hub GCA_001624445.1 genome assembly
shortLabel house mouse CAST_EiJ
longLabel house mouse CAST_EiJ/Mus musculus castaneus/GCA_001624445.1_CAST_EiJ_v1 genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCA_001624445.1_CAST_EiJ_v1.description.html

genome GCA_001624445.1
taxId 10091
groups groups.txt
description house mouse CAST_EiJ
twoBitPath GCA_001624445.1.2bit
twoBitBptUrl GCA_001624445.1.2bit.bpt
chromSizes GCA_001624445.1.chrom.sizes.txt
chromAliasBb GCA_001624445.1.chromAlias.bb
chromAuthority ucsc
organism CAST_EiJ_v1 Apr. 2016
defaultPos CM003994.1:66808189-66818189
scientificName Mus musculus castaneus
htmlPath html/GCA_001624445.1_CAST_EiJ_v1.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/001/624/445/GCA_001624445.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/001/624/445/GCA_001624445.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/001/624/445/GCA_001624445.1
liftOver.mm10 liftOver/GCA_001624445.1ToMm10.over.chain.gz
liftOver.mm39 liftOver/GCA_001624445.1ToMm39.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_001624445.1_CAST_EiJ_v1.assembly.bb
type bigBed 6
html html/GCA_001624445.1_CAST_EiJ_v1.assembly
searchIndex name
searchTrix ixIxx/GCA_001624445.1_CAST_EiJ_v1.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_001624445.1_CAST_EiJ_v1.gap.bb
type bigBed 4
group map
html html/GCA_001624445.1_CAST_EiJ_v1.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.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_001624445.1_CAST_EiJ_v1.gc5Base.bw
html html/GCA_001624445.1_CAST_EiJ_v1.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_001624445.1_CAST_EiJ_v1.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.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/GCA_001624445.1_CAST_EiJ_v1.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/GCA_001624445.1_CAST_EiJ_v1.repeatMasker

    track repeatMaskerSINE
    parent repeatMasker
    shortLabel SINE
    longLabel SINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 1
    bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.rmsk.SINE.bb

    track repeatMaskerLINE
    parent repeatMasker
    shortLabel LINE
    longLabel LINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 2
    bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.rmsk.LINE.bb

    track repeatMaskerLTR
    parent repeatMasker
    shortLabel LTR
    longLabel LTR Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 3
    bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.rmsk.LTR.bb

    track repeatMaskerDNA
    parent repeatMasker
    shortLabel DNA
    longLabel DNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 4
    bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.rmsk.DNA.bb

    track repeatMaskerSimple
    parent repeatMasker
    shortLabel Simple
    longLabel Simple Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 5
    bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.rmsk.Simple.bb

    track repeatMaskerLowComplexity
    parent repeatMasker
    shortLabel Low Complexity
    longLabel Low Complexity Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 6
    bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.rmsk.Low_complexity.bb

    track repeatMaskerSatellite
    parent repeatMasker
    shortLabel Satellite
    longLabel Satellite Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 7
    bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.rmsk.Satellite.bb

    track repeatMaskerRNA
    parent repeatMasker
    shortLabel RNA
    longLabel RNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 8
    bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.rmsk.RNA.bb

    track repeatMaskerOther
    parent repeatMasker
    shortLabel Other
    longLabel Other Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 9
    bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.rmsk.Other.bb

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.simpleRepeat.bb
html html/GCA_001624445.1_CAST_EiJ_v1.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_001624445.1_CAST_EiJ_v1.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_001624445.1_CAST_EiJ_v1.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_001624445.1_CAST_EiJ_v1.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.windowMasker.bb
html html/GCA_001624445.1_CAST_EiJ_v1.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_001624445.1_CAST_EiJ_v1.allGaps.bb
html html/GCA_001624445.1_CAST_EiJ_v1.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.augustus.bb
html html/GCA_001624445.1_CAST_EiJ_v1.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_001624445.1_CAST_EiJ_v1.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_001624445.1_CAST_EiJ_v1.xenoRefGene.ix
html html/GCA_001624445.1_CAST_EiJ_v1.xenoRefGene

track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes version 104/May 2021
group genes
priority 40
visibility pack
color 150,0,0
itemRgb on
type bigBed 12 .
bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.ensGene.bb
searchIndex name
baseColorUseCds given
baseColorDefault genomicCodons
html html/GCA_001624445.1_CAST_EiJ_v1.ensGene

include rnaSeqData/GCA_001624445.1_CAST_EiJ_v1.trackDb.txt

track GCA_001624445.1_CAST_EiJ_v1ChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain and Net alignments to target sequence: GCA_001624445.1_CAST_EiJ_v1
subGroup1 view Views chain=Chains net=Nets
subGroup2 species Species s000=mm10 s001=mm39
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/GCA_001624445.1_CAST_EiJ_v1.chainNet

    track GCA_001624445.1_CAST_EiJ_v1ChainNetViewchain
    shortLabel  Chains
    view chain
    visibility pack
    subTrack GCA_001624445.1_CAST_EiJ_v1ChainNet
    spectrum on

        track chainMm10
        subTrack GCA_001624445.1_CAST_EiJ_v1ChainNetViewchain off
        subGroups view=chain species=s000 clade=c00
        shortLabel mm10 Chain
        longLabel mm10 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.chainMm10.bb
        linkDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.chainMm10Link.bb
        otherDb mm10
        html html/GCA_001624445.1_CAST_EiJ_v1.chainNet
        priority 1

