hub GCF_004115215.2 genome assembly
shortLabel platypus (Pmale09 v4 2020)
longLabel platypus (Pmale09 v4 2020)/Ornithorhynchus anatinus/GCF_004115215.2_mOrnAna1.pri.v4 genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCF_004115215.2_mOrnAna1.pri.v4.description.html

genome GCF_004115215.2
taxId 9258
groups groups.txt
description platypus (Pmale09 v4 2020)
twoBitPath GCF_004115215.2.2bit
twoBitBptUrl GCF_004115215.2.2bit.bpt
chromSizes GCF_004115215.2.chrom.sizes.txt
chromAliasBb GCF_004115215.2.chromAlias.bb
chromAuthority ucsc
organism mOrnAna1.pri.v4 Nov. 2020
defaultPos NC_041728.1:62168672-62178672
scientificName Ornithorhynchus anatinus
htmlPath html/GCF_004115215.2_mOrnAna1.pri.v4.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/004/115/215/GCF_004115215.2
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/004/115/215/GCF_004115215.2
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/004/115/215/GCF_004115215.2
liftOver.GCA_002966995.1 liftOver/GCF_004115215.2ToGCA_002966995.1.over.chain.gz
liftOver.hg38 liftOver/GCF_004115215.2ToHg38.over.chain.gz

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/GCF_004115215.2_mOrnAna1.pri.v4.assembly.bb
type bigBed 6
html html/GCF_004115215.2_mOrnAna1.pri.v4.assembly
searchIndex name
searchTrix ixIxx/GCF_004115215.2_mOrnAna1.pri.v4.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_004115215.2_mOrnAna1.pri.v4.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/GCF_004115215.2_mOrnAna1.pri.v4.gc5Base.bw
html html/GCF_004115215.2_mOrnAna1.pri.v4.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_004115215.2_mOrnAna1.pri.v4.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.rmsk.bb
xrefDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCF_004115215.2_mOrnAna1.pri.v4.repeatMasker

track repeatModeler
shortLabel RepeatModeler
longLabel RepeatModeler Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.rModel.bb
xrefDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.rModel.align.bb
maxWindowToDraw 5000000
html html/GCF_004115215.2_mOrnAna1.pri.v4.repeatModeler

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.simpleRepeat.bb
html html/GCF_004115215.2_mOrnAna1.pri.v4.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 Ornithorhynchus anatinus Annotation Release 105 (2021-03-08)
html html/GCF_004115215.2_mOrnAna1.pri.v4.refSeqComposite
priority 2

        track ncbiRefSeq
        parent refSeqComposite on
        color 12,12,120
        altColor 120,12,12
        shortLabel RefSeq All
        type bigGenePred
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_004115215.2_mOrnAna1.pri.v4.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.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
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_004115215.2_mOrnAna1.pri.v4.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.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
        labelFields name,geneName,geneName2
        defaultLabelFields geneName2
        searchIndex name
        searchTrix ixIxx/GCF_004115215.2_mOrnAna1.pri.v4.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.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_004115215.2_mOrnAna1.pri.v4.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.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_004115215.2_mOrnAna1.pri.v4.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 pack
type bigBed 4 +
html html/GCF_004115215.2_mOrnAna1.pri.v4.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_004115215.2_mOrnAna1.pri.v4.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_004115215.2_mOrnAna1.pri.v4.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.windowMasker.bb
html html/GCF_004115215.2_mOrnAna1.pri.v4.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/GCF_004115215.2_mOrnAna1.pri.v4.allGaps.bb
html html/GCF_004115215.2_mOrnAna1.pri.v4.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.augustus.bb
html html/GCF_004115215.2_mOrnAna1.pri.v4.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_004115215.2_mOrnAna1.pri.v4.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_004115215.2_mOrnAna1.pri.v4.xenoRefGene.ix
html html/GCF_004115215.2_mOrnAna1.pri.v4.xenoRefGene

track GCF_004115215.2_mOrnAna1.pri.v4ChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain and Net alignments to target sequence: GCF_004115215.2_mOrnAna1.pri.v4
subGroup1 view Views chain=Chains net=Nets
subGroup2 species Species s000=GCA_002966995.1 s001=hg38
subGroup3 clade Clade c00=human
dragAndDrop subTracks
visibility hide
group compGeno
color 0,0,0
altColor 255,255,0
type bed 3
chainLinearGap loose
chainMinScore 5000
dimensions dimensionX=clade dimensionY=species
sortOrder species=+ view=+ clade=+
configurable on
html html/GCF_004115215.2_mOrnAna1.pri.v4.chainNet

