hub GCA_041735815.1 genome assembly
shortLabel Inner Mongolia cashmere goat (2024)
longLabel Inner Mongolia cashmere goat (2024)/Capra hircus/GCA_041735815.1_T2T-goat2.0 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCA_041735815.1_T2T-goat2.0.description.html

genome GCA_041735815.1
taxId 9925
groups groups.txt
description Inner Mongolia cashmere goat (2024)
twoBitPath GCA_041735815.1.2bit
twoBitBptUrl GCA_041735815.1.2bit.bpt
chromSizes GCA_041735815.1.chrom.sizes.txt
chromAliasBb GCA_041735815.1.chromAlias.bb
organism T2T-goat2.0 Sep. 2024
defaultPos CP168611.1:55509578-55519578
scientificName Capra hircus
htmlPath html/GCA_041735815.1_T2T-goat2.0.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/041/735/815/GCA_041735815.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/041/735/815/GCA_041735815.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/041/735/815/GCA_041735815.1
liftOver.GCF_002263795.3 liftOver/GCA_041735815.1ToGCF_002263795.3.over.chain.gz

track assembly
longLabel Assembly
shortLabel Assembly
visibility hide
colorByStrand 150,100,30 230,170,40
color 150,100,30
altColor 230,170,40
bigDataUrl bbi/GCA_041735815.1_T2T-goat2.0.assembly.bb
type bigBed 6
html html/GCA_041735815.1_T2T-goat2.0.assembly
searchIndex name
searchTrix ixIxx/GCA_041735815.1_T2T-goat2.0.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_041735815.1_T2T-goat2.0.cytoBand.bb

track gc5Base
shortLabel GC Percent
longLabel GC Percent in 5-Base Windows
group map
visibility dense
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_041735815.1_T2T-goat2.0.gc5Base.bw
html html/GCA_041735815.1_T2T-goat2.0.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_041735815.1_T2T-goat2.0.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCA_041735815.1_T2T-goat2.0.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_041735815.1_T2T-goat2.0.rmsk.bb
xrefDataUrl bbi/GCA_041735815.1_T2T-goat2.0.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCA_041735815.1_T2T-goat2.0.repeatMasker

track repeatModeler
shortLabel RepeatModeler
longLabel RepeatModeler Repetitive Elements
type bigRmsk 9 +
visibility hide
group varRep
bigDataUrl bbi/GCA_041735815.1_T2T-goat2.0.rModel.bb
xrefDataUrl bbi/GCA_041735815.1_T2T-goat2.0.rModel.align.bb
maxWindowToDraw 5000000
html html/GCA_041735815.1_T2T-goat2.0.repeatModeler

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_041735815.1_T2T-goat2.0.simpleRepeat.bb
html html/GCA_041735815.1_T2T-goat2.0.simpleRepeat

track cpgIslands
compositeTrack on
shortLabel CpG Islands
longLabel CpG Islands (Islands < 300 Bases are Light Green)
group regulation
visibility dense
type bigBed 4 +
html html/GCA_041735815.1_T2T-goat2.0.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_041735815.1_T2T-goat2.0.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_041735815.1_T2T-goat2.0.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_041735815.1_T2T-goat2.0.windowMasker.bb
html html/GCA_041735815.1_T2T-goat2.0.windowMasker

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_041735815.1_T2T-goat2.0.augustus.bb
html html/GCA_041735815.1_T2T-goat2.0.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_041735815.1_T2T-goat2.0.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_041735815.1_T2T-goat2.0.xenoRefGene.ix
html html/GCA_041735815.1_T2T-goat2.0.xenoRefGene

