Difference between revisions of "FlyBase Field Mapping Tables"
From GMOD
(Adding a first draft of the FlyBase gene report mapping table.) |
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Revision as of 20:03, 4 June 2008
| Field Name | |
|---|---|
| General information | |
| Symbol | SELECT distinct(s.name) from feature f, feature_synonym fs, synonym s, cvterm cvt, cvterm cvt2 where f.type_id = cvt.cvterm_id and cvt.name = 'gene' and f.feature_id = fs.feature_id and fs.synonym_id = s.synonym_id and fs.is_current = 't' and fs.is_internal = 'f' and s.type_id = cvt2.cvterm_id and cvt2.name = 'symbol' and f.is_obsolete = 'f' and f.uniquename = 'FBgn0000011'; |
| Species | SELECT f.uniquename, f.name, o.genus, o.species from feature f, cvterm cvt, organism o where f.type_id = cvt.cvterm_id and cvt.name = 'gene' and f.is_obsolete = 'f' and f.uniquename like 'FBgn%' and f.organism_id = o.organism_id; |
| Name | SELECT distinct(s.name) from feature f, feature_synonym fs, synonym s, cvterm cvt, cvterm cvt2 where f.type_id = cvt.cvterm_id and cvt.name = 'gene' and f.feature_id = fs.feature_id and fs.synonym_id = s.synonym_id and fs.is_current = 't' and fs.is_internal = 'f' and s.type_id = cvt2.cvterm_id and cvt2.name = 'fullname' and f.is_obsolete = 'f' and f.uniquename = 'FBgn0000011'; |
| Annotation symbol | SELECT accession from feature f, feature_dbxref fd, dbxref d, db where f.feature_id = fd.feature_id and fd.dbxref_id = d.dbxref_id and fd.is_current = 't' and d.db_id = db.db_id and db.name = 'FlyBase Annotation IDs' and f.uniquename = 'FBgn0000011'; |
| Feature type | SELECT fp.value from feature f, featureprop fp, cvterm cvt where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and cvt.name = 'promoted_gene_type' and f.uniquename = 'FBgn0000011'; |
| FlyBase ID | SELECT f.uniquename from feature f, cvterm cvt where f.type_id = cvt.cvterm_id and cvt.name = 'gene' and f.name = 'ab'; |
| Created/Updated | SELECT timeaccessioned, timelastmodified from feature f where uniquename = 'FBgn0000011' |
| Gene Model Status | SELECT fp.value from feature f, featureprop fp, cvterm cvt where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and cvt.name = 'derived_gene_model_status' and f.uniquename = 'FBgn0000011'; |
| Genetic Status | |
| GENOMIC LOCATION | |
| Chromosome arm | SELECT a.uniquename from feature f, featureloc fl, feature a where f.feature_id = fl.feature_id and fl.srcfeature_id = a.feature_id and f.uniquename = 'FBgn0000011'; |
| Recombination map | SELECT fp.value from feature f, featureprop fp, cvterm cvt where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and cvt.name = 'promoted_genetic_location' and f.uniquename = 'FBgn0000011'; |
| Cytogenetic map | SELECT fp.value from feature f, featureprop fp, cvterm cvt where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and cvt.name = 'derived_computed_cyto' and f.uniquename = 'FBgn0000011'; |
| Sequence location | SELECT s.uniquename, fmin, fmax, strand from feature f, featureloc fl, feature s where f.feature_id = fl.feature_id and fl.srcfeature_id = s.feature_id and f.uniquename = 'FBgn0000011'; |
| DETAILED MAPPING DATA | |
| FlyBase computed cytological location | |
| Cytogenetic map | SELECT fp.value from feature f, featureprop fp, cvterm cvt where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and cvt.name = 'derived_computed_cyto' and f.uniquename = 'FBgn0000011'; |
| Evidence for location | SELECT fp.value from feature f, featureprop fp, cvterm cvt where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and cvt.name = 'derived_computed_cyto' and f.uniquename = 'FBgn0000011'; |
| Experimentally determined cytological location | |
| Cytogenetic map | SELECT fp.value from feature f, featureprop fp, cvterm cvt where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and cvt.name = 'derived_experimental_cyto' and f.uniquename = 'FBgn0000011'; |
| Notes | SELECT fp.value from feature f, featureprop fp, cvterm cvt where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and cvt.name = 'cyto_loc_comment' and f.uniquename = 'FBgn0000011'; |
| Reference | SELECT f.uniquename, fp.value, p.uniquename from feature f, featureprop fp, cvterm cvt, featureprop_pub fpp, pub p where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and cvt.name = 'cyto_loc_comment' and fp.featureprop_id = fpp.featureprop_id and fpp.pub_id = p.pub_id and f.uniquename = 'FBgn0000060'; |
| Experimentally determined recombination data | |
| Location | SELECT fp.value from feature f, featureprop fp, cvterm cvt where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and cvt.name = 'genetic_location' and f.uniquename = 'FBgn0000011'; |
