hub GCA_052040795.1 genome assembly
shortLabel zebrafish (M-AB 2025)
longLabel zebrafish (M-AB 2025)/Danio rerio/GCA_052040795.1_GRCz12ab genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCA_052040795.1_GRCz12ab.description.html

genome GCA_052040795.1
taxId 7955
groups groups.txt
description zebrafish (M-AB 2025)
twoBitPath GCA_052040795.1.2bit
twoBitBptUrl GCA_052040795.1.2bit.bpt
chromSizes GCA_052040795.1.chrom.sizes.txt
chromAliasBb GCA_052040795.1.chromAlias.bb
chromAuthority ucsc
organism GRCz12ab Aug. 2025
defaultPos CM124813.1:27085069-27095069
scientificName Danio rerio
htmlPath html/GCA_052040795.1_GRCz12ab.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/052/040/795/GCA_052040795.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/052/040/795/GCA_052040795.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/052/040/795/GCA_052040795.1
liftOver.danRer11 liftOver/GCA_052040795.1ToDanRer11.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/GCA_052040795.1_GRCz12ab.assembly.bb
type bigBed 6
html html/GCA_052040795.1_GRCz12ab.assembly
searchIndex name
searchTrix ixIxx/GCA_052040795.1_GRCz12ab.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_052040795.1_GRCz12ab.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_052040795.1_GRCz12ab.gc5Base.bw
html html/GCA_052040795.1_GRCz12ab.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_052040795.1_GRCz12ab.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_052040795.1_GRCz12ab.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_052040795.1_GRCz12ab.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_052040795.1_GRCz12ab.rmsk.bb
xrefDataUrl bbi/GCA_052040795.1_GRCz12ab.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCA_052040795.1_GRCz12ab.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_052040795.1_GRCz12ab.simpleRepeat.bb
html html/GCA_052040795.1_GRCz12ab.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_052040795.1_GRCz12ab.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_052040795.1_GRCz12ab.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_052040795.1_GRCz12ab.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_052040795.1_GRCz12ab.windowMasker.bb
html html/GCA_052040795.1_GRCz12ab.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_052040795.1_GRCz12ab.allGaps.bb
html html/GCA_052040795.1_GRCz12ab.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_052040795.1_GRCz12ab.augustus.bb
html html/GCA_052040795.1_GRCz12ab.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_052040795.1_GRCz12ab.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_052040795.1_GRCz12ab.xenoRefGene.ix
html html/GCA_052040795.1_GRCz12ab.xenoRefGene

##############################################################################
# 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/GCA_052040795.1_GRCz12ab.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/GCA_052040795.1_GRCz12ab.chainDanRer11.bb
        linkDataUrl bbi/GCA_052040795.1_GRCz12ab.chainDanRer11Link.bb
        priority 1

        track chainLiftOverDanRer11
        parent chainNetDanRer11Viewchain
        subGroups view=chain
        shortLabel Zebrafish loChain
        longLabel Zebrafish (May 2017 (GRCz11/danRer11)) Lift Over Chained Alignments
        type bigChain danRer11
        bigDataUrl bbi/GCA_052040795.1_GRCz12ab.chainLiftOverDanRer11.bb
        linkDataUrl bbi/GCA_052040795.1_GRCz12ab.chainLiftOverDanRer11Link.bb
        priority 2