hub GCA_964270355.1 genome assembly
shortLabel moose/elk (2024)
longLabel moose/elk (2024)/Alces alces/GCA_964270355.1_Elg.assembly.v.1.0 genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCA_964270355.1_Elg.assembly.v.1.0.description.html

genome GCA_964270355.1
taxId 9852
groups groups.txt
description moose/elk (2024)
twoBitPath GCA_964270355.1.2bit
twoBitBptUrl GCA_964270355.1.2bit.bpt
chromSizes GCA_964270355.1.chrom.sizes.txt
chromAliasBb GCA_964270355.1.chromAlias.bb
organism Elg.assembly.v.1.0 Sep. 2024
defaultPos CAXWQY010000569.1:34952279-34962279
scientificName Alces alces
htmlPath html/GCA_964270355.1_Elg.assembly.v.1.0.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/964/270/355/GCA_964270355.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/964/270/355/GCA_964270355.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/964/270/355/GCA_964270355.1
liftOver.GCA_007570765.1 liftOver/GCA_964270355.1ToGCA_007570765.1.over.chain.gz
liftOver.GCA_015832495.2 liftOver/GCA_964270355.1ToGCA_015832495.2.over.chain.gz

track assembly
longLabel Assembly
shortLabel Assembly
visibility pack
colorByStrand 150,100,30 230,170,40
color 150,100,30
altColor 230,170,40
bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.assembly.bb
type bigBed 6
html html/GCA_964270355.1_Elg.assembly.v.1.0.assembly
searchIndex name
searchTrix ixIxx/GCA_964270355.1_Elg.assembly.v.1.0.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 dense
color 0,0,0
bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.gap.bb
type bigBed 4
group map
html html/GCA_964270355.1_Elg.assembly.v.1.0.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.cytoBand.bb

track gc5Base
shortLabel GC Percent
longLabel GC Percent in 5-Base Windows
group map
visibility full
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_964270355.1_Elg.assembly.v.1.0.gc5Base.bw
html html/GCA_964270355.1_Elg.assembly.v.1.0.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_964270355.1_Elg.assembly.v.1.0.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.rmsk.bb
xrefDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCA_964270355.1_Elg.assembly.v.1.0.repeatMasker

track repeatModeler
shortLabel RepeatModeler
longLabel RepeatModeler Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.rModel.bb
xrefDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.rModel.align.bb
maxWindowToDraw 5000000
html html/GCA_964270355.1_Elg.assembly.v.1.0.repeatModeler

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.simpleRepeat.bb
html html/GCA_964270355.1_Elg.assembly.v.1.0.simpleRepeat

track cpgIslands
compositeTrack on
shortLabel CpG Islands
longLabel CpG Islands (Islands < 300 Bases are Light Green)
group regulation
visibility pack
type bigBed 4 +
html html/GCA_964270355.1_Elg.assembly.v.1.0.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_964270355.1_Elg.assembly.v.1.0.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_964270355.1_Elg.assembly.v.1.0.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.windowMasker.bb
html html/GCA_964270355.1_Elg.assembly.v.1.0.windowMasker

track allGaps
shortLabel All Gaps
longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps
group map
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.allGaps.bb
html html/GCA_964270355.1_Elg.assembly.v.1.0.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.augustus.bb
html html/GCA_964270355.1_Elg.assembly.v.1.0.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_964270355.1_Elg.assembly.v.1.0.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_964270355.1_Elg.assembly.v.1.0.xenoRefGene.ix
html html/GCA_964270355.1_Elg.assembly.v.1.0.xenoRefGene

track GCA_964270355.1_Elg.assembly.v.1.0ChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCA_964270355.1_Elg.assembly.v.1.0
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=GCA_007570765.1 s001=GCA_015832495.2
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/GCA_964270355.1_Elg.assembly.v.1.0.chainNet

    track GCA_964270355.1_Elg.assembly.v.1.0ChainNetViewchain
    shortLabel Chains
    view chain
    visibility dense
    parent GCA_964270355.1_Elg.assembly.v.1.0ChainNet
    spectrum on

    track GCA_964270355.1_Elg.assembly.v.1.0ChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility hide
    parent GCA_964270355.1_Elg.assembly.v.1.0ChainNet
    spectrum on

    track GCA_964270355.1_Elg.assembly.v.1.0ChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility hide
    parent GCA_964270355.1_Elg.assembly.v.1.0ChainNet
    spectrum on

    track GCA_964270355.1_Elg.assembly.v.1.0ChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility hide
    parent GCA_964270355.1_Elg.assembly.v.1.0ChainNet
    spectrum on