| Left of (cM) | select f.uniquename, f.name, cvt.name, o.uniquename, o.name, p.uniquename from feature f, feature_relationship fr, cvterm cvt, feature o, feature_relationship_pub frp, pub p where f.feature_id = subject_id and object_id = o.feature_id and fr.feature_relationship_id = frp.feature_relationship_id and frp.pub_id = p.pub_id and fr.type_id = cvt.cvterm_id and cvt.name = 'recom_right_end' and f.uniquename = 'FBgn0000051'; |
| Right of (cM) | select f.uniquename, f.name, cvt.name, o.uniquename, o.name, p.uniquename from feature f, feature_relationship fr, cvterm cvt, feature o, feature_relationship_pub frp, pub p where f.feature_id = subject_id and object_id = o.feature_id and fr.feature_relationship_id = frp.feature_relationship_id and frp.pub_id = p.pub_id and fr.type_id = cvt.cvterm_id and cvt.name = 'recom_left_end' and f.uniquename = 'FBgn0000051'; |
| Notes | SELECT f.uniquename, fp.value, p.uniquename from feature f, featureprop fp, cvterm cvt, featureprop_pub fpp, pub p where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and cvt.name = 'cyto_loc_comment' and fp.featureprop_id = fpp.featureprop_id and fpp.pub_id = p.pub_id and f.uniquename = 'FBgn0000060'; |
| Reference | |
| Molecular map data | |
| Gene Order (in direction of increasing cytology) |
SELECT fp.value, p.uniquename from feature f, featureprop fp, cvterm cvt, featureprop_pub fpp, pub p where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and fp.featureprop_id = fpp.featureprop_id and fpp.pub_id = p.pub_id and cvt.name = 'gene_order' and fp.value like 'Gene order: In direction%' and f.uniquename = 'FBgn0000011'; |
| Reference | |
| Gene Order (overall orientation not stated) |
SELECT fp.value, p.uniquename from feature f, featureprop fp, cvterm cvt, featureprop_pub fpp, pub p where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and fp.featureprop_id = fpp.featureprop_id and fpp.pub_id = p.pub_id and cvt.name = 'gene_order' and fp.value like 'Gene order: In direction%' and f.uniquename = 'FBgn0000053'; |
| Reference | |
| SYNONYMS AND SECONDARY IDs | |
| REPORTED AS | |
| Symbol Synonym | SELECT f.uniquename, f.name, s.name as synonym, synonym_sgml, cvt.name, p.uniquename FROM cvterm cvt, feature f, feature_synonym fs, synonym s, pub p WHERE f.feature_id = fs.feature_id and fs.synonym_id = s.synonym_id and fs.pub_id = p.pub_id and s.type_id = cvt.cvterm_id and cvt.name = 'symbol' and fs.is_current = 'f' and f.uniquename = 'FBgn0000011'; |
| Name Synonym | SELECT f.uniquename, f.name, s.name as synonym, synonym_sgml, cvt.name, p.uniquename FROM cvterm cvt, feature f, feature_synonym fs, synonym s, pub p WHERE f.feature_id = fs.feature_id and fs.synonym_id = s.synonym_id and fs.pub_id = p.pub_id and s.type_id = cvt.cvterm_id and cvt.name = 'fullname' and fs.is_current = 'f' and f.uniquename = 'FBgn0000011'; |
| SECONDARY FLYBASE IDs | SELECT f.uniquename, f.name, accession, db.name from feature f, feature_dbxref fd, dbxref d, db where f.feature_id = fd.feature_id and fd.dbxref_id = d.dbxref_id and fd.is_current = 'f' and d.db_id = db.db_id and db.name = 'FlyBase' and f.uniquename = 'FBgn0000011'; |
| GENE PRODUCTS & EXPRESSION | |
| GENE MODEL & FEATURES | |
| COMMENTS ON GENE MODEL | SELECT f.uniquename, fp.value, p.uniquename from feature f, featureprop fp, cvterm cvt, featureprop_pub fpp, pub p, cv where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and fp.featureprop_id = fpp.featureprop_id and fpp.pub_id = p.pub_id and cvt.cv_id = cv.cv_id and cv.name = 'annotation property type' and cvt.name = 'comment' and f.uniquename = 'FBgn0000011'; |
| SEQUENCES SUPPORTING THE GENE MODEL | |
| DNA sequence | SELECT f.uniquename, fp.value from feature f, featureprop fp, cvterm cvt where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and cvt.name = 'derived_supporting_accessions' and f.uniquename = 'FBgn0000011'; |
| Protein sequence | |
| Name | |
| UniProtKB/Swiss-Prot | SELECT g.uniquename, g.name, fd.is_current, db.name, dbx.accession from feature g, feature_dbxref fd, dbxref dbx, db, cvterm gt where g.type_id = gt.cvterm_id and gt.name = 'gene' and g.uniquename like 'FBgn%' and g.is_obsolete = 'f' and g.feature_id = fd.feature_id and fd.dbxref_id = dbx.dbxref_id and dbx.db_id = d\
b.db_id and db.name = 'UniProt/Swiss-Prot' and g.uniquename = 'FBgn0000011'; |
| UniProtKB/TrEMBL | SELECT g.uniquename, g.name, fd.is_current, db.name, dbx.accession from feature g, feature_dbxref fd, dbxref dbx, db, cvterm gt where g.type_id = gt.cvterm_id and gt.name = 'gene' and g.uniquename like 'FBgn%' and g.is_obsolete = 'f' and g.feature_id = fd.feature_id and fd.dbxref_id = dbx.dbxref_id and dbx.db_id = d\
