hub GCA_001624675.1 genome assembly
shortLabel house mouse (NOD_ShiLtJ v1 2016)
longLabel house mouse (NOD_ShiLtJ v1 2016)/Mus musculus/GCA_001624675.1_NOD_ShiLtJ_v1 genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCA_001624675.1_NOD_ShiLtJ_v1.description.html

genome GCA_001624675.1
taxId 10090
groups groups.txt
description house mouse (NOD_ShiLtJ v1 2016)
twoBitPath GCA_001624675.1.2bit
twoBitBptUrl GCA_001624675.1.2bit.bpt
chromSizes GCA_001624675.1.chrom.sizes.txt
chromAliasBb GCA_001624675.1.chromAlias.bb
chromAuthority ucsc
organism NOD_ShiLtJ_v1 Apr. 2016
defaultPos CM004134.1:74444598-74454598
scientificName Mus musculus
htmlPath html/GCA_001624675.1_NOD_ShiLtJ_v1.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/001/624/675/GCA_001624675.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/001/624/675/GCA_001624675.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/001/624/675/GCA_001624675.1
liftOver.mm10 liftOver/GCA_001624675.1ToMm10.over.chain.gz
liftOver.mm39 liftOver/GCA_001624675.1ToMm39.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_001624675.1_NOD_ShiLtJ_v1.assembly.bb
type bigBed 6
html html/GCA_001624675.1_NOD_ShiLtJ_v1.assembly
searchIndex name
searchTrix ixIxx/GCA_001624675.1_NOD_ShiLtJ_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_001624675.1_NOD_ShiLtJ_v1.gap.bb
type bigBed 4
group map
html html/GCA_001624675.1_NOD_ShiLtJ_v1.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_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_001624675.1_NOD_ShiLtJ_v1.gc5Base.bw
html html/GCA_001624675.1_NOD_ShiLtJ_v1.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_001624675.1_NOD_ShiLtJ_v1.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_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_001624675.1_NOD_ShiLtJ_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_001624675.1_NOD_ShiLtJ_v1.repeatMasker

    track repeatMaskerSINE
    parent repeatMasker
    shortLabel SINE
    longLabel SINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 1
    bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.rmsk.SINE.bb

    track repeatMaskerLINE
    parent repeatMasker
    shortLabel LINE
    longLabel LINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 2
    bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.rmsk.LINE.bb

    track repeatMaskerLTR
    parent repeatMasker
    shortLabel LTR
    longLabel LTR Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 3
    bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.rmsk.LTR.bb

    track repeatMaskerDNA
    parent repeatMasker
    shortLabel DNA
    longLabel DNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 4
    bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.rmsk.DNA.bb

    track repeatMaskerSimple
    parent repeatMasker
    shortLabel Simple
    longLabel Simple Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 5
    bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_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_001624675.1_NOD_ShiLtJ_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_001624675.1_NOD_ShiLtJ_v1.rmsk.Satellite.bb

    track repeatMaskerRNA
    parent repeatMasker
    shortLabel RNA
    longLabel RNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 8
    bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.rmsk.RNA.bb

    track repeatMaskerOther
    parent repeatMasker
    shortLabel Other
    longLabel Other Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 9
    bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_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_001624675.1_NOD_ShiLtJ_v1.simpleRepeat.bb
html html/GCA_001624675.1_NOD_ShiLtJ_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_001624675.1_NOD_ShiLtJ_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_001624675.1_NOD_ShiLtJ_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_001624675.1_NOD_ShiLtJ_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_001624675.1_NOD_ShiLtJ_v1.windowMasker.bb
html html/GCA_001624675.1_NOD_ShiLtJ_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_001624675.1_NOD_ShiLtJ_v1.allGaps.bb
html html/GCA_001624675.1_NOD_ShiLtJ_v1.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.augustus.bb
html html/GCA_001624675.1_NOD_ShiLtJ_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_001624675.1_NOD_ShiLtJ_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_001624675.1_NOD_ShiLtJ_v1.xenoRefGene.ix
html html/GCA_001624675.1_NOD_ShiLtJ_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_001624675.1_NOD_ShiLtJ_v1.ensGene.bb
searchIndex name
baseColorUseCds given
baseColorDefault genomicCodons
html html/GCA_001624675.1_NOD_ShiLtJ_v1.ensGene

include rnaSeqData/GCA_001624675.1_NOD_ShiLtJ_v1.trackDb.txt

track GCA_001624675.1_NOD_ShiLtJ_v1ChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCA_001624675.1_NOD_ShiLtJ_v1
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=mm39 s001=mm10
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_001624675.1_NOD_ShiLtJ_v1.chainNet

    track GCA_001624675.1_NOD_ShiLtJ_v1ChainNetViewchain
    shortLabel Chains
    view chain
    visibility dense
    parent GCA_001624675.1_NOD_ShiLtJ_v1ChainNet
    spectrum on

    track GCA_001624675.1_NOD_ShiLtJ_v1ChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility hide
    parent GCA_001624675.1_NOD_ShiLtJ_v1ChainNet
    spectrum on

    track GCA_001624675.1_NOD_ShiLtJ_v1ChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility hide
    parent GCA_001624675.1_NOD_ShiLtJ_v1ChainNet
    spectrum on

    track GCA_001624675.1_NOD_ShiLtJ_v1ChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility hide
    parent GCA_001624675.1_NOD_ShiLtJ_v1ChainNet
    spectrum on

        track chainMm39
        parent GCA_001624675.1_NOD_ShiLtJ_v1ChainNetViewchain on
        subGroups view=chain species=s000 chainType=c00
        shortLabel Mouse/mm39 Chain
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.chainMm39.bb
        linkDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.chainMm39Link.bb
        otherDb mm39
        html html/GCA_001624675.1_NOD_ShiLtJ_v1.chainNet
        priority 25.400

