hub GCA_036323735.1 genome assembly
shortLabel Norway rat (BN/NHsdMcwi 2024 genbank)
longLabel Norway rat (BN/NHsdMcwi 2024 genbank)/Rattus norvegicus/GCA_036323735.1_GRCr8 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCA_036323735.1_GRCr8.description.html

genome GCA_036323735.1
taxId 10116
groups groups.txt
description Norway rat (BN/NHsdMcwi 2024 genbank)
twoBitPath GCA_036323735.1.2bit
twoBitBptUrl GCA_036323735.1.2bit.bpt
chromSizes GCA_036323735.1.chrom.sizes.txt
chromAliasBb GCA_036323735.1.chromAlias.bb
chromAuthority ucsc
organism GRCr8 Jan. 2024
defaultPos CM070391.1:90172726-90182726
scientificName Rattus norvegicus
htmlPath html/GCA_036323735.1_GRCr8.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/036/323/735/GCA_036323735.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/036/323/735/GCA_036323735.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/036/323/735/GCA_036323735.1
liftOver.GCF_001704415.2 liftOver/GCA_036323735.1ToGCF_001704415.2.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_036323735.1_GRCr8.assembly.bb
type bigBed 6
html html/GCA_036323735.1_GRCr8.assembly
searchIndex name
searchTrix ixIxx/GCA_036323735.1_GRCr8.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_036323735.1_GRCr8.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_036323735.1_GRCr8.gc5Base.bw
html html/GCA_036323735.1_GRCr8.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_036323735.1_GRCr8.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_036323735.1_GRCr8.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_036323735.1_GRCr8.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_036323735.1_GRCr8.rmsk.bb
xrefDataUrl bbi/GCA_036323735.1_GRCr8.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCA_036323735.1_GRCr8.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_036323735.1_GRCr8.simpleRepeat.bb
html html/GCA_036323735.1_GRCr8.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_036323735.1-RS_2024_02 (2024-02-24)
html html/GCA_036323735.1_GRCr8.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 name2,geneName,geneName2
        defaultLabelFields name2
        searchIndex name
        searchTrix ixIxx/GCA_036323735.1_GRCr8.ncbiRefSeq.ix
        bigDataUrl bbi/GCA_036323735.1_GRCr8.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 name2,geneName,geneName2
        defaultLabelFields name2
        searchIndex name
        searchTrix ixIxx/GCA_036323735.1_GRCr8.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCA_036323735.1_GRCr8.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 name2,geneName,geneName2
        defaultLabelFields name2
        searchIndex name
        searchTrix ixIxx/GCA_036323735.1_GRCr8.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCA_036323735.1_GRCr8.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/GCA_036323735.1_GRCr8.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCA_036323735.1_GRCr8.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/GCA_036323735.1_GRCr8.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 ncbiRefSeqSelect
        parent refSeqComposite off
        priority 7
        type bigGenePred
        shortLabel RefSeq Select
        longLabel NCBI RefSeq/MANE Select: one representative transcript per protein-coding gene
        idXref ncbiRefSeqLink mrnaAcc name
        color 20,20,160
        labelFields name,geneName,geneName2
        searchIndex name
        searchTrix ixIxx/GCA_036323735.1_GRCr8.ncbiRefSeqSelectCurated.ix
        bigDataUrl bbi/GCA_036323735.1_GRCr8.ncbiRefSeqSelectCurated.bb
        baseColorUseCds given
        baseColorDefault genomicCodons

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_036323735.1_GRCr8.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_036323735.1_GRCr8.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_036323735.1_GRCr8.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_036323735.1_GRCr8.windowMasker.bb
html html/GCA_036323735.1_GRCr8.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_036323735.1_GRCr8.allGaps.bb
html html/GCA_036323735.1_GRCr8.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_036323735.1_GRCr8.augustus.bb
html html/GCA_036323735.1_GRCr8.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_036323735.1_GRCr8.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_036323735.1_GRCr8.xenoRefGene.ix
html html/GCA_036323735.1_GRCr8.xenoRefGene

