hub GCA_013371645.1 genome assembly
shortLabel rabbit (A946 2020)
longLabel rabbit (A946 2020)/Oryctolagus cuniculus cuniculus/GCA_013371645.1_OryCun3.0 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCA_013371645.1_OryCun3.0.description.html

genome GCA_013371645.1
taxId 568996
groups groups.txt
description rabbit (A946 2020)
twoBitPath GCA_013371645.1.2bit
twoBitBptUrl GCA_013371645.1.2bit.bpt
chromSizes GCA_013371645.1.chrom.sizes.txt
chromAliasBb GCA_013371645.1.chromAlias.bb
chromAuthority ucsc
organism OryCun3.0 Jun. 2020
defaultPos CM023772.1:80647778-80657778
scientificName Oryctolagus cuniculus cuniculus
htmlPath html/GCA_013371645.1_OryCun3.0.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/013/371/645/GCA_013371645.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/013/371/645/GCA_013371645.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/013/371/645/GCA_013371645.1
liftOver.GCA_033439345.1 liftOver/GCA_013371645.1ToGCA_033439345.1.over.chain.gz
liftOver.hg38 liftOver/GCA_013371645.1ToHg38.over.chain.gz
liftOver.micMur2 liftOver/GCA_013371645.1ToMicMur2.over.chain.gz
liftOver.mm10 liftOver/GCA_013371645.1ToMm10.over.chain.gz
liftOver.susScr11 liftOver/GCA_013371645.1ToSusScr11.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_013371645.1_OryCun3.0.assembly.bb
type bigBed 6
html html/GCA_013371645.1_OryCun3.0.assembly
searchIndex name
searchTrix ixIxx/GCA_013371645.1_OryCun3.0.assembly.ix
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
group map

track gap
longLabel AGP gap
shortLabel Gap (AGP defined)
visibility hide
color 0,0,0
bigDataUrl bbi/GCA_013371645.1_OryCun3.0.gap.bb
type bigBed 4
group map
html html/GCA_013371645.1_OryCun3.0.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_013371645.1_OryCun3.0.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_013371645.1_OryCun3.0.gc5Base.bw
html html/GCA_013371645.1_OryCun3.0.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_013371645.1_OryCun3.0.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_013371645.1_OryCun3.0.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/GCA_013371645.1_OryCun3.0.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_013371645.1_OryCun3.0.rmsk.bb
maxWindowToDraw 5000000
html html/GCA_013371645.1_OryCun3.0.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_013371645.1_OryCun3.0.simpleRepeat.bb
html html/GCA_013371645.1_OryCun3.0.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_013371645.1_OryCun3.0.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_013371645.1_OryCun3.0.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_013371645.1_OryCun3.0.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_013371645.1_OryCun3.0.windowMasker.bb
html html/GCA_013371645.1_OryCun3.0.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/GCA_013371645.1_OryCun3.0.allGaps.bb
html html/GCA_013371645.1_OryCun3.0.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_013371645.1_OryCun3.0.augustus.bb
html html/GCA_013371645.1_OryCun3.0.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_013371645.1_OryCun3.0.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_013371645.1_OryCun3.0.xenoRefGene.ix
html html/GCA_013371645.1_OryCun3.0.xenoRefGene

track GCA_013371645.1_OryCun3.0ChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCA_013371645.1_OryCun3.0
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=hg38 s001=micMur2 s002=susScr11 s003=GCA_033439345.1 s004=mm10
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/GCA_013371645.1_OryCun3.0.chainNet

    track GCA_013371645.1_OryCun3.0ChainNetViewchain
    shortLabel Chains
    view chain
    visibility dense
    parent GCA_013371645.1_OryCun3.0ChainNet
    spectrum on

        track chainHg38
        parent GCA_013371645.1_OryCun3.0ChainNetViewchain on
        subGroups view=chain species=s000 chainType=c00
        shortLabel Human/hg38 Chain
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainHg38.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainHg38Link.bb
        otherDb hg38
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 52.124

        track chainMicMur2
        parent GCA_013371645.1_OryCun3.0ChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel Mouse lemur/micMur2 Chain
        longLabel Mouse lemur/micMur2/micMur2 (May 2015) Chained Alignments
        type bigChain micMur2
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainMicMur2.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainMicMur2Link.bb
        otherDb micMur2
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 54.070

        track chainSusScr11
        parent GCA_013371645.1_OryCun3.0ChainNetViewchain off
        subGroups view=chain species=s002 chainType=c00
        shortLabel Pig/susScr11 Chain
        longLabel Pig/susScr11/susScr11 (Feb. 2017) Chained Alignments
        type bigChain susScr11
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainSusScr11.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainSusScr11Link.bb
        otherDb susScr11
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 59.332

