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/human/hg38/wgEncodeGencodeV49.ra src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV49.ra index 68a2d35d12d..e28a99b96e2 100644 --- src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV49.ra +++ src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV49.ra @@ -1,247 +1,248 @@ track wgEncodeGencodeV49 compositeTrack on superTrack wgEncodeGencodeSuper pack shortLabel All GENCODE V49 longLabel All GENCODE annotations from V49 (Ensembl 115) group genes dragAndDrop subTracks priority 34.156 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 49 maxTransEnabled on +pennantIcon New red ../goldenPath/newsarch.html#103125 "Released Oct. 31, 2025" track wgEncodeGencodeV49ViewGenes shortLabel Genes view aGenes configurable on visibility pack subTrack wgEncodeGencodeV49 type genePred idXref wgEncodeGencodeAttrsV49 transcriptId geneId itemClassTbl wgEncodeGencodeAttrsV49 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 wgEncodeGencodeAttrsV49 order by transcriptType' hg38 # - 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 wgEncodeGencodeTagV49 order by tag' hg38 # - 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=artifact,IG_C_gene,IG_C_pseudogene,IG_D_gene,IG_J_gene,IG_J_pseudogene,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,rRNA_pseudogene,scaRNA,snoRNA,snRNA,sRNA,TEC,transcribed_processed_pseudogene,transcribed_unitary_pseudogene,transcribed_unprocessed_pseudogene,translated_processed_pseudogene,TR_C_gene,TR_D_gene,TR_J_gene,TR_J_pseudogene,TR_V_gene,TR_V_pseudogene,unitary_pseudogene,unprocessed_pseudogene,vault_RNA \ tag:Tag=3_nested_supported_extension,3_standard_supported_extension,454_RNA_Seq_supported,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,artifactual_duplication,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,fragmented_mixed_strand_locus,GENCODE_Primary,inferred_exon_combination,inferred_transcript_model,low_sequence_quality,MANE_Plus_Clinical,MANE_Select,mRNA_end_NF,mRNA_start_NF,NAGNAG_splice_site,ncRNA_host,nested_454_RNA_Seq_supported,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,pseudo_consens,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=artifact,IG_C_gene,IG_C_pseudogene,IG_D_gene,IG_J_gene,IG_J_pseudogene,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,rRNA_pseudogene,scaRNA,snoRNA,snRNA,sRNA,TEC,transcribed_processed_pseudogene,transcribed_unitary_pseudogene,transcribed_unprocessed_pseudogene,translated_processed_pseudogene,TR_C_gene,TR_D_gene,TR_J_gene,TR_J_pseudogene,TR_V_gene,TR_V_pseudogene,unitary_pseudogene,unprocessed_pseudogene,vault_RNA \ tag:Tag=3_nested_supported_extension,3_standard_supported_extension,454_RNA_Seq_supported,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,artifactual_duplication,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,fragmented_mixed_strand_locus,GENCODE_Primary,inferred_exon_combination,inferred_transcript_model,low_sequence_quality,MANE_Plus_Clinical,MANE_Select,mRNA_end_NF,mRNA_start_NF,NAGNAG_splice_site,ncRNA_host,nested_454_RNA_Seq_supported,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,pseudo_consens,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 wgEncodeGencodeBasicV49 trackHandler wgEncodeGencode subTrack wgEncodeGencodeV49ViewGenes on shortLabel Basic subGroups view=aGenes name=Basic longLabel Basic Gene Annotation Set from GENCODE Version 49 (Ensembl 115) type genePred priority 1 track wgEncodeGencodeCompV49 trackHandler wgEncodeGencode subTrack wgEncodeGencodeV49ViewGenes off subGroups view=aGenes name=Comprehensive shortLabel Comprehensive longLabel Comprehensive Gene Annotation Set from GENCODE Version 49 (Ensembl 115) type genePred priority 2 track wgEncodeGencodePseudoGeneV49 trackHandler wgEncodeGencode subTrack wgEncodeGencodeV49ViewGenes on subGroups view=aGenes name=Pseudogenes shortLabel Pseudogenes longLabel Pseudogene Annotation Set from GENCODE Version 49 (Ensembl 115) type genePred color 255,51,255 priority 3 track wgEncodeGencodeV49ViewPolya shortLabel PolyA view cPolya visibility hide subTrack wgEncodeGencodeV49 type genePred configurable off track wgEncodeGencodePolyaV49 trackHandler wgEncodeGencode subTrack wgEncodeGencodeV49ViewPolya off subGroups view=bPolya name=zPolyA shortLabel PolyA longLabel PolyA Transcript Annotation Set from GENCODE Version 49 (Ensembl 115) type genePred color 0,0,0 priority 5 # searches for basic searchName wgEncodeGencodeBasicV49 searchTable wgEncodeGencodeBasicV49 searchMethod prefix searchType genePred termRegex ENST[0-9.]