b.db_id and db.name = 'UniProt/TrEMBL' and g.uniquename = 'FBgn0000011'; |
| Maps to | SELECT f.uniquename, f.name, c.uniquename, c.name from feature f, feature_relationship fr, cvterm cvt, feature c where f.feature_id = subject_id and object_id = c.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'maps_to_clone' and f.uniquename = 'FBgn0000011'; |
| Does NOT map to | SELECT f.uniquename, f.name, c.uniquename, c.name from feature f, feature_relationship fr, cvterm cvt, feature c where f.feature_id = subject_id and object_id = c.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'nomaps_to_clone' and f.uniquename = 'FBgn0003308'; |
| Identified with | SELECT f.uniquename, f.name, c.uniquename, c.name from feature f, feature_relationship fr, cvterm cvt, feature c where f.feature_id = subject_id and object_id = c.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'identified_with' and f.uniquename = 'FBgn0000011' |
| MAPPED FEATURES AND MUTATIONS | |
| Type | SELECT cvt.name from feature f, feature_relationship fr, feature m, cvterm cvt where f.uniquename like 'FBgn%' and f.feature_id = object_id and subject_id = m.feature_id and m.type_id = cvt.cvterm_id and cvt.name in ('aberration_junction','complex_substitution','deletion','enhancer','insertion_site','point_mutation', 'protein_binding_site','regulatory_region','rescue_fragment','sequence_variant','transposable_element_target_site_duplication','uncharacterized_change_in_nucleotide_sequence') and f.uniquename = 'FBgn0000011'; |
| Symbol & Location | SELECT m.uniquename as mutation, s.uniquename as arm, strand, fmin, fmax from featureloc fl, feature f, feature_relationship fr, feature m, cvterm cvt, feature s where f.uniquename like 'FBgn%' and f.feature_id = object_id and subject_id = m.feature_id and m.type_id = cvt.cvterm_id and cvt.name in ('aberration_junction','complex_substitution','deletion','enhancer','insertion_site','point_mutation', 'protein_binding_site','regulatory_region','rescue_fragment','sequence_variant','transposable_element_target_site_duplication','uncharacterized_change_in_nucleotide_sequence') and m.feature_id = fl.feature_id and fl.srcfeature_id = s.feature_id and f.uniquename = 'FBgn0000011'; |
| Additional Notes | SELECT m.uniquename, p.uniquename, cvt2.name, fp.value from feature f, feature_relationship fr, feature m, feature_pub mp, pub p, cvterm cvt, cvterm cvt2, featureprop fp where f.uniquename like 'FBgn%' and f.feature_id = object_id and su\
bject_id = m.feature_id and m.type_id = cvt.cvterm_id and cvt.name in ('aberration_junction','complex_substitution','deletion','enhancer','insertion_site','point_mutation', 'protein_binding_site','regulatory_region','rescue_fragment','sequence_variant','transposable_element_target_site_duplication','uncharacterized_change_in_nucleotide_sequence') and m.feature_id = mp.feature_id and mp.pub_id = p.pub_id and m.feature_id = fp.feature_id and fp.type_id = cvt2.cvterm_id and f.uniquename = 'FBgn0000011'; |
| References | |
| EXTERNAL DATA | |
| DEDB (LinkOut) | |
| EPD | SELECT f.uniquename, accession from feature f, feature_dbxref fd, dbxref d, db where f.feature_id = fd.feature_id and fd.dbxref_id = d.dbxref_id and fd.is_current = 't' and d.db_id = db.db_id and db.name = 'EPD' and f.uniquename = 'FBgn0000042'; |
| TRANSCRIPT DATA | |
| ANNOTATED TRANSCRIPTS | |
| Name | SELECT p.uniquename, p.name, p.seqlen, fmin, fmax, strand, a.uniquename as arm from feature f, feature p, feature_relationship fr, cvterm cvt, featureloc fl, feature a, cvterm cvt2 where f.feature_id = object_id and subject_id = p.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'partof' and p.type_id = cvt2.cvterm_id and cvt2.name in ('mRNA', 'snoRNA', 'ncRNA', 'snRNA','tRNA','rRNA','miRNA', 'pseudogene') and p.feature_id = fl.feature_id and fl.srcfeature_id = a.feature_id and f.uniquename = 'FBgn0000011'; |
| FlyBase ID | |
| Length (nt) | |
| Associated CDS (aa) | SELECT t.uniquename, t.name, p.uniquename, p.name, p.seqlen from feature g, feature_relationship fr, cvterm cvt, feature t, cvterm cvt2, feature p, feature_relationship fr2, cvterm cvt3, cvterm cvt4 where g.feature_id = fr.object_id and fr.subject_id = t.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'partof' and t.type_id = cvt2.cvterm_id and cvt2.name in ('mRNA', 'snoRNA', 'ncRNA', 'snRNA','tRNA','rRNA','miRNA', 'pseudogene') and t.feature_id = fr2.object_id and fr2.subject_id = p.feature_id and fr2.type_id = cvt3.cvterm_id and cvt3.name = 'producedby' and p.type_id = cvt4.cvterm_id and cvt4.name = 'protein' and p.seqlen is not null and g.uniquename = 'FBgn0000011'; |