        track chainSynMm10
        subTrack GCA_001624445.1_CAST_EiJ_v1ChainNetViewchain off
        subGroups view=chain species=s000 clade=c00
        shortLabel mm10 synChain
        longLabel mm10 (Dec. 2011) Syntenic Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.chainSynMm10.bb
        linkDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.chainSynMm10Link.bb
        otherDb mm10
        html html/GCA_001624445.1_CAST_EiJ_v1.chainNet
        priority 2

        track chainRBestMm10
        subTrack GCA_001624445.1_CAST_EiJ_v1ChainNetViewchain off
        subGroups view=chain species=s000 clade=c00
        shortLabel mm10 rbChain
        longLabel mm10 (Dec. 2011) Reciprocal Best Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.chainRBestMm10.bb
        linkDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.chainRBestMm10Link.bb
        otherDb mm10
        html html/GCA_001624445.1_CAST_EiJ_v1.chainNet
        priority 3

        track chainLiftOverMm10
        subTrack GCA_001624445.1_CAST_EiJ_v1ChainNetViewchain off
        subGroups view=chain species=s000 clade=c00
        shortLabel mm10 loChain
        longLabel mm10 (Dec. 2011) Lift Over Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.chainLiftOverMm10.bb
        linkDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.chainLiftOverMm10Link.bb
        otherDb mm10
        html html/GCA_001624445.1_CAST_EiJ_v1.chainNet
        priority 4

        track chainMm39
        subTrack GCA_001624445.1_CAST_EiJ_v1ChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel mm39 Chain
        longLabel mm39 (Jun. 2020) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.chainMm39.bb
        linkDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.chainMm39Link.bb
        otherDb mm39
        html html/GCA_001624445.1_CAST_EiJ_v1.chainNet
        priority 5

        track chainSynMm39
        subTrack GCA_001624445.1_CAST_EiJ_v1ChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel mm39 synChain
        longLabel mm39 (Jun. 2020) Syntenic Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.chainSynMm39.bb
        linkDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.chainSynMm39Link.bb
        otherDb mm39
        html html/GCA_001624445.1_CAST_EiJ_v1.chainNet
        priority 6

        track chainRBestMm39
        subTrack GCA_001624445.1_CAST_EiJ_v1ChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel mm39 rbChain
        longLabel mm39 (Jun. 2020) Reciprocal Best Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.chainRBestMm39.bb
        linkDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.chainRBestMm39Link.bb
        otherDb mm39
        html html/GCA_001624445.1_CAST_EiJ_v1.chainNet
        priority 7

    track GCA_001624445.1_CAST_EiJ_v1MafNetViewnet
    shortLabel Nets
    view net
    visibility dense
    subTrack GCA_001624445.1_CAST_EiJ_v1ChainNet

        track synNetMm10
        parent GCA_001624445.1_CAST_EiJ_v1MafNetViewnet
        subGroups view=net species=s000 clade=c00
        shortLabel mm10 synNet
        longLabel mm10 (some date) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.mm10.synNet.bb
        summary bbi/GCA_001624445.1_CAST_EiJ_v1.mm10.synNet.summary.bb
        speciesOrder mm10
        html html/GCA_001624445.1_CAST_EiJ_v1.chainNet
        priority 1

        track rbestNetMm10
        parent GCA_001624445.1_CAST_EiJ_v1MafNetViewnet
        subGroups view=net species=s000 clade=c00
        shortLabel mm10 rbestNet
        longLabel mm10 (some date) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.mm10.rbestNet.bb
        summary bbi/GCA_001624445.1_CAST_EiJ_v1.mm10.rbestNet.summary.bb
        speciesOrder mm10
        html html/GCA_001624445.1_CAST_EiJ_v1.chainNet
        priority 2

        track liftOverNetMm10
        parent GCA_001624445.1_CAST_EiJ_v1MafNetViewnet
        subGroups view=net species=s000 clade=c00
        shortLabel mm10 liftOverNet
        longLabel mm10 (some date) Lift Over Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.mm10.liftOverNet.bb
        summary bbi/GCA_001624445.1_CAST_EiJ_v1.mm10.liftOverNet.summary.bb
        speciesOrder mm10
        html html/GCA_001624445.1_CAST_EiJ_v1.chainNet
        priority 3

        track synNetMm39
        parent GCA_001624445.1_CAST_EiJ_v1MafNetViewnet
        subGroups view=net species=s001 clade=c00
        shortLabel mm39 synNet
        longLabel mm39 (some date) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.mm39.synNet.bb
        summary bbi/GCA_001624445.1_CAST_EiJ_v1.mm39.synNet.summary.bb
        speciesOrder mm39
        html html/GCA_001624445.1_CAST_EiJ_v1.chainNet
        priority 4

        track rbestNetMm39
        parent GCA_001624445.1_CAST_EiJ_v1MafNetViewnet
        subGroups view=net species=s001 clade=c00
        shortLabel mm39 rbestNet
        longLabel mm39 (some date) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_001624445.1_CAST_EiJ_v1.mm39.rbestNet.bb
        summary bbi/GCA_001624445.1_CAST_EiJ_v1.mm39.rbestNet.summary.bb
        speciesOrder mm39
        html html/GCA_001624445.1_CAST_EiJ_v1.chainNet
        priority 5