hub GCF_000002315.6 genome assembly
shortLabel chicken (GRCg6a 2018)
longLabel chicken (GRCg6a 2018)/Gallus gallus/GCF_000002315.6_GRCg6a genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCF_000002315.6_GRCg6a.description.html

genome GCF_000002315.6
taxId 9031
groups groups.txt
description chicken (GRCg6a 2018)
twoBitPath GCF_000002315.6.2bit
twoBitBptUrl GCF_000002315.6.2bit.bpt
chromSizes GCF_000002315.6.chrom.sizes.txt
chromAliasBb GCF_000002315.6.chromAlias.bb
chromAuthority ucsc
organism GRCg6a Mar. 2018
defaultPos NC_006088.5:65869462-65879462
scientificName Gallus gallus
htmlPath html/GCF_000002315.6_GRCg6a.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/315/GCF_000002315.6
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/315/GCF_000002315.6
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/315/GCF_000002315.6
liftOver.GCF_004027225.2 liftOver/GCF_000002315.6ToGCF_004027225.2.over.chain.gz
liftOver.GCF_964237555.1 liftOver/GCF_000002315.6ToGCF_964237555.1.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_000002315.6_GRCg6a.assembly.bb
type bigBed 6
html html/GCF_000002315.6_GRCg6a.assembly
searchIndex name
searchTrix ixIxx/GCF_000002315.6_GRCg6a.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_000002315.6_GRCg6a.gap.bb
type bigBed 4
group map
html html/GCF_000002315.6_GRCg6a.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_000002315.6_GRCg6a.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_000002315.6_GRCg6a.gc5Base.bw
html html/GCF_000002315.6_GRCg6a.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_000002315.6_GRCg6a.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCF_000002315.6_GRCg6a.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCF_000002315.6_GRCg6a.rmsk.bb
maxWindowToDraw 5000000
html html/GCF_000002315.6_GRCg6a.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_000002315.6_GRCg6a.simpleRepeat.bb
html html/GCF_000002315.6_GRCg6a.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 Gallus gallus Annotation Release 104 (2020-03-29)
html html/GCF_000002315.6_GRCg6a.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_000002315.6_GRCg6a.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.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_000002315.6_GRCg6a.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.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_000002315.6_GRCg6a.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.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_000002315.6_GRCg6a.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.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_000002315.6_GRCg6a.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_000002315.6_GRCg6a.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_000002315.6_GRCg6a.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_000002315.6_GRCg6a.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_000002315.6_GRCg6a.windowMasker.bb
html html/GCF_000002315.6_GRCg6a.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_000002315.6_GRCg6a.allGaps.bb
html html/GCF_000002315.6_GRCg6a.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_000002315.6_GRCg6a.augustus.bb
html html/GCF_000002315.6_GRCg6a.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_000002315.6_GRCg6a.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_000002315.6_GRCg6a.xenoRefGene.ix
html html/GCF_000002315.6_GRCg6a.xenoRefGene

track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes 2022_01
group genes
priority 40
visibility pack
color 150,0,0
itemRgb on
type bigGenePred
bigDataUrl bbi/GCF_000002315.6_GRCg6a.ensGene.bb
searchTrix ixIxx/GCF_000002315.6_GRCg6a.ensGene.ix
searchIndex name
labelFields name,name2
defaultLabelFields name2
baseColorUseCds given
baseColorDefault genomicCodons
labelSeparator " "
html html/GCF_000002315.6_GRCg6a.ensGene

track GCF_000002315.6_GRCg6aChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCF_000002315.6_GRCg6a
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=GCF_004027225.2 s001=GCF_964237555.1
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_000002315.6_GRCg6a.chainNet

    track GCF_000002315.6_GRCg6aChainNetViewchain
    shortLabel Chains
    view chain
    visibility dense
    parent GCF_000002315.6_GRCg6aChainNet
    spectrum on

        track chainGCF_004027225.2
        parent GCF_000002315.6_GRCg6aChainNetViewchain on
        subGroups view=chain species=s000 chainType=c00
        shortLabel kakapo Chain
        longLabel kakapo/GCF_004027225.2_bStrHab1.2.pri (2020-03-04) Chained Alignments
        type bigChain GCF_004027225.2
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.chainGCF_004027225.2.bb
        linkDataUrl bbi/GCF_000002315.6_GRCg6a.chainGCF_004027225.2Link.bb
        otherDb GCF_004027225.2
        html html/GCF_000002315.6_GRCg6a.chainNet
        priority 23.401

