From 333e71595b5dd5bc2723770262eec3c253c6c9ee Mon Sep 17 00:00:00 2001
From: Marek Szuba <marek.szuba@ebi.ac.uk>
Date: Tue, 18 Jun 2019 09:36:18 +0100
Subject: [PATCH] Test DB: sync the ontology database with the one from
_ensembl_
For some reason ensembl-io test ontology database went out of sync some
time prior to release 97. See the discussion of PR #85.
---
.../ontology/ontology/SQLite/table.sql | 336 +++++++++---------
.../ontology/ontology/ontology.txt | 12 +-
.../ontology/ontology/table.sql | 99 +++---
.../ontology/ontology/term.txt | 333 ++++++++---------
4 files changed, 392 insertions(+), 388 deletions(-)
diff --git a/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql b/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
index a333ca8e..1d89695b 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
@@ -1,300 +1,302 @@
--
-- Created by SQL::Translator::Producer::SQLite
--- Created on Tue Mar 28 11:01:00 2017
+-- Created on Mon Jun 17 16:51:58 2019
--
BEGIN TRANSACTION;
--
--- Table: alt_id
+-- Table: "alt_id"
--
-CREATE TABLE alt_id (
- alt_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
- term_id integer NOT NULL,
- accession varchar(64) NOT NULL
+CREATE TABLE "alt_id" (
+ "alt_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+ "term_id" integer NOT NULL,
+ "accession" varchar(64) NOT NULL
);
-CREATE UNIQUE INDEX term_alt_idx ON alt_id (term_id, alt_id);
+CREATE UNIQUE INDEX "term_alt_idx" ON "alt_id" ("term_id", "alt_id");
--
--- Table: aux_GO_Cross_product_review_map
+-- Table: "aux_GO_Cross_product_review_map"
--
-CREATE TABLE aux_GO_Cross_product_review_map (
- term_id integer NOT NULL,
- subset_term_id integer NOT NULL,
- distance tinyint NOT NULL
+CREATE TABLE "aux_GO_Cross_product_review_map" (
+ "term_id" integer NOT NULL,
+ "subset_term_id" integer NOT NULL,
+ "distance" tinyint NOT NULL
);
-CREATE UNIQUE INDEX map_idx ON aux_GO_Cross_product_review_map (term_id, subset_term_id);
+CREATE UNIQUE INDEX "map_idx" ON "aux_GO_Cross_product_review_map" ("term_id", "subset_term_id");
--
--- Table: aux_GO_goslim_aspergillus_map
+-- Table: "aux_GO_goslim_aspergillus_map"
--
-CREATE TABLE aux_GO_goslim_aspergillus_map (
- term_id integer NOT NULL,
- subset_term_id integer NOT NULL,
- distance tinyint NOT NULL
+CREATE TABLE "aux_GO_goslim_aspergillus_map" (
+ "term_id" integer NOT NULL,
+ "subset_term_id" integer NOT NULL,
+ "distance" tinyint NOT NULL
);
-CREATE UNIQUE INDEX map_idx02 ON aux_GO_goslim_aspergillus_map (term_id, subset_term_id);
+CREATE UNIQUE INDEX "map_idx02" ON "aux_GO_goslim_aspergillus_map" ("term_id", "subset_term_id");
--
--- Table: aux_GO_goslim_candida_map
+-- Table: "aux_GO_goslim_candida_map"
--
-CREATE TABLE aux_GO_goslim_candida_map (
- term_id integer NOT NULL,
- subset_term_id integer NOT NULL,
- distance tinyint NOT NULL
+CREATE TABLE "aux_GO_goslim_candida_map" (
+ "term_id" integer NOT NULL,
+ "subset_term_id" integer NOT NULL,
+ "distance" tinyint NOT NULL
);
-CREATE UNIQUE INDEX map_idx03 ON aux_GO_goslim_candida_map (term_id, subset_term_id);
+CREATE UNIQUE INDEX "map_idx03" ON "aux_GO_goslim_candida_map" ("term_id", "subset_term_id");
--
--- Table: aux_GO_goslim_generic_map
+-- Table: "aux_GO_goslim_generic_map"
--
-CREATE TABLE aux_GO_goslim_generic_map (
- term_id integer NOT NULL,
- subset_term_id integer NOT NULL,
- distance tinyint NOT NULL
+CREATE TABLE "aux_GO_goslim_generic_map" (
+ "term_id" integer NOT NULL,
+ "subset_term_id" integer NOT NULL,
+ "distance" tinyint NOT NULL
);
-CREATE UNIQUE INDEX map_idx04 ON aux_GO_goslim_generic_map (term_id, subset_term_id);
+CREATE UNIQUE INDEX "map_idx04" ON "aux_GO_goslim_generic_map" ("term_id", "subset_term_id");
--
--- Table: aux_GO_goslim_metagenomics_map
+-- Table: "aux_GO_goslim_metagenomics_map"
--
-CREATE TABLE aux_GO_goslim_metagenomics_map (
- term_id integer NOT NULL,
- subset_term_id integer NOT NULL,
- distance tinyint NOT NULL
+CREATE TABLE "aux_GO_goslim_metagenomics_map" (
+ "term_id" integer NOT NULL,
+ "subset_term_id" integer NOT NULL,
+ "distance" tinyint NOT NULL
);
-CREATE UNIQUE INDEX map_idx05 ON aux_GO_goslim_metagenomics_map (term_id, subset_term_id);
+CREATE UNIQUE INDEX "map_idx05" ON "aux_GO_goslim_metagenomics_map" ("term_id", "subset_term_id");
--
--- Table: aux_GO_goslim_pir_map
+-- Table: "aux_GO_goslim_pir_map"
--
-CREATE TABLE aux_GO_goslim_pir_map (
- term_id integer NOT NULL,
- subset_term_id integer NOT NULL,
- distance tinyint NOT NULL
+CREATE TABLE "aux_GO_goslim_pir_map" (
+ "term_id" integer NOT NULL,
+ "subset_term_id" integer NOT NULL,
+ "distance" tinyint NOT NULL
);
-CREATE UNIQUE INDEX map_idx06 ON aux_GO_goslim_pir_map (term_id, subset_term_id);
+CREATE UNIQUE INDEX "map_idx06" ON "aux_GO_goslim_pir_map" ("term_id", "subset_term_id");
--
--- Table: aux_GO_goslim_plant_map
+-- Table: "aux_GO_goslim_plant_map"
--
-CREATE TABLE aux_GO_goslim_plant_map (
- term_id integer NOT NULL,
- subset_term_id integer NOT NULL,
- distance tinyint NOT NULL
+CREATE TABLE "aux_GO_goslim_plant_map" (
+ "term_id" integer NOT NULL,
+ "subset_term_id" integer NOT NULL,
+ "distance" tinyint NOT NULL
);
-CREATE UNIQUE INDEX map_idx07 ON aux_GO_goslim_plant_map (term_id, subset_term_id);
+CREATE UNIQUE INDEX "map_idx07" ON "aux_GO_goslim_plant_map" ("term_id", "subset_term_id");
--
--- Table: aux_GO_goslim_pombe_map
+-- Table: "aux_GO_goslim_pombe_map"
--
-CREATE TABLE aux_GO_goslim_pombe_map (
- term_id integer NOT NULL,
- subset_term_id integer NOT NULL,
- distance tinyint NOT NULL
+CREATE TABLE "aux_GO_goslim_pombe_map" (
+ "term_id" integer NOT NULL,
+ "subset_term_id" integer NOT NULL,
+ "distance" tinyint NOT NULL
);
-CREATE UNIQUE INDEX map_idx08 ON aux_GO_goslim_pombe_map (term_id, subset_term_id);
+CREATE UNIQUE INDEX "map_idx08" ON "aux_GO_goslim_pombe_map" ("term_id", "subset_term_id");
--
--- Table: aux_GO_goslim_yeast_map
+-- Table: "aux_GO_goslim_yeast_map"
--
-CREATE TABLE aux_GO_goslim_yeast_map (
- term_id integer NOT NULL,
- subset_term_id integer NOT NULL,
- distance tinyint NOT NULL
+CREATE TABLE "aux_GO_goslim_yeast_map" (
+ "term_id" integer NOT NULL,
+ "subset_term_id" integer NOT NULL,
+ "distance" tinyint NOT NULL
);
-CREATE UNIQUE INDEX map_idx09 ON aux_GO_goslim_yeast_map (term_id, subset_term_id);
+CREATE UNIQUE INDEX "map_idx09" ON "aux_GO_goslim_yeast_map" ("term_id", "subset_term_id");
--
--- Table: aux_GO_gosubset_prok_map
+-- Table: "aux_GO_gosubset_prok_map"
--
-CREATE TABLE aux_GO_gosubset_prok_map (
- term_id integer NOT NULL,
- subset_term_id integer NOT NULL,
- distance tinyint NOT NULL
+CREATE TABLE "aux_GO_gosubset_prok_map" (
+ "term_id" integer NOT NULL,
+ "subset_term_id" integer NOT NULL,
+ "distance" tinyint NOT NULL
);
-CREATE UNIQUE INDEX map_idx10 ON aux_GO_gosubset_prok_map (term_id, subset_term_id);
+CREATE UNIQUE INDEX "map_idx10" ON "aux_GO_gosubset_prok_map" ("term_id", "subset_term_id");
--
--- Table: aux_GO_high_level_annotation_qc_map
+-- Table: "aux_GO_high_level_annotation_qc_map"
--
-CREATE TABLE aux_GO_high_level_annotation_qc_map (
- term_id integer NOT NULL,
- subset_term_id integer NOT NULL,
- distance tinyint NOT NULL
+CREATE TABLE "aux_GO_high_level_annotation_qc_map" (
+ "term_id" integer NOT NULL,
+ "subset_term_id" integer NOT NULL,
+ "distance" tinyint NOT NULL
);
-CREATE UNIQUE INDEX map_idx11 ON aux_GO_high_level_annotation_qc_map (term_id, subset_term_id);
+CREATE UNIQUE INDEX "map_idx11" ON "aux_GO_high_level_annotation_qc_map" ("term_id", "subset_term_id");
--
--- Table: aux_GO_mf_needs_review_map
+-- Table: "aux_GO_mf_needs_review_map"
--
-CREATE TABLE aux_GO_mf_needs_review_map (
- term_id integer NOT NULL,
- subset_term_id integer NOT NULL,
- distance tinyint NOT NULL
+CREATE TABLE "aux_GO_mf_needs_review_map" (
+ "term_id" integer NOT NULL,
+ "subset_term_id" integer NOT NULL,
+ "distance" tinyint NOT NULL
);
-CREATE UNIQUE INDEX map_idx12 ON aux_GO_mf_needs_review_map (term_id, subset_term_id);
+CREATE UNIQUE INDEX "map_idx12" ON "aux_GO_mf_needs_review_map" ("term_id", "subset_term_id");
--
--- Table: aux_GO_virus_checked_map
+-- Table: "aux_GO_virus_checked_map"
--
-CREATE TABLE aux_GO_virus_checked_map (
- term_id integer NOT NULL,
- subset_term_id integer NOT NULL,
- distance tinyint NOT NULL
+CREATE TABLE "aux_GO_virus_checked_map" (
+ "term_id" integer NOT NULL,
+ "subset_term_id" integer NOT NULL,
+ "distance" tinyint NOT NULL
);
-CREATE UNIQUE INDEX map_idx13 ON aux_GO_virus_checked_map (term_id, subset_term_id);
+CREATE UNIQUE INDEX "map_idx13" ON "aux_GO_virus_checked_map" ("term_id", "subset_term_id");
--
--- Table: aux_SO_DBVAR_map
+-- Table: "aux_SO_DBVAR_map"
--
-CREATE TABLE aux_SO_DBVAR_map (
- term_id integer NOT NULL,
- subset_term_id integer NOT NULL,
- distance tinyint NOT NULL
+CREATE TABLE "aux_SO_DBVAR_map" (
+ "term_id" integer NOT NULL,
+ "subset_term_id" integer NOT NULL,
+ "distance" tinyint NOT NULL
);
-CREATE UNIQUE INDEX map_idx14 ON aux_SO_DBVAR_map (term_id, subset_term_id);
+CREATE UNIQUE INDEX "map_idx14" ON "aux_SO_DBVAR_map" ("term_id", "subset_term_id");
--
--- Table: aux_SO_SOFA_map
+-- Table: "aux_SO_SOFA_map"
--
-CREATE TABLE aux_SO_SOFA_map (
- term_id integer NOT NULL,
- subset_term_id integer NOT NULL,
- distance tinyint NOT NULL
+CREATE TABLE "aux_SO_SOFA_map" (
+ "term_id" integer NOT NULL,
+ "subset_term_id" integer NOT NULL,
+ "distance" tinyint NOT NULL
);
-CREATE UNIQUE INDEX map_idx15 ON aux_SO_SOFA_map (term_id, subset_term_id);
+CREATE UNIQUE INDEX "map_idx15" ON "aux_SO_SOFA_map" ("term_id", "subset_term_id");
--
--- Table: aux_SO_biosapiens_map
+-- Table: "aux_SO_biosapiens_map"
--
-CREATE TABLE aux_SO_biosapiens_map (
- term_id integer NOT NULL,
- subset_term_id integer NOT NULL,
- distance tinyint NOT NULL
+CREATE TABLE "aux_SO_biosapiens_map" (
+ "term_id" integer NOT NULL,
+ "subset_term_id" integer NOT NULL,
+ "distance" tinyint NOT NULL
);
-CREATE UNIQUE INDEX map_idx16 ON aux_SO_biosapiens_map (term_id, subset_term_id);
+CREATE UNIQUE INDEX "map_idx16" ON "aux_SO_biosapiens_map" ("term_id", "subset_term_id");
--
--- Table: closure
+-- Table: "closure"
--
-CREATE TABLE closure (
- closure_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
- child_term_id integer NOT NULL,
- parent_term_id integer NOT NULL,
- subparent_term_id integer,
- distance tinyint NOT NULL,
- ontology_id integer NOT NULL,
- confident_relationship tinyint NOT NULL DEFAULT 0
+CREATE TABLE "closure" (
+ "closure_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+ "child_term_id" integer NOT NULL,
+ "parent_term_id" integer NOT NULL,
+ "subparent_term_id" integer,
+ "distance" tinyint NOT NULL,
+ "ontology_id" integer NOT NULL,
+ "confident_relationship" tinyint NOT NULL
);
-CREATE UNIQUE INDEX child_parent_idx ON closure (child_term_id, parent_term_id, subparent_term_id, ontology_id);
+CREATE UNIQUE INDEX "closure_child_parent_idx" ON "closure" ("child_term_id", "parent_term_id", "subparent_term_id", "ontology_id");
--
--- Table: meta
+-- Table: "meta"
--
-CREATE TABLE meta (
- meta_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
- meta_key varchar(64) NOT NULL,
- meta_value varchar(128),
- species_id integer
+CREATE TABLE "meta" (
+ "meta_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+ "meta_key" varchar(64) NOT NULL,
+ "meta_value" varchar(128),
+ "species_id" integer
);
-CREATE UNIQUE INDEX key_value_idx ON meta (meta_key, meta_value);
+CREATE UNIQUE INDEX "key_value_idx" ON "meta" ("meta_key", "meta_value");
--
--- Table: ontology
+-- Table: "ontology"
--
-CREATE TABLE ontology (
- ontology_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
- name varchar(64) NOT NULL,
- namespace varchar(64) NOT NULL,
- data_version varchar(64)
+CREATE TABLE "ontology" (
+ "ontology_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+ "name" varchar(64) NOT NULL,
+ "namespace" varchar(64) NOT NULL,
+ "data_version" varchar(64),
+ "title" varchar(255)
);
-CREATE UNIQUE INDEX name_namespace_idx ON ontology (name, namespace);
+CREATE UNIQUE INDEX "ontology_name_namespace_idx" ON "ontology" ("name", "namespace");
--
--- Table: relation
+-- Table: "relation"
--
-CREATE TABLE relation (
- relation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
- child_term_id integer NOT NULL,
- parent_term_id integer NOT NULL,
- relation_type_id integer NOT NULL,
- intersection_of tinyint NOT NULL DEFAULT 0,
- ontology_id integer NOT NULL
+CREATE TABLE "relation" (
+ "relation_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+ "child_term_id" integer NOT NULL,
+ "parent_term_id" integer NOT NULL,