        track chainGCA_007570765.1
        parent GCA_964270355.1_Elg.assembly.v.1.0ChainNetViewchain on
        subGroups view=chain species=s000 chainType=c00
        shortLabel GCA_007570765.1 Chain
        longLabel GCA_007570765.1/GCA_007570765.1_GSC_moose_1.0 (2019-07-12) Chained Alignments
        type bigChain GCA_007570765.1
        bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.chainGCA_007570765.1.bb
        linkDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.chainGCA_007570765.1Link.bb
        otherDb GCA_007570765.1
        html html/GCA_964270355.1_Elg.assembly.v.1.0.chainNet
        priority 2.587

        track chainSynGCA_007570765.1
        parent GCA_964270355.1_Elg.assembly.v.1.0ChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel GCA_007570765.1 synChain
        longLabel GCA_007570765.1/GCA_007570765.1_GSC_moose_1.0 (2019-07-12) Chained Alignments
        type bigChain GCA_007570765.1
        bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.chainSynGCA_007570765.1.bb
        linkDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.chainSynGCA_007570765.1Link.bb
        otherDb GCA_007570765.1
        html html/GCA_964270355.1_Elg.assembly.v.1.0.chainNet
        priority 2.587

        track chainRBestGCA_007570765.1
        parent GCA_964270355.1_Elg.assembly.v.1.0ChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel GCA_007570765.1 rbChain
        longLabel GCA_007570765.1/GCA_007570765.1_GSC_moose_1.0 (2019-07-12) Chained Alignments
        type bigChain GCA_007570765.1
        bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.chainRBestGCA_007570765.1.bb
        linkDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.chainRBestGCA_007570765.1Link.bb
        otherDb GCA_007570765.1
        html html/GCA_964270355.1_Elg.assembly.v.1.0.chainNet
        priority 2.587

        track chainLiftOverGCA_007570765.1
        parent GCA_964270355.1_Elg.assembly.v.1.0ChainNetViewLiftOver off
        subGroups view=liftover species=s000 chainType=c03
        shortLabel GCA_007570765.1 loChain
        longLabel GCA_007570765.1/GCA_007570765.1_GSC_moose_1.0 (2019-07-12) Chained Alignments
        type bigChain GCA_007570765.1
        bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.chainLiftOverGCA_007570765.1.bb
        linkDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.chainLiftOverGCA_007570765.1Link.bb
        otherDb GCA_007570765.1
        html html/GCA_964270355.1_Elg.assembly.v.1.0.chainNet
        priority 2.587

        track chainGCA_015832495.2
        parent GCA_964270355.1_Elg.assembly.v.1.0ChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel GCA_015832495.2 Chain
        longLabel GCA_015832495.2/GCA_015832495.2_NRM_Aalces_2_0.fsa (2023-05-22) Chained Alignments
        type bigChain GCA_015832495.2
        bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.chainGCA_015832495.2.bb
        linkDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.chainGCA_015832495.2Link.bb
        otherDb GCA_015832495.2
        html html/GCA_964270355.1_Elg.assembly.v.1.0.chainNet
        priority 4.694

        track chainSynGCA_015832495.2
        parent GCA_964270355.1_Elg.assembly.v.1.0ChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel GCA_015832495.2 synChain
        longLabel GCA_015832495.2/GCA_015832495.2_NRM_Aalces_2_0.fsa (2023-05-22) Chained Alignments
        type bigChain GCA_015832495.2
        bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.chainSynGCA_015832495.2.bb
        linkDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.chainSynGCA_015832495.2Link.bb
        otherDb GCA_015832495.2
        html html/GCA_964270355.1_Elg.assembly.v.1.0.chainNet
        priority 4.694

        track chainRBestGCA_015832495.2
        parent GCA_964270355.1_Elg.assembly.v.1.0ChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel GCA_015832495.2 rbChain
        longLabel GCA_015832495.2/GCA_015832495.2_NRM_Aalces_2_0.fsa (2023-05-22) Chained Alignments
        type bigChain GCA_015832495.2
        bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.chainRBestGCA_015832495.2.bb
        linkDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.chainRBestGCA_015832495.2Link.bb
        otherDb GCA_015832495.2
        html html/GCA_964270355.1_Elg.assembly.v.1.0.chainNet
        priority 4.694