##############################################################################
# GCF_002263795.3 - domestic cattle - Bos taurus - taxId: 9913
##############################################################################
track chainNetGCF_002263795.3
compositeTrack on
shortLabel domestic cattle Chain/Net
longLabel domestic cattle (2023-07-01), 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 GCF_002263795.3
html html/GCA_041735815.1_T2T-goat2.0.chainNet

    track chainNetGCF_002263795.3Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetGCF_002263795.3
    spectrum on

        track chainGCF_002263795.3
        parent chainNetGCF_002263795.3Viewchain
        subGroups view=chain
        shortLabel domestic cattle Chain
        longLabel domestic cattle (2023-07-01) Chained Alignments
        type bigChain GCF_002263795.3
        bigDataUrl bbi/GCA_041735815.1_T2T-goat2.0.chainGCF_002263795.3.bb
        linkDataUrl bbi/GCA_041735815.1_T2T-goat2.0.chainGCF_002263795.3Link.bb
        priority 1

        track chainSynGCF_002263795.3
        parent chainNetGCF_002263795.3Viewchain
        subGroups view=chain
        shortLabel domestic cattle synChain
        longLabel domestic cattle (2023-07-01) Syntenic Chained Alignments
        type bigChain GCF_002263795.3
        bigDataUrl bbi/GCA_041735815.1_T2T-goat2.0.chainSynGCF_002263795.3.bb
        linkDataUrl bbi/GCA_041735815.1_T2T-goat2.0.chainSynGCF_002263795.3Link.bb
        priority 2

        track chainRBestGCF_002263795.3
        parent chainNetGCF_002263795.3Viewchain
        subGroups view=chain
        shortLabel domestic cattle rbChain
        longLabel domestic cattle (2023-07-01) Reciprocal Best Chained Alignments
        type bigChain GCF_002263795.3
        bigDataUrl bbi/GCA_041735815.1_T2T-goat2.0.chainRBestGCF_002263795.3.bb
        linkDataUrl bbi/GCA_041735815.1_T2T-goat2.0.chainRBestGCF_002263795.3Link.bb
        priority 3

        track chainLiftOverGCF_002263795.3
        parent chainNetGCF_002263795.3Viewchain
        subGroups view=chain
        shortLabel domestic cattle loChain
        longLabel domestic cattle (2023-07-01) Lift Over Chained Alignments
        type bigChain GCF_002263795.3
        bigDataUrl bbi/GCA_041735815.1_T2T-goat2.0.chainLiftOverGCF_002263795.3.bb
        linkDataUrl bbi/GCA_041735815.1_T2T-goat2.0.chainLiftOverGCF_002263795.3Link.bb
        priority 4

    track mafNetGCF_002263795.3Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetGCF_002263795.3

        track netGCF_002263795.3
        parent mafNetGCF_002263795.3Viewnet
        subGroups view=net
        shortLabel domestic cattle net
        longLabel domestic cattle (2023-07-01) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_041735815.1_T2T-goat2.0.GCF_002263795.3.net.bb
        summary bbi/GCA_041735815.1_T2T-goat2.0.GCF_002263795.3.net.summary.bb
        speciesOrder GCF_002263795.3
        priority 5

        track synNetGCF_002263795.3
        parent mafNetGCF_002263795.3Viewnet
        subGroups view=net
        shortLabel domestic cattle synNet
        longLabel domestic cattle (2023-07-01) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_041735815.1_T2T-goat2.0.GCF_002263795.3.synNet.bb
        summary bbi/GCA_041735815.1_T2T-goat2.0.GCF_002263795.3.synNet.summary.bb
        speciesOrder GCF_002263795.3
        priority 6

        track rbestNetGCF_002263795.3
        parent mafNetGCF_002263795.3Viewnet
        subGroups view=net
        shortLabel domestic cattle rbestNet
        longLabel domestic cattle (2023-07-01) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_041735815.1_T2T-goat2.0.GCF_002263795.3.rbestNet.bb
        summary bbi/GCA_041735815.1_T2T-goat2.0.GCF_002263795.3.rbestNet.summary.bb
        speciesOrder GCF_002263795.3
        priority 7


track TOGAv2
shortLabel TOGA V2
longLabel TOGA 2.0 annotations, multiple reference
group genes
visibility hide
type bigBed 12 +
superTrack on
html contrib/TOGAv2/TOGAv2

