hub GCF_002263795.3 genome assembly
shortLabel cattle (Hereford L1 Dominette 01449 42190680 v2.0 2023 USDA)
longLabel cattle (Hereford L1 Dominette 01449 42190680 v2.0 2023 USDA)/Bos taurus/GCF_002263795.3_ARS-UCD2.0 genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCF_002263795.3_ARS-UCD2.0.description.html

genome GCF_002263795.3
taxId 9913
groups groups.txt
description cattle (Hereford L1 Dominette 01449 42190680 v2.0 2023 USDA)
twoBitPath GCF_002263795.3.2bit
twoBitBptUrl GCF_002263795.3.2bit.bpt
chromSizes GCF_002263795.3.chrom.sizes.txt
chromAliasBb GCF_002263795.3.chromAlias.bb
chromAuthority ucsc
organism ARS-UCD2.0 Jul. 2023
defaultPos NC_037328.1:52844703-52854703
scientificName Bos taurus
htmlPath html/GCF_002263795.3_ARS-UCD2.0.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/002/263/795/GCF_002263795.3
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/002/263/795/GCF_002263795.3
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/002/263/795/GCF_002263795.3
liftOver.GCA_000003205.6 liftOver/GCF_002263795.3ToGCA_000003205.6.over.chain.gz
liftOver.GCA_005887515.3 liftOver/GCF_002263795.3ToGCA_005887515.3.over.chain.gz
liftOver.GCA_039881165.1 liftOver/GCF_002263795.3ToGCA_039881165.1.over.chain.gz
liftOver.GCF_000003025.6 liftOver/GCF_002263795.3ToGCF_000003025.6.over.chain.gz
liftOver.GCF_000003055.6 liftOver/GCF_002263795.3ToGCF_000003055.6.over.chain.gz
liftOver.GCF_000767855.1 liftOver/GCF_002263795.3ToGCF_000767855.1.over.chain.gz
liftOver.GCF_001704415.2 liftOver/GCF_002263795.3ToGCF_001704415.2.over.chain.gz
liftOver.GCF_002263795.2 liftOver/GCF_002263795.3ToGCF_002263795.2.over.chain.gz
liftOver.GCF_016699485.2 liftOver/GCF_002263795.3ToGCF_016699485.2.over.chain.gz
liftOver.GCF_016772045.2 liftOver/GCF_002263795.3ToGCF_016772045.2.over.chain.gz
liftOver.GCF_019923935.1 liftOver/GCF_002263795.3ToGCF_019923935.1.over.chain.gz
liftOver.bosTau9 liftOver/GCF_002263795.3ToBosTau9.over.chain.gz
liftOver.hg38 liftOver/GCF_002263795.3ToHg38.over.chain.gz
liftOver.mm39 liftOver/GCF_002263795.3ToMm39.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/GCF_002263795.3_ARS-UCD2.0.assembly.bb
type bigBed 6
html html/GCF_002263795.3_ARS-UCD2.0.assembly
searchIndex name
searchTrix ixIxx/GCF_002263795.3_ARS-UCD2.0.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/GCF_002263795.3_ARS-UCD2.0.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/GCF_002263795.3_ARS-UCD2.0.gc5Base.bw
html html/GCF_002263795.3_ARS-UCD2.0.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_002263795.3_ARS-UCD2.0.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.gapOverlap.bb
    type bigBed 12

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.rmsk.bb
xrefDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCF_002263795.3_ARS-UCD2.0.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.simpleRepeat.bb
html html/GCF_002263795.3_ARS-UCD2.0.simpleRepeat

track refSeqComposite
compositeTrack on
shortLabel NCBI RefSeq
longLabel RefSeq gene predictions from NCBI
group genes
visibility pack
type bigBed
dragAndDrop subTracks
allButtonPair on
dataVersion NCBI RefSeq GCF_002263795.3-RS_2023_09 (2023-10-03)
html html/GCF_002263795.3_ARS-UCD2.0.refSeqComposite
priority 2

        track ncbiRefSeq
        parent refSeqComposite on
        color 12,12,120
        shortLabel RefSeq All
        type bigGenePred
        urls name2="https://www.ncbi.nlm.nih.gov/gene/$D/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$"
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_002263795.3_ARS-UCD2.0.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.ncbiRefSeq.bb
        longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*)
        idXref ncbiRefSeqLink mrnaAcc name
        baseColorUseCds given
        baseColorDefault genomicCodons
        priority 1

        track ncbiRefSeqCurated
        color 12,12,120
        parent refSeqComposite on
        shortLabel RefSeq Curated
        longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*)
        type bigGenePred
        urls name2="https://www.ncbi.nlm.nih.gov/gene/$D/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$"
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_002263795.3_ARS-UCD2.0.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.ncbiRefSeqCurated.bb
        baseColorUseCds given
        baseColorDefault genomicCodons
        priority 2