+ "relation_type_id" integer NOT NULL,
+ "intersection_of" tinyint NOT NULL,
+ "ontology_id" integer NOT NULL
);
-CREATE UNIQUE INDEX child_parent_idx02 ON relation (child_term_id, parent_term_id, relation_type_id, intersection_of, ontology_id);
+CREATE UNIQUE INDEX "child_parent_idx" ON "relation" ("child_term_id", "parent_term_id", "relation_type_id", "intersection_of", "ontology_id");
--
--- Table: relation_type
+-- Table: "relation_type"
--
-CREATE TABLE relation_type (
- relation_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
- name varchar(64) NOT NULL
+CREATE TABLE "relation_type" (
+ "relation_type_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+ "name" varchar(64) NOT NULL
);
-CREATE UNIQUE INDEX name_idx ON relation_type (name);
+CREATE UNIQUE INDEX "name" ON "relation_type" ("name");
--
--- Table: subset
+-- Table: "subset"
--
-CREATE TABLE subset (
- subset_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
- name varchar(64) NOT NULL,
- definition varchar(128) NOT NULL
+CREATE TABLE "subset" (
+ "subset_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+ "name" varchar(64) NOT NULL,
+ "definition" varchar(1023) NOT NULL DEFAULT ''
);
-CREATE UNIQUE INDEX name_idx02 ON subset (name);
+CREATE UNIQUE INDEX "name02" ON "subset" ("name");
--
--- Table: synonym
+-- Table: "synonym"
--
-CREATE TABLE synonym (
- synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
- term_id integer NOT NULL,
- name mediumtext NOT NULL,
- type enum,
- dbxref varchar(256) NOT NULL
+CREATE TABLE "synonym" (
+ "synonym_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+ "term_id" integer NOT NULL,
+ "name" text NOT NULL,
+ "type" enum,
+ "dbxref" varchar(500)
);
-CREATE UNIQUE INDEX term_synonym_idx ON synonym (term_id, synonym_id);
+CREATE UNIQUE INDEX "synonym_term_idx" ON "synonym" ("term_id", "synonym_id");
--
--- Table: term
+-- Table: "term"
--
-CREATE TABLE term (
- term_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
- ontology_id integer NOT NULL,
- subsets text,
- accession varchar(64) NOT NULL,
- name varchar(255) NOT NULL,
- definition text,
- is_root integer,
- is_obsolete integer
+CREATE TABLE "term" (
+ "term_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+ "ontology_id" integer NOT NULL,
+ "subsets" text,
+ "accession" varchar(64) NOT NULL,
+ "name" varchar(255) NOT NULL,
+ "definition" text,
+ "is_root" integer NOT NULL DEFAULT 0,
+ "is_obsolete" integer NOT NULL DEFAULT 0,
+ "iri" text
);
-CREATE UNIQUE INDEX accession_idx ON term (accession);
+CREATE UNIQUE INDEX "accession" ON "term" ("accession");
-CREATE UNIQUE INDEX ontology_acc_idx ON term (ontology_id, accession);
+CREATE UNIQUE INDEX "term_ontology_acc_idx" ON "term" ("ontology_id", "accession");
COMMIT;
diff --git a/modules/t/test-genome-DBs/ontology/ontology/ontology.txt b/modules/t/test-genome-DBs/ontology/ontology/ontology.txt
index c455a303..a689b8a7 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/ontology.txt
+++ b/modules/t/test-genome-DBs/ontology/ontology/ontology.txt
@@ -1,6 +1,6 @@
-1 GO biological_process releases/2016-03-30
-2 GO cellular_component releases/2016-03-30
-3 GO molecular_function releases/2016-03-30
-5 SO sequence so-xp/releases/2015-11-24/so-xp.owl
-6 EFO BrendaTissueOBO \N
-7 EFO EFO \N
+1 GO biological_process releases/2016-03-30 \N
+2 GO cellular_component releases/2016-03-30 \N
+3 GO molecular_function releases/2016-03-30 \N
+5 SO sequence so-xp/releases/2015-11-24/so-xp.owl \N
+6 EFO BrendaTissueOBO \N \N
+7 EFO EFO \N \N
diff --git a/modules/t/test-genome-DBs/ontology/ontology/table.sql b/modules/t/test-genome-DBs/ontology/ontology/table.sql
index cad0e915..7e732851 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/table.sql
+++ b/modules/t/test-genome-DBs/ontology/ontology/table.sql
@@ -4,7 +4,7 @@ CREATE TABLE `alt_id` (
`accession` varchar(64) NOT NULL,
PRIMARY KEY (`alt_id`),
UNIQUE KEY `term_alt_idx` (`term_id`,`alt_id`),
- KEY `accession_idx` (`accession`(50))
+ KEY `ix_alt_id_accession` (`accession`)
) ENGINE=MyISAM AUTO_INCREMENT=7 DEFAULT CHARSET=latin1;
CREATE TABLE `aux_GO_Cross_product_review_map` (
@@ -12,112 +12,112 @@ CREATE TABLE `aux_GO_Cross_product_review_map` (
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_aspergillus_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_candida_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_generic_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_metagenomics_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_pir_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_plant_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_pombe_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_goslim_yeast_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_gosubset_prok_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_high_level_annotation_qc_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_mf_needs_review_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_GO_virus_checked_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_SO_DBVAR_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_SO_SOFA_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `aux_SO_biosapiens_map` (
`term_id` int(10) unsigned NOT NULL,
`subset_term_id` int(10) unsigned NOT NULL,
`distance` tinyint(3) unsigned NOT NULL,
UNIQUE KEY `map_idx` (`term_id`,`subset_term_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=utf8;
CREATE TABLE `closure` (
`closure_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -126,31 +126,31 @@ CREATE TABLE `closure` (
`subparent_term_id` int(10) unsigned DEFAULT NULL,
`distance` tinyint(3) unsigned NOT NULL,
`ontology_id` int(10) unsigned NOT NULL,
- `confident_relationship` tinyint(1) NOT NULL DEFAULT 0,
+ `confident_relationship` tinyint(1) NOT NULL,
PRIMARY KEY (`closure_id`),
- UNIQUE KEY `child_parent_idx` (`child_term_id`,`parent_term_id`,`subparent_term_id`,`ontology_id`),
- KEY `parent_subparent_idx` (`parent_term_id`,`subparent_term_id`),
+ UNIQUE KEY `closure_child_parent_idx` (`child_term_id`,`parent_term_id`,`subparent_term_id`,`ontology_id`),
KEY `ix_closure_subparent_term_id` (`subparent_term_id`),
- KEY `ix_closure_ontology_id` (`ontology_id`)
+ KEY `ix_closure_ontology_id` (`ontology_id`),
+ KEY `parent_subparent_idx` (`parent_term_id`,`subparent_term_id`)
) ENGINE=MyISAM AUTO_INCREMENT=1453438 DEFAULT CHARSET=latin1;
CREATE TABLE `meta` (
`meta_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `meta_key` varchar(64) CHARACTER SET latin1 NOT NULL,
- `meta_value` varchar(128) CHARACTER SET latin1 DEFAULT NULL,
- `species_id` int(1) unsigned DEFAULT NULL,
+ `meta_key` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
+ `meta_value` varchar(128) COLLATE utf8_unicode_ci DEFAULT NULL,
+ `species_id` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`meta_id`),
UNIQUE KEY `key_value_idx` (`meta_key`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=47 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
CREATE TABLE `ontology` (
`ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(64) CHARACTER SET latin1 NOT NULL,
- `namespace` varchar(64) CHARACTER SET latin1 NOT NULL,
- `data_version` varchar(64) CHARACTER SET latin1 DEFAULT NULL,
- `title` varchar(255) CHARACTER SET latin1 DEFAULT NULL,
+ `name` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
+ `namespace` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
+ `data_version` varchar(64) COLLATE utf8_unicode_ci DEFAULT NULL,
+ `title` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL,
PRIMARY KEY (`ontology_id`),
- UNIQUE KEY `name_namespace_idx` (`name`,`namespace`)
+ UNIQUE KEY `ontology_name_namespace_idx` (`name`,`namespace`)
) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
CREATE TABLE `relation` (
@@ -158,11 +158,10 @@ CREATE TABLE `relation` (
`child_term_id` int(10) unsigned NOT NULL,
`parent_term_id` int(10) unsigned NOT NULL,
`relation_type_id` int(10) unsigned NOT NULL,
- `intersection_of` tinyint(3) unsigned NOT NULL DEFAULT 0,
+ `intersection_of` tinyint(1) NOT NULL,
`ontology_id` int(10) unsigned NOT NULL,
PRIMARY KEY (`relation_id`),
UNIQUE KEY `child_parent_idx` (`child_term_id`,`parent_term_id`,`relation_type_id`,`intersection_of`,`ontology_id`),
- KEY `parent_idx` (`parent_term_id`),
KEY `ix_relation_parent_term_id` (`parent_term_id`),
KEY `ix_relation_relation_type_id` (`relation_type_id`),
KEY `ix_relation_ontology_id` (`ontology_id`)
@@ -172,41 +171,41 @@ CREATE TABLE `relation_type` (
`relation_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(64) NOT NULL,
PRIMARY KEY (`relation_type_id`),
- UNIQUE KEY `name_idx` (`name`)
+ UNIQUE KEY `name` (`name`)
) ENGINE=MyISAM AUTO_INCREMENT=85 DEFAULT CHARSET=latin1;
CREATE TABLE `subset` (
`subset_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
- `name` varchar(64) CHARACTER SET latin1 NOT NULL,
+ `name` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
`definition` varchar(1023) COLLATE utf8_unicode_ci NOT NULL DEFAULT '',
PRIMARY KEY (`subset_id`),
- UNIQUE KEY `name_idx` (`name`)
+ UNIQUE KEY `name` (`name`)
) ENGINE=MyISAM AUTO_INCREMENT=18 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
CREATE TABLE `synonym` (
`synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`term_id` int(10) unsigned NOT NULL,
- `name` mediumtext CHARACTER SET utf8 COLLATE utf8_swedish_ci NOT NULL,
- `type` enum('EXACT','BROAD','NARROW','RELATED') CHARACTER SET utf8 COLLATE utf8_swedish_ci DEFAULT NULL,
- `dbxref` varchar(256) CHARACTER SET utf8 COLLATE utf8_swedish_ci NOT NULL,
+ `name` text CHARACTER SET utf8 NOT NULL,
+ `type` enum('EXACT','BROAD','NARROW','RELATED') COLLATE utf8_unicode_ci DEFAULT NULL,
+ `dbxref` varchar(500) COLLATE utf8_unicode_ci DEFAULT NULL,
PRIMARY KEY (`synonym_id`),
- UNIQUE KEY `term_synonym_idx` (`term_id`,`synonym_id`),
- KEY `name_idx` (`name`(50))
+ UNIQUE KEY `synonym_term_idx` (`term_id`,`synonym_id`),
+ KEY `synonym_name_idx` (`name`(100))
) ENGINE=MyISAM AUTO_INCREMENT=104283 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
CREATE TABLE `term` (
`term_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`ontology_id` int(10) unsigned NOT NULL,
- `subsets` text CHARACTER SET latin1 DEFAULT NULL,
- `accession` varchar(64) CHARACTER SET latin1 NOT NULL,
- `name` varchar(255) CHARACTER SET latin1 NOT NULL,
- `definition` text CHARACTER SET latin1 DEFAULT NULL,
- `is_root` int(11) DEFAULT NULL,
- `is_obsolete` int(11) DEFAULT NULL,
- `iri` text CHARACTER SET latin1 DEFAULT NULL,
+ `subsets` text COLLATE utf8_unicode_ci DEFAULT NULL,
+ `accession` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
+ `name` varchar(255) CHARACTER SET utf8 NOT NULL,
+ `definition` text CHARACTER SET utf8 DEFAULT NULL,
+ `is_root` int(11) NOT NULL DEFAULT 0,
+ `is_obsolete` int(11) NOT NULL DEFAULT 0,
+ `iri` text COLLATE utf8_unicode_ci DEFAULT NULL,
PRIMARY KEY (`term_id`),
- UNIQUE KEY `accession_idx` (`accession`),
- UNIQUE KEY `ontology_acc_idx` (`ontology_id`,`accession`),
- KEY `name_idx` (`name`)
-) ENGINE=MyISAM AUTO_INCREMENT=44356 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
+ UNIQUE KEY `accession` (`accession`),
+ UNIQUE KEY `term_ontology_acc_idx` (`ontology_id`,`accession`),
+ KEY `term_name_idx` (`name`(100))
+) ENGINE=MyISAM AUTO_INCREMENT=45001 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
diff --git a/modules/t/test-genome-DBs/ontology/ontology/term.txt b/modules/t/test-genome-DBs/ontology/ontology/term.txt
index 411d6cc9..b1866899 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/term.txt
+++ b/modules/t/test-genome-DBs/ontology/ontology/term.txt
@@ -1,165 +1,168 @@
-144 3 N GO:0000182 rDNA binding "Interacting selectively and non-covalently with DNA sequences encoding ribosomal RNA." [GOC:mah] 0 1
-166 3 N GO:0000217 DNA secondary structure binding "Interacting selectively and non-covalently with DNA containing secondary structure elements such as four-way junctions, bubbles, loops, Y-form DNA, or double-strand/single-strand junctions." [GOC:krc] 0 1
-259 3 N GO:0000332 template for synthesis of G-rich strand of telomere DNA activity "Provision of the template used by reverse transcriptase to synthesize the G-rich strand of telomeric DNA." [PMID:11812242] 0 0
-304 3 N GO:0000400 four-way junction DNA binding "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC:krc, ISBN:0815332181, PMID:15563464] 0 0
-305 3 N GO:0000401 open form four-way junction DNA binding "Interacting selectively and non-covalently with DNA containing the open form of a four-way junction, also known as a Holliday junction, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. The open form of a four-way junction can be diagrammed without any of the strands crossing over." [GOC:krc, ISBN:0815332181, PMID:15563464] 0 0
