hub GCF_902635505.1 genome assembly
shortLabel Tasmanian devil (primary hap 2019)
longLabel Tasmanian devil (primary hap 2019)/Sarcophilus harrisii/GCF_902635505.1_mSarHar1.11 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCF_902635505.1_mSarHar1.11.description.html

genome GCF_902635505.1
taxId 9305
groups groups.txt
description Tasmanian devil (primary hap 2019)
twoBitPath GCF_902635505.1.2bit
twoBitBptUrl GCF_902635505.1.2bit.bpt
chromSizes GCF_902635505.1.chrom.sizes.txt
chromAliasBb GCF_902635505.1.chromAlias.bb
chromAuthority ucsc
organism mSarHar1.11 Nov. 2019
defaultPos NC_045426.1:238804543-238814543
scientificName Sarcophilus harrisii
htmlPath html/GCF_902635505.1_mSarHar1.11.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/902/635/505/GCF_902635505.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/902/635/505/GCF_902635505.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/902/635/505/GCF_902635505.1
liftOver.GCF_001704415.2 liftOver/GCF_902635505.1ToGCF_001704415.2.over.chain.gz
liftOver.rn7 liftOver/GCF_902635505.1ToRn7.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_902635505.1_mSarHar1.11.assembly.bb
type bigBed 6
html html/GCF_902635505.1_mSarHar1.11.assembly
searchIndex name
searchTrix ixIxx/GCF_902635505.1_mSarHar1.11.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_902635505.1_mSarHar1.11.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_902635505.1_mSarHar1.11.gc5Base.bw
html html/GCF_902635505.1_mSarHar1.11.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_902635505.1_mSarHar1.11.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.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_902635505.1_mSarHar1.11.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.rmsk.bb
maxWindowToDraw 5000000
html html/GCF_902635505.1_mSarHar1.11.repeatMasker

track repeatModeler
shortLabel RepeatModeler
longLabel RepeatModeler Repetitive Elements
type bigRmsk 9 +
visibility hide
group varRep
bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.rModel.bb
xrefDataUrl bbi/GCF_902635505.1_mSarHar1.11.rModel.align.bb
maxWindowToDraw 5000000
html html/GCF_902635505.1_mSarHar1.11.repeatModeler

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.simpleRepeat.bb
html html/GCF_902635505.1_mSarHar1.11.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 Sarcophilus harrisii Annotation Release 103 (2022-09-28)
html html/GCF_902635505.1_mSarHar1.11.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/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$"
        labelFields name2,geneName,geneName2
        defaultLabelFields name2
        searchIndex name
        searchTrix ixIxx/GCF_902635505.1_mSarHar1.11.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.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/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$"
        labelFields name2,geneName,geneName2
        defaultLabelFields name2
        searchIndex name
        searchTrix ixIxx/GCF_902635505.1_mSarHar1.11.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.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/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$"
        labelFields name2,geneName,geneName2
        defaultLabelFields name2
        searchIndex name
        searchTrix ixIxx/GCF_902635505.1_mSarHar1.11.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.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_902635505.1_mSarHar1.11.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.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_902635505.1_mSarHar1.11.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_902635505.1_mSarHar1.11.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_902635505.1_mSarHar1.11.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_902635505.1_mSarHar1.11.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.windowMasker.bb
html html/GCF_902635505.1_mSarHar1.11.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_902635505.1_mSarHar1.11.allGaps.bb
html html/GCF_902635505.1_mSarHar1.11.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.augustus.bb
html html/GCF_902635505.1_mSarHar1.11.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_902635505.1_mSarHar1.11.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_902635505.1_mSarHar1.11.xenoRefGene.ix
html html/GCF_902635505.1_mSarHar1.11.xenoRefGene

track GCF_902635505.1_mSarHar1.11ChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCF_902635505.1_mSarHar1.11
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=GCF_001704415.2 s001=rn7
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_902635505.1_mSarHar1.11.chainNet