        track chainGCA_033439345.1
        parent GCA_013371645.1_OryCun3.0ChainNetViewchain off
        subGroups view=chain species=s003 chainType=c00
        shortLabel Chinese tree shrew Chain
        longLabel Chinese tree shrew/GCA_033439345.1_KIZ_version_2 (2023-11-09) Chained Alignments
        type bigChain GCA_033439345.1
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainGCA_033439345.1.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainGCA_033439345.1Link.bb
        otherDb GCA_033439345.1
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 59.793

        track chainMm10
        parent GCA_013371645.1_OryCun3.0ChainNetViewchain off
        subGroups view=chain species=s004 chainType=c00
        shortLabel Mouse/mm10 Chain
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainMm10.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainMm10Link.bb
        otherDb mm10
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 74.721

    track GCA_013371645.1_OryCun3.0ChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility hide
    parent GCA_013371645.1_OryCun3.0ChainNet
    spectrum on

        track chainSynHg38
        parent GCA_013371645.1_OryCun3.0ChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel Human/hg38 synChain
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainSynHg38.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainSynHg38Link.bb
        otherDb hg38
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 52.124

        track chainSynMicMur2
        parent GCA_013371645.1_OryCun3.0ChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel Mouse lemur/micMur2 synChain
        longLabel Mouse lemur/micMur2/micMur2 (May 2015) Chained Alignments
        type bigChain micMur2
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainSynMicMur2.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainSynMicMur2Link.bb
        otherDb micMur2
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 54.070

        track chainSynSusScr11
        parent GCA_013371645.1_OryCun3.0ChainNetViewSynTen off
        subGroups view=synten species=s002 chainType=c01
        shortLabel Pig/susScr11 synChain
        longLabel Pig/susScr11/susScr11 (Feb. 2017) Chained Alignments
        type bigChain susScr11
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainSynSusScr11.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainSynSusScr11Link.bb
        otherDb susScr11
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 59.332

        track chainSynGCA_033439345.1
        parent GCA_013371645.1_OryCun3.0ChainNetViewSynTen off
        subGroups view=synten species=s003 chainType=c01
        shortLabel Chinese tree shrew synChain
        longLabel Chinese tree shrew/GCA_033439345.1_KIZ_version_2 (2023-11-09) Chained Alignments
        type bigChain GCA_033439345.1
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainSynGCA_033439345.1.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainSynGCA_033439345.1Link.bb
        otherDb GCA_033439345.1
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 59.793

        track chainSynMm10
        parent GCA_013371645.1_OryCun3.0ChainNetViewSynTen off
        subGroups view=synten species=s004 chainType=c01
        shortLabel Mouse/mm10 synChain
        longLabel Mouse/mm10/mm10_KIZ_version_2 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainSynMm10.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainSynMm10Link.bb
        otherDb mm10
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 74.721

    track GCA_013371645.1_OryCun3.0ChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility hide
    parent GCA_013371645.1_OryCun3.0ChainNet
    spectrum on

        track chainRBestHg38
        parent GCA_013371645.1_OryCun3.0ChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel Human/hg38 rbChain
        longLabel Human/hg38/hg38_KIZ_version_2 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainRBestHg38.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainRBestHg38Link.bb
        otherDb hg38
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 52.124

        track chainRBestMicMur2
        parent GCA_013371645.1_OryCun3.0ChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel Mouse lemur/micMur2 rbChain
        longLabel Mouse lemur/micMur2/micMur2_KIZ_version_2 (May 2015) Chained Alignments
        type bigChain micMur2
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainRBestMicMur2.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainRBestMicMur2Link.bb
        otherDb micMur2
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 54.070

        track chainRBestSusScr11
        parent GCA_013371645.1_OryCun3.0ChainNetViewRBest off
        subGroups view=rbest species=s002 chainType=c02
        shortLabel Pig/susScr11 rbChain
        longLabel Pig/susScr11/susScr11_KIZ_version_2 (Feb. 2017) Chained Alignments
        type bigChain susScr11
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainRBestSusScr11.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainRBestSusScr11Link.bb
        otherDb susScr11
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 59.332

        track chainRBestGCA_033439345.1
        parent GCA_013371645.1_OryCun3.0ChainNetViewRBest off
        subGroups view=rbest species=s003 chainType=c02
        shortLabel Chinese tree shrew rbChain
        longLabel Chinese tree shrew/GCA_033439345.1_KIZ_version_2 (2023-11-09) Chained Alignments
        type bigChain GCA_033439345.1
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainRBestGCA_033439345.1.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainRBestGCA_033439345.1Link.bb
        otherDb GCA_033439345.1
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 59.793