-306 3 N GO:0000402 crossed form four-way junction DNA binding "Interacting selectively and non-covalently with DNA containing the crossed form of a four-way junction, also known as a Holliday junction, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. The crossed form of a four-way junction cannot be diagrammed without any of the strands crossing over, and instead contains a single crossover between two of the strands." [GOC:krc, ISBN:0815332181, PMID:15563464] 0 0
-307 3 N GO:0000403 Y-form DNA binding "Interacting selectively and non-covalently with segment of DNA shaped like a Y. This shape occurs when DNA contains a region of paired double-stranded DNA on one end and a region of unpaired DNA strands on the opposite end." [GOC:elh, PMID:16781730] 0 0
-308 3 N GO:0000404 loop DNA binding "Interacting selectively and non-covalently with DNA containing a loop. A loop occurs when DNA contains a large insertion or deletion that causes a region of unpaired single-stranded DNA to loop out, while the rest of the DNA is in a paired double-stranded configuration." [GOC:elh, PMID:16781730] 0 0
-309 3 N GO:0000405 bubble DNA binding "Interacting selectively and non-covalently with DNA that contains a bubble. A bubble occurs when DNA contains a region of unpaired, single-stranded DNA flanked on both sides by regions of paired, double-stranded DNA." [GOC:elh, GOC:vw, PMID:16781730] 0 0
-310 3 N GO:0000406 double-strand/single-strand DNA junction binding "Interacting selectively and non-covalently with a region of DNA that contains double-stranded DNA flanked by a region of single-stranded DNA." [GOC:elh, PMID:16781730] 0 0
-399 3 N GO:0000497 base pairing with DNA "Interacting selectively and non-covalently with nucleic acid via hydrogen bonds between the bases of a gene product molecule and the bases of a target DNA molecule." [GOC:krc] 0 0
-614 3 N GO:0000975 regulatory region DNA binding "Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair." [GOC:txnOH] 0 1
-615 3 N GO:0000976 transcription regulatory region sequence-specific DNA binding "Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH] 0 0
-616 3 N GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding "Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II." [GOC:txnOH] 0 0
-617 3 N GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II." [GOC:txnOH] 0 1
-618 3 N GO:0000979 RNA polymerase II core promoter sequence-specific DNA binding "Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery." [GOC:txnOH] 0 0
-619 3 N GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding "Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter." [GOC:txnOH] 0 0
-623 3 gosubset_prok GO:0000984 bacterial-type RNA polymerase regulatory region sequence-specific DNA binding "Interacting selectively and non-covalently with a sequence of DNA that is part of a regulatory region that controls the transcription of a gene or operon by a bacterial-type RNA polymerase." [GOC:txnOH] 0 0
-624 3 gosubset_prok GO:0000985 bacterial-type RNA polymerase core promoter sequence-specific DNA binding "Interacting selectively and non-covalently with a specific DNA sequence in a bacterial-type RNA polymerase core promoter, the region composed of the transcription start site and binding sites for transcription factors of the basal transcription machinery, in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] 0 0
-625 3 gosubset_prok GO:0000986 bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase." [GOC:txnOH] 0 0
-626 3 N GO:0000987 core promoter proximal region sequence-specific DNA binding "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH] 0 0
-631 3 N GO:0000992 polymerase III regulatory region sequence-specific DNA binding "Interacting selectively and non-covalently with a sequence of DNA that is part of a regulatory region that controls transcription by RNA polymerase III. The transcribed region might be contain a single gene or a cistron containing multiple genes." [GOC:txnOH, PMID:12381659] 0 0
-636 3 N GO:0000997 mitochondrial RNA polymerase core promoter sequence-specific DNA binding "Interacting selectively and non-covalently with a sequence of DNA that is part of the core promoter for the mitochondrial RNA polymerase." [GOC:txnOH] 0 0
-640 3 N GO:0001002 RNA polymerase III type 1 promoter sequence-specific DNA binding "Interacting selectively and non-covalently with a sequence of DNA that is a part of a type 1 promoter that controls transcription by RNA polymerase III. Type 1 promoters are found in 5S rRNA genes, downstream of the transcription start site within the sequence of the mature RNA, and require TFIIIA for recognition." [GOC:txnOH, PMID:12381659] 0 0
-641 3 N GO:0001003 RNA polymerase III type 2 promoter sequence-specific DNA binding "Interacting selectively and non-covalently with a sequence of DNA that is a part of a type 2 promoter that controls transcription by RNA polymerase III. Type 2 promoters consist of an A box and a B box downstream of the transcription start site within the sequence within the sequence of the mature RNA. Type 2 promoters are found in many tRNA genes as well as in other small RNAs." [GOC:txnOH, PMID:12381659] 0 0
-644 3 N GO:0001006 RNA polymerase III type 3 promoter sequence-specific DNA binding "Interacting selectively and non-covalently with a sequence of DNA that is a part of a type 3 promoter that controls transcription by RNA polymerase III (Pol III). A type 3 Pol III promoter is composed of elements upstream of the transcription start site, including a TATA box. The human U6 snRNA gene has a type 3 promoter. Type 3 Pol III promoters have not been observed in S. cerevisiae." [GOC:txnOH, PMID:12381659] 0 0
-650 3 N GO:0001012 RNA polymerase II regulatory region DNA binding "Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by RNA polymerase II. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH, GOC:vw] 0 0
-651 3 N GO:0001013 RNA polymerase I regulatory region DNA binding "Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by RNA polymerase I. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH, GOC:vw] 0 0
-654 3 N GO:0001016 RNA polymerase III regulatory region DNA binding "Interacting selectively and non-covalently with a DNA region that controls the transcription of a gene by RNA polymerase III. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH, GOC:vw, PMID:12381659] 0 0
-655 3 gosubset_prok GO:0001017 bacterial-type RNA polymerase regulatory region DNA binding "Interacting selectively and non-covalently with a DNA region that controls the transcription of a gene or operon by a bacterial-type RNA polymerase. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH] 0 0
-656 3 N GO:0001018 mitochondrial RNA polymerase regulatory region DNA binding "Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by mitochondrial RNA polymerase. Binding may occur as a high affinity and sequence specific interaction or as a lower affinity interaction observed once a factor has been recruited to the DNA by other factors." [GOC:txnOH, GOC:vw, PMID:20056105] 0 0
-657 3 N GO:0001019 plastid RNA polymerase regulatory region DNA binding "Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by a plastid RNA polymerase. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH, GOC:vw] 0 0
-668 3 N GO:0001030 RNA polymerase III type 1 promoter DNA binding "Interacting selectively and non-covalently with a region of DNA that is a part of a type 1 promoter that controls transcription by RNA polymerase III. Type 1 promoters are found in 5S rRNA genes, downstream of the transcription start site within the sequence of the mature RNA, and require TFIIIA for recognition." [GOC:txnOH, PMID:12381659] 0 0
-669 3 N GO:0001031 RNA polymerase III type 2 promoter DNA binding "Interacting selectively and non-covalently with a region of DNA that is a part of a type 2 promoter that controls transcription by RNA polymerase III. Type 2 promoters consist of an A box and a B box downstream of the transcription start site within the sequence within the sequence of the mature RNA. Type 2 promoters are found in many tRNA genes as well as in other small RNAs." [GOC:txnOH, PMID:12381659] 0 0
-670 3 N GO:0001032 RNA polymerase III type 3 promoter DNA binding "Interacting selectively and non-covalently with a region of DNA that is a part of a type 3 promoter that controls transcription by RNA polymerase III. A type 3 Pol III promoter is composed of elements upstream of the transcription start site, including a TATA box. The human U6 snRNA gene has a type 3 promoter. Type 3 Pol III promoters have not been observed in S. cerevisiae." [GOC:txnOH, PMID:12381659] 0 0
-675 3 N GO:0001037 RNA polymerase III hybrid type promoter DNA binding "Interacting selectively and non-covalently with a region of DNA that is a part of a hybrid promoter that controls transcription by RNA polymerase III (Pol III). A hybrid Pol III promoter contains both regulatory elements both upstream and downstream of the transcription initiation site. An example gene with such a promoter is the S. cerevisiae U6 gene." [GOC:txnOH, PMID:12381659] 0 0
-677 3 N GO:0001039 RNA polymerase III hybrid type promoter sequence-specific DNA binding "Interacting selectively and non-covalently with a sequence of DNA that is a part of a hybrid type promoter that controls transcription by RNA polymerase III (Pol III). A hybrid Pol III promoter contains both regulatory elements both upstream and downstream of the transcription initiation site. An example gene with such a promoter is the S. cerevisiae U6 gene." [GOC:txnOH, PMID:12381659] 0 0
-682 3 N GO:0001044 mitochondrial RNA polymerase regulatory region sequence-specific DNA binding "Interacting selectively and non-covalently with a specific sequence of DNA that controls the transcription of a region of DNA by mitochondrial RNA polymerase." [GOC:txnOH] 0 0
-683 3 N GO:0001045 mitochondrial RNA polymerase core promoter proximal region sequence-specific DNA binding "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a mitochondrial RNA polymerase." [GOC:txnOH, PMID:20670382] 0 0
-684 3 N GO:0001046 core promoter sequence-specific DNA binding "Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region composed of the transcription start site and binding sites for the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH] 0 0
-685 3 N GO:0001047 core promoter binding "Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH] 0 0
-782 3 N GO:0001145 mitochondrial RNA polymerase termination site sequence-specific DNA binding "Interacting selectively and non-covalently with a sequence of DNA that is a terminator for mitochondrial RNA polymerase." [GOC:txnOH, PMID:18391175] 0 0
-784 3 N GO:0001147 transcription termination site sequence-specific DNA binding "Interacting selectively and non-covalently with a sequence of DNA that promotes termination by RNA polymerase. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH, PMID:18280161, PMID:18391175] 0 0
-785 3 N GO:0001148 bacterial-type RNA polymerase termination site sequence-specific DNA binding "Interacting selectively and non-covalently with a sequence of DNA that is a terminator for bacterial-type RNA polymerase." [GOC:txnOH, PMID:18280161] 0 0
-787 3 N GO:0001150 bacterial-type RNA polymerase enhancer sequence-specific DNA binding "Interacting selectively and non-covalently with a sequence of DNA that is an enhancer region that helps activate transcription of a gene or operon by a bacterial-type RNA polymerase. Enhancers for sigma-54 holoenzymes are typically located 80 to 150 base pairs upstream from the transcription start site, although they can be further away or may be downstream of the promoter. Some transcription units dependent on sigma-70 holoenzymes may also include enhancer sequences." [GOC:txnOH, PMID:11282468, PMID:20629756] 0 0
-795 3 N GO:0001158 enhancer sequence-specific DNA binding "Interacting selectively and non-covalently with a specific sequence of DNA that is part of an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter." [GOC:txnOH] 0 0
-796 3 N GO:0001159 core promoter proximal region DNA binding "Interacting selectively and non-covalently with a region of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH] 0 0