+ searchPriority 2.24801 searchName wgEncodeGencodeBasicGeneSymV49 searchTable wgEncodeGencodeBasicV49 searchMethod exact searchType genePred searchPriority 2.24802 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodeBasicGeneV49 searchTable wgEncodeGencodeBasicV49 searchMethod prefix searchType genePred termRegex ENSG[0-9.]+ searchPriority 2.24803 xrefTable wgEncodeGencodeAttrsV49 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodeBasicHavanaTranscriptV49 searchTable wgEncodeGencodeBasicV49 searchMethod prefix searchType genePred termRegex OTTHUMT[0-9.]+ searchPriority 2.24804 xrefTable wgEncodeGencodeAttrsV49 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodeBasicHavanaGeneV49 searchTable wgEncodeGencodeBasicV49 searchMethod prefix searchType genePred termRegex OTTHUMG[0-9.]+ searchPriority 2.24806 xrefTable wgEncodeGencodeAttrsV49 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%' searchName wgEncodeGencodeBasicProtV49 searchTable wgEncodeGencodeBasicV49 searchMethod prefix searchType genePred termRegex ENSP[0-9.]+ searchPriority 2.24807 xrefTable wgEncodeGencodeAttrsV49 xrefQuery select transcriptId,proteinId from %s where proteinId like '%s%%' # searches for comp searchName wgEncodeGencodeCompV49 searchTable wgEncodeGencodeCompV49 searchMethod prefix searchType genePred termRegex ENST[0-9.]+ searchPriority 2.24808 searchName wgEncodeGencodeCompGeneSymV49 searchTable wgEncodeGencodeCompV49 searchMethod exact searchType genePred searchPriority 2.24809 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodeCompGeneV49 searchTable wgEncodeGencodeCompV49 searchMethod prefix searchType genePred termRegex ENSG[0-9.]+ searchPriority 2.24810 xrefTable wgEncodeGencodeAttrsV49 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodeCompHavanaTranscriptV49 searchTable wgEncodeGencodeCompV49 searchMethod prefix searchType genePred termRegex OTTHUMT[0-9.]+ searchPriority 2.24811 xrefTable wgEncodeGencodeAttrsV49 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodeCompHavanaGeneV49 searchTable wgEncodeGencodeCompV49 searchMethod prefix searchType genePred termRegex OTTHUMG[0-9.]+ searchPriority 2.24812 xrefTable wgEncodeGencodeAttrsV49 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%' searchName wgEncodeGencodeCompProtV49 searchTable wgEncodeGencodeCompV49 searchMethod prefix searchType genePred termRegex ENSP[0-9.]+ searchPriority 2.24813 xrefTable wgEncodeGencodeAttrsV49 xrefQuery select transcriptId,proteinId from %s where proteinId like '%s%%' # searches for pseudogene searchName wgEncodeGencodePseudoGeneV49 searchTable wgEncodeGencodePseudoGeneV49 searchMethod prefix searchType genePred termRegex ENST[0-9.]+ searchPriority 2.24814 searchName wgEncodeGencodePseudoGeneGeneSymV49 searchTable wgEncodeGencodePseudoGeneV49 searchMethod exact searchType genePred searchPriority 2.24815 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodePseudoGeneGeneV49 searchTable wgEncodeGencodePseudoGeneV49 searchMethod prefix searchType genePred termRegex ENSG[0-9.]+ searchPriority 2.24816 xrefTable wgEncodeGencodeAttrsV49 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodePseudoGeneHavanaTranscriptV49 searchTable wgEncodeGencodePseudoGeneV49 searchMethod prefix searchType genePred termRegex OTTHUMT[0-9.]+ searchPriority 2.24817 xrefTable wgEncodeGencodeAttrsV49 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodePseudoGeneHavanaGeneV49 searchTable wgEncodeGencodePseudoGeneV49 searchMethod prefix searchType genePred termRegex OTTHUMG[0-9.]+ searchPriority 2.24818 xrefTable wgEncodeGencodeAttrsV49 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%'