| ADDITIONAL TRANSCRIPT DATA AND COMMENTS | |
| Reported transcript sizes |
SELECT f.uniquename, fp.value from feature f, featureprop fp, cvterm cvt where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and cvt.name = 'derived_transcript_reported_sizes' and f.uniquename = 'FBgn0000011'; |
| Comments | SELECT f.uniquename, fp.value from feature f, featureprop fp, cvterm cvt where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and cvt.name = 'derived_transcript_comment' and f.uniquename = 'FBgn0000038'; |
| EXTERNAL DATA | |
| MIR | SELECT f.uniquename, accession from feature f, feature_dbxref fd, dbxref d, db where f.feature_id = fd.feature_id and fd.dbxref_id = d.dbxref_id and fd.is_current = 't' and d.db_id = db.db_id and db.name = 'MIR' and f.uniquename = 'FBgn0064191'; |
| Rfam | SELECT f.uniquename, accession from feature f, feature_dbxref fd, dbxref d, db where f.feature_id = fd.feature_id and fd.dbxref_id = d.dbxref_id and fd.is_current = 't' and d.db_id = db.db_id and db.name = 'Rfam' and f.uniquename = 'FBgn0000810'; |
| POLYPEPTIDE DATA | |
| ANNOTATED POLYPEPTIDES | |
| Name | SELECT g.uniquename, g.name, t.uniquename, t.name, p.uniquename, p.name, p.seqlen, fmin, fmax, strand, a.uniquename, cvt5.name, fp.value from feature g, feature_relationship fr, cvterm cvt, feature t, cvterm cvt2, feature p, feature_relationship fr2, cvterm cvt3, cvterm cvt4, featureloc fl, feature a, featureprop fp, cvterm cvt5 where g.feature_id = fr.object_id and fr.subject_id = t.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'partof' and t.type_id = cvt2.cvterm_id and cvt2.name in ('mRNA', 'snoRNA', 'ncRNA', 'snRNA', 'tRNA', 'rRNA', 'miRNA', 'pseudogene') and t.feature_id = fr2.object_id and fr2.subject_id = p.feature_id and fr2.type_id = cvt3.cvterm_id and cvt3.name = 'producedby' and p.type_id = cvt4.cvterm_id and cvt4.name = 'protein' and p.seqlen is not null and p.feature_id = fl.feature_id and fl.srcfeature_id = a.feature_id and p.feature_id = fp.feature_id and fp.type_id = cvt5.cvterm_id and g.uniquename = 'FBgn0000011'; |
| FlyBase ID | |
| Predicted MW (kD) | |
| Length (aa) | |
| Theoretical pI | |
| Genbank protein | SELECT g.uniquename, g.name, t.uniquename, t.name, p.uniquename, p.name, p.seqlen, fmin, fmax, strand, a.uniquename, d.accession from feature g, feature_relationship fr, cvterm cvt, feature t, cvterm cvt2, feature p, feature_relationship fr2, cvterm cvt3, cvterm cvt4, featureloc fl, feature a, feature_dbxref fd, dbxref d, db where g.feature_id = fr.object_id and fr.subject_id = t.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'partof' and t.type_id = cvt2.cvterm_id and cvt2.name in ('mRNA', 'snoRNA', 'ncRNA', 'snRNA', 'tRNA', 'rRNA', 'miRNA', 'pseudogene') and t.feature_id = fr2.object_id and fr2.subject_id = p.feature_id and fr2.type_id = cvt3.cvterm_id and cvt3.name = 'producedby' and p.type_id = cvt4.cvterm_id and cvt4.name = 'protein' and p.seqlen is not null and p.feature_id = fl.feature_id and fl.srcfeature_id = a.feature_id and p.feature_id = fd.feature_id and fd.dbxref_id = d.dbxref_id and d.db_id = db.db_id and db.name = 'GB_protein' and g.uniquename = 'FBgn0051371'; |
| ADDITIONAL POLYPEPTIDE DATA AND COMMENTS | |
| Reported protein sizes | |
| Comments | |
| EXTERNAL DATA | |
| GCR | SELECT f.uniquename, accession from feature f, feature_dbxref fd, dbxref d, db where f.feature_id = fd.feature_id and fd.dbxref_id = d.dbxref_id and fd.is_current = 't' and d.db_id = db.db_id and db.name = 'GCR' and f.uniquename = 'FBgn0004168'; |
| InterPro domains | SELECT f.uniquename, accession from feature f, feature_dbxref fd, dbxref d, db where f.feature_id = fd.feature_id and fd.dbxref_id = d.dbxref_id and fd.is_current = 't' and d.db_id = db.db_id and db.name = 'INTERPRO' and f.uniquename = 'FBgn0015570'; |
| MEROPS | SELECT f.uniquename, accession from feature f, feature_dbxref fd, dbxref d, db where f.feature_id = fd.feature_id and fd.dbxref_id = d.dbxref_id and fd.is_current = 't' and d.db_id = db.db_id and db.name = 'MEROPS' and f.uniquename = 'FBgn0004648'; |
| MITODROME | SELECT f.uniquename, accession from feature f, feature_dbxref fd, dbxref d, db where f.feature_id = fd.feature_id and fd.dbxref_id = d.dbxref_id and fd.is_current = 't' and d.db_id = db.db_id and db.name = 'MITODROME' and f.uniquename = 'FBgn0027085'; |
