hub GCF_000002285.5 genome assembly
shortLabel dog (boxer Tasha 2020)
longLabel dog (boxer Tasha 2020)/Canis lupus familiaris/GCF_000002285.5_Dog10K_Boxer_Tasha genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCF_000002285.5_Dog10K_Boxer_Tasha.description.html

genome GCF_000002285.5
taxId 9615
groups groups.txt
description dog (boxer Tasha 2020)
twoBitPath GCF_000002285.5.2bit
twoBitBptUrl GCF_000002285.5.2bit.bpt
chromSizes GCF_000002285.5.chrom.sizes.txt
chromAliasBb GCF_000002285.5.chromAlias.bb
chromAuthority ucsc
organism Dog10K_Boxer_Tasha Oct. 2020
defaultPos NC_006583.4:40671356-40681356
scientificName Canis lupus familiaris
htmlPath html/GCF_000002285.5_Dog10K_Boxer_Tasha.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/285/GCF_000002285.5
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/285/GCF_000002285.5
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/285/GCF_000002285.5
liftOver.GCA_905319855.2 liftOver/GCF_000002285.5ToGCA_905319855.2.over.chain.gz
liftOver.rn7 liftOver/GCF_000002285.5ToRn7.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/GCF_000002285.5_Dog10K_Boxer_Tasha.assembly.bb
type bigBed 6
html html/GCF_000002285.5_Dog10K_Boxer_Tasha.assembly
searchIndex name
searchTrix ixIxx/GCF_000002285.5_Dog10K_Boxer_Tasha.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_000002285.5_Dog10K_Boxer_Tasha.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/GCF_000002285.5_Dog10K_Boxer_Tasha.gc5Base.bw
html html/GCF_000002285.5_Dog10K_Boxer_Tasha.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_000002285.5_Dog10K_Boxer_Tasha.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.tandemDups.bb
    type bigBed 12

track repeatMasker
compositeTrack on
shortLabel RepeatMasker
longLabel Repeating Elements by RepeatMasker
group varRep
visibility dense
type bigBed 6 +
colorByStrand 50,50,150 150,50,50
maxWindowToDraw 10000000
spectrum on
html html/GCF_000002285.5_Dog10K_Boxer_Tasha.repeatMasker

    track repeatMaskerSINE
    parent repeatMasker
    shortLabel SINE
    longLabel SINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 1
    bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.rmsk.SINE.bb

    track repeatMaskerLINE
    parent repeatMasker
    shortLabel LINE
    longLabel LINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 2
    bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.rmsk.LINE.bb

    track repeatMaskerLTR
    parent repeatMasker
    shortLabel LTR
    longLabel LTR Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 3
    bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.rmsk.LTR.bb

    track repeatMaskerDNA
    parent repeatMasker
    shortLabel DNA
    longLabel DNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 4
    bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.rmsk.DNA.bb

    track repeatMaskerSimple
    parent repeatMasker
    shortLabel Simple
    longLabel Simple Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 5
    bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.rmsk.Simple.bb

    track repeatMaskerLowComplexity
    parent repeatMasker
    shortLabel Low Complexity
    longLabel Low Complexity Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 6
    bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.rmsk.Low_complexity.bb

    track repeatMaskerSatellite
    parent repeatMasker
    shortLabel Satellite
    longLabel Satellite Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 7
    bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.rmsk.Satellite.bb

    track repeatMaskerRNA
    parent repeatMasker
    shortLabel RNA
    longLabel RNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 8
    bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.rmsk.RNA.bb

    track repeatMaskerOther
    parent repeatMasker
    shortLabel Other
    longLabel Other Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 9
    bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.rmsk.Other.bb

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.simpleRepeat.bb
html html/GCF_000002285.5_Dog10K_Boxer_Tasha.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 Canis lupus familiaris Annotation Release 106 (2021-01-11)
html html/GCF_000002285.5_Dog10K_Boxer_Tasha.refSeqComposite
priority 2