        track chainRBestMm10
        parent GCA_013371645.1_OryCun3.0ChainNetViewRBest off
        subGroups view=rbest species=s004 chainType=c02
        shortLabel Mouse/mm10 rbChain
        longLabel Mouse/mm10/mm10_KIZ_version_2 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainRBestMm10.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainRBestMm10Link.bb
        otherDb mm10
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 74.721

    track GCA_013371645.1_OryCun3.0ChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility hide
    parent GCA_013371645.1_OryCun3.0ChainNet
    spectrum on

        track chainLiftOverHg38
        parent GCA_013371645.1_OryCun3.0ChainNetViewLiftOver off
        subGroups view=liftover species=s000 chainType=c03
        shortLabel Human/hg38 loChain
        longLabel Human/hg38/hg38_KIZ_version_2 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainLiftOverHg38.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainLiftOverHg38Link.bb
        otherDb hg38
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 52.124

        track chainLiftOverMicMur2
        parent GCA_013371645.1_OryCun3.0ChainNetViewLiftOver off
        subGroups view=liftover species=s001 chainType=c03
        shortLabel Mouse lemur/micMur2 loChain
        longLabel Mouse lemur/micMur2/micMur2_KIZ_version_2 (May 2015) Chained Alignments
        type bigChain micMur2
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainLiftOverMicMur2.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainLiftOverMicMur2Link.bb
        otherDb micMur2
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 54.070

        track chainLiftOverSusScr11
        parent GCA_013371645.1_OryCun3.0ChainNetViewLiftOver off
        subGroups view=liftover species=s002 chainType=c03
        shortLabel Pig/susScr11 loChain
        longLabel Pig/susScr11/susScr11_KIZ_version_2 (Feb. 2017) Chained Alignments
        type bigChain susScr11
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainLiftOverSusScr11.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainLiftOverSusScr11Link.bb
        otherDb susScr11
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 59.332

        track chainLiftOverGCA_033439345.1
        parent GCA_013371645.1_OryCun3.0ChainNetViewLiftOver off
        subGroups view=liftover species=s003 chainType=c03
        shortLabel Chinese tree shrew loChain
        longLabel Chinese tree shrew/GCA_033439345.1_KIZ_version_2 (2023-11-09) Chained Alignments
        type bigChain GCA_033439345.1
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainLiftOverGCA_033439345.1.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainLiftOverGCA_033439345.1Link.bb
        otherDb GCA_033439345.1
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 59.793

        track chainLiftOverMm10
        parent GCA_013371645.1_OryCun3.0ChainNetViewLiftOver off
        subGroups view=liftover species=s004 chainType=c03
        shortLabel Mouse/mm10 loChain
        longLabel Mouse/mm10/mm10_KIZ_version_2 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.chainLiftOverMm10.bb
        linkDataUrl bbi/GCA_013371645.1_OryCun3.0.chainLiftOverMm10Link.bb
        otherDb mm10
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 74.721

    track GCA_013371645.1_OryCun3.0MafNetViewnet
    shortLabel Nets
    view align
    visibility hide
    parent GCA_013371645.1_OryCun3.0ChainNet

        track netHg38
        parent GCA_013371645.1_OryCun3.0MafNetViewnet off
        subGroups view=align species=s000 chainType=c04
        shortLabel Human/hg38 mafNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.hg38.net.bb
        summary bbi/GCA_013371645.1_OryCun3.0.hg38.net.summary.bb
        speciesOrder hg38
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 52.124

        track synNetHg38
        parent GCA_013371645.1_OryCun3.0MafNetViewnet off
        subGroups view=align species=s000 chainType=c05
        shortLabel Human/hg38 synNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.hg38.synNet.bb
        summary bbi/GCA_013371645.1_OryCun3.0.hg38.synNet.summary.bb
        speciesOrder hg38
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 52.124

        track rbestNetHg38
        parent GCA_013371645.1_OryCun3.0MafNetViewnet off
        subGroups view=align species=s000 chainType=c06
        shortLabel Human/hg38 rbestNet
        longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.hg38.rbestNet.bb
        summary bbi/GCA_013371645.1_OryCun3.0.hg38.rbestNet.summary.bb
        speciesOrder hg38
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 52.124

        track netMicMur2
        parent GCA_013371645.1_OryCun3.0MafNetViewnet off
        subGroups view=align species=s001 chainType=c04
        shortLabel Mouse lemur/micMur2 mafNet
        longLabel Mouse lemur/micMur2/micMur2 (May 2015) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.micMur2.net.bb
        summary bbi/GCA_013371645.1_OryCun3.0.micMur2.net.summary.bb
        speciesOrder micMur2
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 54.070

        track synNetMicMur2
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        subGroups view=align species=s001 chainType=c05
        shortLabel Mouse lemur/micMur2 synNet
        longLabel Mouse lemur/micMur2/micMur2 (May 2015) Chained Alignments
        type bigMaf
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        summary bbi/GCA_013371645.1_OryCun3.0.micMur2.synNet.summary.bb
        speciesOrder micMur2
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 54.070