-797 3 N GO:0001160 transcription termination site DNA binding "Interacting selectively and non-covalently with a region of DNA that promotes termination by RNA polymerase. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH] 0 0
-798 3 N GO:0001161 intronic transcription regulatory region sequence-specific DNA binding "Interacting selectively and non-covalently with an intronic DNA sequence that regulates the transcription of the transcript it is contained within." [GOC:txnOH] 0 0
-799 3 N GO:0001162 RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding "Interacting selectively and non-covalently with an RNA polymerase II intronic DNA sequence that regulates the transcription of the transcript it is contained within." [GOC:txnOH] 0 0
-800 3 N GO:0001163 RNA polymerase I regulatory region sequence-specific DNA binding "Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase I." [GOC:txnOH] 0 0
-801 3 N GO:0001164 RNA polymerase I CORE element sequence-specific DNA binding "Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery. This site is often referred to as the CORE element. In mammalian cells, the CORE element functions in conjunction with the Upstream Control Element (UCE), while in fungi, protozoa, and plants, the CORE element functions without a UCE." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832] 0 0
-802 3 N GO:0001165 RNA polymerase I upstream control element sequence-specific DNA binding "Interacting selectively and non-covalently with the upstream control element (UCE, or alternately referred to as the upstream element), a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase I." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832] 0 0
-803 3 N GO:0001166 RNA polymerase I enhancer sequence-specific DNA binding "Interacting selectively and non-covalently with a RNA polymerase I (Pol I) enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832] 0 0
-2688 3 goslim_aspergillus,goslim_candida,goslim_generic,goslim_metagenomics,goslim_pir,goslim_plant,goslim_yeast,gosubset_prok GO:0003674 molecular_function "Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions." [GOC:go_curators] 1 0
-2689 3 goslim_metagenomics,goslim_pir,goslim_plant,gosubset_prok GO:0003676 nucleic acid binding "Interacting selectively and non-covalently with any nucleic acid." [GOC:jl] 0 0
-2690 3 goslim_aspergillus,goslim_candida,goslim_generic,goslim_plant,goslim_yeast,gosubset_prok GO:0003677 DNA binding "Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid)." [GOC:dph, GOC:jl, GOC:tb, GOC:vw] 0 0
-2692 3 N GO:0003680 AT DNA binding "Interacting selectively and non-covalently with oligo(A) and oligo(T) tracts of DNA (AT DNA)." [GOC:jl, PMID:2670564] 0 0
-2693 3 gosubset_prok GO:0003681 bent DNA binding "Interacting selectively and non-covalently with DNA in a bent conformation." [GOC:jl, PMID:12627977] 0 0
-2695 3 gosubset_prok GO:0003684 damaged DNA binding "Interacting selectively and non-covalently with damaged DNA." [GOC:jl] 0 0
-2696 3 gosubset_prok GO:0003688 DNA replication origin binding "Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally." [GOC:curators] 0 0
-2697 3 gosubset_prok GO:0003689 DNA clamp loader activity "Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the opening of the ring structure of the PCNA complex, or any of the related sliding clamp complexes, and their closing around the DNA duplex." [GOC:mah, GOC:vw, PMID:16082778] 0 0
-2698 3 gosubset_prok GO:0003690 double-stranded DNA binding "Interacting selectively and non-covalently with double-stranded DNA." [GOC:elh] 0 0
-2699 3 N GO:0003691 double-stranded telomeric DNA binding "Interacting selectively and non-covalently with double-stranded telomere-associated DNA." [GOC:jl, ISBN:0321000382] 0 0
-2700 3 N GO:0003692 left-handed Z-DNA binding "Interacting selectively and non-covalently with DNA in the Z form, i.e. a left-handed helix in which the phosphate backbone zigzags." [ISBN:0716720094] 0 0
-2701 3 N GO:0003693 P-element binding "Interacting selectively and non-covalently with any P-element, a class of Drosophila transposon responsible for hybrid dysgenesis." [GOC:jl, PMID:9440262] 0 0
-2702 3 N GO:0003695 random coil DNA binding "Interacting selectively and non-covalently with DNA in a random coil configuration." [GOC:mah] 0 0
-2703 3 N GO:0003696 satellite DNA binding "Interacting selectively and non-covalently with satellite DNA, the many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [GOC:jl, SO:0000005] 0 0
-2704 3 gosubset_prok GO:0003697 single-stranded DNA binding "Interacting selectively and non-covalently with single-stranded DNA." [GOC:elh] 0 0
-2811 3 gosubset_prok GO:0003916 DNA topoisomerase activity "Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA." [GOC:mah, PMID:8811192] 0 0
-2812 3 gosubset_prok GO:0003917 DNA topoisomerase type I activity "Catalysis of a DNA topological transformation by transiently cleaving one DNA strand at a time to allow passage of another strand; changes the linking number by +1 per catalytic cycle." [PMID:8811192] 0 0
-2813 3 gosubset_prok GO:0003918 DNA topoisomerase type II (ATP-hydrolyzing) activity "Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2." [PMID:8811192] 0 0
-3916 3 goslim_pir,goslim_plant,gosubset_prok GO:0005488 binding "The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732] 0 0
-5856 3 gosubset_prok GO:0008301 DNA binding, bending "The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence." [GOC:krc, GOC:vw, PMID:10710711, PMID:19037758] 0 0
-5875 3 N GO:0008327 methyl-CpG binding "Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide." [GOC:jl, PMID:11746232] 0 0
-7628 3 N GO:0010385 double-stranded methylated DNA binding "Interacting selectively and non-covalently with double-stranded methylated DNA. Cytosine methylation in DNA is an important mechanism for establishing stable heritable epigenetic marks." [PMID:17242155] 0 0
-7966 3 N GO:0010736 serum response element binding "Interacting selectively and non-covalently with the serum response element (SRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum." [GOC:BHF, GOC:dph, GOC:rl, GOC:tb] 0 0
-8072 3 N GO:0010844 recombination hotspot binding "Interacting selectively and non-covalently with a region in a genome which promotes recombination." [GOC:dph, GOC:tb] 0 0
-8912 3 N GO:0015616 DNA translocase activity "Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded DNA molecule." [GOC:mah, PMID:16428451, PMID:17631491] 0 0
-11234 3 N GO:0019237 centromeric DNA binding "Interacting selectively and non-covalently with a centromere, a region of chromosome where the spindle fibers attach during mitosis and meiosis." [GOC:jl, SO:0000577] 0 0
-13423 3 N GO:0030983 mismatched DNA binding "Interacting selectively and non-covalently with double-stranded DNA containing one or more mismatches." [GOC:mah] 0 0
-13890 3 N GO:0031490 chromatin DNA binding "Interacting selectively and non-covalently with DNA that is assembled into chromatin." [GOC:mah] 0 0
-13892 3 N GO:0031492 nucleosomal DNA binding "Interacting selectively and non-covalently with the DNA portion of a nucleosome." [GOC:mah] 0 0
-14031 3 N GO:0031634 replication fork barrier binding "Interacting selectively and non-covalently with replication fork barriers, sites that inhibit the progress of replication forks." [GOC:mah] 0 0
-14511 3 N GO:0032131 alkylated DNA binding "Interacting selectively and non-covalently with alkylated residues in DNA." [GOC:mah] 0 0
-14512 3 N GO:0032132 O6-alkylguanine-DNA binding "Interacting selectively and non-covalently with O6-alkylguanine adducts in DNA." [GOC:mah, PMID:16679453] 0 0
-14514 3 N GO:0032135 DNA insertion or deletion binding "Interacting selectively and non-covalently with double-stranded DNA containing insertions or deletions." [GOC:vk] 0 0
-14515 3 N GO:0032136 adenine/cytosine mispair binding "Interacting selectively and non-covalently with double-stranded DNA containing an A/C mispair." [GOC:vk] 0 0
-14516 3 N GO:0032137 guanine/thymine mispair binding "Interacting selectively and non-covalently with double-stranded DNA containing a G/T mispair." [GOC:vk] 0 0
-14517 3 N GO:0032138 single base insertion or deletion binding "Interacting selectively and non-covalently with double-stranded DNA containing a single base insertion or deletion." [GOC:vk] 0 0
-14518 3 N GO:0032139 dinucleotide insertion or deletion binding "Interacting selectively and non-covalently with double-stranded DNA containing a dinucleotide insertion or deletion." [GOC:vk] 0 0
-14519 3 N GO:0032140 single adenine insertion binding "Interacting selectively and non-covalently with double-stranded DNA containing a single adenine insertion or a deletion that results in an unpaired adenine." [GOC:mah, GOC:vk] 0 0
-14520 3 N GO:0032141 single cytosine insertion binding "Interacting selectively and non-covalently with double-stranded DNA containing a single cytosine insertion or a deletion that results in an unpaired cytosine." [GOC:mah, GOC:vk] 0 0
-14521 3 N GO:0032142 single guanine insertion binding "Interacting selectively and non-covalently with double-stranded DNA containing a single guanine insertion or a deletion that results in an unpaired guanine." [GOC:mah, GOC:vk] 0 0
-14522 3 N GO:0032143 single thymine insertion binding "Interacting selectively and non-covalently with double-stranded DNA containing a single thymine insertion or a deletion that results in an unpaired thymine." [GOC:mah, GOC:vk] 0 0
-14559 3 N GO:0032181 dinucleotide repeat insertion binding "Interacting selectively and non-covalently with double-stranded DNA containing a dinucleotide repeat insertion or a deletion resulting in unpaired dinucleotide repeats." [GOC:mah, GOC:vk] 0 0
-14729 3 N GO:0032356 oxidized DNA binding "Interacting selectively and non-covalently with oxidized residues in DNA." [GOC:vk] 0 0
-14730 3 N GO:0032357 oxidized purine DNA binding "Interacting selectively and non-covalently with oxidized purine residues in DNA." [GOC:vk] 0 0
-14731 3 N GO:0032358 oxidized pyrimidine DNA binding "Interacting selectively and non-covalently with oxidized pyrimidine residues in DNA." [GOC:vk] 0 0
-14794 3 N GO:0032422 purine-rich negative regulatory element binding "Interacting selectively and non-covalently with a 30-bp purine-rich negative regulatory element; the best characterized such element is found in the first intronic region of the rat cardiac alpha-myosin heavy chain gene, and contains two palindromic high-affinity Ets-binding sites (CTTCCCTGGAAG). The presence of this element restricts expression of the gene containing it to cardiac myocytes." [GOC:mah, PMID:9819411] 0 0
-14820 3 N GO:0032448 DNA hairpin binding "Interacting selectively and non-covalently with DNA containing a hairpin. A hairpin structure forms when a DNA strand folds back on itself and intrachain base pairing occurs between inverted repeat sequences." [GOC:mah, ISBN:0198506732] 0 0
-15175 3 N GO:0032810 sterol response element binding "Interacting selectively and non-covalently with the sterol response element (SRE), a nonpalindromic sequence found in the promoters of genes involved in lipid metabolism." [GOC:vk, PMID:11994399] 0 0
-16393 3 N GO:0034056 estrogen response element binding "Interacting selectively and non-covalently with the estrogen response element (ERE), a conserved sequence found in the promoters of genes whose expression is regulated in response to estrogen." [GOC:ecd, PMID:15036253, PMID:17975005] 0 0
-17624 3 N GO:0035326 enhancer binding "Interacting selectively and non-covalently with an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter." [GOC:sart, GOC:txnOH, SO:0000165] 0 0
-17777 3 N GO:0035484 adenine/adenine mispair binding "Interacting selectively and non-covalently with double-stranded DNA containing an A/A mispair." [GOC:bf, GOC:jh] 0 0
-17778 3 N GO:0035485 adenine/guanine mispair binding "Interacting selectively and non-covalently with double-stranded DNA containing an A/G mispair." [GOC:bf, GOC:jh] 0 0
-17779 3 N GO:0035486 cytosine/cytosine mispair binding "Interacting selectively and non-covalently with double-stranded DNA containing a C/C mispair." [GOC:bf, GOC:jh] 0 0
-17780 3 N GO:0035487 thymine/thymine mispair binding "Interacting selectively and non-covalently with double-stranded DNA containing a T/T mispair." [GOC:bf, GOC:jh] 0 0
-17781 3 N GO:0035488 cytosine/thymine mispair binding "Interacting selectively and non-covalently with double-stranded DNA containing a C/T mispair." [GOC:bf, GOC:jh] 0 0
-17782 3 N GO:0035489 guanine/guanine mispair binding "Interacting selectively and non-covalently with double-stranded DNA containing a G/G mispair." [GOC:bf, GOC:jh] 0 0
