hub GCF_905237065.1 genome assembly
shortLabel Atlantic salmon (refseq 2021)
longLabel Atlantic salmon (refseq 2021)/Salmo salar/GCF_905237065.1_Ssal_v3.1 genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCF_905237065.1_Ssal_v3.1.description.html

genome GCF_905237065.1
taxId 8030
groups groups.txt
description Atlantic salmon (refseq 2021)
twoBitPath GCF_905237065.1.2bit
twoBitBptUrl GCF_905237065.1.2bit.bpt
chromSizes GCF_905237065.1.chrom.sizes.txt
chromAliasBb GCF_905237065.1.chromAlias.bb
chromAuthority ucsc
organism Ssal_v3.1 Apr. 2021
defaultPos NC_059442.1:58166243-58176243
scientificName Salmo salar
htmlPath html/GCF_905237065.1_Ssal_v3.1.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/905/237/065/GCF_905237065.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/905/237/065/GCF_905237065.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/905/237/065/GCF_905237065.1
liftOver.danRer11 liftOver/GCF_905237065.1ToDanRer11.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/GCF_905237065.1_Ssal_v3.1.assembly.bb
type bigBed 6
html html/GCF_905237065.1_Ssal_v3.1.assembly
searchIndex name
searchTrix ixIxx/GCF_905237065.1_Ssal_v3.1.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 hide
color 0,0,0
bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.gap.bb
type bigBed 4
group map
html html/GCF_905237065.1_Ssal_v3.1.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.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_905237065.1_Ssal_v3.1.gc5Base.bw
html html/GCF_905237065.1_Ssal_v3.1.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_905237065.1_Ssal_v3.1.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.rmsk.bb
xrefDataUrl bbi/GCF_905237065.1_Ssal_v3.1.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCF_905237065.1_Ssal_v3.1.repeatMasker

track repeatModeler
shortLabel RepeatModeler
longLabel RepeatModeler Repetitive Elements
type bigRmsk 9 +
visibility hide
group varRep
bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.rModel.bb
xrefDataUrl bbi/GCF_905237065.1_Ssal_v3.1.rModel.align.bb
maxWindowToDraw 5000000
html html/GCF_905237065.1_Ssal_v3.1.repeatModeler

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.simpleRepeat.bb
html html/GCF_905237065.1_Ssal_v3.1.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_905237065.1-RS_2025_05 (2025-05-23)
html html/GCF_905237065.1_Ssal_v3.1.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/?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_905237065.1_Ssal_v3.1.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.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/?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_905237065.1_Ssal_v3.1.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.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/?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_905237065.1_Ssal_v3.1.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.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_905237065.1_Ssal_v3.1.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.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_905237065.1_Ssal_v3.1.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_905237065.1_Ssal_v3.1.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_905237065.1_Ssal_v3.1.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_905237065.1_Ssal_v3.1.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.windowMasker.bb
html html/GCF_905237065.1_Ssal_v3.1.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_905237065.1_Ssal_v3.1.allGaps.bb
html html/GCF_905237065.1_Ssal_v3.1.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.augustus.bb
html html/GCF_905237065.1_Ssal_v3.1.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_905237065.1_Ssal_v3.1.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_905237065.1_Ssal_v3.1.xenoRefGene.ix
html html/GCF_905237065.1_Ssal_v3.1.xenoRefGene

track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes 2021_07
group genes
priority 40
visibility pack
color 150,0,0
itemRgb on
type bigGenePred
bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.ensGene.bb
searchTrix ixIxx/GCF_905237065.1_Ssal_v3.1.ensGene.ix
searchIndex name
labelFields name,name2
defaultLabelFields name2
baseColorUseCds given
baseColorDefault genomicCodons
labelSeparator " "
html html/GCF_905237065.1_Ssal_v3.1.ensGene

##############################################################################
# danRer11 - Zebrafish - Danio rerio - taxId: 7955
##############################################################################
track chainNetDanRer11
compositeTrack on
shortLabel Zebrafish Chain/Net
longLabel Zebrafish (May 2017 (GRCz11/danRer11)), 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=+
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
chainMinScore 5000
chainLinearGap loose
matrixHeader A, C, G, T
otherDb danRer11
html html/GCF_905237065.1_Ssal_v3.1.chainNet

    track chainNetDanRer11Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetDanRer11
    spectrum on

        track chainDanRer11
        parent chainNetDanRer11Viewchain
        subGroups view=chain
        shortLabel Zebrafish Chain
        longLabel Zebrafish (May 2017 (GRCz11/danRer11)) Chained Alignments
        type bigChain danRer11
        bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.chainDanRer11.bb
        linkDataUrl bbi/GCF_905237065.1_Ssal_v3.1.chainDanRer11Link.bb
        priority 1

        track chainSynDanRer11
        parent chainNetDanRer11Viewchain
        subGroups view=chain
        shortLabel Zebrafish synChain
        longLabel Zebrafish (May 2017 (GRCz11/danRer11)) Syntenic Chained Alignments
        type bigChain danRer11
        bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.chainSynDanRer11.bb
        linkDataUrl bbi/GCF_905237065.1_Ssal_v3.1.chainSynDanRer11Link.bb
        priority 2

        track chainRBestDanRer11
        parent chainNetDanRer11Viewchain
        subGroups view=chain
        shortLabel Zebrafish rbChain
        longLabel Zebrafish (May 2017 (GRCz11/danRer11)) Reciprocal Best Chained Alignments
        type bigChain danRer11
        bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.chainRBestDanRer11.bb
        linkDataUrl bbi/GCF_905237065.1_Ssal_v3.1.chainRBestDanRer11Link.bb
        priority 3

    track mafNetDanRer11Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetDanRer11

        track netDanRer11
        parent mafNetDanRer11Viewnet
        subGroups view=net
        shortLabel Zebrafish net
        longLabel Zebrafish (May 2017 (GRCz11/danRer11)) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.danRer11.net.bb
        summary bbi/GCF_905237065.1_Ssal_v3.1.danRer11.net.summary.bb
        speciesOrder danRer11
        priority 4

        track synNetDanRer11
        parent mafNetDanRer11Viewnet
        subGroups view=net
        shortLabel Zebrafish synNet
        longLabel Zebrafish (May 2017 (GRCz11/danRer11)) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.danRer11.synNet.bb
        summary bbi/GCF_905237065.1_Ssal_v3.1.danRer11.synNet.summary.bb
        speciesOrder danRer11
        priority 5

        track rbestNetDanRer11
        parent mafNetDanRer11Viewnet
        subGroups view=net
        shortLabel Zebrafish rbestNet
        longLabel Zebrafish (May 2017 (GRCz11/danRer11)) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_905237065.1_Ssal_v3.1.danRer11.rbestNet.bb
        summary bbi/GCF_905237065.1_Ssal_v3.1.danRer11.rbestNet.summary.bb
        speciesOrder danRer11
        priority 6