hub GCF_042767895.1 genome assembly
shortLabel Pacific white shrimp (JL-2024 2024)
longLabel Pacific white shrimp (JL-2024 2024)/Penaeus vannamei/GCF_042767895.1_ASM4276789v1 genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCF_042767895.1_ASM4276789v1.description.html
genome GCF_042767895.1
taxId 6689
groups groups.txt
description Pacific white shrimp (JL-2024 2024)
twoBitPath GCF_042767895.1.2bit
twoBitBptUrl GCF_042767895.1.2bit.bpt
chromSizes GCF_042767895.1.chrom.sizes.txt
chromAliasBb GCF_042767895.1.chromAlias.bb
chromAuthority ucsc
organism ASM4276789v1 Oct. 2024
defaultPos NC_091549.1:18900061-18910061
scientificName Penaeus vannamei
htmlPath html/GCF_042767895.1_ASM4276789v1.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/042/767/895/GCF_042767895.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/042/767/895/GCF_042767895.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/042/767/895/GCF_042767895.1
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/GCF_042767895.1_ASM4276789v1.assembly.bb
type bigBed 6
html html/GCF_042767895.1_ASM4276789v1.assembly
searchIndex name
searchTrix ixIxx/GCF_042767895.1_ASM4276789v1.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/GCF_042767895.1_ASM4276789v1.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/GCF_042767895.1_ASM4276789v1.gc5Base.bw
html html/GCF_042767895.1_ASM4276789v1.gc5Base
track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_042767895.1_ASM4276789v1.tanDups
track gapOverlap
parent tanDups on
shortLabel Gap Overlaps
longLabel Paired exactly identical sequence on each side of a gap
bigDataUrl bbi/GCF_042767895.1_ASM4276789v1.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/GCF_042767895.1_ASM4276789v1.tandemDups.bb
type bigBed 12
track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCF_042767895.1_ASM4276789v1.rmsk.bb
xrefDataUrl bbi/GCF_042767895.1_ASM4276789v1.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCF_042767895.1_ASM4276789v1.repeatMasker
track repeatModeler
shortLabel RepeatModeler
longLabel RepeatModeler Repetitive Elements
type bigRmsk 9 +
visibility hide
group varRep
bigDataUrl bbi/GCF_042767895.1_ASM4276789v1.rModel.bb
xrefDataUrl bbi/GCF_042767895.1_ASM4276789v1.rModel.align.bb
maxWindowToDraw 5000000
html html/GCF_042767895.1_ASM4276789v1.repeatModeler
track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_042767895.1_ASM4276789v1.simpleRepeat.bb
html html/GCF_042767895.1_ASM4276789v1.simpleRepeat
track refSeqComposite
compositeTrack on
shortLabel NCBI RefSeq
longLabel RefSeq gene predictions from NCBI
group genes
visibility pack
type bigBed
dragAndDrop subTracks
allButtonPair on
dataVersion NCBI RefSeq GCF_042767895.1-RS_2024_11 (2024-12-03)
html html/GCF_042767895.1_ASM4276789v1.refSeqComposite
priority 2
track ncbiRefSeq
parent refSeqComposite on
color 12,12,120
shortLabel RefSeq All
type bigGenePred
urls name2="https://www.ncbi.nlm.nih.gov/gene/$D/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$"
labelFields name,geneName,geneName2
defaultLabelFields geneName2
searchIndex name
searchTrix ixIxx/GCF_042767895.1_ASM4276789v1.ncbiRefSeq.ix
bigDataUrl bbi/GCF_042767895.1_ASM4276789v1.ncbiRefSeq.bb
longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*)
idXref ncbiRefSeqLink mrnaAcc name
baseColorUseCds given
baseColorDefault genomicCodons
priority 1
track ncbiRefSeqCurated
color 12,12,120
parent refSeqComposite on
shortLabel RefSeq Curated
longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*)
type bigGenePred
urls name2="https://www.ncbi.nlm.nih.gov/gene/$D/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$"
labelFields name,geneName,geneName2
defaultLabelFields geneName2
searchIndex name
searchTrix ixIxx/GCF_042767895.1_ASM4276789v1.ncbiRefSeqCurated.ix
idXref ncbiRefSeqLink mrnaAcc name
bigDataUrl bbi/GCF_042767895.1_ASM4276789v1.ncbiRefSeqCurated.bb
baseColorUseCds given
baseColorDefault genomicCodons
priority 2
track ncbiRefSeqPredicted
color 12,12,120
parent refSeqComposite on
shortLabel RefSeq Predicted
longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*)
type bigGenePred
urls name2="https://www.ncbi.nlm.nih.gov/gene/$D/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$"
labelFields name,geneName,geneName2
defaultLabelFields geneName2
searchIndex name
searchTrix ixIxx/GCF_042767895.1_ASM4276789v1.ncbiRefSeqPredicted.ix
idXref ncbiRefSeqLink mrnaAcc name
bigDataUrl bbi/GCF_042767895.1_ASM4276789v1.ncbiRefSeqPredicted.bb
baseColorUseCds given
baseColorDefault genomicCodons
priority 3
track ncbiRefSeqOther
color 32,32,32
parent refSeqComposite on
shortLabel RefSeq Other
longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*)
priority 4
searchIndex name
searchTrix ixIxx/GCF_042767895.1_ASM4276789v1.ncbiRefSeqOther.ix
bigDataUrl bbi/GCF_042767895.1_ASM4276789v1.ncbiRefSeqOther.bb
type bigBed 12 +
labelFields name
skipEmptyFields on
urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/$$" HGNC="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="http://www.informatics.jax.org/marker/$$"
track ncbiRefSeqPsl
priority 5
parent refSeqComposite off
shortLabel RefSeq Alignments
longLabel RefSeq Alignments of RNAs
type bigPsl
searchIndex name
bigDataUrl bbi/GCF_042767895.1_ASM4276789v1.bigPsl.bb
indelDoubleInsert on
indelQueryInsert on
showDiffBasesAllScales .
showDiffBasesMaxZoom 10000.0
showCdsMaxZoom 10000.0
showCdsAllScales .
baseColorDefault diffCodons
pslSequence no
baseColorUseSequence lfExtra
baseColorUseCds table given
color 0,0,0
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/GCF_042767895.1_ASM4276789v1.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/GCF_042767895.1_ASM4276789v1.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/GCF_042767895.1_ASM4276789v1.cpgIslandExtUnmasked.bb
track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_042767895.1_ASM4276789v1.windowMasker.bb
html html/GCF_042767895.1_ASM4276789v1.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/GCF_042767895.1_ASM4276789v1.allGaps.bb
html html/GCF_042767895.1_ASM4276789v1.allGaps
track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_042767895.1_ASM4276789v1.augustus.bb
html html/GCF_042767895.1_ASM4276789v1.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/GCF_042767895.1_ASM4276789v1.xenoRefGene.bb
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
labelFields name,geneName,geneName2
defaultLabelFields geneName
searchIndex name
searchTrix ixIxx/GCF_042767895.1_ASM4276789v1.xenoRefGene.ix
html html/GCF_042767895.1_ASM4276789v1.xenoRefGene