-17790 3 N GO:0035497 cAMP response element binding "Interacting selectively and non-covalently with the cyclic AMP response element (CRE), a short palindrome-containing sequence found in the promoters of genes whose expression is regulated in response to cyclic AMP." [PMID:2875459, PMID:2900470] 0 0
-17831 3 N GO:0035538 carbohydrate response element binding "Interacting selectively and non-covalently with the carbohydrate response element (ChoRE) found in the promoters of genes whose expression is regulated in response to carbohydrates, such as the triglyceride synthesis genes." [GOC:BHF, PMID:20001964] 0 0
-18227 3 N GO:0035939 microsatellite binding "Interacting selectively and non-covalently with a microsatellite, a repeat_region in DNA containing repeat units (2 to 4 base pairs) that is repeated multiple times in tandem." [GOC:yaf, PMID:21290414, SO:0000289] 0 0
-18977 3 N GO:0039631 DNA translocase activity involved in viral DNA genome packaging "Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded DNA molecule, that contributes to the packing of viral DNA into a capsid." [GOC:bm, PMID:17501915] 0 0
-19168 3 N GO:0042162 telomeric DNA binding "Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end." [GOC:jl, SO:0000624] 0 0
-19988 3 N GO:0043035 chromatin insulator sequence binding "Interacting selectively and non-covalently and stoichiometrically with a chromatin insulator sequence, a DNA sequence that prevents enhancer-mediated activation or repression of transcription." [GOC:jl, PMID:12783795] 0 0
-19999 3 N GO:0043047 single-stranded telomeric DNA binding "Interacting selectively and non-covalently with single-stranded telomere-associated DNA." [GOC:jl, ISBN:0321000382] 0 0
-20053 3 N GO:0043110 rDNA spacer replication fork barrier binding "Interacting selectively and non-covalently with replication fork barriers found in rDNA spacers, sites that inhibit replication forks in the direction opposite to rDNA transcription." [GOC:jl, GOC:mah, PMID:14645529] 0 0
-20464 3 gosubset_prok GO:0043565 sequence-specific DNA binding "Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding." [GOC:jl] 0 0
-20465 3 gosubset_prok GO:0043566 structure-specific DNA binding "Interacting selectively and non-covalently with DNA of a specific structure or configuration e.g. triplex DNA binding or bent DNA binding." [GOC:jl] 0 0
-21090 3 N GO:0044212 transcription regulatory region DNA binding "Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:jl, GOC:txnOH, SO:0005836] 0 0
-21091 3 N GO:0044213 intronic transcription regulatory region DNA binding "Interacting selectively and non-covalently with an intronic DNA region that regulates the transcription of the transcript it is contained within." [GOC:ecd, GOC:txnOH] 0 0
-21198 3 N GO:0044323 retinoic acid-responsive element binding "Interacting selectively and non-covalently with a retinoic acid-responsive element, a variable direct repeat of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [GOC:jl, GOC:vw, GOC:yaf, PMID:11327309, PMID:19917671] 0 0
-21249 3 gosubset_prok GO:0044374 sequence-specific DNA binding, bending "The activity of binding selectively and non-covalently to DNA in a sequence-specific manner and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence." [GOC:jl, GOC:vw] 0 0
-21252 3 N GO:0044377 RNA polymerase II core promoter proximal region sequence-specific DNA binding, bending "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence." [GOC:jl] 0 0
-21253 3 gosubset_prok GO:0044378 non-sequence-specific DNA binding, bending "The activity of binding selectively and non-covalently to DNA in a sequence-independent manner and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence." [GOC:jl, GOC:vw, PMID:20123079] 0 0
-21597 3 N GO:0044729 hemi-methylated DNA-binding "Interacting selectively and non-covalently with double-stranded hemi-methylated DNA at replication foci (one strand methylated, while the other strand is unmethylated). Cytosine methylation in DNA is an important mechanism for establishing stable heritable epigenetic marks." [GOC:sp, PMID:18772889] 0 0
-21657 3 N GO:0045027 DNA end binding "Interacting selectively and non-covalently with the ends of DNA that are exposed by the creation of double-strand breaks (DSBs)." [GOC:jl] 0 0
-21759 3 N GO:0045142 triplex DNA binding "Interacting selectively and non-covalently with a DNA triple helix. The formation of triple helical DNA has been evoked in several cellular processes including transcription, replication, and recombination." [PMID:10681538] 0 0
-21911 3 N GO:0045322 unmethylated CpG binding "Interacting selectively and non-covalently with unmethylated CpG motifs. Unmethylated CpG dinucleotides are often associated with gene promoters." [GOC:ai, PMID:10688657] 0 0
-27066 3 N GO:0051880 G-quadruplex DNA binding "Interacting selectively and non-covalently with G-quadruplex DNA structures, in which groups of four guanines adopt a flat, cyclic Hoogsteen hydrogen-bonding arrangement known as a guanine tetrad. The stacking of guanine tetrads results in G-quadruplex DNA structures. G-quadruplex DNA can form under physiological conditions from some G-rich sequences, such as those found in telomeres, immunoglobulin switch regions, gene promoters, fragile X repeats, and the dimerization domain in the human immunodeficiency virus (HIV) genome." [PMID:16142245, PMID:9512530] 0 0
-29618 3 N GO:0061505 DNA topoisomerase II activity "Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; changes the linking number in multiples of 2." [GOC:dph] 0 0
-29619 3 N GO:0061506 DNA topoisomerase type II (ATP-independent) activity "Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is not coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2." [GOC:dph] 0 0
-29959 3 gosubset_prok GO:0070336 flap-structured DNA binding "Interacting selectively and non-covalently with a flap structure in DNA. A DNA flap structure is one in which a single-stranded length of DNA or RNA protrudes from a double-stranded DNA molecule." [GOC:mah, PMID:15189154] 0 0
-29960 3 gosubset_prok GO:0070337 3'-flap-structured DNA binding "Interacting selectively and non-covalently with a 3'-flap structure in DNA. A DNA flap structure is one in which a single-stranded 3'-end of DNA or RNA protrudes from a double-stranded DNA molecule." [GOC:mah, PMID:15189154] 0 0
-29961 3 gosubset_prok GO:0070338 5'-flap-structured DNA binding "Interacting selectively and non-covalently with a 5'-flap structure in DNA. A DNA flap structure is one in which a single-stranded 5'-end of DNA or RNA protrudes from a double-stranded DNA molecule. 5'-flap structures can be formed during DNA repair or lagging strand synthesis; in the latter case RNA flaps form from lagging strand RNA primers." [GOC:mah, PMID:15189154] 0 0
-29984 3 N GO:0070361 mitochondrial light strand promoter anti-sense binding "Interacting selectively and non-covalently with the anti-sense strand of the light strand promoter, a promoter located on the light, or cytosine-rich, strand of mitochondrial DNA." [GOC:mah, PMID:9485316] 0 0
-29985 3 N GO:0070362 mitochondrial heavy strand promoter anti-sense binding "Interacting selectively and non-covalently with the anti-sense strand of the heavy strand promoter, a promoter located on the heavy, or guanine-rich, strand of mitochondrial DNA." [GOC:mah, PMID:9485316] 0 0
-29986 3 N GO:0070363 mitochondrial light strand promoter sense binding "Interacting selectively and non-covalently with the sense strand of the light strand promoter, a promoter located on the light, or cytosine-rich, strand of mitochondrial DNA." [GOC:mah, PMID:9485316] 0 0
-29987 3 N GO:0070364 mitochondrial heavy strand promoter sense binding "Interacting selectively and non-covalently with the sense strand of the heavy strand promoter, a promoter located on the heavy, or guanine-rich, strand of mitochondrial DNA." [GOC:mah, PMID:9485316] 0 0
-30217 3 N GO:0070594 juvenile hormone response element binding "Interacting selectively and non-covalently with the juvenile hormone response element (JHRE), a conserved sequence found in the promoters of genes whose expression is regulated in response to juvenile hormone." [GOC:sart, PMID:17956872] 0 0
-30267 3 N GO:0070644 vitamin D response element binding "Interacting selectively and non-covalently with the vitamin D response element (VDRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum." [GOC:BHF, GOC:vk, PMID:17426122] 0 0
-30510 3 N GO:0070888 E-box binding "Interacting selectively and non-covalently with an E-box, a DNA motif with the consensus sequence CANNTG that is found in the promoters of a wide array of genes expressed in neurons, muscle and other tissues." [GOC:BHF, GOC:vk, PMID:11812799] 0 0
-31065 3 N GO:0071443 tDNA binding "Interacting selectively and non-covalently with DNA sequences encoding transfer RNA." [GOC:mah] 0 0
-31441 3 N GO:0071820 N-box binding "Interacting selectively and non-covalently with an N-box, a DNA motif with the consensus sequence CACNAG that is found in the promoters of genes expressed preferentially at synapses." [GOC:yaf, PMID:11498047] 0 0
-32813 3 N GO:0080084 5S rDNA binding "Interacting selectively and non-covalently with the 5S rDNA sequence encoding ribosomal 5S rRNA, which is individually transcribed by RNA polymerase III, rather than by RNA polymerase I, in species where it exists." [PMID:12711688] 0 0
-33677 3 N GO:0097100 supercoiled DNA binding "Interacting selectively and non-covalently with supercoiled DNA. During replication and transcription, template DNA is negatively supercoiled in the receding downstream DNA and positively supercoiled in the approaching downstream DNA." [GOC:pr, GOC:rph, PMID:20723754, PMID:21345933, Wikipedia:DNA_supercoil] 0 0
-33736 3 N GO:0097159 organic cyclic compound binding "Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure." [CHEBI:33832, GOC:sjw, PMID:7583672] 0 0
-35405 3 N GO:1901363 heterocyclic compound binding "Interacting selectively and non-covalently with heterocyclic compound." [GOC:TermGenie] 0 0
-39579 5 SOFA SO:0000001 region """A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids."" [SO:ke]" 0 0
-39724 5 SOFA SO:0000147 exon """A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing."" [SO:ke]" 0 0
-40233 5 SOFA SO:0000657 repeat_region """A region of sequence containing one or more repeat units."" [SO:ke]" 0 0
-40249 5 SOFA SO:0000673 transcript """An RNA synthesized on a DNA or RNA template by an RNA polymerase."" [SO:ma]" 0 0
-40280 5 SOFA SO:0000704 gene """A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions."" [SO:immuno_workshop]" 0 0
-40582 5 NULL SO:0001009 DNA_constraint_sequence """A double-stranded DNA used to control macromolecular structure and function."" [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au]&dispmax=50]" 0 0
-40633 5 NULL SO:0001060 sequence_variant """A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration."" [SO:ke]" 1 0
-40981 5 SOFA SO:0001411 biological_region """A region defined by its disposition to be involved in a biological process."" [SO:cb]" 0 0
-41106 5 NULL SO:0001537 structural_variant """A sequence variant that changes one or more sequence features."" [SO:ke]" 0 0
-41493 5 SOFA SO:0005836 regulatory_region """A region of sequence that is involved in the control of a biological process."" [SO:ke]" 0 0
-40145 5 NULL SO:0000569 retrotransposed """An attribute of a feature that occurred as the product of a reverse transcriptase mediated event."" [SO:ke]" 0 0
-40788 5 NULL SO:0001217 protein_coding_gene """"" []" 0 0
-40842 5 NULL SO:0001272 tRNA_gene """"" []" 0 0
-41072 5 NULL SO:0001503 processed_transcript """A transcript for which no open reading frame has been identified and for which no other function has been determined."" [MGI:hdeen]" 0 0
-41494 5 SOFA SO:0000340 chromosome "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma] 0 0
-44355 5 N SO:0000234 mRNA "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma] 0 0
+144 3 N GO:0000182 rDNA binding Interacting selectively and non-covalently with DNA sequences encoding ribosomal RNA. [GOC:mah] 0 1 \N
+166 3 N GO:0000217 DNA secondary structure binding Interacting selectively and non-covalently with DNA containing secondary structure elements such as four-way junctions, bubbles, loops, Y-form DNA, or double-strand/single-strand junctions. [GOC:krc] 0 1 \N
+259 3 N GO:0000332 template for synthesis of G-rich strand of telomere DNA activity Provision of the template used by reverse transcriptase to synthesize the G-rich strand of telomeric DNA. [PMID:11812242] 0 0 \N