    track GCF_902635505.1_mSarHar1.11ChainNetViewchain
    shortLabel Chains
    view chain
    visibility dense
    parent GCF_902635505.1_mSarHar1.11ChainNet
    spectrum on

        track chainGCF_001704415.2
        parent GCF_902635505.1_mSarHar1.11ChainNetViewchain on
        subGroups view=chain species=s000 chainType=c00
        shortLabel goat Chain
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.chainGCF_001704415.2.bb
        linkDataUrl bbi/GCF_902635505.1_mSarHar1.11.chainGCF_001704415.2Link.bb
        otherDb GCF_001704415.2
        html html/GCF_902635505.1_mSarHar1.11.chainNet
        priority 93.744

        track chainRn7
        parent GCF_902635505.1_mSarHar1.11ChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel Rat/rn7 Chain
        longLabel Rat/rn7/rn7 (Nov. 2020) Chained Alignments
        type bigChain rn7
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.chainRn7.bb
        linkDataUrl bbi/GCF_902635505.1_mSarHar1.11.chainRn7Link.bb
        otherDb rn7
        html html/GCF_902635505.1_mSarHar1.11.chainNet
        priority 95.390

    track GCF_902635505.1_mSarHar1.11ChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility hide
    parent GCF_902635505.1_mSarHar1.11ChainNet
    spectrum on

        track chainSynGCF_001704415.2
        parent GCF_902635505.1_mSarHar1.11ChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel goat synChain
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.chainSynGCF_001704415.2.bb
        linkDataUrl bbi/GCF_902635505.1_mSarHar1.11.chainSynGCF_001704415.2Link.bb
        otherDb GCF_001704415.2
        html html/GCF_902635505.1_mSarHar1.11.chainNet
        priority 93.744

        track chainSynRn7
        parent GCF_902635505.1_mSarHar1.11ChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel Rat/rn7 synChain
        longLabel Rat/rn7/rn7_ARS1.2 (Nov. 2020) Chained Alignments
        type bigChain rn7
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.chainSynRn7.bb
        linkDataUrl bbi/GCF_902635505.1_mSarHar1.11.chainSynRn7Link.bb
        otherDb rn7
        html html/GCF_902635505.1_mSarHar1.11.chainNet
        priority 95.390

    track GCF_902635505.1_mSarHar1.11ChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility hide
    parent GCF_902635505.1_mSarHar1.11ChainNet
    spectrum on

        track chainRBestGCF_001704415.2
        parent GCF_902635505.1_mSarHar1.11ChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel goat rbChain
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.chainRBestGCF_001704415.2.bb
        linkDataUrl bbi/GCF_902635505.1_mSarHar1.11.chainRBestGCF_001704415.2Link.bb
        otherDb GCF_001704415.2
        html html/GCF_902635505.1_mSarHar1.11.chainNet
        priority 93.744

        track chainRBestRn7
        parent GCF_902635505.1_mSarHar1.11ChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel Rat/rn7 rbChain
        longLabel Rat/rn7/rn7_ARS1.2 (Nov. 2020) Chained Alignments
        type bigChain rn7
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.chainRBestRn7.bb
        linkDataUrl bbi/GCF_902635505.1_mSarHar1.11.chainRBestRn7Link.bb
        otherDb rn7
        html html/GCF_902635505.1_mSarHar1.11.chainNet
        priority 95.390

    track GCF_902635505.1_mSarHar1.11ChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility hide
    parent GCF_902635505.1_mSarHar1.11ChainNet
    spectrum on

        track chainLiftOverGCF_001704415.2
        parent GCF_902635505.1_mSarHar1.11ChainNetViewLiftOver off
        subGroups view=liftover species=s000 chainType=c03
        shortLabel goat loChain
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.chainLiftOverGCF_001704415.2.bb
        linkDataUrl bbi/GCF_902635505.1_mSarHar1.11.chainLiftOverGCF_001704415.2Link.bb
        otherDb GCF_001704415.2
        html html/GCF_902635505.1_mSarHar1.11.chainNet
        priority 93.744

