hub GCA_004027735.1 genome assembly
shortLabel Seba's short-tailed bat
longLabel Seba's short-tailed bat/Carollia perspicillata/GCA_004027735.1_CarPer_v1_BIUU genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCA_004027735.1_CarPer_v1_BIUU.description.html

genome GCA_004027735.1
taxId 40233
groups groups.txt
description Seba's short-tailed bat
twoBitPath GCA_004027735.1.2bit
twoBitBptUrl GCA_004027735.1.2bit.bpt
chromSizes GCA_004027735.1.chrom.sizes.txt
chromAliasBb GCA_004027735.1.chromAlias.bb
organism CarPer_v1_BIUU Jan. 2019
defaultPos PVKM010000001.1:91644-101644
scientificName Carollia perspicillata
htmlPath html/GCA_004027735.1_CarPer_v1_BIUU.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/004/027/735/GCA_004027735.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/004/027/735/GCA_004027735.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/004/027/735/GCA_004027735.1
liftOver.mm39 liftOver/GCA_004027735.1ToMm39.over.chain.gz
liftOver.susScr11 liftOver/GCA_004027735.1ToSusScr11.over.chain.gz

track assembly
longLabel Assembly
shortLabel Assembly
visibility hide
colorByStrand 150,100,30 230,170,40
color 150,100,30
altColor 230,170,40
bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.assembly.bb
type bigBed 6
html html/GCA_004027735.1_CarPer_v1_BIUU.assembly
searchIndex name
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
group map

track gap
longLabel AGP gap
shortLabel Gap (AGP defined)
visibility hide
color 0,0,0
bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.gap.bb
type bigBed 4
group map
html html/GCA_004027735.1_CarPer_v1_BIUU.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.cytoBand.bb

track gc5Base
shortLabel GC Percent
longLabel GC Percent in 5-Base Windows
group map
visibility dense
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_004027735.1_CarPer_v1_BIUU.gc5Base.bw
html html/GCA_004027735.1_CarPer_v1_BIUU.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_004027735.1_CarPer_v1_BIUU.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.gapOverlap.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_004027735.1_CarPer_v1_BIUU.repeatMasker

    track repeatMaskerSINE
    parent repeatMasker
    shortLabel SINE
    longLabel SINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 1
    bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.rmsk.SINE.bb

    track repeatMaskerLINE
    parent repeatMasker
    shortLabel LINE
    longLabel LINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 2
    bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.rmsk.LINE.bb

    track repeatMaskerLTR
    parent repeatMasker
    shortLabel LTR
    longLabel LTR Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 3
    bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.rmsk.LTR.bb

    track repeatMaskerDNA
    parent repeatMasker
    shortLabel DNA
    longLabel DNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 4
    bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.rmsk.DNA.bb

    track repeatMaskerSimple
    parent repeatMasker
    shortLabel Simple
    longLabel Simple Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 5
    bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.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_004027735.1_CarPer_v1_BIUU.rmsk.Low_complexity.bb

    track repeatMaskerRNA
    parent repeatMasker
    shortLabel RNA
    longLabel RNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 8
    bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.rmsk.RNA.bb

    track repeatMaskerOther
    parent repeatMasker
    shortLabel Other
    longLabel Other Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 9
    bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.rmsk.Other.bb

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.simpleRepeat.bb
html html/GCA_004027735.1_CarPer_v1_BIUU.simpleRepeat

track cpgIslands
compositeTrack on
shortLabel CpG Islands
longLabel CpG Islands (Islands < 300 Bases are Light Green)
group regulation
visibility dense
type bigBed 4 +
html html/GCA_004027735.1_CarPer_v1_BIUU.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_004027735.1_CarPer_v1_BIUU.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_004027735.1_CarPer_v1_BIUU.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.windowMasker.bb
html html/GCA_004027735.1_CarPer_v1_BIUU.windowMasker