+304 3 N GO:0000400 four-way junction DNA binding Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. [GOC:krc, ISBN:0815332181, PMID:15563464] 0 0 \N
+305 3 N GO:0000401 open form four-way junction DNA binding Interacting selectively and non-covalently with DNA containing the open form of a four-way junction, also known as a Holliday junction, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. The open form of a four-way junction can be diagrammed without any of the strands crossing over. [GOC:krc, ISBN:0815332181, PMID:15563464] 0 0 \N
+306 3 N GO:0000402 crossed form four-way junction DNA binding Interacting selectively and non-covalently with DNA containing the crossed form of a four-way junction, also known as a Holliday junction, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. The crossed form of a four-way junction cannot be diagrammed without any of the strands crossing over, and instead contains a single crossover between two of the strands. [GOC:krc, ISBN:0815332181, PMID:15563464] 0 0 \N
+307 3 N GO:0000403 Y-form DNA binding Interacting selectively and non-covalently with segment of DNA shaped like a Y. This shape occurs when DNA contains a region of paired double-stranded DNA on one end and a region of unpaired DNA strands on the opposite end. [GOC:elh, PMID:16781730] 0 0 \N
+308 3 N GO:0000404 loop DNA binding Interacting selectively and non-covalently with DNA containing a loop. A loop occurs when DNA contains a large insertion or deletion that causes a region of unpaired single-stranded DNA to loop out, while the rest of the DNA is in a paired double-stranded configuration. [GOC:elh, PMID:16781730] 0 0 \N
+309 3 N GO:0000405 bubble DNA binding Interacting selectively and non-covalently with DNA that contains a bubble. A bubble occurs when DNA contains a region of unpaired, single-stranded DNA flanked on both sides by regions of paired, double-stranded DNA. [GOC:elh, GOC:vw, PMID:16781730] 0 0 \N
+310 3 N GO:0000406 double-strand/single-strand DNA junction binding Interacting selectively and non-covalently with a region of DNA that contains double-stranded DNA flanked by a region of single-stranded DNA. [GOC:elh, PMID:16781730] 0 0 \N
+399 3 N GO:0000497 base pairing with DNA Interacting selectively and non-covalently with nucleic acid via hydrogen bonds between the bases of a gene product molecule and the bases of a target DNA molecule. [GOC:krc] 0 0 \N
+614 3 N GO:0000975 regulatory region DNA binding Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair. [GOC:txnOH] 0 1 \N
+615 3 N GO:0000976 transcription regulatory region sequence-specific DNA binding Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon. [GOC:txnOH] 0 0 \N
+616 3 N GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II. [GOC:txnOH] 0 0 \N
+617 3 N GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II. [GOC:txnOH] 0 1 \N
+618 3 N GO:0000979 RNA polymerase II core promoter sequence-specific DNA binding Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery. [GOC:txnOH] 0 0 \N
+619 3 N GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter. [GOC:txnOH] 0 0 \N
+623 3 gosubset_prok GO:0000984 bacterial-type RNA polymerase regulatory region sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that is part of a regulatory region that controls the transcription of a gene or operon by a bacterial-type RNA polymerase. [GOC:txnOH] 0 0 \N
+624 3 gosubset_prok GO:0000985 bacterial-type RNA polymerase core promoter sequence-specific DNA binding Interacting selectively and non-covalently with a specific DNA sequence in a bacterial-type RNA polymerase core promoter, the region composed of the transcription start site and binding sites for transcription factors of the basal transcription machinery, in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. [GOC:txnOH] 0 0 \N
+625 3 gosubset_prok GO:0000986 bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase. [GOC:txnOH] 0 0 \N
+626 3 N GO:0000987 core promoter proximal region sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon. [GOC:txnOH] 0 0 \N
+631 3 N GO:0000992 polymerase III regulatory region sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that is part of a regulatory region that controls transcription by RNA polymerase III. The transcribed region might be contain a single gene or a cistron containing multiple genes. [GOC:txnOH, PMID:12381659] 0 0 \N
+636 3 N GO:0000997 mitochondrial RNA polymerase core promoter sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that is part of the core promoter for the mitochondrial RNA polymerase. [GOC:txnOH] 0 0 \N
+640 3 N GO:0001002 RNA polymerase III type 1 promoter sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that is a part of a type 1 promoter that controls transcription by RNA polymerase III. Type 1 promoters are found in 5S rRNA genes, downstream of the transcription start site within the sequence of the mature RNA, and require TFIIIA for recognition. [GOC:txnOH, PMID:12381659] 0 0 \N
+641 3 N GO:0001003 RNA polymerase III type 2 promoter sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that is a part of a type 2 promoter that controls transcription by RNA polymerase III. Type 2 promoters consist of an A box and a B box downstream of the transcription start site within the sequence within the sequence of the mature RNA. Type 2 promoters are found in many tRNA genes as well as in other small RNAs. [GOC:txnOH, PMID:12381659] 0 0 \N
+644 3 N GO:0001006 RNA polymerase III type 3 promoter sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that is a part of a type 3 promoter that controls transcription by RNA polymerase III (Pol III). A type 3 Pol III promoter is composed of elements upstream of the transcription start site, including a TATA box. The human U6 snRNA gene has a type 3 promoter. Type 3 Pol III promoters have not been observed in S. cerevisiae. [GOC:txnOH, PMID:12381659] 0 0 \N
+650 3 N GO:0001012 RNA polymerase II regulatory region DNA binding Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by RNA polymerase II. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. [GOC:txnOH, GOC:vw] 0 0 \N
+651 3 N GO:0001013 RNA polymerase I regulatory region DNA binding Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by RNA polymerase I. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. [GOC:txnOH, GOC:vw] 0 0 \N
+654 3 N GO:0001016 RNA polymerase III regulatory region DNA binding Interacting selectively and non-covalently with a DNA region that controls the transcription of a gene by RNA polymerase III. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. [GOC:txnOH, GOC:vw, PMID:12381659] 0 0 \N
+655 3 gosubset_prok GO:0001017 bacterial-type RNA polymerase regulatory region DNA binding Interacting selectively and non-covalently with a DNA region that controls the transcription of a gene or operon by a bacterial-type RNA polymerase. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. [GOC:txnOH] 0 0 \N
+656 3 N GO:0001018 mitochondrial RNA polymerase regulatory region DNA binding Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by mitochondrial RNA polymerase. Binding may occur as a high affinity and sequence specific interaction or as a lower affinity interaction observed once a factor has been recruited to the DNA by other factors. [GOC:txnOH, GOC:vw, PMID:20056105] 0 0 \N
+657 3 N GO:0001019 plastid RNA polymerase regulatory region DNA binding Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by a plastid RNA polymerase. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. [GOC:txnOH, GOC:vw] 0 0 \N
+668 3 N GO:0001030 RNA polymerase III type 1 promoter DNA binding Interacting selectively and non-covalently with a region of DNA that is a part of a type 1 promoter that controls transcription by RNA polymerase III. Type 1 promoters are found in 5S rRNA genes, downstream of the transcription start site within the sequence of the mature RNA, and require TFIIIA for recognition. [GOC:txnOH, PMID:12381659] 0 0 \N
+669 3 N GO:0001031 RNA polymerase III type 2 promoter DNA binding Interacting selectively and non-covalently with a region of DNA that is a part of a type 2 promoter that controls transcription by RNA polymerase III. Type 2 promoters consist of an A box and a B box downstream of the transcription start site within the sequence within the sequence of the mature RNA. Type 2 promoters are found in many tRNA genes as well as in other small RNAs. [GOC:txnOH, PMID:12381659] 0 0 \N
+670 3 N GO:0001032 RNA polymerase III type 3 promoter DNA binding Interacting selectively and non-covalently with a region of DNA that is a part of a type 3 promoter that controls transcription by RNA polymerase III. A type 3 Pol III promoter is composed of elements upstream of the transcription start site, including a TATA box. The human U6 snRNA gene has a type 3 promoter. Type 3 Pol III promoters have not been observed in S. cerevisiae. [GOC:txnOH, PMID:12381659] 0 0 \N
+675 3 N GO:0001037 RNA polymerase III hybrid type promoter DNA binding Interacting selectively and non-covalently with a region of DNA that is a part of a hybrid promoter that controls transcription by RNA polymerase III (Pol III). A hybrid Pol III promoter contains both regulatory elements both upstream and downstream of the transcription initiation site. An example gene with such a promoter is the S. cerevisiae U6 gene. [GOC:txnOH, PMID:12381659] 0 0 \N
+677 3 N GO:0001039 RNA polymerase III hybrid type promoter sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that is a part of a hybrid type promoter that controls transcription by RNA polymerase III (Pol III). A hybrid Pol III promoter contains both regulatory elements both upstream and downstream of the transcription initiation site. An example gene with such a promoter is the S. cerevisiae U6 gene. [GOC:txnOH, PMID:12381659] 0 0 \N
+682 3 N GO:0001044 mitochondrial RNA polymerase regulatory region sequence-specific DNA binding Interacting selectively and non-covalently with a specific sequence of DNA that controls the transcription of a region of DNA by mitochondrial RNA polymerase. [GOC:txnOH] 0 0 \N
+683 3 N GO:0001045 mitochondrial RNA polymerase core promoter proximal region sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a mitochondrial RNA polymerase. [GOC:txnOH, PMID:20670382] 0 0 \N
+684 3 N GO:0001046 core promoter sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region composed of the transcription start site and binding sites for the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon. [GOC:txnOH] 0 0 \N
+685 3 N GO:0001047 core promoter binding Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. [GOC:txnOH] 0 0 \N
+782 3 N GO:0001145 mitochondrial RNA polymerase termination site sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that is a terminator for mitochondrial RNA polymerase. [GOC:txnOH, PMID:18391175] 0 0 \N
+784 3 N GO:0001147 transcription termination site sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that promotes termination by RNA polymerase. The transcribed region might be described as a gene, cistron, or operon. [GOC:txnOH, PMID:18280161, PMID:18391175] 0 0 \N
+785 3 N GO:0001148 bacterial-type RNA polymerase termination site sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that is a terminator for bacterial-type RNA polymerase. [GOC:txnOH, PMID:18280161] 0 0 \N
+787 3 N GO:0001150 bacterial-type RNA polymerase enhancer sequence-specific DNA binding Interacting selectively and non-covalently with a sequence of DNA that is an enhancer region that helps activate transcription of a gene or operon by a bacterial-type RNA polymerase. Enhancers for sigma-54 holoenzymes are typically located 80 to 150 base pairs upstream from the transcription start site, although they can be further away or may be downstream of the promoter. Some transcription units dependent on sigma-70 holoenzymes may also include enhancer sequences. [GOC:txnOH, PMID:11282468, PMID:20629756] 0 0 \N
+795 3 N GO:0001158 enhancer sequence-specific DNA binding Interacting selectively and non-covalently with a specific sequence of DNA that is part of an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter. [GOC:txnOH] 0 0 \N
+796 3 N GO:0001159 core promoter proximal region DNA binding Interacting selectively and non-covalently with a region of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon. [GOC:txnOH] 0 0 \N