        track ncbiRefSeq
        parent refSeqComposite on
        color 12,12,120
        altColor 120,12,12
        shortLabel RefSeq All
        type bigGenePred
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_000002285.5_Dog10K_Boxer_Tasha.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.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
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_000002285.5_Dog10K_Boxer_Tasha.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.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
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_000002285.5_Dog10K_Boxer_Tasha.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.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_000002285.5_Dog10K_Boxer_Tasha.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.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_000002285.5_Dog10K_Boxer_Tasha.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 pack
type bigBed 4 +
html html/GCF_000002285.5_Dog10K_Boxer_Tasha.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_000002285.5_Dog10K_Boxer_Tasha.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_000002285.5_Dog10K_Boxer_Tasha.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.windowMasker.bb
html html/GCF_000002285.5_Dog10K_Boxer_Tasha.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/GCF_000002285.5_Dog10K_Boxer_Tasha.allGaps.bb
html html/GCF_000002285.5_Dog10K_Boxer_Tasha.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.augustus.bb
html html/GCF_000002285.5_Dog10K_Boxer_Tasha.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_000002285.5_Dog10K_Boxer_Tasha.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_000002285.5_Dog10K_Boxer_Tasha.xenoRefGene.ix
html html/GCF_000002285.5_Dog10K_Boxer_Tasha.xenoRefGene

track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes 2020_10
group genes
priority 40
visibility pack
color 150,0,0
itemRgb on
type bigGenePred
bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.ensGene.bb
searchTrix ixIxx/GCF_000002285.5_Dog10K_Boxer_Tasha.ensGene.ix
searchIndex name
labelFields name,name2
defaultLabelFields name2
baseColorUseCds given
baseColorDefault genomicCodons
labelSeperator " "
html html/GCF_000002285.5_Dog10K_Boxer_Tasha.ensGene

track GCF_000002285.5_Dog10K_Boxer_TashaChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain and Net alignments to target sequence: GCF_000002285.5_Dog10K_Boxer_Tasha
subGroup1 view Views chain=Chains net=Nets
subGroup2 species Species s000=GCA_905319855.2 s001=rn7
subGroup3 clade Clade c00=human
dragAndDrop subTracks
visibility hide
group compGeno
color 0,0,0
altColor 255,255,0
type bed 3
chainLinearGap loose
chainMinScore 5000
dimensions dimensionX=clade dimensionY=species
sortOrder species=+ view=+ clade=+
configurable on
html html/GCF_000002285.5_Dog10K_Boxer_Tasha.chainNet

    track GCF_000002285.5_Dog10K_Boxer_TashaChainNetViewchain
    shortLabel  Chains
    view chain
    visibility pack
    subTrack GCF_000002285.5_Dog10K_Boxer_TashaChainNet
    spectrum on

        track chainGCA_905319855.2
        subTrack GCF_000002285.5_Dog10K_Boxer_TashaChainNetViewchain off
        subGroups view=chain species=s000 clade=c00
        shortLabel GCA_905319855.2 Chain
        longLabel GCA_905319855.2_mCanLor1.2 (2021-03-26) Chained Alignments
        type bigChain GCA_905319855.2
        bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.chainGCA_905319855.2.bb
        linkDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.chainGCA_905319855.2Link.bb
        otherDb GCA_905319855.2
        html html/GCF_000002285.5_Dog10K_Boxer_Tasha.chainNet
        priority 1

        track chainSynGCA_905319855.2
        subTrack GCF_000002285.5_Dog10K_Boxer_TashaChainNetViewchain off
        subGroups view=chain species=s000 clade=c00
        shortLabel GCA_905319855.2 synChain
        longLabel GCA_905319855.2_mCanLor1.2 (2021-03-26) Syntenic Chained Alignments
        type bigChain GCA_905319855.2
        bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.chainSynGCA_905319855.2.bb
        linkDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.chainSynGCA_905319855.2Link.bb
        otherDb GCA_905319855.2
        html html/GCF_000002285.5_Dog10K_Boxer_Tasha.chainNet
        priority 2

        track chainRBestGCA_905319855.2
        subTrack GCF_000002285.5_Dog10K_Boxer_TashaChainNetViewchain off
        subGroups view=chain species=s000 clade=c00
        shortLabel GCA_905319855.2 rbChain
        longLabel GCA_905319855.2_mCanLor1.2 (2021-03-26) Reciprocal Best Chained Alignments
        type bigChain GCA_905319855.2
        bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.chainRBestGCA_905319855.2.bb
        linkDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.chainRBestGCA_905319855.2Link.bb
        otherDb GCA_905319855.2
        html html/GCF_000002285.5_Dog10K_Boxer_Tasha.chainNet
        priority 3