        track chainSynMm39
        parent GCA_001624675.1_NOD_ShiLtJ_v1ChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel Mouse/mm39 synChain
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.chainSynMm39.bb
        linkDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.chainSynMm39Link.bb
        otherDb mm39
        html html/GCA_001624675.1_NOD_ShiLtJ_v1.chainNet
        priority 25.400

        track chainRBestMm39
        parent GCA_001624675.1_NOD_ShiLtJ_v1ChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel Mouse/mm39 rbChain
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.chainRBestMm39.bb
        linkDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.chainRBestMm39Link.bb
        otherDb mm39
        html html/GCA_001624675.1_NOD_ShiLtJ_v1.chainNet
        priority 25.400

        track chainLiftOverMm39
        parent GCA_001624675.1_NOD_ShiLtJ_v1ChainNetViewLiftOver off
        subGroups view=liftover species=s000 chainType=c03
        shortLabel Mouse/mm39 loChain
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.chainLiftOverMm39.bb
        linkDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.chainLiftOverMm39Link.bb
        otherDb mm39
        html html/GCA_001624675.1_NOD_ShiLtJ_v1.chainNet
        priority 25.400

        track chainMm10
        parent GCA_001624675.1_NOD_ShiLtJ_v1ChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel Mouse/mm10 Chain
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.chainMm10.bb
        linkDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.chainMm10Link.bb
        otherDb mm10
        html html/GCA_001624675.1_NOD_ShiLtJ_v1.chainNet
        priority 25.405

        track chainSynMm10
        parent GCA_001624675.1_NOD_ShiLtJ_v1ChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel Mouse/mm10 synChain
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.chainSynMm10.bb
        linkDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.chainSynMm10Link.bb
        otherDb mm10
        html html/GCA_001624675.1_NOD_ShiLtJ_v1.chainNet
        priority 25.405

        track chainRBestMm10
        parent GCA_001624675.1_NOD_ShiLtJ_v1ChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel Mouse/mm10 rbChain
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigChain mm10
        bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.chainRBestMm10.bb
        linkDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.chainRBestMm10Link.bb
        otherDb mm10
        html html/GCA_001624675.1_NOD_ShiLtJ_v1.chainNet
        priority 25.405

    track GCA_001624675.1_NOD_ShiLtJ_v1MafNetViewnet
    shortLabel Nets
    view align
    visibility hide
    parent GCA_001624675.1_NOD_ShiLtJ_v1ChainNet

        track netMm39
        parent GCA_001624675.1_NOD_ShiLtJ_v1MafNetViewnet off
        subGroups view=align species=s000 chainType=c04
        shortLabel Mouse/mm39 mafNet
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.mm39.net.bb
        summary bbi/GCA_001624675.1_NOD_ShiLtJ_v1.mm39.net.summary.bb
        speciesOrder mm39
        html html/GCA_001624675.1_NOD_ShiLtJ_v1.chainNet
        priority 25.400

        track synNetMm39
        parent GCA_001624675.1_NOD_ShiLtJ_v1MafNetViewnet off
        subGroups view=align species=s000 chainType=c05
        shortLabel Mouse/mm39 synNet
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.mm39.synNet.bb
        summary bbi/GCA_001624675.1_NOD_ShiLtJ_v1.mm39.synNet.summary.bb
        speciesOrder mm39
        html html/GCA_001624675.1_NOD_ShiLtJ_v1.chainNet
        priority 25.400

        track rbestNetMm39
        parent GCA_001624675.1_NOD_ShiLtJ_v1MafNetViewnet off
        subGroups view=align species=s000 chainType=c06
        shortLabel Mouse/mm39 rbestNet
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.mm39.rbestNet.bb
        summary bbi/GCA_001624675.1_NOD_ShiLtJ_v1.mm39.rbestNet.summary.bb
        speciesOrder mm39
        html html/GCA_001624675.1_NOD_ShiLtJ_v1.chainNet
        priority 25.400

        track netMm10
        parent GCA_001624675.1_NOD_ShiLtJ_v1MafNetViewnet off
        subGroups view=align species=s001 chainType=c04
        shortLabel Mouse/mm10 mafNet
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.mm10.net.bb
        summary bbi/GCA_001624675.1_NOD_ShiLtJ_v1.mm10.net.summary.bb
        speciesOrder mm10
        html html/GCA_001624675.1_NOD_ShiLtJ_v1.chainNet
        priority 25.405

        track synNetMm10
        parent GCA_001624675.1_NOD_ShiLtJ_v1MafNetViewnet off
        subGroups view=align species=s001 chainType=c05
        shortLabel Mouse/mm10 synNet
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.mm10.synNet.bb
        summary bbi/GCA_001624675.1_NOD_ShiLtJ_v1.mm10.synNet.summary.bb
        speciesOrder mm10
        html html/GCA_001624675.1_NOD_ShiLtJ_v1.chainNet
        priority 25.405

        track rbestNetMm10
        parent GCA_001624675.1_NOD_ShiLtJ_v1MafNetViewnet off
        subGroups view=align species=s001 chainType=c06
        shortLabel Mouse/mm10 rbestNet
        longLabel Mouse/mm10/mm10 (Dec. 2011) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_001624675.1_NOD_ShiLtJ_v1.mm10.rbestNet.bb
        summary bbi/GCA_001624675.1_NOD_ShiLtJ_v1.mm10.rbestNet.summary.bb
        speciesOrder mm10
        html html/GCA_001624675.1_NOD_ShiLtJ_v1.chainNet
        priority 25.405