hub GCA_002880775.3 genome assembly
shortLabel Sumatran orangutan (Susie 2018 genbank)
longLabel Sumatran orangutan (Susie 2018 genbank)/Pongo abelii/GCA_002880775.3_Susie_PABv2 genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCA_002880775.3_Susie_PABv2.description.html

genome GCA_002880775.3
taxId 9601
groups groups.txt
description Sumatran orangutan (Susie 2018 genbank)
twoBitPath GCA_002880775.3.2bit
twoBitBptUrl GCA_002880775.3.2bit.bpt
chromSizes GCA_002880775.3.chrom.sizes.txt
chromAliasBb GCA_002880775.3.chromAlias.bb
chromAuthority ucsc
organism Susie_PABv2 Jan. 2018
defaultPos CM009262.2:75971234-75981234
scientificName Pongo abelii
htmlPath html/GCA_002880775.3_Susie_PABv2.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/002/880/775/GCA_002880775.3
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/002/880/775/GCA_002880775.3
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/002/880/775/GCA_002880775.3

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_002880775.3_Susie_PABv2.assembly.bb
type bigBed 6
html html/GCA_002880775.3_Susie_PABv2.assembly
searchIndex name
searchTrix ixIxx/GCA_002880775.3_Susie_PABv2.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_002880775.3_Susie_PABv2.gap.bb
type bigBed 4
group map
html html/GCA_002880775.3_Susie_PABv2.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_002880775.3_Susie_PABv2.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_002880775.3_Susie_PABv2.gc5Base.bw
html html/GCA_002880775.3_Susie_PABv2.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_002880775.3_Susie_PABv2.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCA_002880775.3_Susie_PABv2.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_002880775.3_Susie_PABv2.repeatMasker

    track repeatMaskerSINE
    parent repeatMasker
    shortLabel SINE
    longLabel SINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 1
    bigDataUrl bbi/GCA_002880775.3_Susie_PABv2.rmsk.SINE.bb

    track repeatMaskerLINE
    parent repeatMasker
    shortLabel LINE
    longLabel LINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 2
    bigDataUrl bbi/GCA_002880775.3_Susie_PABv2.rmsk.LINE.bb

    track repeatMaskerLTR
    parent repeatMasker
    shortLabel LTR
    longLabel LTR Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 3
    bigDataUrl bbi/GCA_002880775.3_Susie_PABv2.rmsk.LTR.bb

    track repeatMaskerDNA
    parent repeatMasker
    shortLabel DNA
    longLabel DNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 4
    bigDataUrl bbi/GCA_002880775.3_Susie_PABv2.rmsk.DNA.bb

    track repeatMaskerSimple
    parent repeatMasker
    shortLabel Simple
    longLabel Simple Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 5
    bigDataUrl bbi/GCA_002880775.3_Susie_PABv2.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_002880775.3_Susie_PABv2.rmsk.Low_complexity.bb

    track repeatMaskerSatellite
    parent repeatMasker
    shortLabel Satellite
    longLabel Satellite Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 7
    bigDataUrl bbi/GCA_002880775.3_Susie_PABv2.rmsk.Satellite.bb

    track repeatMaskerRNA
    parent repeatMasker
    shortLabel RNA
    longLabel RNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 8
    bigDataUrl bbi/GCA_002880775.3_Susie_PABv2.rmsk.RNA.bb

    track repeatMaskerOther
    parent repeatMasker
    shortLabel Other
    longLabel Other Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 9
    bigDataUrl bbi/GCA_002880775.3_Susie_PABv2.rmsk.Other.bb

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_002880775.3_Susie_PABv2.simpleRepeat.bb
html html/GCA_002880775.3_Susie_PABv2.simpleRepeat

track ncbiGene
longLabel Gene models submitted to NCBI
shortLabel Gene models
visibility pack
color 0,80,150
altColor 150,80,0
colorByStrand 0,80,150 150,80,0
bigDataUrl bbi/GCA_002880775.3_Susie_PABv2.ncbiGene.bb
type bigGenePred
html html/GCA_002880775.3_Susie_PABv2.ncbiGene
searchIndex name
searchTrix ixIxx/GCA_002880775.3_Susie_PABv2.ncbiGene.ix
url https://www.ncbi.nlm.nih.gov/gene/?term=$$
urlLabel Entrez gene:
labelFields geneName,geneName2
defaultLabelFields geneName2
group genes

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_002880775.3_Susie_PABv2.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_002880775.3_Susie_PABv2.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_002880775.3_Susie_PABv2.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_002880775.3_Susie_PABv2.windowMasker.bb
html html/GCA_002880775.3_Susie_PABv2.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_002880775.3_Susie_PABv2.allGaps.bb
html html/GCA_002880775.3_Susie_PABv2.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_002880775.3_Susie_PABv2.augustus.bb
html html/GCA_002880775.3_Susie_PABv2.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_002880775.3_Susie_PABv2.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_002880775.3_Susie_PABv2.xenoRefGene.ix
html html/GCA_002880775.3_Susie_PABv2.xenoRefGene

track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes 2021_01
group genes
priority 40
visibility pack
color 150,0,0
itemRgb on
type bigGenePred
bigDataUrl bbi/GCA_002880775.3_Susie_PABv2.ensGene.bb
searchTrix ixIxx/GCA_002880775.3_Susie_PABv2.ensGene.ix
searchIndex name
labelFields name,name2
defaultLabelFields name2
baseColorUseCds given
baseColorDefault genomicCodons
labelSeperator " "
html html/GCA_002880775.3_Susie_PABv2.ensGene