+797 3 N GO:0001160 transcription termination site DNA binding Interacting selectively and non-covalently with a region of DNA that promotes termination by RNA polymerase. The transcribed region might be described as a gene, cistron, or operon. [GOC:txnOH] 0 0 \N
+798 3 N GO:0001161 intronic transcription regulatory region sequence-specific DNA binding Interacting selectively and non-covalently with an intronic DNA sequence that regulates the transcription of the transcript it is contained within. [GOC:txnOH] 0 0 \N
+799 3 N GO:0001162 RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding Interacting selectively and non-covalently with an RNA polymerase II intronic DNA sequence that regulates the transcription of the transcript it is contained within. [GOC:txnOH] 0 0 \N
+800 3 N GO:0001163 RNA polymerase I regulatory region sequence-specific DNA binding Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase I. [GOC:txnOH] 0 0 \N
+801 3 N GO:0001164 RNA polymerase I CORE element sequence-specific DNA binding Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery. This site is often referred to as the CORE element. In mammalian cells, the CORE element functions in conjunction with the Upstream Control Element (UCE), while in fungi, protozoa, and plants, the CORE element functions without a UCE. [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832] 0 0 \N
+802 3 N GO:0001165 RNA polymerase I upstream control element sequence-specific DNA binding Interacting selectively and non-covalently with the upstream control element (UCE, or alternately referred to as the upstream element), a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase I. [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832] 0 0 \N
+803 3 N GO:0001166 RNA polymerase I enhancer sequence-specific DNA binding Interacting selectively and non-covalently with a RNA polymerase I (Pol I) enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter. [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832] 0 0 \N
+2688 3 goslim_aspergillus,goslim_candida,goslim_generic,goslim_metagenomics,goslim_pir,goslim_plant,goslim_yeast,gosubset_prok GO:0003674 molecular_function Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. [GOC:go_curators] 1 0 \N
+2689 3 goslim_metagenomics,goslim_pir,goslim_plant,gosubset_prok GO:0003676 nucleic acid binding Interacting selectively and non-covalently with any nucleic acid. [GOC:jl] 0 0 \N
+2690 3 goslim_aspergillus,goslim_candida,goslim_generic,goslim_plant,goslim_yeast,gosubset_prok GO:0003677 DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). [GOC:dph, GOC:jl, GOC:tb, GOC:vw] 0 0 \N
+2692 3 N GO:0003680 AT DNA binding Interacting selectively and non-covalently with oligo(A) and oligo(T) tracts of DNA (AT DNA). [GOC:jl, PMID:2670564] 0 0 \N
+2693 3 gosubset_prok GO:0003681 bent DNA binding Interacting selectively and non-covalently with DNA in a bent conformation. [GOC:jl, PMID:12627977] 0 0 \N
+2695 3 gosubset_prok GO:0003684 damaged DNA binding Interacting selectively and non-covalently with damaged DNA. [GOC:jl] 0 0 \N
+2696 3 gosubset_prok GO:0003688 DNA replication origin binding Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally. [GOC:curators] 0 0 \N
+2697 3 gosubset_prok GO:0003689 DNA clamp loader activity Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the opening of the ring structure of the PCNA complex, or any of the related sliding clamp complexes, and their closing around the DNA duplex. [GOC:mah, GOC:vw, PMID:16082778] 0 0 \N
+2698 3 gosubset_prok GO:0003690 double-stranded DNA binding Interacting selectively and non-covalently with double-stranded DNA. [GOC:elh] 0 0 \N
+2699 3 N GO:0003691 double-stranded telomeric DNA binding Interacting selectively and non-covalently with double-stranded telomere-associated DNA. [GOC:jl, ISBN:0321000382] 0 0 \N
+2700 3 N GO:0003692 left-handed Z-DNA binding Interacting selectively and non-covalently with DNA in the Z form, i.e. a left-handed helix in which the phosphate backbone zigzags. [ISBN:0716720094] 0 0 \N
+2701 3 N GO:0003693 P-element binding Interacting selectively and non-covalently with any P-element, a class of Drosophila transposon responsible for hybrid dysgenesis. [GOC:jl, PMID:9440262] 0 0 \N
+2702 3 N GO:0003695 random coil DNA binding Interacting selectively and non-covalently with DNA in a random coil configuration. [GOC:mah] 0 0 \N
+2703 3 N GO:0003696 satellite DNA binding Interacting selectively and non-covalently with satellite DNA, the many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA. [GOC:jl, SO:0000005] 0 0 \N
+2704 3 gosubset_prok GO:0003697 single-stranded DNA binding Interacting selectively and non-covalently with single-stranded DNA. [GOC:elh] 0 0 \N
+2811 3 gosubset_prok GO:0003916 DNA topoisomerase activity Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA. [GOC:mah, PMID:8811192] 0 0 \N
+2812 3 gosubset_prok GO:0003917 DNA topoisomerase type I activity Catalysis of a DNA topological transformation by transiently cleaving one DNA strand at a time to allow passage of another strand; changes the linking number by +1 per catalytic cycle. [PMID:8811192] 0 0 \N
+2813 3 gosubset_prok GO:0003918 DNA topoisomerase type II (ATP-hydrolyzing) activity Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2. [PMID:8811192] 0 0 \N
+3916 3 goslim_pir,goslim_plant,gosubset_prok GO:0005488 binding The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. [GOC:ceb, GOC:mah, ISBN:0198506732] 0 0 \N
+5856 3 gosubset_prok GO:0008301 DNA binding, bending The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence. [GOC:krc, GOC:vw, PMID:10710711, PMID:19037758] 0 0 \N
+5875 3 N GO:0008327 methyl-CpG binding Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide. [GOC:jl, PMID:11746232] 0 0 \N
+7628 3 N GO:0010385 double-stranded methylated DNA binding Interacting selectively and non-covalently with double-stranded methylated DNA. Cytosine methylation in DNA is an important mechanism for establishing stable heritable epigenetic marks. [PMID:17242155] 0 0 \N
+7966 3 N GO:0010736 serum response element binding Interacting selectively and non-covalently with the serum response element (SRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum. [GOC:BHF, GOC:dph, GOC:rl, GOC:tb] 0 0 \N
+8072 3 N GO:0010844 recombination hotspot binding Interacting selectively and non-covalently with a region in a genome which promotes recombination. [GOC:dph, GOC:tb] 0 0 \N
+8912 3 N GO:0015616 DNA translocase activity Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded DNA molecule. [GOC:mah, PMID:16428451, PMID:17631491] 0 0 \N
+11234 3 N GO:0019237 centromeric DNA binding Interacting selectively and non-covalently with a centromere, a region of chromosome where the spindle fibers attach during mitosis and meiosis. [GOC:jl, SO:0000577] 0 0 \N
+13423 3 N GO:0030983 mismatched DNA binding Interacting selectively and non-covalently with double-stranded DNA containing one or more mismatches. [GOC:mah] 0 0 \N
+13890 3 N GO:0031490 chromatin DNA binding Interacting selectively and non-covalently with DNA that is assembled into chromatin. [GOC:mah] 0 0 \N
+13892 3 N GO:0031492 nucleosomal DNA binding Interacting selectively and non-covalently with the DNA portion of a nucleosome. [GOC:mah] 0 0 \N
+14031 3 N GO:0031634 replication fork barrier binding Interacting selectively and non-covalently with replication fork barriers, sites that inhibit the progress of replication forks. [GOC:mah] 0 0 \N
+14511 3 N GO:0032131 alkylated DNA binding Interacting selectively and non-covalently with alkylated residues in DNA. [GOC:mah] 0 0 \N
+14512 3 N GO:0032132 O6-alkylguanine-DNA binding Interacting selectively and non-covalently with O6-alkylguanine adducts in DNA. [GOC:mah, PMID:16679453] 0 0 \N
+14514 3 N GO:0032135 DNA insertion or deletion binding Interacting selectively and non-covalently with double-stranded DNA containing insertions or deletions. [GOC:vk] 0 0 \N
+14515 3 N GO:0032136 adenine/cytosine mispair binding Interacting selectively and non-covalently with double-stranded DNA containing an A/C mispair. [GOC:vk] 0 0 \N
+14516 3 N GO:0032137 guanine/thymine mispair binding Interacting selectively and non-covalently with double-stranded DNA containing a G/T mispair. [GOC:vk] 0 0 \N
+14517 3 N GO:0032138 single base insertion or deletion binding Interacting selectively and non-covalently with double-stranded DNA containing a single base insertion or deletion. [GOC:vk] 0 0 \N
+14518 3 N GO:0032139 dinucleotide insertion or deletion binding Interacting selectively and non-covalently with double-stranded DNA containing a dinucleotide insertion or deletion. [GOC:vk] 0 0 \N
+14519 3 N GO:0032140 single adenine insertion binding Interacting selectively and non-covalently with double-stranded DNA containing a single adenine insertion or a deletion that results in an unpaired adenine. [GOC:mah, GOC:vk] 0 0 \N
+14520 3 N GO:0032141 single cytosine insertion binding Interacting selectively and non-covalently with double-stranded DNA containing a single cytosine insertion or a deletion that results in an unpaired cytosine. [GOC:mah, GOC:vk] 0 0 \N
+14521 3 N GO:0032142 single guanine insertion binding Interacting selectively and non-covalently with double-stranded DNA containing a single guanine insertion or a deletion that results in an unpaired guanine. [GOC:mah, GOC:vk] 0 0 \N
+14522 3 N GO:0032143 single thymine insertion binding Interacting selectively and non-covalently with double-stranded DNA containing a single thymine insertion or a deletion that results in an unpaired thymine. [GOC:mah, GOC:vk] 0 0 \N
+14559 3 N GO:0032181 dinucleotide repeat insertion binding Interacting selectively and non-covalently with double-stranded DNA containing a dinucleotide repeat insertion or a deletion resulting in unpaired dinucleotide repeats. [GOC:mah, GOC:vk] 0 0 \N
+14729 3 N GO:0032356 oxidized DNA binding Interacting selectively and non-covalently with oxidized residues in DNA. [GOC:vk] 0 0 \N
+14730 3 N GO:0032357 oxidized purine DNA binding Interacting selectively and non-covalently with oxidized purine residues in DNA. [GOC:vk] 0 0 \N
+14731 3 N GO:0032358 oxidized pyrimidine DNA binding Interacting selectively and non-covalently with oxidized pyrimidine residues in DNA. [GOC:vk] 0 0 \N
+14794 3 N GO:0032422 purine-rich negative regulatory element binding Interacting selectively and non-covalently with a 30-bp purine-rich negative regulatory element; the best characterized such element is found in the first intronic region of the rat cardiac alpha-myosin heavy chain gene, and contains two palindromic high-affinity Ets-binding sites (CTTCCCTGGAAG). The presence of this element restricts expression of the gene containing it to cardiac myocytes. [GOC:mah, PMID:9819411] 0 0 \N
+14820 3 N GO:0032448 DNA hairpin binding Interacting selectively and non-covalently with DNA containing a hairpin. A hairpin structure forms when a DNA strand folds back on itself and intrachain base pairing occurs between inverted repeat sequences. [GOC:mah, ISBN:0198506732] 0 0 \N
+15175 3 N GO:0032810 sterol response element binding Interacting selectively and non-covalently with the sterol response element (SRE), a nonpalindromic sequence found in the promoters of genes involved in lipid metabolism. [GOC:vk, PMID:11994399] 0 0 \N
+16393 3 N GO:0034056 estrogen response element binding Interacting selectively and non-covalently with the estrogen response element (ERE), a conserved sequence found in the promoters of genes whose expression is regulated in response to estrogen. [GOC:ecd, PMID:15036253, PMID:17975005] 0 0 \N
+17624 3 N GO:0035326 enhancer binding Interacting selectively and non-covalently with an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter. [GOC:sart, GOC:txnOH, SO:0000165] 0 0 \N
+17777 3 N GO:0035484 adenine/adenine mispair binding Interacting selectively and non-covalently with double-stranded DNA containing an A/A mispair. [GOC:bf, GOC:jh] 0 0 \N
+17778 3 N GO:0035485 adenine/guanine mispair binding Interacting selectively and non-covalently with double-stranded DNA containing an A/G mispair. [GOC:bf, GOC:jh] 0 0 \N
+17779 3 N GO:0035486 cytosine/cytosine mispair binding Interacting selectively and non-covalently with double-stranded DNA containing a C/C mispair. [GOC:bf, GOC:jh] 0 0 \N
+17780 3 N GO:0035487 thymine/thymine mispair binding Interacting selectively and non-covalently with double-stranded DNA containing a T/T mispair. [GOC:bf, GOC:jh] 0 0 \N
