17b7d3c37be41135afaf8e91e365e3847af96ca5 lrnassar Mon Jun 22 10:56:56 2026 -0700 Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt). diff --git src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra index 9cde9928fea..bae36b9f0af 100644 --- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra +++ src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra @@ -1,431 +1,433 @@ 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 mouseDevTimecourse.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 beta,public include trackDb.encode3.alpha.ra alpha include encode3RenEnhancerGene.ra include encode.cCREs.override.ra include encode4Reg.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=$$ color 180,0,134 priority 2 include dbSnpArchiveMm10.ra include reMap.ra track allGaps shortLabel All Gaps longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps group map visibility dense type bigBed 3 bigDataUrl /gbdb/mm10/bbi/allGaps.bb html allGaps track vistaEnhancersBb shortLabel VISTA Enhancers longLabel VISTA Enhancers group regulation url https://enhancer.lbl.gov/vista/element?vistaId=$$ 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 include long_read_transcripts.ra track ucscGenePfam override shortLabel Pfam in GENCODE longLabel Pfam Domains in GENCODE Genes html gencodePfam track jaspar2024 override parent jaspar on + +include tad.ra alpha