        track ncbiRefSeqPredicted
        color 12,12,120
        parent refSeqComposite on
        shortLabel RefSeq Predicted
        longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*)
        type bigGenePred
        urls name2="https://www.ncbi.nlm.nih.gov/gene/$D/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$"
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_002263795.3_ARS-UCD2.0.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.ncbiRefSeqPredicted.bb
        baseColorUseCds given
        baseColorDefault genomicCodons
        priority 3

        track ncbiRefSeqOther
        color 32,32,32
        parent refSeqComposite on
        shortLabel RefSeq Other
        longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*)
        priority 4
        searchIndex name
        searchTrix ixIxx/GCF_002263795.3_ARS-UCD2.0.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.ncbiRefSeqOther.bb
        type bigBed 12 +
        labelFields name
        skipEmptyFields on
        urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/$$" HGNC="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="http://www.informatics.jax.org/marker/$$"

        track ncbiRefSeqPsl
        priority 5
        parent refSeqComposite off
        shortLabel RefSeq Alignments
        longLabel RefSeq Alignments of RNAs
        type bigPsl
        searchIndex name
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.bigPsl.bb
        indelDoubleInsert on
        indelQueryInsert on
        showDiffBasesAllScales .
        showDiffBasesMaxZoom 10000.0
        showCdsMaxZoom 10000.0
        showCdsAllScales .
        baseColorDefault diffCodons
        pslSequence no
        baseColorUseSequence lfExtra
        baseColorUseCds table given
        color 0,0,0

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/GCF_002263795.3_ARS-UCD2.0.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/GCF_002263795.3_ARS-UCD2.0.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/GCF_002263795.3_ARS-UCD2.0.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.windowMasker.bb
html html/GCF_002263795.3_ARS-UCD2.0.windowMasker

track allGaps
shortLabel All Gaps
longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps
group map
visibility hide
type bigBed 3
bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.allGaps.bb
html html/GCF_002263795.3_ARS-UCD2.0.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.augustus.bb
html html/GCF_002263795.3_ARS-UCD2.0.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/GCF_002263795.3_ARS-UCD2.0.xenoRefGene.bb
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
labelFields name,geneName,geneName2
defaultLabelFields geneName
searchIndex name
searchTrix ixIxx/GCF_002263795.3_ARS-UCD2.0.xenoRefGene.ix
html html/GCF_002263795.3_ARS-UCD2.0.xenoRefGene

track GCF_002263795.3_ARS-UCD2.0ChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCF_002263795.3_ARS-UCD2.0
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=GCF_002263795.2 s001=bosTau9 s002=GCA_000003205.6 s003=GCF_000003055.6 s004=GCA_039881165.1 s005=GCA_005887515.3 s006=GCF_019923935.1 s007=GCF_001704415.2 s008=GCF_016772045.2 s009=GCF_000767855.1 s010=GCF_000003025.6 s011=hg38 s012=mm39 s013=GCF_016699485.2
subGroup3 chainType chain_type c00=chain c01=syntenic c02=reciprocal_best c03=lift_over c04=chain_align c05=syntenic_align c06=reciprocal_align c07=lift_over_align
dragAndDrop subTracks
visibility hide
group compGeno
color 0,0,0
altColor 255,255,0
type bed 3
chainLinearGap loose
chainMinScore 5000
dimensions dimensionX=chainType dimensionY=species
sortOrder species=+ view=+ chainType=+
configurable on
html html/GCF_002263795.3_ARS-UCD2.0.chainNet

    track GCF_002263795.3_ARS-UCD2.0ChainNetViewchain
    shortLabel Chains
    view chain
    visibility dense
    parent GCF_002263795.3_ARS-UCD2.0ChainNet
    spectrum on

    track GCF_002263795.3_ARS-UCD2.0ChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility hide
    parent GCF_002263795.3_ARS-UCD2.0ChainNet
    spectrum on

    track GCF_002263795.3_ARS-UCD2.0ChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility hide
    parent GCF_002263795.3_ARS-UCD2.0ChainNet
    spectrum on

    track GCF_002263795.3_ARS-UCD2.0ChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility hide
    parent GCF_002263795.3_ARS-UCD2.0ChainNet
    spectrum on

        track chainGCF_002263795.2
        parent GCF_002263795.3_ARS-UCD2.0ChainNetViewchain on
        subGroups view=chain species=s000 chainType=c00
        shortLabel cattle Chain
        longLabel cattle/GCF_002263795.2_ARS-UCD1.3 (2018-04-11) Chained Alignments
        type bigChain GCF_002263795.2
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainGCF_002263795.2.bb
        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainGCF_002263795.2Link.bb
        otherDb GCF_002263795.2
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 1.716