| NRL_3D | SELECT f.uniquename, accession from feature f, feature_dbxref fd, dbxref d, db where f.feature_id = fd.feature_id and fd.dbxref_id = d.dbxref_id and fd.is_current = 't' and d.db_id = db.db_id and db.name = 'NRL_3D' and f.uniquename = 'FBgn0003470'; |
| PANTHER (LinkOut) | SELECT f.uniquename, f.name, db.name, accession from feature f, feature_dbxref fd, db, dbxref dx, dbxrefprop dxp, cvterm cvt where f.feature_id = fd.feature_id and fd.dbxref_id = dx.dbxref_id and dx.db_id = db.db_id and dx.dbxref_id = dxp.dbxref_id and dxp.type_id = cvt.cvterm_id and cvt.name = 'linkout' and db.name = 'panther' and f.uniquename = 'FBgn0000011'; |
| PDB | SELECT f.uniquename, accession from feature f, feature_dbxref fd, dbxref d, db where f.feature_id = fd.feature_id and fd.dbxref_id = d.dbxref_id and fd.is_current = 't' and d.db_id = db.db_id and db.name = 'PDB' and f.uniquename = 'FBgn0003659'; |
| TransFac | SELECT f.uniquename, accession from feature f, feature_dbxref fd, dbxref d, db where f.feature_id = fd.feature_id and fd.dbxref_id = d.dbxref_id and fd.is_current = 't' and d.db_id = db.db_id and db.name = 'TF' and f.uniquename = 'FBgn0000014'; |
| EXPRESSION DATA | |
| BDGP in situ (LinkOut) | SELECT f.uniquename, f.name, db.name, accession from feature f, feature_dbxref fd, db, dbxref dx, dbxrefprop dxp, cvterm cvt where f.feature_id = fd.feature_id and fd.dbxref_id = dx.dbxref_id and dx.db_id = db.db_id and dx.dbxref_id = dxp.dbxref_id and dxp.type_id = cvt.cvterm_id and cvt.name = 'linkout' and db.name = 'bdgpinsituexpr' and f.uniquename = 'FBgn0000011'; |
| Yale Dev. Expression (LinkOut) | SELECT f.uniquename, f.name, db.name, accession from feature f, feature_dbxref fd, db, dbxref dx, dbxrefprop dxp, cvterm cvt where f.feature_id = fd.feature_id and fd.dbxref_id = dx.dbxref_id and dx.db_id = db.db_id and dx.dbxref_id = dxp.dbxref_id and dxp.type_id = cvt.cvterm_id and cvt.name = 'linkout' and db.name = 'kwexpression' and f.uniquename = 'FBgn0000014'; |
| RELATED COMMENTS | |
| SELECT f.uniquename, f.name, fp.value from feature f, featureprop fp, cvterm cvt where f.feature_id = fp.feature_id and fp.type_id = cvt.cvterm_id and cvt.name = 'molecular_info' and f.uniquename = 'FBgn0000014'; | |
| ALLELES | |
| CLASSICAL ALLELES | |
| Allele of (gene name) | SELECT g.uniquename, g.name, a.uniquename, a.name from feature g, feature_relationship fr, feature a, cvterm cvt where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and not exists (select * from feature_relationship fr2, feature t, cvterm cvt2, cvterm cvt3 where fr2.subject_id = a.feature_id and fr2.type_id = cvt2.cvterm_id and cvt2.name = 'associated_with' and fr2.object_id = t.feature_id and t.type_id = cvt3.cvterm_id and cvt3.name = 'transgenic_transposon') and g.uniquename = 'FBgn0000011'; |
| Class | SELECT g.uniquename, g.name, a.uniquename, a.name, fp.value from feature g, feature_relationship fr, feature a, cvterm cvt, featureprop fp, cvterm cvt3 where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and not exists (select * from feature_relationship fr2, feature t, cvterm cvt2, cvterm cvt3 where fr2.subject_id = a.feature_id and fr2.type_id = cvt2.cvterm_id and cvt2.name = 'associated_with' and fr2.object_id = t.feature_id and t.type_id = cvt3.cvterm_id and cvt3.name = 'transgenic_transposon') and a.feature_id = fp.feature_id and fp.type_id = cvt3.cvterm_id and cvt3.name = 'promoted_allele_class' and g.uniquename = 'FBgn0000011'; |
| Mutagen | SELECT g.uniquename, g.name, a.uniquename, a.name, cvt4.name from feature g, feature_relationship fr, feature a, cvterm cvt, cvterm cvt4, cvtermprop cvtp, feature_cvterm fcv where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and not exists (select * from feature_relationship fr2, feature t, cvterm cvt2, cvterm cvt3 where fr2.subject_id = a.feature_id and fr2.type_id = cvt2.cvterm_id and cvt2.name = 'associated_with' and fr2.object_id = t.feature_id and t.type_id = cvt3.cvterm_id and cvt3.name = 'transgenic_transposon') and a.feature_id = fcv.feature_id and fcv.cvterm_id = cvt4.cvterm_id and cvt4.cvterm_id = cvtp.cvterm_id and cvtp.value = 'origin_of_mutation' and g.uniquename = 'FBgn0000011'; |
| Stocks | SELECT g.uniquename, g.name, a.uniquename, a.name, cvt3.name, fp.value from feature g, feature_relationship fr, feature a, cvterm cvt, featureprop fp, cvterm cvt3 where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and not exists (select * from feature_relationship fr2, feature t, cvterm cvt2, cvterm cvt3 where fr2.subject_id = a.feature_id and fr2.type_id = cvt2.cvterm_id and cvt2.name = 'associated_with' and fr2.object_id = t.feature_id and t.type_id = cvt3.cvterm_id and cvt3.name = 'transgenic_transposon') and a.feature_id = fp.feature_id and fp.type_id = cvt3.cvterm_id and cvt3.name like 'derived_stock_%' and g.uniquename = 'FBgn0000011'; |
