hub GCA_921999005.2 genome assembly
shortLabel Southeastern Asian house mouse (2022)
longLabel Southeastern Asian house mouse (2022)/Mus musculus castaneus/GCA_921999005.2_CAST_EiJ_v3 genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCA_921999005.2_CAST_EiJ_v3.description.html

genome GCA_921999005.2
taxId 10091
groups groups.txt
description Southeastern Asian house mouse (2022)
twoBitPath GCA_921999005.2.2bit
twoBitBptUrl GCA_921999005.2.2bit.bpt
chromSizes GCA_921999005.2.chrom.sizes.txt
chromAliasBb GCA_921999005.2.chromAlias.bb
chromAuthority ucsc
organism CAST_EiJ_v3 Jul. 2022
defaultPos OW971825.1:63485534-63495534
scientificName Mus musculus castaneus
htmlPath html/GCA_921999005.2_CAST_EiJ_v3.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/921/999/005/GCA_921999005.2
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/921/999/005/GCA_921999005.2
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/921/999/005/GCA_921999005.2
liftOver.mm39 liftOver/GCA_921999005.2ToMm39.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_921999005.2_CAST_EiJ_v3.assembly.bb
type bigBed 6
html html/GCA_921999005.2_CAST_EiJ_v3.assembly
searchIndex name
searchTrix ixIxx/GCA_921999005.2_CAST_EiJ_v3.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_921999005.2_CAST_EiJ_v3.gap.bb
type bigBed 4
group map
html html/GCA_921999005.2_CAST_EiJ_v3.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.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_921999005.2_CAST_EiJ_v3.gc5Base.bw
html html/GCA_921999005.2_CAST_EiJ_v3.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_921999005.2_CAST_EiJ_v3.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.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_921999005.2_CAST_EiJ_v3.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.rmsk.bb
xrefDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCA_921999005.2_CAST_EiJ_v3.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.simpleRepeat.bb
html html/GCA_921999005.2_CAST_EiJ_v3.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_921999005.2_CAST_EiJ_v3.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_921999005.2_CAST_EiJ_v3.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_921999005.2_CAST_EiJ_v3.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.windowMasker.bb
html html/GCA_921999005.2_CAST_EiJ_v3.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_921999005.2_CAST_EiJ_v3.allGaps.bb
html html/GCA_921999005.2_CAST_EiJ_v3.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.augustus.bb
html html/GCA_921999005.2_CAST_EiJ_v3.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_921999005.2_CAST_EiJ_v3.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_921999005.2_CAST_EiJ_v3.xenoRefGene.ix
html html/GCA_921999005.2_CAST_EiJ_v3.xenoRefGene

track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes 2023_06
group genes
priority 40
visibility pack
color 150,0,0
itemRgb on
type bigGenePred
bigDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.ensGene.bb
searchTrix ixIxx/GCA_921999005.2_CAST_EiJ_v3.ensGene.ix
searchIndex name
labelFields name,name2
defaultLabelFields name2
baseColorUseCds given
baseColorDefault genomicCodons
labelSeperator " "
html html/GCA_921999005.2_CAST_EiJ_v3.ensGene

##############################################################################
# mm39 - Mouse - Mus musculus - taxId: 10090
##############################################################################
track chainNetMm39
compositeTrack on
shortLabel Mouse Chain/Net
longLabel Mouse (Jun. 2020 (GRCm39/mm39)), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
group compGeno
priority 100.1
color 0,0,0
altColor 100,50,0
type bed 3
sortOrder view=+
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
chainMinScore 3000
chainLinearGap medium
matrixHeader A, C, G, T
otherDb mm39
html html/GCA_921999005.2_CAST_EiJ_v3.chainNet

    track chainNetMm39Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetMm39
    spectrum on

        track chainMm39
        parent chainNetMm39Viewchain
        subGroups view=chain
        shortLabel Mouse Chain
        longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.chainMm39.bb
        linkDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.chainMm39Link.bb
        priority 1

        track chainSynMm39
        parent chainNetMm39Viewchain
        subGroups view=chain
        shortLabel Mouse synChain
        longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Syntenic Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.chainSynMm39.bb
        linkDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.chainSynMm39Link.bb
        priority 2

        track chainRBestMm39
        parent chainNetMm39Viewchain
        subGroups view=chain
        shortLabel Mouse rbChain
        longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Reciprocal Best Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.chainRBestMm39.bb
        linkDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.chainRBestMm39Link.bb
        priority 3

        track chainLiftOverMm39
        parent chainNetMm39Viewchain
        subGroups view=chain
        shortLabel Mouse loChain
        longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Lift Over Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.chainLiftOverMm39.bb
        linkDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.chainLiftOverMm39Link.bb
        priority 4

    track mafNetMm39Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetMm39

        track netMm39
        parent mafNetMm39Viewnet
        subGroups view=net
        shortLabel Mouse net
        longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.mm39.net.bb
        summary bbi/GCA_921999005.2_CAST_EiJ_v3.mm39.net.summary.bb
        speciesOrder mm39
        priority 5

        track synNetMm39
        parent mafNetMm39Viewnet
        subGroups view=net
        shortLabel Mouse synNet
        longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.mm39.synNet.bb
        summary bbi/GCA_921999005.2_CAST_EiJ_v3.mm39.synNet.summary.bb
        speciesOrder mm39
        priority 6

        track rbestNetMm39
        parent mafNetMm39Viewnet
        subGroups view=net
        shortLabel Mouse rbestNet
        longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_921999005.2_CAST_EiJ_v3.mm39.rbestNet.bb
        summary bbi/GCA_921999005.2_CAST_EiJ_v3.mm39.rbestNet.summary.bb
        speciesOrder mm39
        priority 7