track allGaps
shortLabel All Gaps
longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps
group map
visibility hide
type bigBed 3
bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.allGaps.bb
html html/GCA_004027735.1_CarPer_v1_BIUU.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.augustus.bb
html html/GCA_004027735.1_CarPer_v1_BIUU.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_004027735.1_CarPer_v1_BIUU.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_004027735.1_CarPer_v1_BIUU.xenoRefGene.ix
html html/GCA_004027735.1_CarPer_v1_BIUU.xenoRefGene

track GCA_004027735.1_CarPer_v1_BIUUChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCA_004027735.1_CarPer_v1_BIUU
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=susScr11 s001=mm39
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_004027735.1_CarPer_v1_BIUU.chainNet

    track GCA_004027735.1_CarPer_v1_BIUUChainNetViewchain
    shortLabel Chains
    view chain
    visibility dense
    parent GCA_004027735.1_CarPer_v1_BIUUChainNet
    spectrum on

    track GCA_004027735.1_CarPer_v1_BIUUChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility hide
    parent GCA_004027735.1_CarPer_v1_BIUUChainNet
    spectrum on

    track GCA_004027735.1_CarPer_v1_BIUUChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility hide
    parent GCA_004027735.1_CarPer_v1_BIUUChainNet
    spectrum on

    track GCA_004027735.1_CarPer_v1_BIUUChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility hide
    parent GCA_004027735.1_CarPer_v1_BIUUChainNet
    spectrum on

        track chainSusScr11
        parent GCA_004027735.1_CarPer_v1_BIUUChainNetViewchain on
        subGroups view=chain species=s000 chainType=c00
        shortLabel Pig/susScr11 Chain
        longLabel Pig/susScr11/susScr11 (Feb. 2017) Chained Alignments
        type bigChain susScr11
        bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.chainSusScr11.bb
        linkDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.chainSusScr11Link.bb
        otherDb susScr11
        html html/GCA_004027735.1_CarPer_v1_BIUU.chainNet
        priority 46.124

        track chainSynSusScr11
        parent GCA_004027735.1_CarPer_v1_BIUUChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel Pig/susScr11 synChain
        longLabel Pig/susScr11/susScr11 (Feb. 2017) Chained Alignments
        type bigChain susScr11
        bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.chainSynSusScr11.bb
        linkDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.chainSynSusScr11Link.bb
        otherDb susScr11
        html html/GCA_004027735.1_CarPer_v1_BIUU.chainNet
        priority 46.124

        track chainRBestSusScr11
        parent GCA_004027735.1_CarPer_v1_BIUUChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel Pig/susScr11 rbChain
        longLabel Pig/susScr11/susScr11 (Feb. 2017) Chained Alignments
        type bigChain susScr11
        bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.chainRBestSusScr11.bb
        linkDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.chainRBestSusScr11Link.bb
        otherDb susScr11
        html html/GCA_004027735.1_CarPer_v1_BIUU.chainNet
        priority 46.124

        track chainMm39
        parent GCA_004027735.1_CarPer_v1_BIUUChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel Mouse/mm39 Chain
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.chainMm39.bb
        linkDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.chainMm39Link.bb
        otherDb mm39
        html html/GCA_004027735.1_CarPer_v1_BIUU.chainNet
        priority 74.439

        track chainSynMm39
        parent GCA_004027735.1_CarPer_v1_BIUUChainNetViewSynTen off
        subGroups view=synten species=s001 chainType=c01
        shortLabel Mouse/mm39 synChain
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.chainSynMm39.bb
        linkDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.chainSynMm39Link.bb
        otherDb mm39
        html html/GCA_004027735.1_CarPer_v1_BIUU.chainNet
        priority 74.439

        track chainRBestMm39
        parent GCA_004027735.1_CarPer_v1_BIUUChainNetViewRBest off
        subGroups view=rbest species=s001 chainType=c02
        shortLabel Mouse/mm39 rbChain
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigChain mm39
        bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.chainRBestMm39.bb
        linkDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.chainRBestMm39Link.bb
        otherDb mm39
        html html/GCA_004027735.1_CarPer_v1_BIUU.chainNet
        priority 74.439