    track HLTOGAannotvsHLbosTau10v2
    parent TOGAv2
    shortLabel TOGA2 zebrafinch annotations
    longLabel TOGA 2.0 annotations using zebrafinch taeGut5 as reference
    group genes
    priority 3
    visibility pack
    itemRgb on
    type bigBed 12 +
    bigDataUrl contrib/TOGAv2/TOGAvBosTau10v2/HLTOGAannotVsHLbosTau10v2.bb
    labelFields name
    searchIndex name
    searchTrix contrib/TOGAv2/TOGAvBosTau10v2/HLTOGAannotVsHLbosTau10v2.ix
    decorator.default.bigDataUrl contrib/TOGAv2/TOGAvBosTau10v2/HLTOGAannotVsHLbosTau10v2.decorator.bb
    decorator.default.maxLabelBases 5000
    html contrib/TOGAv2/TOGAv2

    track HLTOGAannotvsMm10v2
    parent TOGAv2
    shortLabel TOGA2 zebrafinch annotations
    longLabel TOGA 2.0 annotations using zebrafinch taeGut5 as reference
    group genes
    priority 3
    visibility pack
    itemRgb on
    type bigBed 12 +
    bigDataUrl contrib/TOGAv2/TOGAvMm10v2/HLTOGAannotVsMm10v2.bb
    labelFields name
    searchIndex name
    searchTrix contrib/TOGAv2/TOGAvMm10v2/HLTOGAannotVsMm10v2.ix
    decorator.default.bigDataUrl contrib/TOGAv2/TOGAvMm10v2/HLTOGAannotVsMm10v2.decorator.bb
    decorator.default.maxLabelBases 5000
    html contrib/TOGAv2/TOGAv2

    track HLTOGAannotvsHLeleMaxInd3Av2
    parent TOGAv2
    shortLabel TOGA2 zebrafinch annotations
    longLabel TOGA 2.0 annotations using zebrafinch taeGut5 as reference
    group genes
    priority 3
    visibility pack
    itemRgb on
    type bigBed 12 +
    bigDataUrl contrib/TOGAv2/TOGAvGCF_024166365.1v2/HLTOGAannotVsHLeleMaxInd3Av2.bb
    labelFields name
    searchIndex name
    searchTrix contrib/TOGAv2/TOGAvGCF_024166365.1v2/HLTOGAannotVsHLeleMaxInd3Av2.ix
    decorator.default.bigDataUrl contrib/TOGAv2/TOGAvGCF_024166365.1v2/HLTOGAannotVsHLeleMaxInd3Av2.decorator.bb
    decorator.default.maxLabelBases 5000
    html contrib/TOGAv2/TOGAv2

    track HLTOGAannotvsHg38v2
    parent TOGAv2
    shortLabel TOGA2 zebrafinch annotations
    longLabel TOGA 2.0 annotations using zebrafinch taeGut5 as reference
    group genes
    priority 3
    visibility pack
    itemRgb on
    type bigBed 12 +
    bigDataUrl contrib/TOGAv2/TOGAvHg38v2/HLTOGAannotVsHg38v2.bb
    labelFields name
    searchIndex name
    searchTrix contrib/TOGAv2/TOGAvHg38v2/HLTOGAannotVsHg38v2.ix
    decorator.default.bigDataUrl contrib/TOGAv2/TOGAvHg38v2/HLTOGAannotVsHg38v2.decorator.bb
    decorator.default.maxLabelBases 5000
    html contrib/TOGAv2/TOGAv2

track Tiberius
bigDataUrl contrib/tiberius/tiberius.bigGenePred.bb
shortLabel Tiberius genes
longLabel Tiberius ab initio gene prediction
type bigGenePred
visibility pack
color 0,102,204
noScoreFilter on
html contrib/tiberius/Tiberius.html
group genes
dataVersion Tiberius version 2025-11-10
baseColorDefault genomicCodons