+17781 3 N GO:0035488 cytosine/thymine mispair binding Interacting selectively and non-covalently with double-stranded DNA containing a C/T mispair. [GOC:bf, GOC:jh] 0 0 \N
+17782 3 N GO:0035489 guanine/guanine mispair binding Interacting selectively and non-covalently with double-stranded DNA containing a G/G mispair. [GOC:bf, GOC:jh] 0 0 \N
+17790 3 N GO:0035497 cAMP response element binding Interacting selectively and non-covalently with the cyclic AMP response element (CRE), a short palindrome-containing sequence found in the promoters of genes whose expression is regulated in response to cyclic AMP. [PMID:2875459, PMID:2900470] 0 0 \N
+17831 3 N GO:0035538 carbohydrate response element binding Interacting selectively and non-covalently with the carbohydrate response element (ChoRE) found in the promoters of genes whose expression is regulated in response to carbohydrates, such as the triglyceride synthesis genes. [GOC:BHF, PMID:20001964] 0 0 \N
+18227 3 N GO:0035939 microsatellite binding Interacting selectively and non-covalently with a microsatellite, a repeat_region in DNA containing repeat units (2 to 4 base pairs) that is repeated multiple times in tandem. [GOC:yaf, PMID:21290414, SO:0000289] 0 0 \N
+18977 3 N GO:0039631 DNA translocase activity involved in viral DNA genome packaging Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded DNA molecule, that contributes to the packing of viral DNA into a capsid. [GOC:bm, PMID:17501915] 0 0 \N
+19168 3 N GO:0042162 telomeric DNA binding Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end. [GOC:jl, SO:0000624] 0 0 \N
+19988 3 N GO:0043035 chromatin insulator sequence binding Interacting selectively and non-covalently and stoichiometrically with a chromatin insulator sequence, a DNA sequence that prevents enhancer-mediated activation or repression of transcription. [GOC:jl, PMID:12783795] 0 0 \N
+19999 3 N GO:0043047 single-stranded telomeric DNA binding Interacting selectively and non-covalently with single-stranded telomere-associated DNA. [GOC:jl, ISBN:0321000382] 0 0 \N
+20053 3 N GO:0043110 rDNA spacer replication fork barrier binding Interacting selectively and non-covalently with replication fork barriers found in rDNA spacers, sites that inhibit replication forks in the direction opposite to rDNA transcription. [GOC:jl, GOC:mah, PMID:14645529] 0 0 \N
+20464 3 gosubset_prok GO:0043565 sequence-specific DNA binding Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. [GOC:jl] 0 0 \N
+20465 3 gosubset_prok GO:0043566 structure-specific DNA binding Interacting selectively and non-covalently with DNA of a specific structure or configuration e.g. triplex DNA binding or bent DNA binding. [GOC:jl] 0 0 \N
+21090 3 N GO:0044212 transcription regulatory region DNA binding Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors. [GOC:jl, GOC:txnOH, SO:0005836] 0 0 \N
+21091 3 N GO:0044213 intronic transcription regulatory region DNA binding Interacting selectively and non-covalently with an intronic DNA region that regulates the transcription of the transcript it is contained within. [GOC:ecd, GOC:txnOH] 0 0 \N
+21198 3 N GO:0044323 retinoic acid-responsive element binding Interacting selectively and non-covalently with a retinoic acid-responsive element, a variable direct repeat of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind. [GOC:jl, GOC:vw, GOC:yaf, PMID:11327309, PMID:19917671] 0 0 \N
+21249 3 gosubset_prok GO:0044374 sequence-specific DNA binding, bending The activity of binding selectively and non-covalently to DNA in a sequence-specific manner and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence. [GOC:jl, GOC:vw] 0 0 \N
+21252 3 N GO:0044377 RNA polymerase II core promoter proximal region sequence-specific DNA binding, bending Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence. [GOC:jl] 0 0 \N
+21253 3 gosubset_prok GO:0044378 non-sequence-specific DNA binding, bending The activity of binding selectively and non-covalently to DNA in a sequence-independent manner and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence. [GOC:jl, GOC:vw, PMID:20123079] 0 0 \N
+21597 3 N GO:0044729 hemi-methylated DNA-binding Interacting selectively and non-covalently with double-stranded hemi-methylated DNA at replication foci (one strand methylated, while the other strand is unmethylated). Cytosine methylation in DNA is an important mechanism for establishing stable heritable epigenetic marks. [GOC:sp, PMID:18772889] 0 0 \N
+21657 3 N GO:0045027 DNA end binding Interacting selectively and non-covalently with the ends of DNA that are exposed by the creation of double-strand breaks (DSBs). [GOC:jl] 0 0 \N
+21759 3 N GO:0045142 triplex DNA binding Interacting selectively and non-covalently with a DNA triple helix. The formation of triple helical DNA has been evoked in several cellular processes including transcription, replication, and recombination. [PMID:10681538] 0 0 \N
+21911 3 N GO:0045322 unmethylated CpG binding Interacting selectively and non-covalently with unmethylated CpG motifs. Unmethylated CpG dinucleotides are often associated with gene promoters. [GOC:ai, PMID:10688657] 0 0 \N
+27066 3 N GO:0051880 G-quadruplex DNA binding Interacting selectively and non-covalently with G-quadruplex DNA structures, in which groups of four guanines adopt a flat, cyclic Hoogsteen hydrogen-bonding arrangement known as a guanine tetrad. The stacking of guanine tetrads results in G-quadruplex DNA structures. G-quadruplex DNA can form under physiological conditions from some G-rich sequences, such as those found in telomeres, immunoglobulin switch regions, gene promoters, fragile X repeats, and the dimerization domain in the human immunodeficiency virus (HIV) genome. [PMID:16142245, PMID:9512530] 0 0 \N
+29618 3 N GO:0061505 DNA topoisomerase II activity Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; changes the linking number in multiples of 2. [GOC:dph] 0 0 \N
+29619 3 N GO:0061506 DNA topoisomerase type II (ATP-independent) activity Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is not coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2. [GOC:dph] 0 0 \N
+29959 3 gosubset_prok GO:0070336 flap-structured DNA binding Interacting selectively and non-covalently with a flap structure in DNA. A DNA flap structure is one in which a single-stranded length of DNA or RNA protrudes from a double-stranded DNA molecule. [GOC:mah, PMID:15189154] 0 0 \N
+29960 3 gosubset_prok GO:0070337 3'-flap-structured DNA binding Interacting selectively and non-covalently with a 3'-flap structure in DNA. A DNA flap structure is one in which a single-stranded 3'-end of DNA or RNA protrudes from a double-stranded DNA molecule. [GOC:mah, PMID:15189154] 0 0 \N
+29961 3 gosubset_prok GO:0070338 5'-flap-structured DNA binding Interacting selectively and non-covalently with a 5'-flap structure in DNA. A DNA flap structure is one in which a single-stranded 5'-end of DNA or RNA protrudes from a double-stranded DNA molecule. 5'-flap structures can be formed during DNA repair or lagging strand synthesis; in the latter case RNA flaps form from lagging strand RNA primers. [GOC:mah, PMID:15189154] 0 0 \N
+29984 3 N GO:0070361 mitochondrial light strand promoter anti-sense binding Interacting selectively and non-covalently with the anti-sense strand of the light strand promoter, a promoter located on the light, or cytosine-rich, strand of mitochondrial DNA. [GOC:mah, PMID:9485316] 0 0 \N
+29985 3 N GO:0070362 mitochondrial heavy strand promoter anti-sense binding Interacting selectively and non-covalently with the anti-sense strand of the heavy strand promoter, a promoter located on the heavy, or guanine-rich, strand of mitochondrial DNA. [GOC:mah, PMID:9485316] 0 0 \N
+29986 3 N GO:0070363 mitochondrial light strand promoter sense binding Interacting selectively and non-covalently with the sense strand of the light strand promoter, a promoter located on the light, or cytosine-rich, strand of mitochondrial DNA. [GOC:mah, PMID:9485316] 0 0 \N
+29987 3 N GO:0070364 mitochondrial heavy strand promoter sense binding Interacting selectively and non-covalently with the sense strand of the heavy strand promoter, a promoter located on the heavy, or guanine-rich, strand of mitochondrial DNA. [GOC:mah, PMID:9485316] 0 0 \N
+30217 3 N GO:0070594 juvenile hormone response element binding Interacting selectively and non-covalently with the juvenile hormone response element (JHRE), a conserved sequence found in the promoters of genes whose expression is regulated in response to juvenile hormone. [GOC:sart, PMID:17956872] 0 0 \N
+30267 3 N GO:0070644 vitamin D response element binding Interacting selectively and non-covalently with the vitamin D response element (VDRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum. [GOC:BHF, GOC:vk, PMID:17426122] 0 0 \N
+30510 3 N GO:0070888 E-box binding Interacting selectively and non-covalently with an E-box, a DNA motif with the consensus sequence CANNTG that is found in the promoters of a wide array of genes expressed in neurons, muscle and other tissues. [GOC:BHF, GOC:vk, PMID:11812799] 0 0 \N
+31065 3 N GO:0071443 tDNA binding Interacting selectively and non-covalently with DNA sequences encoding transfer RNA. [GOC:mah] 0 0 \N
+31441 3 N GO:0071820 N-box binding Interacting selectively and non-covalently with an N-box, a DNA motif with the consensus sequence CACNAG that is found in the promoters of genes expressed preferentially at synapses. [GOC:yaf, PMID:11498047] 0 0 \N
+32813 3 N GO:0080084 5S rDNA binding Interacting selectively and non-covalently with the 5S rDNA sequence encoding ribosomal 5S rRNA, which is individually transcribed by RNA polymerase III, rather than by RNA polymerase I, in species where it exists. [PMID:12711688] 0 0 \N
+33677 3 N GO:0097100 supercoiled DNA binding Interacting selectively and non-covalently with supercoiled DNA. During replication and transcription, template DNA is negatively supercoiled in the receding downstream DNA and positively supercoiled in the approaching downstream DNA. [GOC:pr, GOC:rph, PMID:20723754, PMID:21345933, Wikipedia:DNA_supercoil] 0 0 \N
+33736 3 N GO:0097159 organic cyclic compound binding Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure. [CHEBI:33832, GOC:sjw, PMID:7583672] 0 0 \N
+35405 3 N GO:1901363 heterocyclic compound binding Interacting selectively and non-covalently with heterocyclic compound. [GOC:TermGenie] 0 0 \N
+39579 5 SOFA SO:0000001 region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. [SO:ke] 0 0 \N
+39724 5 SOFA SO:0000147 exon A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. [SO:ke] 0 0 \N
+40233 5 SOFA SO:0000657 repeat_region A region of sequence containing one or more repeat units. [SO:ke] 0 0 \N
+40249 5 SOFA SO:0000673 transcript An RNA synthesized on a DNA or RNA template by an RNA polymerase. [SO:ma] 0 0 \N
+40280 5 SOFA SO:0000704 gene A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. [SO:immuno_workshop] 0 0 \N
+40582 5 NULL SO:0001009 DNA_constraint_sequence A double-stranded DNA used to control macromolecular structure and function. [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au]&dispmax=50] 0 0 \N
+40633 5 NULL SO:0001060 sequence_variant A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. [SO:ke] 1 0 \N
+40981 5 SOFA SO:0001411 biological_region A region defined by its disposition to be involved in a biological process. [SO:cb] 0 0 \N
+41106 5 NULL SO:0001537 structural_variant A sequence variant that changes one or more sequence features. [SO:ke] 0 0 \N
+41493 5 SOFA SO:0005836 regulatory_region A region of sequence that is involved in the control of a biological process. [SO:ke] 0 0 \N
+40145 5 NULL SO:0000569 retrotransposed An attribute of a feature that occurred as the product of a reverse transcriptase mediated event. [SO:ke] 0 0 \N
+40788 5 NULL SO:0001217 protein_coding_gene [] 0 0 \N
+40842 5 NULL SO:0001272 tRNA_gene. [] 0 0 \N
+41072 5 NULL SO:0001503 processed_transcript A transcript for which no open reading frame has been identified and for which no other function has been determined. [MGI:hdeen] 0 0 \N
+41494 5 SOFA SO:0000340 chromosome Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication. [SO:ma] 0 0 \N
+43394 5 SOFA SO:0000253 tRNA Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732] 0 0 \N
+44395 5 NULL SO:0001263 ncRNA_gene [] 0 0 \N
+45000 5 NULL SO:0001877 lnc_RNA A non-coding RNA over 200nucleotides in length. [HGNC:mw] 0 0 \N
+43375 5 SOFA SO:0000234 mRNA Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. [SO:ma] 0 0 \N
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