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/hg19/wgEncodeGencodeV49lift37.ra src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV49lift37.ra index 3ba5f56a6ad..624c53c9c6d 100644 --- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV49lift37.ra +++ src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV49lift37.ra @@ -1,210 +1,211 @@ track wgEncodeGencodeV49lift37 compositeTrack on superTrack wgEncodeGencodeSuper pack shortLabel GENCODE V49lift37 longLabel GENCODE lifted annotations from V49lift37 (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 49lift37 +pennantIcon New red ../goldenPath/newsarch.html#103125 "Released Oct. 31, 2025" track wgEncodeGencodeV49lift37ViewGenes shortLabel Genes view aGenes configurable on visibility pack subTrack wgEncodeGencodeV49lift37 type genePred idXref wgEncodeGencodeAttrsV49lift37 transcriptId geneId itemClassTbl wgEncodeGencodeAttrsV49lift37 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 wgEncodeGencodeAttrsV49lift37 order by transcriptType' hg19 # - 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 wgEncodeGencodeTagV49lift37 order by tag' hg19 # - 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=antisense,artifact,IG_C_gene,IG_C_pseudogene,IG_D_gene,IG_J_gene,IG_J_pseudogene,IG_pseudogene,IG_V_gene,IG_V_pseudogene,lincRNA,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,sense_intronic,sense_overlapping,snoRNA,snRNA,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_candidate,appris_candidate_longest,appris_principal,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,PAR,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=antisense,artifact,IG_C_gene,IG_C_pseudogene,IG_D_gene,IG_J_gene,IG_J_pseudogene,IG_pseudogene,IG_V_gene,IG_V_pseudogene,lincRNA,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,sense_intronic,sense_overlapping,snoRNA,snRNA,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_candidate,appris_candidate_longest,appris_principal,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,PAR,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 wgEncodeGencodeBasicV49lift37 trackHandler wgEncodeGencode subTrack wgEncodeGencodeV49lift37ViewGenes on shortLabel Basic subGroups view=aGenes name=Basic longLabel Basic Gene Annotation Set from GENCODE Version 49lift37 (Ensembl 115) type genePred priority 1 track wgEncodeGencodeCompV49lift37 trackHandler wgEncodeGencode subTrack wgEncodeGencodeV49lift37ViewGenes off subGroups view=aGenes name=Comprehensive shortLabel Comprehensive longLabel Comprehensive Gene Annotation Set from GENCODE Version 49lift37 (Ensembl 115) type genePred priority 2 track wgEncodeGencodePseudoGeneV49lift37 trackHandler wgEncodeGencode subTrack wgEncodeGencodeV49lift37ViewGenes on subGroups view=aGenes name=Pseudogenes shortLabel Pseudogenes longLabel Pseudogene Annotation Set from GENCODE Version 49lift37 (Ensembl 115) type genePred color 255,51,255 priority 3 # searches for basic searchName wgEncodeGencodeBasicV49lift37 searchTable wgEncodeGencodeBasicV49lift37 searchMethod prefix searchType genePred termRegex ENST[0-9._]+ searchPriority 2.24801 searchName wgEncodeGencodeBasicGeneSymV49lift37 searchTable wgEncodeGencodeBasicV49lift37 searchMethod exact searchType genePred searchPriority 2.24802 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodeBasicGeneV49lift37 searchTable wgEncodeGencodeBasicV49lift37 searchMethod prefix searchType genePred termRegex ENSG[0-9._]+ searchPriority 2.24803 xrefTable wgEncodeGencodeAttrsV49lift37 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodeBasicHavanaTranscriptV49lift37 searchTable wgEncodeGencodeBasicV49lift37 searchMethod prefix searchType genePred termRegex OTTHUMT[0-9._]+ searchPriority 2.24804 xrefTable wgEncodeGencodeAttrsV49lift37 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodeBasicHavanaGeneV49lift37 searchTable wgEncodeGencodeBasicV49lift37 searchMethod prefix searchType genePred termRegex OTTHUMG[0-9._]+ searchPriority 2.24806 xrefTable wgEncodeGencodeAttrsV49lift37 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%' # searches for comp searchName wgEncodeGencodeCompV49lift37 searchTable wgEncodeGencodeCompV49lift37 searchMethod prefix searchType genePred termRegex ENST[0-9._]+ searchPriority 2.24808 searchName wgEncodeGencodeCompGeneSymV49lift37 searchTable wgEncodeGencodeCompV49lift37 searchMethod exact searchType genePred searchPriority 2.24809 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodeCompGeneV49lift37 searchTable wgEncodeGencodeCompV49lift37 searchMethod prefix searchType genePred termRegex ENSG[0-9._]+ searchPriority 2.24810 xrefTable wgEncodeGencodeAttrsV49lift37 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodeCompHavanaTranscriptV49lift37 searchTable wgEncodeGencodeCompV49lift37 searchMethod prefix searchType genePred termRegex OTTHUMT[0-9._]+ searchPriority 2.24811 xrefTable wgEncodeGencodeAttrsV49lift37 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodeCompHavanaGeneV49lift37 searchTable wgEncodeGencodeCompV49lift37 searchMethod prefix searchType genePred termRegex OTTHUMG[0-9._]+ searchPriority 2.24812 xrefTable wgEncodeGencodeAttrsV49lift37 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%' # searches for pseudogene searchName wgEncodeGencodePseudoGeneV49lift37 searchTable wgEncodeGencodePseudoGeneV49lift37 searchMethod prefix searchType genePred termRegex ENST[0-9._]+ searchPriority 2.24814 searchName wgEncodeGencodePseudoGeneGeneSymV49lift37 searchTable wgEncodeGencodePseudoGeneV49lift37 searchMethod exact searchType genePred searchPriority 2.24815 query select chrom, txStart, txEnd, name2 from %s where name2 like '%s' searchName wgEncodeGencodePseudoGeneGeneV49lift37 searchTable wgEncodeGencodePseudoGeneV49lift37 searchMethod prefix searchType genePred termRegex ENSG[0-9._]+ searchPriority 2.24816 xrefTable wgEncodeGencodeAttrsV49lift37 xrefQuery select transcriptId,geneId from %s where geneId like '%s%%' searchName wgEncodeGencodePseudoGeneHavanaTranscriptV49lift37 searchTable wgEncodeGencodePseudoGeneV49lift37 searchMethod prefix searchType genePred termRegex OTTHUMT[0-9._]+ searchPriority 2.24817 xrefTable wgEncodeGencodeAttrsV49lift37 xrefQuery select transcriptId,havanaTranscriptId from %s where havanaTranscriptId like '%s%%' searchName wgEncodeGencodePseudoGeneHavanaGeneV49lift37 searchTable wgEncodeGencodePseudoGeneV49lift37 searchMethod prefix searchType genePred termRegex OTTHUMG[0-9._]+ searchPriority 2.24818 xrefTable wgEncodeGencodeAttrsV49lift37 xrefQuery select transcriptId,havanaGeneId from %s where havanaGeneId like '%s%%'