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_000002035.6_GRCz11.assembly.bb
type bigBed 6
html html/GCF_000002035.6_GRCz11.assembly
searchIndex name
searchTrix ixIxx/GCF_000002035.6_GRCz11.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/GCF_000002035.6_GRCz11.gap.bb
type bigBed 4
group map
html html/GCF_000002035.6_GRCz11.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_000002035.6_GRCz11.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_000002035.6_GRCz11.gc5Base.bw
html html/GCF_000002035.6_GRCz11.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_000002035.6_GRCz11.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCF_000002035.6_GRCz11.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_000002035.6_GRCz11.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCF_000002035.6_GRCz11.rmsk.bb
maxWindowToDraw 5000000
html html/GCF_000002035.6_GRCz11.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_000002035.6_GRCz11.simpleRepeat.bb
html html/GCF_000002035.6_GRCz11.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_000002035.6-RS_2024_08 (2024-09-12)
html html/GCF_000002035.6_GRCz11.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 name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_000002035.6_GRCz11.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_000002035.6_GRCz11.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 name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_000002035.6_GRCz11.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_000002035.6_GRCz11.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 name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_000002035.6_GRCz11.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_000002035.6_GRCz11.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_000002035.6_GRCz11.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_000002035.6_GRCz11.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_000002035.6_GRCz11.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_000002035.6_GRCz11.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_000002035.6_GRCz11.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_000002035.6_GRCz11.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_000002035.6_GRCz11.windowMasker.bb
html html/GCF_000002035.6_GRCz11.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_000002035.6_GRCz11.allGaps.bb
html html/GCF_000002035.6_GRCz11.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_000002035.6_GRCz11.augustus.bb
html html/GCF_000002035.6_GRCz11.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_000002035.6_GRCz11.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_000002035.6_GRCz11.xenoRefGene.ix
html html/GCF_000002035.6_GRCz11.xenoRefGene

track GCF_000002035.6_GRCz11ChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCF_000002035.6_GRCz11
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=xenTro10 s001=GCF_010993605.1
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_000002035.6_GRCz11.chainNet

    track GCF_000002035.6_GRCz11ChainNetViewchain
    shortLabel Chains
    view chain
    visibility dense
    parent GCF_000002035.6_GRCz11ChainNet
    spectrum on

    track GCF_000002035.6_GRCz11ChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility hide
    parent GCF_000002035.6_GRCz11ChainNet
    spectrum on

    track GCF_000002035.6_GRCz11ChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility hide
    parent GCF_000002035.6_GRCz11ChainNet
    spectrum on

    track GCF_000002035.6_GRCz11ChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility hide
    parent GCF_000002035.6_GRCz11ChainNet
    spectrum on

        track chainXenTro10
        parent GCF_000002035.6_GRCz11ChainNetViewchain on
        subGroups view=chain species=s000 chainType=c00
        shortLabel X. tropicalis/xenTro10 Chain
        longLabel X. tropicalis/xenTro10/xenTro10 (Nov. 2019) Chained Alignments
        type bigChain xenTro10
        bigDataUrl bbi/GCF_000002035.6_GRCz11.chainXenTro10.bb
        linkDataUrl bbi/GCF_000002035.6_GRCz11.chainXenTro10Link.bb
        otherDb xenTro10
        html html/GCF_000002035.6_GRCz11.chainNet
        priority 97.030

        track chainSynXenTro10
        parent GCF_000002035.6_GRCz11ChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel X. tropicalis/xenTro10 synChain
        longLabel X. tropicalis/xenTro10/xenTro10 (Nov. 2019) Chained Alignments
        type bigChain xenTro10
        bigDataUrl bbi/GCF_000002035.6_GRCz11.chainSynXenTro10.bb
        linkDataUrl bbi/GCF_000002035.6_GRCz11.chainSynXenTro10Link.bb
        otherDb xenTro10
        html html/GCF_000002035.6_GRCz11.chainNet
        priority 97.030