| Known lesion | SELECT g.uniquename, g.name, a.uniquename, a.name, cvt3.name, fp.value from feature g, feature_relationship fr, feature a, cvterm cvt, featureprop fp, cvterm cvt3 where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and not exists (select * from feature_relationship fr2, feature t, cvterm cvt2, cvterm cvt3 where fr2.subject_id = a.feature_id and fr2.type_id = cvt2.cvterm_id and cvt2.name = 'associated_with' and fr2.object_id = t.feature_id and t.type_id = cvt3.cvterm_id and cvt3.name = 'transgenic_transposon') and a.feature_id = fp.feature_id and fp.type_id = cvt3.cvterm_id and cvt3.name in ('molecular_info','aminoacid_rep','nucleotide_rep') and g.uniquename = 'FBgn0000011'; |
| ALLELES CARRIED ON TRANSGENIC CONSTRUCTS | |
| Allele of (gene name) | SELECT g.uniquename, g.name, a.uniquename, a.name from feature g, feature_relationship fr, feature a, cvterm cvt where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and exists (select * from feature_relationship fr2, feature t, cvterm cvt2, cvterm cvt3 where fr2.subject_id = a.feature_id and fr2.type_id = cvt2.cvterm_id and cvt2.name = 'associated_with' and fr2.object_id = t.feature_id and t.type_id = cvt3.cvterm_id and cvt3.name = 'transgenic_transposon') and g.uniquename = 'FBgn0000011'; |
| Class | SELECT g.uniquename, g.name, a.uniquename, a.name, fp.value from feature g, feature_relationship fr, feature a, cvterm cvt, featureprop fp, cvterm cvt3 where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and exists (select * from feature_relationship fr2, feature t, cvterm cvt2, cvterm cvt3 where fr2.subject_id = a.feature_id and fr2.type_id = cvt2.cvterm_id and cvt2.name = 'associated_with' and fr2.object_id = t.feature_id and t.type_id = cvt3.cvterm_id and cvt3.name = 'transgenic_transposon') and a.feature_id = fp.feature_id and fp.type_id = cvt3.cvterm_id and cvt3.name = 'promoted_allele_class' and g.uniquename = 'FBgn0000011'; |
| Mutagen | SELECT g.uniquename, g.name, a.uniquename, a.name, cvt4.name from feature g, feature_relationship fr, feature a, cvterm cvt, cvterm cvt4, cvtermprop cvtp, feature_cvterm fcv where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and exists (select * from feature_relationship fr2, feature t, cvterm cvt2, cvterm cvt3 where fr2.subject_id = a.feature_id and fr2.type_id = cvt2.cvterm_id and cvt2.name = 'associated_with' and fr2.object_id = t.feature_id and t.type_id = cvt3.cvterm_id and cvt3.name = 'transgenic_transposon') and a.feature_id = fcv.feature_id and fcv.cvterm_id = cvt4.cvterm_id and cvt4.cvterm_id = cvtp.cvterm_id and cvtp.value = 'origin_of_mutation' and g.uniquename = 'FBgn0000011'; |
| Stocks | SELECT g.uniquename, g.name, a.uniquename, a.name, cvt3.name, fp.value from feature g, feature_relationship fr, feature a, cvterm cvt, featureprop fp, cvterm cvt3 where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and exists (select * from feature_relationship fr2, feature t, cvterm cvt2, cvterm cvt3 where fr2.subject_id = a.feature_id and fr2.type_id = cvt2.cvterm_id and cvt2.name = 'associated_with' and fr2.object_id = t.feature_id and t.type_id = cvt3.cvterm_id and cvt3.name = 'transgenic_transposon') and a.feature_id = fp.feature_id and fp.type_id = cvt3.cvterm_id and cvt3.name like 'derived_stock_%' and g.uniquename = 'FBgn0000011'; |
| Known lesion | SELECT g.uniquename, g.name, a.uniquename, a.name, cvt3.name, fp.value from feature g, feature_relationship fr, feature a, cvterm cvt, featureprop fp, cvterm cvt3 where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and exists (select * from feature_relationship fr2, feature t, cvterm cvt2, cvterm cvt3 where fr2.subject_id = a.feature_id and fr2.type_id = cvt2.cvterm_id and cvt2.name = 'associated_with' and fr2.object_id = t.feature_id and t.type_id = cvt3.cvterm_id and cvt3.name = 'transgenic_transposon') and a.feature_id = fp.feature_id and fp.type_id = cvt3.cvterm_id and cvt3.name in ('molecular_info','aminoacid_rep','nucleotide_rep') and g.uniquename = 'FBgn0000011'; |
| SUMMARY OF ALLELE PHENOTYPES | |
| Lethality | SELECT g.uniquename, g.name, a.uniquename, a.name, cvt4.name, fp.value from feature g, feature_relationship fr, feature a, cvterm cvt, cvterm cvt4, featureprop fp where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and a.feature_id = fp.feature_id and fp.type_id = cvt4.cvterm_id and cvt4.name = 'derived_pheno_class'and fp.value like '%lethal%' and g.uniquename = 'FBgn0000011'
