hub GCA_028533165.1 genome assembly shortLabel golden lion tamarin (Coari 2023) longLabel golden lion tamarin (Coari 2023)/Leontopithecus rosalia/GCA_028533165.1_Leontopithecus_rosalia_HiC genome assembly useOneFile on email hclawson@ucsc.edu descriptionUrl html/GCA_028533165.1_Leontopithecus_rosalia_HiC.description.html genome GCA_028533165.1 taxId 30588 groups groups.txt description golden lion tamarin (Coari 2023) twoBitPath GCA_028533165.1.2bit twoBitBptUrl GCA_028533165.1.2bit.bpt chromSizes GCA_028533165.1.chrom.sizes.txt chromAliasBb GCA_028533165.1.chromAlias.bb chromAuthority ucsc organism Leontopithecus_rosalia_HiC Feb. 2023 defaultPos CM052648.1:64698360-64708360 scientificName Leontopithecus rosalia htmlPath html/GCA_028533165.1_Leontopithecus_rosalia_HiC.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/028/533/165/GCA_028533165.1 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/028/533/165/GCA_028533165.1 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/028/533/165/GCA_028533165.1 liftOver.GCA_011100555.2 liftOver/GCA_028533165.1ToGCA_011100555.2.over.chain.gz track assembly longLabel Assembly shortLabel Assembly visibility pack colorByStrand 150,100,30 230,170,40 color 150,100,30 altColor 230,170,40 bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.assembly.bb type bigBed 6 html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.assembly searchIndex name searchTrix ixIxx/GCA_028533165.1_Leontopithecus_rosalia_HiC.assembly.ix url https://www.ncbi.nlm.nih.gov/nuccore/$$ urlLabel NCBI Nucleotide database: group map track cytoBandIdeo shortLabel Chromosome Band (Ideogram) longLabel Ideogram for Orientation group map visibility dense type bigBed 4 + bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.cytoBand.bb track gc5Base shortLabel GC Percent longLabel GC Percent in 5-Base Windows group map visibility full autoScale Off maxHeightPixels 128:36:16 graphTypeDefault Bar gridDefault OFF windowingFunction Mean color 0,0,0 altColor 128,128,128 viewLimits 30:70 type bigWig 0 100 bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.gc5Base.bw html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.tanDups track gapOverlap parent tanDups on shortLabel Gap Overlaps longLabel Paired exactly identical sequence on each side of a gap bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.gapOverlap.bb type bigBed 12 track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.rmsk.bb xrefDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.rmsk.align.bb maxWindowToDraw 5000000 html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.repeatMasker track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.simpleRepeat.bb html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.simpleRepeat track cpgIslands compositeTrack on shortLabel CpG Islands longLabel CpG Islands (Islands < 300 Bases are Light Green) group regulation visibility pack type bigBed 4 + html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.cpgIslands track cpgIslandExt parent cpgIslands off shortLabel CpG Islands longLabel CpG Islands (Islands < 300 Bases are Light Green) type bigBed 4 + priority 1 bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.cpgIslandExt.bb track cpgIslandExtUnmasked parent cpgIslands on shortLabel Unmasked CpG longLabel CpG Islands on All Sequence (Islands < 300 Bases are Light Green) type bigBed 4 + priority 2 bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.windowMasker.bb html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.windowMasker 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 bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.allGaps.bb html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility pack color 180,0,0 type bigGenePred bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.augustus.bb html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.augustus track xenoRefGene shortLabel RefSeq mRNAs longLabel RefSeq mRNAs mapped to this assembly group rna visibility pack color 180,0,0 type bigGenePred bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.xenoRefGene.bb url https://www.ncbi.nlm.nih.gov/nuccore/$$ urlLabel NCBI Nucleotide database: labelFields name,geneName,geneName2 defaultLabelFields geneName searchIndex name searchTrix ixIxx/GCA_028533165.1_Leontopithecus_rosalia_HiC.xenoRefGene.ix html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.xenoRefGene ############################################################################## # GCA_011100555.2 - golden lion tamarin - Leontopithecus rosalia - taxId: 30588 ############################################################################## track chainNetGCA_011100555.2 compositeTrack on shortLabel golden lion tamarin Chain/Net longLabel golden lion tamarin (2023-02-09), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno priority 100.1 color 0,0,0 altColor 100,50,0 type bed 3 sortOrder view=+ otherDb GCA_011100555.2 html html/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainNet track chainNetGCA_011100555.2Viewchain shortLabel Chain view chain visibility pack parent chainNetGCA_011100555.2 spectrum on track chainGCA_011100555.2 parent chainNetGCA_011100555.2Viewchain subGroups view=chain shortLabel golden lion tamarin Chain longLabel golden lion tamarin (2023-02-09) Chained Alignments type bigChain GCA_011100555.2 bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainGCA_011100555.2.bb linkDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainGCA_011100555.2Link.bb priority 1 track chainSynGCA_011100555.2 parent chainNetGCA_011100555.2Viewchain subGroups view=chain shortLabel golden lion tamarin synChain longLabel golden lion tamarin (2023-02-09) Syntenic Chained Alignments type bigChain GCA_011100555.2 bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainSynGCA_011100555.2.bb linkDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainSynGCA_011100555.2Link.bb priority 2 track chainRBestGCA_011100555.2 parent chainNetGCA_011100555.2Viewchain subGroups view=chain shortLabel golden lion tamarin rbChain longLabel golden lion tamarin (2023-02-09) Reciprocal Best Chained Alignments type bigChain GCA_011100555.2 bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainRBestGCA_011100555.2.bb linkDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainRBestGCA_011100555.2Link.bb priority 3 track chainLiftOverGCA_011100555.2 parent chainNetGCA_011100555.2Viewchain subGroups view=chain shortLabel golden lion tamarin loChain longLabel golden lion tamarin (2023-02-09) Lift Over Chained Alignments type bigChain GCA_011100555.2 bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainLiftOverGCA_011100555.2.bb linkDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.chainLiftOverGCA_011100555.2Link.bb priority 4 track mafNetGCA_011100555.2Viewnet shortLabel Net view net visibility full parent chainNetGCA_011100555.2 track netGCA_011100555.2 parent mafNetGCA_011100555.2Viewnet subGroups view=net shortLabel golden lion tamarin net longLabel golden lion tamarin (2023-02-09) Net Alignment type bigMaf bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.GCA_011100555.2.net.bb summary bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.GCA_011100555.2.net.summary.bb speciesOrder GCA_011100555.2 priority 5 track synNetGCA_011100555.2 parent mafNetGCA_011100555.2Viewnet subGroups view=net shortLabel golden lion tamarin synNet longLabel golden lion tamarin (2023-02-09) Syntenic Net Alignment type bigMaf bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.GCA_011100555.2.synNet.bb summary bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.GCA_011100555.2.synNet.summary.bb speciesOrder GCA_011100555.2 priority 6 track rbestNetGCA_011100555.2 parent mafNetGCA_011100555.2Viewnet subGroups view=net shortLabel golden lion tamarin rbestNet longLabel golden lion tamarin (2023-02-09) Reciprocal Best Net Alignment type bigMaf bigDataUrl bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.GCA_011100555.2.rbestNet.bb summary bbi/GCA_028533165.1_Leontopithecus_rosalia_HiC.GCA_011100555.2.rbestNet.summary.bb speciesOrder GCA_011100555.2 priority 7