hub GCA_009764565.4 genome assembly
shortLabel leatherback sea turtle (primary hap 2021)
longLabel leatherback sea turtle (primary hap 2021)/Dermochelys coriacea/GCA_009764565.4_rDerCor1.pri.v4 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCA_009764565.4_rDerCor1.pri.v4.description.html

genome GCA_009764565.4
taxId 27794
groups groups.txt
description leatherback sea turtle (primary hap 2021)
twoBitPath GCA_009764565.4.2bit
twoBitBptUrl GCA_009764565.4.2bit.bpt
chromSizes GCA_009764565.4.chrom.sizes.txt
chromAliasBb GCA_009764565.4.chromAlias.bb
chromAuthority ucsc
organism rDerCor1.pri.v4 Aug. 2021
defaultPos CM019935.3:118150962-118160962
scientificName Dermochelys coriacea
htmlPath html/GCA_009764565.4_rDerCor1.pri.v4.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/009/764/565/GCA_009764565.4
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/009/764/565/GCA_009764565.4
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/009/764/565/GCA_009764565.4
liftOver.GCA_015237465.2 liftOver/GCA_009764565.4ToGCA_015237465.2.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_009764565.4_rDerCor1.pri.v4.assembly.bb
type bigBed 6
html html/GCA_009764565.4_rDerCor1.pri.v4.assembly
searchIndex name
searchTrix ixIxx/GCA_009764565.4_rDerCor1.pri.v4.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/GCA_009764565.4_rDerCor1.pri.v4.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_009764565.4_rDerCor1.pri.v4.gc5Base.bw
html html/GCA_009764565.4_rDerCor1.pri.v4.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_009764565.4_rDerCor1.pri.v4.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.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_009764565.4_rDerCor1.pri.v4.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.rmsk.bb
xrefDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCA_009764565.4_rDerCor1.pri.v4.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.simpleRepeat.bb
html html/GCA_009764565.4_rDerCor1.pri.v4.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_009764565.4_rDerCor1.pri.v4.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_009764565.4_rDerCor1.pri.v4.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_009764565.4_rDerCor1.pri.v4.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.windowMasker.bb
html html/GCA_009764565.4_rDerCor1.pri.v4.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_009764565.4_rDerCor1.pri.v4.allGaps.bb
html html/GCA_009764565.4_rDerCor1.pri.v4.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.augustus.bb
html html/GCA_009764565.4_rDerCor1.pri.v4.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_009764565.4_rDerCor1.pri.v4.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_009764565.4_rDerCor1.pri.v4.xenoRefGene.ix
html html/GCA_009764565.4_rDerCor1.pri.v4.xenoRefGene

##############################################################################
# GCA_015237465.2 - leatherback sea turtle - Dermochelys coriacea - taxId: 27794
##############################################################################
track chainNetGCA_015237465.2
compositeTrack on
shortLabel leatherback sea turtle Chain/Net
longLabel leatherback sea turtle (2021-08-25), 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=+
otherDb GCA_015237465.2
html html/GCA_009764565.4_rDerCor1.pri.v4.chainNet

    track chainNetGCA_015237465.2Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetGCA_015237465.2
    spectrum on

        track chainGCA_015237465.2
        parent chainNetGCA_015237465.2Viewchain
        subGroups view=chain
        shortLabel leatherback sea turtle Chain
        longLabel leatherback sea turtle (2021-08-25) Chained Alignments
        type bigChain GCA_015237465.2
        bigDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.chainGCA_015237465.2.bb
        linkDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.chainGCA_015237465.2Link.bb
        priority 1

        track chainSynGCA_015237465.2
        parent chainNetGCA_015237465.2Viewchain
        subGroups view=chain
        shortLabel leatherback sea turtle synChain
        longLabel leatherback sea turtle (2021-08-25) Syntenic Chained Alignments
        type bigChain GCA_015237465.2
        bigDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.chainSynGCA_015237465.2.bb
        linkDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.chainSynGCA_015237465.2Link.bb
        priority 2

        track chainRBestGCA_015237465.2
        parent chainNetGCA_015237465.2Viewchain
        subGroups view=chain
        shortLabel leatherback sea turtle rbChain
        longLabel leatherback sea turtle (2021-08-25) Reciprocal Best Chained Alignments
        type bigChain GCA_015237465.2
        bigDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.chainRBestGCA_015237465.2.bb
        linkDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.chainRBestGCA_015237465.2Link.bb
        priority 3

        track chainLiftOverGCA_015237465.2
        parent chainNetGCA_015237465.2Viewchain
        subGroups view=chain
        shortLabel leatherback sea turtle loChain
        longLabel leatherback sea turtle (2021-08-25) Lift Over Chained Alignments
        type bigChain GCA_015237465.2
        bigDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.chainLiftOverGCA_015237465.2.bb
        linkDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.chainLiftOverGCA_015237465.2Link.bb
        priority 4

    track mafNetGCA_015237465.2Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetGCA_015237465.2

        track netGCA_015237465.2
        parent mafNetGCA_015237465.2Viewnet
        subGroups view=net
        shortLabel leatherback sea turtle net
        longLabel leatherback sea turtle (2021-08-25) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.GCA_015237465.2.net.bb
        summary bbi/GCA_009764565.4_rDerCor1.pri.v4.GCA_015237465.2.net.summary.bb
        speciesOrder GCA_015237465.2
        priority 5

        track synNetGCA_015237465.2
        parent mafNetGCA_015237465.2Viewnet
        subGroups view=net
        shortLabel leatherback sea turtle synNet
        longLabel leatherback sea turtle (2021-08-25) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.GCA_015237465.2.synNet.bb
        summary bbi/GCA_009764565.4_rDerCor1.pri.v4.GCA_015237465.2.synNet.summary.bb
        speciesOrder GCA_015237465.2
        priority 6

        track rbestNetGCA_015237465.2
        parent mafNetGCA_015237465.2Viewnet
        subGroups view=net
        shortLabel leatherback sea turtle rbestNet
        longLabel leatherback sea turtle (2021-08-25) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_009764565.4_rDerCor1.pri.v4.GCA_015237465.2.rbestNet.bb
        summary bbi/GCA_009764565.4_rDerCor1.pri.v4.GCA_015237465.2.rbestNet.summary.bb
        speciesOrder GCA_015237465.2
        priority 7