        track chainSynGCF_002263795.2
        parent GCF_002263795.3_ARS-UCD2.0ChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel cattle synChain
        longLabel cattle/GCF_002263795.2_ARS-UCD1.3 (2018-04-11) Chained Alignments
        type bigChain GCF_002263795.2
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainSynGCF_002263795.2.bb
        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainSynGCF_002263795.2Link.bb
        otherDb GCF_002263795.2
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 1.716

        track chainRBestGCF_002263795.2
        parent GCF_002263795.3_ARS-UCD2.0ChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel cattle rbChain
        longLabel cattle/GCF_002263795.2_ARS-UCD1.3 (2018-04-11) Chained Alignments
        type bigChain GCF_002263795.2
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainRBestGCF_002263795.2.bb
        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainRBestGCF_002263795.2Link.bb
        otherDb GCF_002263795.2
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 1.716

        track chainLiftOverGCF_002263795.2
        parent GCF_002263795.3_ARS-UCD2.0ChainNetViewLiftOver off
        subGroups view=liftover species=s000 chainType=c03
        shortLabel cattle loChain
        longLabel cattle/GCF_002263795.2_ARS-UCD1.3 (2018-04-11) Chained Alignments
        type bigChain GCF_002263795.2
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainLiftOverGCF_002263795.2.bb
        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainLiftOverGCF_002263795.2Link.bb
        otherDb GCF_002263795.2
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 1.716

        track chainBosTau9
        parent GCF_002263795.3_ARS-UCD2.0ChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel Cow/bosTau9 Chain
        longLabel Cow/bosTau9/bosTau9 (Apr. 2018) Chained Alignments
        type bigChain bosTau9
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainBosTau9.bb
        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainBosTau9Link.bb
        otherDb bosTau9
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 1.760

        track chainSynBosTau9
        parent GCF_002263795.3_ARS-UCD2.0ChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel Cow/bosTau9 synChain
        longLabel Cow/bosTau9/bosTau9 (Apr. 2018) Chained Alignments
        type bigChain bosTau9
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainSynBosTau9.bb
        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainSynBosTau9Link.bb
        otherDb bosTau9
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 1.760

        track chainRBestBosTau9
        parent GCF_002263795.3_ARS-UCD2.0ChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel Cow/bosTau9 rbChain
        longLabel Cow/bosTau9/bosTau9 (Apr. 2018) Chained Alignments
        type bigChain bosTau9
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainRBestBosTau9.bb
        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainRBestBosTau9Link.bb
        otherDb bosTau9
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 1.760

        track chainLiftOverBosTau9
        parent GCF_002263795.3_ARS-UCD2.0ChainNetViewLiftOver off
        subGroups view=liftover species=s001 chainType=c03
        shortLabel Cow/bosTau9 loChain
        longLabel Cow/bosTau9/bosTau9 (Apr. 2018) Chained Alignments
        type bigChain bosTau9
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainLiftOverBosTau9.bb
        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainLiftOverBosTau9Link.bb
        otherDb bosTau9
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 1.760

        track chainGCA_000003205.6
        parent GCF_002263795.3_ARS-UCD2.0ChainNetViewchain off
        subGroups view=chain species=s002 chainType=c00
        shortLabel cattle Chain
        longLabel cattle/GCA_000003205.6_Btau_5.0.1 (2015-11-19) Chained Alignments
        type bigChain GCA_000003205.6
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainGCA_000003205.6.bb
        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainGCA_000003205.6Link.bb
        otherDb GCA_000003205.6
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 2.818

        track chainSynGCA_000003205.6
        parent GCF_002263795.3_ARS-UCD2.0ChainNetViewSynTen off
        subGroups view=synten species=s002 chainType=c01
        shortLabel cattle synChain
        longLabel cattle/GCA_000003205.6_Btau_5.0.1 (2015-11-19) Chained Alignments
        type bigChain GCA_000003205.6
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainSynGCA_000003205.6.bb
        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainSynGCA_000003205.6Link.bb
        otherDb GCA_000003205.6
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 2.818

        track chainRBestGCA_000003205.6
        parent GCF_002263795.3_ARS-UCD2.0ChainNetViewRBest off
        subGroups view=rbest species=s002 chainType=c02
        shortLabel cattle rbChain
        longLabel cattle/GCA_000003205.6_Btau_5.0.1 (2015-11-19) Chained Alignments
        type bigChain GCA_000003205.6
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainRBestGCA_000003205.6.bb
        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainRBestGCA_000003205.6Link.bb
        otherDb GCA_000003205.6
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 2.818

