hub GCA_007399415.1 genome assembly
shortLabel Goodes thornscrub tortoise (Sinaloan lineage primary hap 2019)
longLabel Goodes thornscrub tortoise (Sinaloan lineage primary hap 2019)/Gopherus evgoodei/GCA_007399415.1_rGopEvg1_v1.p genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCA_007399415.1_rGopEvg1_v1.p.description.html

genome GCA_007399415.1
taxId 1825980
groups groups.txt
description Goodes thornscrub tortoise (Sinaloan lineage primary hap 2019)
twoBitPath GCA_007399415.1.2bit
twoBitBptUrl GCA_007399415.1.2bit.bpt
chromSizes GCA_007399415.1.chrom.sizes.txt
chromAliasBb GCA_007399415.1.chromAlias.bb
organism rGopEvg1_v1.p Jul. 2019
defaultPos chr1:123445048-123455048
scientificName Gopherus evgoodei
htmlPath html/GCA_007399415.1_rGopEvg1_v1.p.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/007/399/415/GCA_007399415.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/007/399/415/GCA_007399415.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/007/399/415/GCA_007399415.1

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_007399415.1_rGopEvg1_v1.p.assembly.bb
type bigBed 6
html html/GCA_007399415.1_rGopEvg1_v1.p.assembly
searchIndex name
searchTrix ixIxx/GCA_007399415.1_rGopEvg1_v1.p.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_007399415.1_rGopEvg1_v1.p.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_007399415.1_rGopEvg1_v1.p.gc5Base.bw
html html/GCA_007399415.1_rGopEvg1_v1.p.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_007399415.1_rGopEvg1_v1.p.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCA_007399415.1_rGopEvg1_v1.p.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_007399415.1_rGopEvg1_v1.p.repeatMasker

    track repeatMaskerSINE
    parent repeatMasker
    shortLabel SINE
    longLabel SINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 1
    bigDataUrl bbi/GCA_007399415.1_rGopEvg1_v1.p.rmsk.SINE.bb

    track repeatMaskerLINE
    parent repeatMasker
    shortLabel LINE
    longLabel LINE Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 2
    bigDataUrl bbi/GCA_007399415.1_rGopEvg1_v1.p.rmsk.LINE.bb

    track repeatMaskerLTR
    parent repeatMasker
    shortLabel LTR
    longLabel LTR Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 3
    bigDataUrl bbi/GCA_007399415.1_rGopEvg1_v1.p.rmsk.LTR.bb

    track repeatMaskerDNA
    parent repeatMasker
    shortLabel DNA
    longLabel DNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 4
    bigDataUrl bbi/GCA_007399415.1_rGopEvg1_v1.p.rmsk.DNA.bb

    track repeatMaskerSimple
    parent repeatMasker
    shortLabel Simple
    longLabel Simple Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 5
    bigDataUrl bbi/GCA_007399415.1_rGopEvg1_v1.p.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_007399415.1_rGopEvg1_v1.p.rmsk.Low_complexity.bb

    track repeatMaskerRNA
    parent repeatMasker
    shortLabel RNA
    longLabel RNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 8
    bigDataUrl bbi/GCA_007399415.1_rGopEvg1_v1.p.rmsk.RNA.bb

    track repeatMaskerOther
    parent repeatMasker
    shortLabel Other
    longLabel Other Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 9
    bigDataUrl bbi/GCA_007399415.1_rGopEvg1_v1.p.rmsk.Other.bb

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_007399415.1_rGopEvg1_v1.p.simpleRepeat.bb
html html/GCA_007399415.1_rGopEvg1_v1.p.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_007399415.1_rGopEvg1_v1.p.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_007399415.1_rGopEvg1_v1.p.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_007399415.1_rGopEvg1_v1.p.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_007399415.1_rGopEvg1_v1.p.windowMasker.bb
html html/GCA_007399415.1_rGopEvg1_v1.p.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_007399415.1_rGopEvg1_v1.p.allGaps.bb
html html/GCA_007399415.1_rGopEvg1_v1.p.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_007399415.1_rGopEvg1_v1.p.augustus.bb
html html/GCA_007399415.1_rGopEvg1_v1.p.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_007399415.1_rGopEvg1_v1.p.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_007399415.1_rGopEvg1_v1.p.xenoRefGene.ix
html html/GCA_007399415.1_rGopEvg1_v1.p.xenoRefGene

track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes version 103/Feb. 2021
group genes
priority 40
visibility pack
color 150,0,0
itemRgb on
type bigBed 12 .
bigDataUrl bbi/GCA_007399415.1_rGopEvg1_v1.p.ensGene.bb
searchIndex name
baseColorUseCds given
baseColorDefault genomicCodons
html html/GCA_007399415.1_rGopEvg1_v1.p.ensGene