        track chainRBestXenTro10
        parent GCF_000002035.6_GRCz11ChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel X. tropicalis/xenTro10 rbChain
        longLabel X. tropicalis/xenTro10/xenTro10 (Nov. 2019) Chained Alignments
        type bigChain xenTro10
        bigDataUrl bbi/GCF_000002035.6_GRCz11.chainRBestXenTro10.bb
        linkDataUrl bbi/GCF_000002035.6_GRCz11.chainRBestXenTro10Link.bb
        otherDb xenTro10
        html html/GCF_000002035.6_GRCz11.chainNet
        priority 97.030

        track chainLiftOverXenTro10
        parent GCF_000002035.6_GRCz11ChainNetViewLiftOver off
        subGroups view=liftover species=s000 chainType=c03
        shortLabel X. tropicalis/xenTro10 loChain
        longLabel X. tropicalis/xenTro10/xenTro10 (Nov. 2019) Chained Alignments
        type bigChain xenTro10
        bigDataUrl bbi/GCF_000002035.6_GRCz11.chainLiftOverXenTro10.bb
        linkDataUrl bbi/GCF_000002035.6_GRCz11.chainLiftOverXenTro10Link.bb
        otherDb xenTro10
        html html/GCF_000002035.6_GRCz11.chainNet
        priority 97.030

        track chainGCF_010993605.1
        parent GCF_000002035.6_GRCz11ChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel sea lamprey Chain
        longLabel sea lamprey/GCF_010993605.1_kPetMar1.pri (2020-02-24) Chained Alignments
        type bigChain GCF_010993605.1
        bigDataUrl bbi/GCF_000002035.6_GRCz11.chainGCF_010993605.1.bb
        linkDataUrl bbi/GCF_000002035.6_GRCz11.chainGCF_010993605.1Link.bb
        otherDb GCF_010993605.1
        html html/GCF_000002035.6_GRCz11.chainNet
        priority 98.181

        track chainSynGCF_010993605.1
        parent GCF_000002035.6_GRCz11ChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel sea lamprey synChain
        longLabel sea lamprey/GCF_010993605.1_kPetMar1.pri (2020-02-24) Chained Alignments
        type bigChain GCF_010993605.1
        bigDataUrl bbi/GCF_000002035.6_GRCz11.chainSynGCF_010993605.1.bb
        linkDataUrl bbi/GCF_000002035.6_GRCz11.chainSynGCF_010993605.1Link.bb
        otherDb GCF_010993605.1
        html html/GCF_000002035.6_GRCz11.chainNet
        priority 98.181

        track chainRBestGCF_010993605.1
        parent GCF_000002035.6_GRCz11ChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel sea lamprey rbChain
        longLabel sea lamprey/GCF_010993605.1_kPetMar1.pri (2020-02-24) Chained Alignments
        type bigChain GCF_010993605.1
        bigDataUrl bbi/GCF_000002035.6_GRCz11.chainRBestGCF_010993605.1.bb
        linkDataUrl bbi/GCF_000002035.6_GRCz11.chainRBestGCF_010993605.1Link.bb
        otherDb GCF_010993605.1
        html html/GCF_000002035.6_GRCz11.chainNet
        priority 98.181

        track chainLiftOverGCF_010993605.1
        parent GCF_000002035.6_GRCz11ChainNetViewLiftOver off
        subGroups view=liftover species=s001 chainType=c03
        shortLabel sea lamprey loChain
        longLabel sea lamprey/GCF_010993605.1_kPetMar1.pri (2020-02-24) Chained Alignments
        type bigChain GCF_010993605.1
        bigDataUrl bbi/GCF_000002035.6_GRCz11.chainLiftOverGCF_010993605.1.bb
        linkDataUrl bbi/GCF_000002035.6_GRCz11.chainLiftOverGCF_010993605.1Link.bb
        otherDb GCF_010993605.1
        html html/GCF_000002035.6_GRCz11.chainNet
        priority 98.181