        track chainLiftOverGCA_000003205.6
        parent GCF_002263795.3_ARS-UCD2.0ChainNetViewLiftOver off
        subGroups view=liftover species=s002 chainType=c03
        shortLabel cattle loChain
        longLabel cattle/GCA_000003205.6_Btau_5.0.1 (2015-11-19) Chained Alignments
        type bigChain GCA_000003205.6
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainLiftOverGCA_000003205.6.bb
        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainLiftOverGCA_000003205.6Link.bb
        otherDb GCA_000003205.6
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 2.818

        track chainGCF_000003055.6
        parent GCF_002263795.3_ARS-UCD2.0ChainNetViewchain off
        subGroups view=chain species=s003 chainType=c00
        shortLabel cattle Chain
        longLabel cattle/GCF_000003055.6_Bos_taurus_UMD_3.1.1 (2014-11-25) Chained Alignments
        type bigChain GCF_000003055.6
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainGCF_000003055.6.bb
        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainGCF_000003055.6Link.bb
        otherDb GCF_000003055.6
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 4.098

        track chainSynGCF_000003055.6
        parent GCF_002263795.3_ARS-UCD2.0ChainNetViewSynTen off
        subGroups view=synten species=s003 chainType=c01
        shortLabel cattle synChain
        longLabel cattle/GCF_000003055.6_Bos_taurus_UMD_3.1.1 (2014-11-25) Chained Alignments
        type bigChain GCF_000003055.6
        bigDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainSynGCF_000003055.6.bb
        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainSynGCF_000003055.6Link.bb
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        track chainRBestGCF_019923935.1
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        track chainLiftOverGCF_019923935.1
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        priority 7.802

        track chainGCF_001704415.2
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        priority 11.599

        track chainSynGCF_001704415.2
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        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainSynGCF_001704415.2Link.bb
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        priority 11.599

        track chainRBestGCF_001704415.2
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        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainRBestGCF_001704415.2Link.bb
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        track chainLiftOverGCF_001704415.2
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        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainLiftOverGCF_001704415.2Link.bb
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        priority 11.599

        track chainGCF_016772045.2
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        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainGCF_016772045.2Link.bb
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        priority 11.709

        track chainSynGCF_016772045.2
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        linkDataUrl bbi/GCF_002263795.3_ARS-UCD2.0.chainSynGCF_016772045.2Link.bb
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        track chainRBestGCF_016772045.2
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        priority 11.709

        track chainLiftOverGCF_016772045.2
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        priority 11.709

        track chainGCF_000767855.1
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        priority 44.046

        track chainSynGCF_000767855.1
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        priority 44.046

        track chainRBestGCF_000767855.1
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        priority 44.046

        track chainLiftOverGCF_000767855.1
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        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 44.046

        track chainGCF_000003025.6
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        priority 44.254

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        track chainLiftOverHg38
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        track chainSynMm39
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        track chainRBestMm39
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        track chainLiftOverMm39
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        track chainGCF_016699485.2
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    view align
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        speciesOrder bosTau9
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        speciesOrder GCA_000003205.6
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
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        track netGCF_000003055.6
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        speciesOrder GCF_000003055.6
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 4.098

        track synNetGCF_000003055.6
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        speciesOrder GCF_000003055.6
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        track rbestNetGCF_000003055.6
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        speciesOrder GCF_000003055.6
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
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        track netGCA_039881165.1
        parent GCF_002263795.3_ARS-UCD2.0MafNetViewnet off
        subGroups view=align species=s004 chainType=c04
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        type bigMaf
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        speciesOrder GCA_039881165.1
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 4.516

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        type bigMaf
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        speciesOrder GCA_039881165.1
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
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        track netGCA_005887515.3
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        type bigMaf
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        speciesOrder GCA_005887515.3
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 6.445

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        speciesOrder GCA_005887515.3
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
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        speciesOrder GCA_005887515.3
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        priority 6.445

        track netGCF_019923935.1
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        type bigMaf
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        speciesOrder GCF_019923935.1
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 7.802

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        speciesOrder GCF_019923935.1
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        speciesOrder GCF_019923935.1
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 7.802

        track netGCF_001704415.2
        parent GCF_002263795.3_ARS-UCD2.0MafNetViewnet off
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        speciesOrder GCF_001704415.2
        html html/GCF_002263795.3_ARS-UCD2.0.chainNet
        priority 11.599

        track synNetGCF_001704415.2
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        track netGCF_016772045.2
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        track netHg38
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        track netMm39
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