410bc23ea2ad4369745b5f80f2f805bd81e201e4 gperez2 Wed Oct 29 17:41:51 2025 -0700 Staging 3 All GENCODE tracks, refs #36170 #36168 #36166 diff --git src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM38.ra src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM38.ra index ea3b16349c5..37b5ad4f179 100644 --- src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM38.ra +++ src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM38.ra @@ -1,247 +1,248 @@ track wgEncodeGencodeVM38 compositeTrack on superTrack wgEncodeGencodeSuper pack shortLabel All GENCODE VM38 longLabel All GENCODE annotations from VM38 (Ensembl 115) group genes dragAndDrop subTracks priority 2.946 visibility pack subGroup1 view View aGenes=Genes bPolya=PolyA subGroup2 name Name Basic=Basic Comprehensive=Comprehensive Pseudogenes=Pseudogenes zPolyA=PolyA allButtonPair on sortOrder name=+ view=+ fileSortOrder labVersion=Contents dccAccession=UCSC_Accession type genePred configurable off wgEncodeGencodeVersion M38 maxTransEnabled on +pennantIcon New red ../goldenPath/newsarch.html#103125 "Released Oct. 31, 2025" track wgEncodeGencodeVM38ViewGenes shortLabel Genes view aGenes configurable on visibility pack subTrack wgEncodeGencodeVM38 type genePred idXref wgEncodeGencodeAttrsVM38 transcriptId geneId itemClassTbl wgEncodeGencodeAttrsVM38 itemClassNameColumn transcriptId itemClassClassColumn transcriptClass cdsDrawDefault genomic\ codons baseColorUseCds given baseColorDefault genomicCodons geneClasses coding nonCoding pseudo problem gClass_coding 12,12,120 gClass_nonCoding 0,153,0 gClass_pseudo 255,51,255 gClass_problem 254,0,0 highlightColor 255,255,0 # filterBy notes: # - attrs is an alias for the current wgEncodeGencodeAttrs in the sql # - transcriptMethod is a pseudo-column name, which is handled explictly in the code # - attrs.transcriptType are transcript biotypes. This will get the current list of values: # hgsql -Ne 'select distinct(transcriptType) from wgEncodeGencodeAttrsVM38 order by transcriptType' mm39 # - tag - is s pseudo-column name for join with the tag table. This will get the current list of values: # hgsql -Ne 'select distinct(tag) from wgEncodeGencodeTagVM38 order by tag' mm39 # - supportLevel is a pseudo-column name handled in the code filterBy attrs.transcriptClass:Transcript_Class=coding,nonCoding,pseudo,problem \ transcriptMethod:Transcript_Annotation_Method=manual,automatic,manual_only,automatic_only \ attrs.transcriptType:Transcript_Biotype=IG_C_gene,IG_C_pseudogene,IG_D_gene,IG_D_pseudogene,IG_J_gene,IG_LV_gene,IG_pseudogene,IG_V_gene,IG_V_pseudogene,lncRNA,miRNA,misc_RNA,Mt_rRNA,Mt_tRNA,nonsense_mediated_decay,non_stop_decay,processed_pseudogene,processed_transcript,protein_coding,protein_coding_CDS_not_defined,protein_coding_LoF,pseudogene,retained_intron,ribozyme,rRNA,scaRNA,scRNA,snoRNA,snRNA,sRNA,TEC,transcribed_processed_pseudogene,transcribed_unitary_pseudogene,transcribed_unprocessed_pseudogene,translated_unprocessed_pseudogene,TR_C_gene,TR_D_gene,TR_J_gene,TR_J_pseudogene,TR_V_gene,TR_V_pseudogene,unitary_pseudogene,unprocessed_pseudogene \ tag:Tag=3_nested_supported_extension,3_standard_supported_extension,5_nested_supported_extension,5_standard_supported_extension,alternative_3_UTR,alternative_5_UTR,appris_alternative_1,appris_alternative_2,appris_principal_1,appris_principal_2,appris_principal_3,appris_principal_4,appris_principal_5,basic,bicistronic,CAGE_supported_TSS,CCDS,cds_end_NF,cds_start_NF,confirm_experimentally,dotter_confirmed,downstream_ATG,Ensembl_canonical,EnsEMBL_merge_exception,exp_conf,fragmented_locus,GENCODE_Primary,inferred_exon_combination,inferred_transcript_model,low_sequence_quality,mRNA_end_NF,mRNA_start_NF,NAGNAG_splice_site,ncRNA_host,NMD_exception,NMD_likely_if_extended,non_ATG_start,non_canonical_conserved,non_canonical_genome_sequence_error,non_canonical_other,non_canonical_polymorphism,non_canonical_TEC,non_canonical_U12,non_submitted_evidence,not_best_in_genome_evidence,not_organism_supported,overlapping_locus,overlapping_uORF,overlaps_pseudogene,polymorphic_pseudogene_no_stop,precursor_RNA,readthrough_gene,readthrough_transcript,reference_genome_error,retained_intron_CDS,retained_intron_final,retained_intron_first,retrogene,RNA_Seq_supported_only,RNA_Seq_supported_partial,RP_supported_TIS,seleno,Selenoprotein,semi_processed,sequence_error,stop_codon_readthrough,TAGENE,upstream_ATG,upstream_uORF \ supportLevel:Support_Level=tsl1,tsl2,tsl3,tsl4,tsl5,tslNA highlightBy transcriptMethod:Transcript_Annotation_Method=manual,automatic,manual_only,automatic_only \ attrs.transcriptType:Transcript_Biotype=IG_C_gene,IG_C_pseudogene,IG_D_gene,IG_D_pseudogene,IG_J_gene,IG_LV_gene,IG_pseudogene,IG_V_gene,IG_V_pseudogene,lncRNA,miRNA,misc_RNA,Mt_rRNA,Mt_tRNA,nonsense_mediated_decay,non_stop_decay,processed_pseudogene,processed_transcript,protein_coding,protein_coding_CDS_not_defined,protein_coding_LoF,pseudogene,retained_intron,ribozyme,rRNA,scaRNA,scRNA,snoRNA,snRNA,sRNA,TEC,transcribed_processed_pseudogene,transcribed_unitary_pseudogene,transcribed_unprocessed_pseudogene,translated_unprocessed_pseudogene,TR_C_gene,TR_D_gene,TR_J_gene,TR_J_pseudogene,TR_V_gene,TR_V_pseudogene,unitary_pseudogene,unprocessed_pseudogene \ tag:Tag=3_nested_supported_extension,3_standard_supported_extension,5_nested_supported_extension,5_standard_supported_extension,alternative_3_UTR,alternative_5_UTR,appris_alternative_1,appris_alternative_2,appris_principal_1,appris_principal_2,appris_principal_3,appris_principal_4,appris_principal_5,basic,bicistronic,CAGE_supported_TSS,CCDS,cds_end_NF,cds_start_NF,confirm_experimentally,dotter_confirmed,downstream_ATG,Ensembl_canonical,EnsEMBL_merge_exception,exp_conf,fragmented_locus,GENCODE_Primary,inferred_exon_combination,inferred_transcript_model,low_sequence_quality,mRNA_end_NF,mRNA_start_NF,NAGNAG_splice_site,ncRNA_host,NMD_exception,NMD_likely_if_extended,non_ATG_start,non_canonical_conserved,non_canonical_genome_sequence_error,non_canonical_other,non_canonical_polymorphism,non_canonical_TEC,non_canonical_U12,non_submitted_evidence,not_best_in_genome_evidence,not_organism_supported,overlapping_locus,overlapping_uORF,overlaps_pseudogene,polymorphic_pseudogene_no_stop,precursor_RNA,readthrough_gene,readthrough_transcript,reference_genome_error,retained_intron_CDS,retained_intron_final,retained_intron_first,retrogene,RNA_Seq_supported_only,RNA_Seq_supported_partial,RP_supported_TIS,seleno,Selenoprotein,semi_processed,sequence_error,stop_codon_readthrough,TAGENE,upstream_ATG,upstream_uORF \ supportLevel:Support_Level=tsl1,tsl2,tsl3,tsl4,tsl5,tslNA track wgEncodeGencodeBasicVM38 trackHandler wgEncodeGencode subTrack wgEncodeGencodeVM38ViewGenes on shortLabel Basic subGroups view=aGenes name=Basic longLabel Basic Gene Annotation Set from GENCODE Version M38 (Ensembl 115) type genePred priority 1 track wgEncodeGencodeCompVM38 trackHandler wgEncodeGencode subTrack wgEncodeGencodeVM38ViewGenes off subGroups view=aGenes name=Comprehensive shortLabel Comprehensive longLabel Comprehensive Gene Annotation Set from GENCODE Version M38 (Ensembl 115) type genePred priority 2 track wgEncodeGencodePseudoGeneVM38 trackHandler wgEncodeGencode subTrack wgEncodeGencodeVM38ViewGenes on subGroups view=aGenes name=Pseudogenes shortLabel Pseudogenes longLabel Pseudogene Annotation Set from GENCODE Version M38 (Ensembl 115) type genePred color 255,51,255 priority 3 track wgEncodeGencodeVM38ViewPolya shortLabel PolyA view cPolya visibility hide subTrack wgEncodeGencodeVM38 type genePred configurable off track wgEncodeGencodePolyaVM38 trackHandler wgEncodeGencode subTrack wgEncodeGencodeVM38ViewPolya off subGroups view=bPolya name=zPolyA shortLabel PolyA longLabel PolyA Transcript Annotation Set from GENCODE Version M38 (Ensembl 115) type genePred color 0,0,0 priority 5 # searches for basic searchName wgEncodeGencodeBasicVM38 searchTable wgEncodeGencodeBasicVM38 searchMethod prefix searchType genePred termRegex ENSMUST[0-9.]