    track GCF_000002035.6_GRCz11MafNetViewnet
    shortLabel Nets
    view align
    visibility hide
    parent GCF_000002035.6_GRCz11ChainNet

        track netXenTro10
        parent GCF_000002035.6_GRCz11MafNetViewnet off
        subGroups view=align species=s000 chainType=c04
        shortLabel X. tropicalis/xenTro10 mafNet
        longLabel X. tropicalis/xenTro10/xenTro10 (Nov. 2019) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_000002035.6_GRCz11.xenTro10.net.bb
        summary bbi/GCF_000002035.6_GRCz11.xenTro10.net.summary.bb
        speciesOrder xenTro10
        html html/GCF_000002035.6_GRCz11.chainNet
        priority 97.030

        track synNetXenTro10
        parent GCF_000002035.6_GRCz11MafNetViewnet off
        subGroups view=align species=s000 chainType=c05
        shortLabel X. tropicalis/xenTro10 synNet
        longLabel X. tropicalis/xenTro10/xenTro10 (Nov. 2019) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_000002035.6_GRCz11.xenTro10.synNet.bb
        summary bbi/GCF_000002035.6_GRCz11.xenTro10.synNet.summary.bb
        speciesOrder xenTro10
        html html/GCF_000002035.6_GRCz11.chainNet
        priority 97.030

        track rbestNetXenTro10
        parent GCF_000002035.6_GRCz11MafNetViewnet off
        subGroups view=align species=s000 chainType=c06
        shortLabel X. tropicalis/xenTro10 rbestNet
        longLabel X. tropicalis/xenTro10/xenTro10 (Nov. 2019) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_000002035.6_GRCz11.xenTro10.rbestNet.bb
        summary bbi/GCF_000002035.6_GRCz11.xenTro10.rbestNet.summary.bb
        speciesOrder xenTro10
        html html/GCF_000002035.6_GRCz11.chainNet
        priority 97.030

        track netGCF_010993605.1
        parent GCF_000002035.6_GRCz11MafNetViewnet off
        subGroups view=align species=s001 chainType=c04
        shortLabel sea lamprey mafNet
        longLabel sea lamprey/GCF_010993605.1_kPetMar1.pri (2020-02-24) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_000002035.6_GRCz11.GCF_010993605.1.net.bb
        summary bbi/GCF_000002035.6_GRCz11.GCF_010993605.1.net.summary.bb
        speciesOrder GCF_010993605.1
        html html/GCF_000002035.6_GRCz11.chainNet
        priority 98.181

        track synNetGCF_010993605.1
        parent GCF_000002035.6_GRCz11MafNetViewnet off
        subGroups view=align species=s001 chainType=c05
        shortLabel sea lamprey synNet
        longLabel sea lamprey/GCF_010993605.1_kPetMar1.pri (2020-02-24) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_000002035.6_GRCz11.GCF_010993605.1.synNet.bb
        summary bbi/GCF_000002035.6_GRCz11.GCF_010993605.1.synNet.summary.bb
        speciesOrder GCF_010993605.1
        html html/GCF_000002035.6_GRCz11.chainNet
        priority 98.181

        track rbestNetGCF_010993605.1
        parent GCF_000002035.6_GRCz11MafNetViewnet off
        subGroups view=align species=s001 chainType=c06
        shortLabel sea lamprey rbestNet
        longLabel sea lamprey/GCF_010993605.1_kPetMar1.pri (2020-02-24) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_000002035.6_GRCz11.GCF_010993605.1.rbestNet.bb
        summary bbi/GCF_000002035.6_GRCz11.GCF_010993605.1.rbestNet.summary.bb
        speciesOrder GCF_010993605.1
        html html/GCF_000002035.6_GRCz11.chainNet
        priority 98.181