7e008fe9bc0fd5adbba182fd74adfc4b8fbd5fca hiram Thu Dec 4 13:46:14 2025 -0800 no need to define HLTOGAannotvsHg38v1 here, it is at the top level refs #35776 diff --git src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra index 8c32e41420b..9f6344c9ec4 100644 --- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra +++ src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra @@ -1,438 +1,424 @@ include ../../crispr10K.ra include knownGene.ra # chainNet tracks include trackDb.gliresChainNet.ra include trackDb.euarchontoglireChainNet.ra include trackDb.placentalsChainNet.ra include trackDb.vertebrateChainNet.ra include trackDb.previousVersionsChainNet.ra alpha include tabulaMurisSenis.ra include tabulamuris.ra include liftOverMm39.ra # Local declaration so that local gold.html is picked up. track gold override html gold # Local declaration so that local gap.html is picked up. track gap override html gap # Local declaration so that patents are in the right group track patSeq override group pub track patNonBulk override group pub track patBulk override group pub track assemblyFrags shortLabel Contigs longLabel Contig fragments used in the assembly group map visibility hide colorByStrand 150,100,30 100,50,0 type bed 6 urlLabel NCBI Nucleotide: url https://www.ncbi.nlm.nih.gov/nuccore/$$ # different type of gold search here so the fragments can be found with # or without their trailing .1 searchTable gold searchMethod prefix searchType bed shortCircuit 1 termRegex [ACGJ][ACLHRTY][A0-9]+(\.[0-9]+)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 include trackDb.60way.ra include trackDb.4way.ra alpha track mm9UcscGenes shortLabel mm9 Ucsc Genes longLabel mm9 Ucsc Genes group genes visibility hide color 20,20,170 type bed 12 track xenoClinvar shortLabel Human Variants longLabel ClinVar Variants mapped to Mouse type bigBed 9 + itemRgb on bigDataUrl /gbdb/mm10/bbi/xenoClinvar.bb group x mouseOverField _mouseOver urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/" release alpha include mm10Strains1SuperTrack.ra track qPcrPrimers override group regulation url http://www.weizmann.ac.il/cgi-bin/USERcompphys/primers/mouse/extract_primer_by_line.cgi?$$ urlLabel Click here for primer details: track ucscRetroAli2 shortLabel Retroposed Genes longLabel Retroposed Genes V2, Including Pseudogenes group genes type psl color 20,0,250 visibility hide ucscRetroInfo ucscRetroInfo2 baseColorDefault diffCodons baseColorUseCds table ucscRetroCds2 baseColorUseSequence extFile ucscRetroSeq2 ucscRetroExtFile2 indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 dataVersion Apr. 2013 searchName ucscRetroInfoRefSeq2 searchTable ucscRetroAli2 searchDescription Retroposed Genes V2, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' xrefTable hgFixed.refLink, ucscRetroInfo2 dontCheckXrefQueryFormat 1 xrefQuery select ucscRetroInfo2.name, hgFixed.refLink.name from %s where hgFixed.refLink.name like '%s%%' and refSeq = mrnaAcc searchPriority 3.52 searchName ucscRetroInfoMrna2 searchTable ucscRetroAli2 searchDescription Retroposed Genes V2, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' searchPriority 3.55 searchName ucscRetroUniProt2 searchTable ucscRetroAli2 searchDescription Retroposed Genes V2, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' dontCheckXrefQueryFormat 1 xrefTable kgXref, ucscRetroInfo2 xrefQuery select ucscRetroInfo2.name, spDisplayID from %s where spDisplayID like '%s%%' and kgName = kgID searchPriority 3.54 searchName ucscRetroKnownGene2 searchTable ucscRetroAli2 searchDescription Retroposed Genes V2, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' dontCheckXrefQueryFormat 1 xrefTable kgXref, ucscRetroInfo2 xrefQuery select ucscRetroInfo2.name, geneSymbol from %s where geneSymbol like '%s%%' and kgName = kgID searchPriority 3.53 track ucscRetroAli4 shortLabel Retroposed Genes 4.0 longLabel Retroposed Genes V4, Including Pseudogenes group genes type psl color 20,0,250 visibility hide ucscRetroInfo ucscRetroInfo4 baseColorDefault diffCodons baseColorUseCds table ucscRetroCds4 baseColorUseSequence extFile ucscRetroSeq4 ucscRetroExtFile4 indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 dataVersion Feb. 2014 searchName ucscRetroInfoRefSeq4 searchTable ucscRetroAli4 searchDescription Retroposed GenesV4, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' xrefTable hgFixed.refLink, ucscRetroInfo4 dontCheckXrefQueryFormat 1 xrefQuery select ucscRetroInfo4.name, hgFixed.refLink.name from %s where hgFixed.refLink.name like '%s%%' and refSeq = mrnaAcc searchPriority 3.52 searchName ucscRetroInfoMrna4 searchTable ucscRetroAli4 searchDescription Retroposed GenesV4, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' searchPriority 3.55 searchName ucscRetroUniProt4 searchTable ucscRetroAli4 searchDescription Retroposed GenesV4, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' dontCheckXrefQueryFormat 1 xrefTable kgXref, ucscRetroInfo4 xrefQuery select ucscRetroInfo4.name, spDisplayID from %s where spDisplayID like '%s%%' and kgName = kgID searchPriority 3.54 searchName ucscRetroKnownGene4 searchTable ucscRetroAli4 searchDescription Retroposed GenesV4, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' dontCheckXrefQueryFormat 1 xrefTable kgXref, ucscRetroInfo4 xrefQuery select ucscRetroInfo4.name, geneSymbol from %s where geneSymbol like '%s%%' and kgName = kgID searchPriority 3.53 track ucscRetroAli5 shortLabel Retroposed Genes 5.0 longLabel Retroposed Genes V5, Including Pseudogens group genes type psl color 20,0,250 visibility hide ucscRetroInfo ucscRetroInfo5 baseColorDefault diffCodons baseColorUseCds table ucscRetroCds5 baseColorUseSequence extFile ucscRetroSeq5 ucscRetroExtFile5 indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 dataVersion Jul. 2014 searchName ucscRetroInfoRefSeq5 searchTable ucscRetroAli5 searchDescription Retroposed GenesV5, Including Pseudogenes - 2014-07-22 query select tName, tStart,tEnd, qName from %s where qName like '%s%%' xrefTable hgFixed.refLink, ucscRetroInfo5 dontCheckXrefQueryFormat 1 xrefQuery select ucscRetroInfo5.name, hgFixed.refLink.name from %s where hgFixed.refLink.name like '%s%%' and refSeq = mrnaAcc searchPriority 3.52 searchName ucscRetroInfoMrna5 searchTable ucscRetroAli5 searchDescription Retroposed GenesV5, Including Pseudogenes - 2014-07-22 query select tName, tStart,tEnd, qName from %s where qName like '%s%%' searchPriority 3.55 searchName ucscRetroUniProt5 searchTable ucscRetroAli5 searchDescription Retroposed GenesV5, Including Pseudogenes - 2014-07-22 query select tName, tStart,tEnd, qName from %s where qName like '%s%%' dontCheckXrefQueryFormat 1 xrefTable kgXref, ucscRetroInfo5 xrefQuery select ucscRetroInfo5.name, spDisplayID from %s where spDisplayID like '%s%%' and kgName = kgID searchPriority 3.54 searchName ucscRetroKnownGene5 searchTable ucscRetroAli5 searchDescription Retroposed GenesV5, Including Pseudogenes - 2014-07-22 query select tName, tStart,tEnd, qName from %s where qName like '%s%%' dontCheckXrefQueryFormat 1 xrefTable kgXref, ucscRetroInfo5 xrefQuery select ucscRetroInfo5.name, geneSymbol from %s where geneSymbol like '%s%%' and kgName = kgID searchPriority 3.53 track ucscRetroAli6 shortLabel RetroGenes V6 longLabel Retroposed Genes V6, Including Pseudogenes group genes type psl color 20,0,250 visibility hide ucscRetroInfo ucscRetroInfo6 baseColorDefault diffCodons baseColorUseCds table ucscRetroCds6 baseColorUseSequence extFile ucscRetroSeq6 ucscRetroExtFile6 indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 dataVersion Jan. 2015 exonNumbers off searchName ucscRetroInfoRefSeq6 searchTable ucscRetroAli6 searchDescription Retroposed Genes V6, Including Pseudogene query select tName, tStart,tEnd, qName from %s where qName like '%s%%' xrefTable hgFixed.refLink, ucscRetroInfo6 dontCheckXrefQueryFormat 1 xrefQuery select ucscRetroInfo6.name, hgFixed.refLink.name from %s where hgFixed.refLink.name like '%s%%' and refSeq = mrnaAcc searchPriority 3.52 searchName ucscRetroInfoMrna6 searchTable ucscRetroAli6 searchDescription Retroposed Genes V6, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' searchPriority 3.55 searchName ucscRetroUniProt6 searchTable ucscRetroAli6 searchDescription