        track rbestNetMicMur2
        parent GCA_013371645.1_OryCun3.0MafNetViewnet off
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        shortLabel Mouse lemur/micMur2 rbestNet
        longLabel Mouse lemur/micMur2/micMur2 (May 2015) Chained Alignments
        type bigMaf
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        summary bbi/GCA_013371645.1_OryCun3.0.micMur2.rbestNet.summary.bb
        speciesOrder micMur2
        html html/GCA_013371645.1_OryCun3.0.chainNet
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        track netSusScr11
        parent GCA_013371645.1_OryCun3.0MafNetViewnet off
        subGroups view=align species=s002 chainType=c04
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        longLabel Pig/susScr11/susScr11 (Feb. 2017) Chained Alignments
        type bigMaf
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        summary bbi/GCA_013371645.1_OryCun3.0.susScr11.net.summary.bb
        speciesOrder susScr11
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 59.332

        track synNetSusScr11
        parent GCA_013371645.1_OryCun3.0MafNetViewnet off
        subGroups view=align species=s002 chainType=c05
        shortLabel Pig/susScr11 synNet
        longLabel Pig/susScr11/susScr11 (Feb. 2017) Chained Alignments
        type bigMaf
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        summary bbi/GCA_013371645.1_OryCun3.0.susScr11.synNet.summary.bb
        speciesOrder susScr11
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 59.332

        track rbestNetSusScr11
        parent GCA_013371645.1_OryCun3.0MafNetViewnet off
        subGroups view=align species=s002 chainType=c06
        shortLabel Pig/susScr11 rbestNet
        longLabel Pig/susScr11/susScr11 (Feb. 2017) Chained Alignments
        type bigMaf
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        summary bbi/GCA_013371645.1_OryCun3.0.susScr11.rbestNet.summary.bb
        speciesOrder susScr11
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 59.332

        track netGCA_033439345.1
        parent GCA_013371645.1_OryCun3.0MafNetViewnet off
        subGroups view=align species=s003 chainType=c04
        shortLabel Chinese tree shrew mafNet
        longLabel Chinese tree shrew/GCA_033439345.1_KIZ_version_2 (2023-11-09) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.GCA_033439345.1.net.bb
        summary bbi/GCA_013371645.1_OryCun3.0.GCA_033439345.1.net.summary.bb
        speciesOrder GCA_033439345.1
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 59.793

        track synNetGCA_033439345.1
        parent GCA_013371645.1_OryCun3.0MafNetViewnet off
        subGroups view=align species=s003 chainType=c05
        shortLabel Chinese tree shrew synNet
        longLabel Chinese tree shrew/GCA_033439345.1_KIZ_version_2 (2023-11-09) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.GCA_033439345.1.synNet.bb
        summary bbi/GCA_013371645.1_OryCun3.0.GCA_033439345.1.synNet.summary.bb
        speciesOrder GCA_033439345.1
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 59.793

        track rbestNetGCA_033439345.1
        parent GCA_013371645.1_OryCun3.0MafNetViewnet off
        subGroups view=align species=s003 chainType=c06
        shortLabel Chinese tree shrew rbestNet
        longLabel Chinese tree shrew/GCA_033439345.1_KIZ_version_2 (2023-11-09) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.GCA_033439345.1.rbestNet.bb
        summary bbi/GCA_013371645.1_OryCun3.0.GCA_033439345.1.rbestNet.summary.bb
        speciesOrder GCA_033439345.1
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 59.793

        track netMm10
        parent GCA_013371645.1_OryCun3.0MafNetViewnet off
        subGroups view=align species=s004 chainType=c04
        shortLabel Mouse/mm10 mafNet
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.mm10.net.bb
        summary bbi/GCA_013371645.1_OryCun3.0.mm10.net.summary.bb
        speciesOrder mm10
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 74.721

        track synNetMm10
        parent GCA_013371645.1_OryCun3.0MafNetViewnet off
        subGroups view=align species=s004 chainType=c05
        shortLabel Mouse/mm10 synNet
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.mm10.synNet.bb
        summary bbi/GCA_013371645.1_OryCun3.0.mm10.synNet.summary.bb
        speciesOrder mm10
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 74.721

        track rbestNetMm10
        parent GCA_013371645.1_OryCun3.0MafNetViewnet off
        subGroups view=align species=s004 chainType=c06
        shortLabel Mouse/mm10 rbestNet
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_013371645.1_OryCun3.0.mm10.rbestNet.bb
        summary bbi/GCA_013371645.1_OryCun3.0.mm10.rbestNet.summary.bb
        speciesOrder mm10
        html html/GCA_013371645.1_OryCun3.0.chainNet
        priority 74.721


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 2025-01-07
baseColorDefault genomicCodons