        track chainGCF_964237555.1
        parent GCF_000002315.6_GRCg6aChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel rabbit Chain
        longLabel rabbit/GCF_964237555.1_mOryCun1.1 (2024-08-31) Chained Alignments
        type bigChain GCF_964237555.1
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.chainGCF_964237555.1.bb
        linkDataUrl bbi/GCF_000002315.6_GRCg6a.chainGCF_964237555.1Link.bb
        otherDb GCF_964237555.1
        html html/GCF_000002315.6_GRCg6a.chainNet
        priority 94.034

    track GCF_000002315.6_GRCg6aChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility hide
    parent GCF_000002315.6_GRCg6aChainNet
    spectrum on

        track chainSynGCF_004027225.2
        parent GCF_000002315.6_GRCg6aChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel kakapo synChain
        longLabel kakapo/GCF_004027225.2_bStrHab1.2.pri (2020-03-04) Chained Alignments
        type bigChain GCF_004027225.2
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.chainSynGCF_004027225.2.bb
        linkDataUrl bbi/GCF_000002315.6_GRCg6a.chainSynGCF_004027225.2Link.bb
        otherDb GCF_004027225.2
        html html/GCF_000002315.6_GRCg6a.chainNet
        priority 23.401

        track chainSynGCF_964237555.1
        parent GCF_000002315.6_GRCg6aChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel rabbit synChain
        longLabel rabbit/GCF_964237555.1_mOryCun1.1 (2024-08-31) Chained Alignments
        type bigChain GCF_964237555.1
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.chainSynGCF_964237555.1.bb
        linkDataUrl bbi/GCF_000002315.6_GRCg6a.chainSynGCF_964237555.1Link.bb
        otherDb GCF_964237555.1
        html html/GCF_000002315.6_GRCg6a.chainNet
        priority 94.034

    track GCF_000002315.6_GRCg6aChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility hide
    parent GCF_000002315.6_GRCg6aChainNet
    spectrum on

        track chainRBestGCF_004027225.2
        parent GCF_000002315.6_GRCg6aChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel kakapo rbChain
        longLabel kakapo/GCF_004027225.2_bStrHab1.2.pri (2020-03-04) Chained Alignments
        type bigChain GCF_004027225.2
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.chainRBestGCF_004027225.2.bb
        linkDataUrl bbi/GCF_000002315.6_GRCg6a.chainRBestGCF_004027225.2Link.bb
        otherDb GCF_004027225.2
        html html/GCF_000002315.6_GRCg6a.chainNet
        priority 23.401

        track chainRBestGCF_964237555.1
        parent GCF_000002315.6_GRCg6aChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel rabbit rbChain
        longLabel rabbit/GCF_964237555.1_mOryCun1.1 (2024-08-31) Chained Alignments
        type bigChain GCF_964237555.1
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.chainRBestGCF_964237555.1.bb
        linkDataUrl bbi/GCF_000002315.6_GRCg6a.chainRBestGCF_964237555.1Link.bb
        otherDb GCF_964237555.1
        html html/GCF_000002315.6_GRCg6a.chainNet
        priority 94.034

    track GCF_000002315.6_GRCg6aChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility hide
    parent GCF_000002315.6_GRCg6aChainNet
    spectrum on

        track chainLiftOverGCF_004027225.2
        parent GCF_000002315.6_GRCg6aChainNetViewLiftOver off
        subGroups view=liftover species=s000 chainType=c03
        shortLabel kakapo loChain
        longLabel kakapo/GCF_004027225.2_bStrHab1.2.pri (2020-03-04) Chained Alignments
        type bigChain GCF_004027225.2
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.chainLiftOverGCF_004027225.2.bb
        linkDataUrl bbi/GCF_000002315.6_GRCg6a.chainLiftOverGCF_004027225.2Link.bb
        otherDb GCF_004027225.2
        html html/GCF_000002315.6_GRCg6a.chainNet
        priority 23.401