    track GCA_004027735.1_CarPer_v1_BIUUMafNetViewnet
    shortLabel Nets
    view align
    visibility hide
    parent GCA_004027735.1_CarPer_v1_BIUUChainNet

        track netSusScr11
        parent GCA_004027735.1_CarPer_v1_BIUUMafNetViewnet off
        subGroups view=align species=s000 chainType=c04
        shortLabel Pig/susScr11 mafNet
        longLabel Pig/susScr11/susScr11 (Feb. 2017) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.susScr11.net.bb
        summary bbi/GCA_004027735.1_CarPer_v1_BIUU.susScr11.net.summary.bb
        speciesOrder susScr11
        html html/GCA_004027735.1_CarPer_v1_BIUU.chainNet
        priority 46.124

        track synNetSusScr11
        parent GCA_004027735.1_CarPer_v1_BIUUMafNetViewnet off
        subGroups view=align species=s000 chainType=c05
        shortLabel Pig/susScr11 synNet
        longLabel Pig/susScr11/susScr11 (Feb. 2017) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.susScr11.synNet.bb
        summary bbi/GCA_004027735.1_CarPer_v1_BIUU.susScr11.synNet.summary.bb
        speciesOrder susScr11
        html html/GCA_004027735.1_CarPer_v1_BIUU.chainNet
        priority 46.124

        track rbestNetSusScr11
        parent GCA_004027735.1_CarPer_v1_BIUUMafNetViewnet off
        subGroups view=align species=s000 chainType=c06
        shortLabel Pig/susScr11 rbestNet
        longLabel Pig/susScr11/susScr11 (Feb. 2017) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.susScr11.rbestNet.bb
        summary bbi/GCA_004027735.1_CarPer_v1_BIUU.susScr11.rbestNet.summary.bb
        speciesOrder susScr11
        html html/GCA_004027735.1_CarPer_v1_BIUU.chainNet
        priority 46.124

        track netMm39
        parent GCA_004027735.1_CarPer_v1_BIUUMafNetViewnet off
        subGroups view=align species=s001 chainType=c04
        shortLabel Mouse/mm39 mafNet
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.mm39.net.bb
        summary bbi/GCA_004027735.1_CarPer_v1_BIUU.mm39.net.summary.bb
        speciesOrder mm39
        html html/GCA_004027735.1_CarPer_v1_BIUU.chainNet
        priority 74.439

        track synNetMm39
        parent GCA_004027735.1_CarPer_v1_BIUUMafNetViewnet off
        subGroups view=align species=s001 chainType=c05
        shortLabel Mouse/mm39 synNet
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.mm39.synNet.bb
        summary bbi/GCA_004027735.1_CarPer_v1_BIUU.mm39.synNet.summary.bb
        speciesOrder mm39
        html html/GCA_004027735.1_CarPer_v1_BIUU.chainNet
        priority 74.439

        track rbestNetMm39
        parent GCA_004027735.1_CarPer_v1_BIUUMafNetViewnet off
        subGroups view=align species=s001 chainType=c06
        shortLabel Mouse/mm39 rbestNet
        longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCA_004027735.1_CarPer_v1_BIUU.mm39.rbestNet.bb
        summary bbi/GCA_004027735.1_CarPer_v1_BIUU.mm39.rbestNet.summary.bb
        speciesOrder mm39
        html html/GCA_004027735.1_CarPer_v1_BIUU.chainNet
        priority 74.439

track HLTOGAannotvHg38v1
bigDataUrl bbi/HLTOGAannotVsHg38v1.bb
shortLabel TOGA vs. hg38
longLabel TOGA annotations using human/hg38 as reference
group genes
visibility pack
itemRgb on
type bigBed 12
searchIndex name
searchTrix  ixIxx/HLTOGAannotVsHg38v1.ix
html html/TOGAannotation