+ searchPriority 2.23601 searchName wgEncodeGencodeBasicGeneSymVM38 searchTable wgEncodeGencodeBasicVM38 searchMethod exact searchType genePred searchPriority 2.23602 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodeBasicGeneVM38 searchTable wgEncodeGencodeBasicVM38 searchMethod prefix searchType genePred termRegex ENSMUSG[0-9.]+ searchPriority 2.23603 xrefTable wgEncodeGencodeAttrsVM38 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodeBasicHavanaTranscriptVM38 searchTable wgEncodeGencodeBasicVM38 searchMethod prefix searchType genePred termRegex OTTMUST[0-9.]+ searchPriority 2.23604 xrefTable wgEncodeGencodeAttrsVM38 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodeBasicHavanaGeneVM38 searchTable wgEncodeGencodeBasicVM38 searchMethod prefix searchType genePred termRegex OTTMUSG[0-9.]+ searchPriority 2.23606 xrefTable wgEncodeGencodeAttrsVM38 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%' searchName wgEncodeGencodeBasicProtVM38 searchTable wgEncodeGencodeBasicVM38 searchMethod prefix searchType genePred termRegex ENSMUSP[0-9.]+ searchPriority 2.23607 xrefTable wgEncodeGencodeAttrsVM38 xrefQuery select transcriptId,proteinId from %s where proteinId like '%s%%' # searches for comp searchName wgEncodeGencodeCompVM38 searchTable wgEncodeGencodeCompVM38 searchMethod prefix searchType genePred termRegex ENSMUST[0-9.]+ searchPriority 2.23608 searchName wgEncodeGencodeCompGeneSymVM38 searchTable wgEncodeGencodeCompVM38 searchMethod exact searchType genePred searchPriority 2.23609 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodeCompGeneVM38 searchTable wgEncodeGencodeCompVM38 searchMethod prefix searchType genePred termRegex ENSMUSG[0-9.]+ searchPriority 2.23610 xrefTable wgEncodeGencodeAttrsVM38 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodeCompHavanaTranscriptVM38 searchTable wgEncodeGencodeCompVM38 searchMethod prefix searchType genePred termRegex OTTMUST[0-9.]+ searchPriority 2.23611 xrefTable wgEncodeGencodeAttrsVM38 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodeCompHavanaGeneVM38 searchTable wgEncodeGencodeCompVM38 searchMethod prefix searchType genePred termRegex OTTMUSG[0-9.]+ searchPriority 2.23612 xrefTable wgEncodeGencodeAttrsVM38 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%' searchName wgEncodeGencodeCompProtVM38 searchTable wgEncodeGencodeCompVM38 searchMethod prefix searchType genePred termRegex ENSMUSP[0-9.]+ searchPriority 2.23613 xrefTable wgEncodeGencodeAttrsVM38 xrefQuery select transcriptId,proteinId from %s where proteinId like '%s%%' # searches for pseudogene searchName wgEncodeGencodePseudoGeneVM38 searchTable wgEncodeGencodePseudoGeneVM38 searchMethod prefix searchType genePred termRegex ENSMUST[0-9.]+ searchPriority 2.23614 searchName wgEncodeGencodePseudoGeneGeneSymVM38 searchTable wgEncodeGencodePseudoGeneVM38 searchMethod exact searchType genePred searchPriority 2.23615 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodePseudoGeneGeneVM38 searchTable wgEncodeGencodePseudoGeneVM38 searchMethod prefix searchType genePred termRegex ENSMUSG[0-9.]+ searchPriority 2.23616 xrefTable wgEncodeGencodeAttrsVM38 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodePseudoGeneHavanaTranscriptVM38 searchTable wgEncodeGencodePseudoGeneVM38 searchMethod prefix searchType genePred termRegex OTTMUST[0-9.]+ searchPriority 2.23617 xrefTable wgEncodeGencodeAttrsVM38 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodePseudoGeneHavanaGeneVM38 searchTable wgEncodeGencodePseudoGeneVM38 searchMethod prefix searchType genePred termRegex OTTMUSG[0-9.]+ searchPriority 2.23618 xrefTable wgEncodeGencodeAttrsVM38 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%'