        track chainRn7
        subTrack GCF_000002285.5_Dog10K_Boxer_TashaChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel rn7 Chain
        longLabel rn7 (Nov. 2020) Chained Alignments
        type bigChain rn7
        bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.chainRn7.bb
        linkDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.chainRn7Link.bb
        otherDb rn7
        html html/GCF_000002285.5_Dog10K_Boxer_Tasha.chainNet
        priority 4

        track chainSynRn7
        subTrack GCF_000002285.5_Dog10K_Boxer_TashaChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel rn7 synChain
        longLabel rn7 (Nov. 2020) Syntenic Chained Alignments
        type bigChain rn7
        bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.chainSynRn7.bb
        linkDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.chainSynRn7Link.bb
        otherDb rn7
        html html/GCF_000002285.5_Dog10K_Boxer_Tasha.chainNet
        priority 5

        track chainRBestRn7
        subTrack GCF_000002285.5_Dog10K_Boxer_TashaChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel rn7 rbChain
        longLabel rn7 (Nov. 2020) Reciprocal Best Chained Alignments
        type bigChain rn7
        bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.chainRBestRn7.bb
        linkDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.chainRBestRn7Link.bb
        otherDb rn7
        html html/GCF_000002285.5_Dog10K_Boxer_Tasha.chainNet
        priority 6

        track chainLiftOverRn7
        subTrack GCF_000002285.5_Dog10K_Boxer_TashaChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel rn7 loChain
        longLabel rn7 (Nov. 2020) Lift Over Chained Alignments
        type bigChain rn7
        bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.chainLiftOverRn7.bb
        linkDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.chainLiftOverRn7Link.bb
        otherDb rn7
        html html/GCF_000002285.5_Dog10K_Boxer_Tasha.chainNet
        priority 7

    track GCF_000002285.5_Dog10K_Boxer_TashaMafNetViewnet
    shortLabel Nets
    view net
    visibility dense
    subTrack GCF_000002285.5_Dog10K_Boxer_TashaChainNet

        track synNetGCA_905319855.2
        parent GCF_000002285.5_Dog10K_Boxer_TashaMafNetViewnet
        subGroups view=net species=s000 clade=c00
        shortLabel GCA_905319855.2 synNet
        longLabel GCA_905319855.2 (some date) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.GCA_905319855.2.synNet.bb
        summary bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.GCA_905319855.2.synNet.summary.bb
        speciesOrder GCA_905319855.2
        html html/GCF_000002285.5_Dog10K_Boxer_Tasha.chainNet
        priority 1

        track rbestNetGCA_905319855.2
        parent GCF_000002285.5_Dog10K_Boxer_TashaMafNetViewnet
        subGroups view=net species=s000 clade=c00
        shortLabel GCA_905319855.2 rbestNet
        longLabel GCA_905319855.2 (some date) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.GCA_905319855.2.rbestNet.bb
        summary bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.GCA_905319855.2.rbestNet.summary.bb
        speciesOrder GCA_905319855.2
        html html/GCF_000002285.5_Dog10K_Boxer_Tasha.chainNet
        priority 2

        track synNetRn7
        parent GCF_000002285.5_Dog10K_Boxer_TashaMafNetViewnet
        subGroups view=net species=s001 clade=c00
        shortLabel rn7 synNet
        longLabel rn7 (some date) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.rn7.synNet.bb
        summary bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.rn7.synNet.summary.bb
        speciesOrder rn7
        html html/GCF_000002285.5_Dog10K_Boxer_Tasha.chainNet
        priority 3

        track rbestNetRn7
        parent GCF_000002285.5_Dog10K_Boxer_TashaMafNetViewnet
        subGroups view=net species=s001 clade=c00
        shortLabel rn7 rbestNet
        longLabel rn7 (some date) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.rn7.rbestNet.bb
        summary bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.rn7.rbestNet.summary.bb
        speciesOrder rn7
        html html/GCF_000002285.5_Dog10K_Boxer_Tasha.chainNet
        priority 4

        track liftOverNetRn7
        parent GCF_000002285.5_Dog10K_Boxer_TashaMafNetViewnet
        subGroups view=net species=s001 clade=c00
        shortLabel rn7 liftOverNet
        longLabel rn7 (some date) Lift Over Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.rn7.liftOverNet.bb
        summary bbi/GCF_000002285.5_Dog10K_Boxer_Tasha.rn7.liftOverNet.summary.bb
        speciesOrder rn7
        html html/GCF_000002285.5_Dog10K_Boxer_Tasha.chainNet
        priority 5