        track chainLiftOverGCA_015832495.2
        parent GCA_964270355.1_Elg.assembly.v.1.0ChainNetViewLiftOver off
        subGroups view=liftover species=s001 chainType=c03
        shortLabel GCA_015832495.2 loChain
        longLabel GCA_015832495.2/GCA_015832495.2_NRM_Aalces_2_0.fsa (2023-05-22) Chained Alignments
        type bigChain GCA_015832495.2
        bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.chainLiftOverGCA_015832495.2.bb
        linkDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.chainLiftOverGCA_015832495.2Link.bb
        otherDb GCA_015832495.2
        html html/GCA_964270355.1_Elg.assembly.v.1.0.chainNet
        priority 4.694

    track GCA_964270355.1_Elg.assembly.v.1.0MafNetViewnet
    shortLabel Nets
    view align
    visibility hide
    parent GCA_964270355.1_Elg.assembly.v.1.0ChainNet

        track netGCA_007570765.1
        parent GCA_964270355.1_Elg.assembly.v.1.0MafNetViewnet off
        subGroups view=align species=s000 chainType=c04
        shortLabel GCA_007570765.1 mafNet
        longLabel GCA_007570765.1/GCA_007570765.1_GSC_moose_1.0 (2019-07-12) Chained Alignments
        type bigMaf
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        summary bbi/GCA_964270355.1_Elg.assembly.v.1.0.GCA_007570765.1.net.summary.bb
        speciesOrder GCA_007570765.1
        html html/GCA_964270355.1_Elg.assembly.v.1.0.chainNet
        priority 2.587

        track synNetGCA_007570765.1
        parent GCA_964270355.1_Elg.assembly.v.1.0MafNetViewnet off
        subGroups view=align species=s000 chainType=c05
        shortLabel GCA_007570765.1 synNet
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        type bigMaf
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        summary bbi/GCA_964270355.1_Elg.assembly.v.1.0.GCA_007570765.1.synNet.summary.bb
        speciesOrder GCA_007570765.1
        html html/GCA_964270355.1_Elg.assembly.v.1.0.chainNet
        priority 2.587

        track rbestNetGCA_007570765.1
        parent GCA_964270355.1_Elg.assembly.v.1.0MafNetViewnet off
        subGroups view=align species=s000 chainType=c06
        shortLabel GCA_007570765.1 rbestNet
        longLabel GCA_007570765.1/GCA_007570765.1_GSC_moose_1.0 (2019-07-12) Chained Alignments
        type bigMaf
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        summary bbi/GCA_964270355.1_Elg.assembly.v.1.0.GCA_007570765.1.rbestNet.summary.bb
        speciesOrder GCA_007570765.1
        html html/GCA_964270355.1_Elg.assembly.v.1.0.chainNet
        priority 2.587

        track netGCA_015832495.2
        parent GCA_964270355.1_Elg.assembly.v.1.0MafNetViewnet off
        subGroups view=align species=s001 chainType=c04
        shortLabel GCA_015832495.2 mafNet
        longLabel GCA_015832495.2/GCA_015832495.2_NRM_Aalces_2_0.fsa (2023-05-22) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_964270355.1_Elg.assembly.v.1.0.GCA_015832495.2.net.bb
        summary bbi/GCA_964270355.1_Elg.assembly.v.1.0.GCA_015832495.2.net.summary.bb
        speciesOrder GCA_015832495.2
        html html/GCA_964270355.1_Elg.assembly.v.1.0.chainNet
        priority 4.694

        track synNetGCA_015832495.2
        parent GCA_964270355.1_Elg.assembly.v.1.0MafNetViewnet off
        subGroups view=align species=s001 chainType=c05
        shortLabel GCA_015832495.2 synNet
        longLabel GCA_015832495.2/GCA_015832495.2_NRM_Aalces_2_0.fsa (2023-05-22) Chained Alignments
        type bigMaf
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        summary bbi/GCA_964270355.1_Elg.assembly.v.1.0.GCA_015832495.2.synNet.summary.bb
        speciesOrder GCA_015832495.2
        html html/GCA_964270355.1_Elg.assembly.v.1.0.chainNet
        priority 4.694

        track rbestNetGCA_015832495.2
        parent GCA_964270355.1_Elg.assembly.v.1.0MafNetViewnet off
        subGroups view=align species=s001 chainType=c06
        shortLabel GCA_015832495.2 rbestNet
        longLabel GCA_015832495.2/GCA_015832495.2_NRM_Aalces_2_0.fsa (2023-05-22) Chained Alignments
        type bigMaf
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        summary bbi/GCA_964270355.1_Elg.assembly.v.1.0.GCA_015832495.2.rbestNet.summary.bb
        speciesOrder GCA_015832495.2
        html html/GCA_964270355.1_Elg.assembly.v.1.0.chainNet
        priority 4.694