        track chainLiftOverRn7
        parent GCF_902635505.1_mSarHar1.11ChainNetViewLiftOver off
        subGroups view=liftover species=s001 chainType=c03
        shortLabel Rat/rn7 loChain
        longLabel Rat/rn7/rn7_ARS1.2 (Nov. 2020) Chained Alignments
        type bigChain rn7
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.chainLiftOverRn7.bb
        linkDataUrl bbi/GCF_902635505.1_mSarHar1.11.chainLiftOverRn7Link.bb
        otherDb rn7
        html html/GCF_902635505.1_mSarHar1.11.chainNet
        priority 95.390

    track GCF_902635505.1_mSarHar1.11MafNetViewnet
    shortLabel Nets
    view align
    visibility hide
    parent GCF_902635505.1_mSarHar1.11ChainNet

        track netGCF_001704415.2
        parent GCF_902635505.1_mSarHar1.11MafNetViewnet off
        subGroups view=align species=s000 chainType=c04
        shortLabel goat mafNet
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.GCF_001704415.2.net.bb
        summary bbi/GCF_902635505.1_mSarHar1.11.GCF_001704415.2.net.summary.bb
        speciesOrder GCF_001704415.2
        html html/GCF_902635505.1_mSarHar1.11.chainNet
        priority 93.744

        track synNetGCF_001704415.2
        parent GCF_902635505.1_mSarHar1.11MafNetViewnet off
        subGroups view=align species=s000 chainType=c05
        shortLabel goat synNet
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.GCF_001704415.2.synNet.bb
        summary bbi/GCF_902635505.1_mSarHar1.11.GCF_001704415.2.synNet.summary.bb
        speciesOrder GCF_001704415.2
        html html/GCF_902635505.1_mSarHar1.11.chainNet
        priority 93.744

        track rbestNetGCF_001704415.2
        parent GCF_902635505.1_mSarHar1.11MafNetViewnet off
        subGroups view=align species=s000 chainType=c06
        shortLabel goat rbestNet
        longLabel goat/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.GCF_001704415.2.rbestNet.bb
        summary bbi/GCF_902635505.1_mSarHar1.11.GCF_001704415.2.rbestNet.summary.bb
        speciesOrder GCF_001704415.2
        html html/GCF_902635505.1_mSarHar1.11.chainNet
        priority 93.744

        track netRn7
        parent GCF_902635505.1_mSarHar1.11MafNetViewnet off
        subGroups view=align species=s001 chainType=c04
        shortLabel Rat/rn7 mafNet
        longLabel Rat/rn7/rn7 (Nov. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.rn7.net.bb
        summary bbi/GCF_902635505.1_mSarHar1.11.rn7.net.summary.bb
        speciesOrder rn7
        html html/GCF_902635505.1_mSarHar1.11.chainNet
        priority 95.390

        track synNetRn7
        parent GCF_902635505.1_mSarHar1.11MafNetViewnet off
        subGroups view=align species=s001 chainType=c05
        shortLabel Rat/rn7 synNet
        longLabel Rat/rn7/rn7 (Nov. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.rn7.synNet.bb
        summary bbi/GCF_902635505.1_mSarHar1.11.rn7.synNet.summary.bb
        speciesOrder rn7
        html html/GCF_902635505.1_mSarHar1.11.chainNet
        priority 95.390

        track rbestNetRn7
        parent GCF_902635505.1_mSarHar1.11MafNetViewnet off
        subGroups view=align species=s001 chainType=c06
        shortLabel Rat/rn7 rbestNet
        longLabel Rat/rn7/rn7 (Nov. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_902635505.1_mSarHar1.11.rn7.rbestNet.bb
        summary bbi/GCF_902635505.1_mSarHar1.11.rn7.rbestNet.summary.bb
        speciesOrder rn7
        html html/GCF_902635505.1_mSarHar1.11.chainNet
        priority 95.390