Retroposed Genes V6, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' dontCheckXrefQueryFormat 1 xrefTable kgXref, ucscRetroInfo6 xrefQuery select ucscRetroInfo6.name, spDisplayID from %s where spDisplayID like '%s%%' and kgName = kgID searchPriority 3.54 searchName ucscRetroKnownGene6 searchTable ucscRetroAli6 searchDescription Retroposed Genes V6, Including Pseudogenes query select tName, tStart,tEnd, qName from %s where qName like '%s%%' dontCheckXrefQueryFormat 1 xrefTable kgXref, ucscRetroInfo6 xrefQuery select ucscRetroInfo6.name, geneSymbol from %s where geneSymbol like '%s%%' and kgName = kgID searchPriority 3.53 track jaxQtl override shortLabel MGI QTL longLabel Mouse Genome Informatics Quantitative Trait Loci ***Lifted from NCBI 37 (mm9)*** origAssembly mm9 pennantIcon 9.jpg ../goldenPath/help/liftOver.html "These data were converted via liftOver from the July 2007 (NCBI37/mm9) version of the track" track FaceBase24SampleTypesAvg override origAssembly mm9 pennantIcon 9.jpg ../goldenPath/help/liftOver.html "These data were converted via liftOver from the July 2007 (NCBI37/mm9) version of the track" track rmskJoinedBaseline override group varRep include trackDb.gencode.ra include defaultPriority.ra searchTable sgpGene searchType genePred termRegex chr[0-9MUXYn]+[GHJLv0-9_]+(alt_|random_)?[0-9]+(\.[0-9]+)? searchPriority 50 searchTable geneid searchType genePred searchMethod prefix termRegex chr[0-9MUXYn]+[GHJLv0-9_]+(alt_|random_)?[0-9]+(\.[0-9]+)? searchPriority 50 track strainSNPs shortLabel Mouse SNPs longLabel Annotated SNPs from mouse strain comparison analysis group varRep type vcfTabix visibility hide priority 11.5 hapClusterHeight 360 hapClusterEnabled on hapClusterMethod fileOrder maxWindowToDraw 1000000 track nestedRepeats override group varRep priority 10 track microsat override group varRep priority 11 track genomicSuperDups override group varRep track simpleRepeat override group varRep track windowmaskerSdust override group varRep track spMut override group pub bigDataUrl /gbdb/$D/uniprot/unipMut.bb #######################3 # regulation tracks include trackDb.encode3.ra include encode3RenEnhancerGene.ra include fantom5.ra track epdNew compositeTrack on shortLabel EPDnew Promoters longLabel Promoters from EPDnew html ../../epdNewPromoter type bigBed 8 group regulation visibility hide urlLabel EPDnew link: bedNameLabel Promoter ID exonArrows on track epdNewPromoter shortLabel EPDnew v6 longLabel Promoters from EPDnew mouse version 003 parent epdNew on bigDataUrl /gbdb/$D/bbi/epdNewMouse003.$D.bb dataVersion EPDNew Mouse Version 003 (June 2018) url https://epd.epfl.ch/cgi-bin/get_doc?db=mmEpdNew&format=genome&entry=$$ color 50,50,200 priority 1 track epdNewPromoterNonCoding shortLabel EPDnew NC v1 longLabel ncRNA promoters from EPDnewNC mouse version 001 parent epdNew on bigDataUrl /gbdb/$D/bbi/epdNewMouseNc001.$D.bb dataVersion EPDNewNC Mouse Version 001 (August 2019) url https://epd.epfl.ch/cgi-bin/get_doc?db=mmNCEpdNew&format=genome&entry=$$ color 180,0,134 priority 2 include dbSnpArchiveMm10.ra include reMap.ra -# TOGA default annotation for hg38 -track HLTOGAannotvsHg38v1 -shortLabel TOGA hg38 annotations -longLabel TOGA annotations using human hg38 as reference -group genes -priority 2 -visibility pack -itemRgb on -type bed 12 - -searchTable HLTOGAannotvsHg38v1 -searchType bed -searchMethod fuzzy - track allGaps shortLabel All Gaps longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps group map visibility dense type bigBed 3 bigDataUrl /gbdb/mm10/bbi/allGaps.bb html allGaps track vistaEnhancersBb shortLabel VISTA Enhancers longLabel VISTA Enhancers group regulation url https://enhancer.lbl.gov/vista/element?vistaId=$$ type bigBed 9 + mouseOverField patternExpression urlLabel View on the VISTA Enhancer Browser bigDataUrl /gbdb/mm10/vistaEnhancers/vistaEnhancers.bb itemRgb on include ../../trackDb.mgc-orfeome.ra include ../refSeqComposite.mm10.mm39.ra include recount3.ra alpha include long_read_transcripts.ra track ucscGenePfam override shortLabel Pfam in GENCODE longLabel Pfam Domains in GENCODE Genes html gencodePfam