    track GCF_004115215.2_mOrnAna1.pri.v4ChainNetViewchain
    shortLabel  Chains
    view chain
    visibility pack
    subTrack GCF_004115215.2_mOrnAna1.pri.v4ChainNet
    spectrum on

        track chainGCA_002966995.1
        subTrack GCF_004115215.2_mOrnAna1.pri.v4ChainNetViewchain off
        subGroups view=chain species=s000 clade=c00
        shortLabel GCA_002966995.1 Chain
        longLabel GCA_002966995.1_ASM296699v1 (2018-03-02) Chained Alignments
        type bigChain GCA_002966995.1
        bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.chainGCA_002966995.1.bb
        linkDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.chainGCA_002966995.1Link.bb
        otherDb GCA_002966995.1
        html html/GCF_004115215.2_mOrnAna1.pri.v4.chainNet
        priority 1

        track chainSynGCA_002966995.1
        subTrack GCF_004115215.2_mOrnAna1.pri.v4ChainNetViewchain off
        subGroups view=chain species=s000 clade=c00
        shortLabel GCA_002966995.1 synChain
        longLabel GCA_002966995.1_ASM296699v1 (2018-03-02) Syntenic Chained Alignments
        type bigChain GCA_002966995.1
        bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.chainSynGCA_002966995.1.bb
        linkDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.chainSynGCA_002966995.1Link.bb
        otherDb GCA_002966995.1
        html html/GCF_004115215.2_mOrnAna1.pri.v4.chainNet
        priority 2

        track chainHg38
        subTrack GCF_004115215.2_mOrnAna1.pri.v4ChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel hg38 Chain
        longLabel hg38 (Dec. 2013) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.chainHg38.bb
        linkDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.chainHg38Link.bb
        otherDb hg38
        html html/GCF_004115215.2_mOrnAna1.pri.v4.chainNet
        priority 3

        track chainSynHg38
        subTrack GCF_004115215.2_mOrnAna1.pri.v4ChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel hg38 synChain
        longLabel hg38 (Dec. 2013) Syntenic Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.chainSynHg38.bb
        linkDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.chainSynHg38Link.bb
        otherDb hg38
        html html/GCF_004115215.2_mOrnAna1.pri.v4.chainNet
        priority 4

        track chainRBestHg38
        subTrack GCF_004115215.2_mOrnAna1.pri.v4ChainNetViewchain off
        subGroups view=chain species=s001 clade=c00
        shortLabel hg38 rbChain
        longLabel hg38 (Dec. 2013) Reciprocal Best Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.chainRBestHg38.bb
        linkDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.chainRBestHg38Link.bb
        otherDb hg38
        html html/GCF_004115215.2_mOrnAna1.pri.v4.chainNet
        priority 5

    track GCF_004115215.2_mOrnAna1.pri.v4MafNetViewnet
    shortLabel Nets
    view net
    visibility dense
    subTrack GCF_004115215.2_mOrnAna1.pri.v4ChainNet

        track synNetGCA_002966995.1
        parent GCF_004115215.2_mOrnAna1.pri.v4MafNetViewnet
        subGroups view=net species=s000 clade=c00
        shortLabel GCA_002966995.1 synNet
        longLabel GCA_002966995.1 (some date) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.GCA_002966995.1.synNet.bb
        summary bbi/GCF_004115215.2_mOrnAna1.pri.v4.GCA_002966995.1.synNet.summary.bb
        speciesOrder GCA_002966995.1
        html html/GCF_004115215.2_mOrnAna1.pri.v4.chainNet
        priority 1

        track synNetHg38
        parent GCF_004115215.2_mOrnAna1.pri.v4MafNetViewnet
        subGroups view=net species=s001 clade=c00
        shortLabel hg38 synNet
        longLabel hg38 (some date) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.hg38.synNet.bb
        summary bbi/GCF_004115215.2_mOrnAna1.pri.v4.hg38.synNet.summary.bb
        speciesOrder hg38
        html html/GCF_004115215.2_mOrnAna1.pri.v4.chainNet
        priority 2

        track rbestNetHg38
        parent GCF_004115215.2_mOrnAna1.pri.v4MafNetViewnet
        subGroups view=net species=s001 clade=c00
        shortLabel hg38 rbestNet
        longLabel hg38 (some date) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_004115215.2_mOrnAna1.pri.v4.hg38.rbestNet.bb
        summary bbi/GCF_004115215.2_mOrnAna1.pri.v4.hg38.rbestNet.summary.bb
        speciesOrder hg38
        html html/GCF_004115215.2_mOrnAna1.pri.v4.chainNet
        priority 3