UNION SELECT g.uniquename, g.name, a.uniquename, a.name, cvt4.name, fp.value from feature g, feature_relationship fr, feature a, cvterm cvt, cvterm cvt4, featureprop fp where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and a.feature_id = fp.feature_id and fp.type_id = cvt4.cvterm_id and cvt4.name = 'derived_pheno_class' and fp.value like '%viable%' and g.uniquename = 'FBgn0000011'; |
| Allele | |
| Sterility | SELECT g.uniquename, g.name, a.uniquename, a.name, cvt4.name, fp.value from feature g, feature_relationship fr, feature a, cvterm cvt, cvterm cvt4, featureprop fp where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and a.feature_id = fp.feature_id and fp.type_id = cvt4.cvterm_id and cvt4.name = 'derived_pheno_class'and fp.value like '%fertile%' and g.uniquename = 'FBgn0000011'
UNION SELECT g.uniquename, g.name, a.uniquename, a.name, cvt4.name, fp.value from feature g, feature_relationship fr, feature a, cvterm cvt, cvterm cvt4, featureprop fp where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and a.feature_id = fp.feature_id and fp.type_id = cvt4.cvterm_id and cvt4.name = 'derived_pheno_class' and fp.value like '%sterile%' and g.uniquename = 'FBgn0000011'; |
| Allele | |
| Other Phenotypes | SELECT g.uniquename, g.name, a.uniquename, a.name, cvt4.name, fp.value from feature g, feature_relationship fr, feature a, cvterm cvt, cvterm cvt4, featureprop fp where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and a.feature_id = fp.feature_id and fp.type_id = cvt4.cvterm_id and cvt4.name = 'derived_pheno_class'and fp.value not like '%lethal%' and g.uniquename = 'FBgn0000011'
INTERSECT SELECT g.uniquename, g.name, a.uniquename, a.name, cvt4.name, fp.value from feature g, feature_relationship fr, feature a, cvterm cvt, cvterm cvt4, featureprop fp where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and a.feature_id = fp.feature_id and fp.type_id = cvt4.cvterm_id and cvt4.name = 'derived_pheno_class' and fp.value not like '%viable%' and g.uniquename = 'FBgn0000011' INTERSECT SELECT g.uniquename, g.name, a.uniquename, a.name, cvt4.name, fp.value from feature g, feature_relationship fr, feature a, cvterm cvt, cvterm cvt4, featureprop fp where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and a.feature_id = fp.feature_id and fp.type_id = cvt4.cvterm_id and cvt4.name = 'derived_pheno_class'and fp.value not like '%fertile%' and g.uniquename = 'FBgn0000011' INTERSECT SELECT g.uniquename, g.name, a.uniquename, a.name, cvt4.name, fp.value from feature g, feature_relationship fr, feature a, cvterm cvt, cvterm cvt4, featureprop fp where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and a.feature_id = fp.feature_id and fp.type_id = cvt4.cvterm_id and cvt4.name = 'derived_pheno_class' and fp.value not like '%sterile%' and g.uniquename = 'FBgn0000011'; |
| Allele | |
| Phenotype manifest in | SELECT g.uniquename, g.name, a.uniquename, a.name, cvt4.name, fp.value from feature g, feature_relationship fr, feature a, cvterm cvt, cvterm cvt4, featureprop fp where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name = 'alleleof' and a.feature_id = fp.feature_id and fp.type_id = cvt4.cvterm_id and cvt4.name = 'derived_pheno_manifest' and g.uniquename = 'FBgn0000011'; |
| Allele | |
| ANEUPLOID ABERRATIONS | |
| (Useful Duplication) | SELECT g.uniquename, g.name, cvt.name, a.uniquename, a.name from feature g, feature_relationship fr, cvterm cvt, feature a where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name in ('useful_Dp_direct', 'useful_Dp_from_cyto') and g.uniquename = 'FBgn0000022'; |
| (Useful Deficiency) | |
| (Disrupted in) | SELECT g.uniquename, g.name, cvt.name, a.uniquename, a.name from feature g, feature_relationship fr, cvterm cvt, feature a where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name in ('deletes', 'molec_deletes') and g.uniquename = 'FBgn0000011'; |
| (Partially disrupted in) | SELECT g.uniquename, g.name, cvt.name, a.uniquename, a.name from feature g, feature_relationship fr, cvterm cvt, feature a where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name in ('part_deletes', 'molec_partdeletes') and g.uniquename = 'FBgn0000014'; |
| (Not Disrupted in) | SELECT g.uniquename, g.name, cvt.name, a.uniquename, a.name from feature g, feature_relationship fr, cvterm cvt, feature a where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name in ('nondeletes', 'molec_nondeletes') and g.uniquename = 'FBgn0000014'; |