        track chainLiftOverGCF_964237555.1
        parent GCF_000002315.6_GRCg6aChainNetViewLiftOver off
        subGroups view=liftover species=s001 chainType=c03
        shortLabel rabbit loChain
        longLabel rabbit/GCF_964237555.1_mOryCun1.1 (2024-08-31) Chained Alignments
        type bigChain GCF_964237555.1
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.chainLiftOverGCF_964237555.1.bb
        linkDataUrl bbi/GCF_000002315.6_GRCg6a.chainLiftOverGCF_964237555.1Link.bb
        otherDb GCF_964237555.1
        html html/GCF_000002315.6_GRCg6a.chainNet
        priority 94.034

    track GCF_000002315.6_GRCg6aMafNetViewnet
    shortLabel Nets
    view align
    visibility hide
    parent GCF_000002315.6_GRCg6aChainNet

        track netGCF_004027225.2
        parent GCF_000002315.6_GRCg6aMafNetViewnet off
        subGroups view=align species=s000 chainType=c04
        shortLabel kakapo mafNet
        longLabel kakapo/GCF_004027225.2_bStrHab1.2.pri (2020-03-04) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.GCF_004027225.2.net.bb
        summary bbi/GCF_000002315.6_GRCg6a.GCF_004027225.2.net.summary.bb
        speciesOrder GCF_004027225.2
        html html/GCF_000002315.6_GRCg6a.chainNet
        priority 23.401

        track synNetGCF_004027225.2
        parent GCF_000002315.6_GRCg6aMafNetViewnet off
        subGroups view=align species=s000 chainType=c05
        shortLabel kakapo synNet
        longLabel kakapo/GCF_004027225.2_bStrHab1.2.pri (2020-03-04) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.GCF_004027225.2.synNet.bb
        summary bbi/GCF_000002315.6_GRCg6a.GCF_004027225.2.synNet.summary.bb
        speciesOrder GCF_004027225.2
        html html/GCF_000002315.6_GRCg6a.chainNet
        priority 23.401

        track rbestNetGCF_004027225.2
        parent GCF_000002315.6_GRCg6aMafNetViewnet off
        subGroups view=align species=s000 chainType=c06
        shortLabel kakapo rbestNet
        longLabel kakapo/GCF_004027225.2_bStrHab1.2.pri (2020-03-04) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.GCF_004027225.2.rbestNet.bb
        summary bbi/GCF_000002315.6_GRCg6a.GCF_004027225.2.rbestNet.summary.bb
        speciesOrder GCF_004027225.2
        html html/GCF_000002315.6_GRCg6a.chainNet
        priority 23.401

        track netGCF_964237555.1
        parent GCF_000002315.6_GRCg6aMafNetViewnet off
        subGroups view=align species=s001 chainType=c04
        shortLabel rabbit mafNet
        longLabel rabbit/GCF_964237555.1_mOryCun1.1 (2024-08-31) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.GCF_964237555.1.net.bb
        summary bbi/GCF_000002315.6_GRCg6a.GCF_964237555.1.net.summary.bb
        speciesOrder GCF_964237555.1
        html html/GCF_000002315.6_GRCg6a.chainNet
        priority 94.034

        track synNetGCF_964237555.1
        parent GCF_000002315.6_GRCg6aMafNetViewnet off
        subGroups view=align species=s001 chainType=c05
        shortLabel rabbit synNet
        longLabel rabbit/GCF_964237555.1_mOryCun1.1 (2024-08-31) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.GCF_964237555.1.synNet.bb
        summary bbi/GCF_000002315.6_GRCg6a.GCF_964237555.1.synNet.summary.bb
        speciesOrder GCF_964237555.1
        html html/GCF_000002315.6_GRCg6a.chainNet
        priority 94.034

        track rbestNetGCF_964237555.1
        parent GCF_000002315.6_GRCg6aMafNetViewnet off
        subGroups view=align species=s001 chainType=c06
        shortLabel rabbit rbestNet
        longLabel rabbit/GCF_964237555.1_mOryCun1.1 (2024-08-31) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_000002315.6_GRCg6a.GCF_964237555.1.rbestNet.bb
        summary bbi/GCF_000002315.6_GRCg6a.GCF_964237555.1.rbestNet.summary.bb
        speciesOrder GCF_964237555.1
        html html/GCF_000002315.6_GRCg6a.chainNet
        priority 94.034