| (Duplicated in) | SELECT g.uniquename, g.name, cvt.name, a.uniquename, a.name from feature g, feature_relationship fr, cvterm cvt, feature a where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name in ('duplicates', 'molec_dups') and g.uniquename = 'FBgn0000014'; |
| (Partially duplicated in) | SELECT g.uniquename, g.name, cvt.name, a.uniquename, a.name from feature g, feature_relationship fr, cvterm cvt, feature a where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name in ('part_duplicates', 'molec_partdups') and g.uniquename = 'FBgn0000014'; |
| (Not duplicated in) | SELECT g.uniquename, g.name, cvt.name, a.uniquename, a.name from feature g, feature_relationship fr, cvterm cvt, feature a where g.feature_id = object_id and subject_id = a.feature_id and fr.type_id = cvt.cvterm_id and cvt.name in ('nonduplicates', 'molec_nondups') and g.uniquename = 'FBgn0000022'; |
| TRANSGENIC CONSTRUCTS AND INSERTIONS | |
| Transgenic constructs | |
| Type of construct | |
| heat-shock construct | |
| UAS construct | |
| characterization construct | |
| vital-reporter construct | |
| reporter construct | |
| Insertions | |
| insertion of mobile activating element | |
| insertion_of_enhancer_trap | |
| insertion_of_enhancer_trap_binary_system | |
| miscellaneous insertions | |
| RELATED COMMENTS | |
| SEQUENCE ONTOLOGY: Class of gene | |
| GENE ONTOLOGY: Function, Process, and Cellular Component | |
| MOLECULAR FUNCTION | |
| Terms based on experimental evidence | |
| CV term (Includes qualifier) | |
| Evidence code (Includes identifier) | |
| Reference | |
| Terms based on predictions | |
| CV term (Includes qualifier) | |
| Evidence code (Includes identifier) | |
| Reference | |
| BIOLOGICAL PROCESS | |
| Terms based on experimental evidence | |
| CV term (Includes qualifier) | |
| Evidence code (Includes identifier) | |
| Reference | |
| Terms based on predictions | |
| CV term (Includes qualifier) | |
| Evidence code (Includes identifier) | |
| Reference | |
| CELLULAR COMPONENT | |
| Terms based on experimental evidence | |
| CV term (Includes qualifier) | |
| Evidence code (Includes identifier) | |
| Reference | |
| Terms based on predictions | |
| CV term (Includes qualifier) | |
| Evidence code (Includes identifier) | |
| Reference | |
| RELATED COMMENTS | |
| INTERACTIONS AND PATHWAYS | |
| SUMMARY OF GENETIC INTERACTIONS | |
| Interacting Gene | |
| Allele of this gene | |
| Reference | |
| EXTERNAL DATA | |
| BioGRID (LinkOut) | |
| Dros. PIMRider (LinkOut) | |
| ORTHOLOGS | |
| Genome-wide drosophilid orthologs | |
| Curated drosophilid orthologs | |
| InParanoid orthologs (LinkOut) | |
| FUNCTIONAL COMPLEMENTATION BETWEEN SPECIES | |
| Functionally complements | |
| Partially functionally complements | |
| Does NOT functionally complement | |
| Functionally complemented by | |
| Partially functionally complemented by | |
| NOT functionally complemented by | |
| INTER-SPECIES MISEXPRESSION DATA | |
| Produces phenotype in | |
| Produces NO phenotype in | |
| STOCKS AND REAGENTS | |
| STOCKS LISTED IN FLYBASE | |
| Bloomington | |
| Kyoto | |
| Szeged | |
| Tucson | |
| Carpenter | |
| Garcia-Bellido | |
| Harvard | |
| Nusslein-Volhard | |
| Saxton | |
| Notes on availability | |
| GENOMIC CLONES | |
| cDNA CLONES | |
| cDNA clones, fully sequenced | |
| BDGP DGC clones | |
| Other clones | |
| cDNA clones, end sequenced (ESTs) | |
| BDGP DGC clones | |
| Other clones | |
| RNAi & ARRAY INFORMATION | |
| Affy Oligo | |
| NCBI GEO (LinkOut) | |
| Heidelberg RNAi (LinkOut) | |
| DRSC (LinkOut) | |
| ANTIBODY INFORMATION | |
| OTHER INFORMATION | |
| DISCOVERER | |
| ETYMOLOGY | |
| IDENTIFICATION | |
| POSITION EFFECT VARIEGATION DATA | |
| No PEV in | |
| Dominant PEV in | |
| Recessive PEV in | |
| RELATIONSHIP TO OTHER GENES | |
| Source for database identity of | |
| Source for database merge of | |
| (Member gene of) | |
| (Component gene(s)) | |
| (Encoded by) | |
| (Tags) | |
| Additional Comments | |
| OTHER COMMENTS | |
| (FOREIGN GENE DATA) | |
| EXTERNAL CROSSREFERENCES & LINKOUTS | |
| Sequence Crossreferences | |
| DNA sequence | |
| Protein sequence | |
| UniProt/Swiss-Prot | |
| UniProt/TrEMBL | |
| Other Crossreferences | |
| EPD | |
| GCR | |
| InterPro domains | |
| MEROPS | |
| MIR | |
| MITODROME | |
| NRL_3D | |
| PDB | |
| Rfam | |
| TransFac | |
| LinkOuts | |
| BioGRID | |
| BDGP in situ | |
| DEDB Exons | |
| Dros. PIMRider | |
| DRSC | |
| FLIGHT | |
| FlyMine | |
| Heidelberg RNAi | |
| InParanoid | |
| Interactive Fly | |
| NCBI GEO | |
| PANTHER | |
| Yale Dev. Expression | |
| REFERENCES | |
| Research paper | |
| ;Supplementary material | |
| Review | |
| Abstract | |
| Other | |