##############################################################################
# GCF_001704415.2 - Norway rat - Rattus norvegicus - taxId: 10116
##############################################################################
track chainNetGCF_001704415.2
compositeTrack on
shortLabel Norway rat Chain/Net
longLabel Norway rat (2024-01-31), 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=+
otherDb GCF_001704415.2
html html/GCA_036323735.1_GRCr8.chainNet

    track chainNetGCF_001704415.2Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetGCF_001704415.2
    spectrum on

        track chainGCF_001704415.2
        parent chainNetGCF_001704415.2Viewchain
        subGroups view=chain
        shortLabel Norway rat Chain
        longLabel Norway rat (2024-01-31) Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCA_036323735.1_GRCr8.chainGCF_001704415.2.bb
        linkDataUrl bbi/GCA_036323735.1_GRCr8.chainGCF_001704415.2Link.bb
        priority 1

        track chainSynGCF_001704415.2
        parent chainNetGCF_001704415.2Viewchain
        subGroups view=chain
        shortLabel Norway rat synChain
        longLabel Norway rat (2024-01-31) Syntenic Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCA_036323735.1_GRCr8.chainSynGCF_001704415.2.bb
        linkDataUrl bbi/GCA_036323735.1_GRCr8.chainSynGCF_001704415.2Link.bb
        priority 2

        track chainRBestGCF_001704415.2
        parent chainNetGCF_001704415.2Viewchain
        subGroups view=chain
        shortLabel Norway rat rbChain
        longLabel Norway rat (2024-01-31) Reciprocal Best Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCA_036323735.1_GRCr8.chainRBestGCF_001704415.2.bb
        linkDataUrl bbi/GCA_036323735.1_GRCr8.chainRBestGCF_001704415.2Link.bb
        priority 3

        track chainLiftOverGCF_001704415.2
        parent chainNetGCF_001704415.2Viewchain
        subGroups view=chain
        shortLabel Norway rat loChain
        longLabel Norway rat (2024-01-31) Lift Over Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCA_036323735.1_GRCr8.chainLiftOverGCF_001704415.2.bb
        linkDataUrl bbi/GCA_036323735.1_GRCr8.chainLiftOverGCF_001704415.2Link.bb
        priority 4

    track mafNetGCF_001704415.2Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetGCF_001704415.2

        track netGCF_001704415.2
        parent mafNetGCF_001704415.2Viewnet
        subGroups view=net
        shortLabel Norway rat net
        longLabel Norway rat (2024-01-31) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_036323735.1_GRCr8.GCF_001704415.2.net.bb
        summary bbi/GCA_036323735.1_GRCr8.GCF_001704415.2.net.summary.bb
        speciesOrder GCF_001704415.2
        priority 5

        track synNetGCF_001704415.2
        parent mafNetGCF_001704415.2Viewnet
        subGroups view=net
        shortLabel Norway rat synNet
        longLabel Norway rat (2024-01-31) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_036323735.1_GRCr8.GCF_001704415.2.synNet.bb
        summary bbi/GCA_036323735.1_GRCr8.GCF_001704415.2.synNet.summary.bb
        speciesOrder GCF_001704415.2
        priority 6

        track rbestNetGCF_001704415.2
        parent mafNetGCF_001704415.2Viewnet
        subGroups view=net
        shortLabel Norway rat rbestNet
        longLabel Norway rat (2024-01-31) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_036323735.1_GRCr8.GCF_001704415.2.rbestNet.bb
        summary bbi/GCA_036323735.1_GRCr8.GCF_001704415.2.rbestNet.summary.bb
        speciesOrder GCF_001704415.2
        priority 7


track evaSnp8
shortLabel EVA SNP Release 8
longLabel Short Genetic Variants from European Variant Archive Release 8
type bigBed 9 +
visibility dense
group varRep
itemRgb on
bigDataUrl contrib/evaSnp8/evaSnp8.bb
url https://www.ebi.ac.uk/eva/?variant&accessionID=$$
searchIndex name
mouseOver <b>Ref/Alt allele(s)</b>: $ref>$alt<br> <b>Var type</b>: $ucscClass<br> <b>AA change</b>: $aaChange
filterValues.varClass SNV|SNV,deletion|Deletion,indel|Indel,insertion|Insertion,MNV|MNV,sequence_alteration|Sequence alteration
filterLabel.varClass Variant class from EVA SO term
filterLabel.ucscClass Functional effect per UCSC Variant Annotation
filterValues.ucscClass downstream_gene_variant|Downstream gene variant,upstream_gene_variant|Upstream gene variant,intron_variant|Intron variant,NMD_transcript_variant|Nonsense-mediated mRNA decay (NMD) variant,5_prime_UTR_variant|5 prime UTR variant,3_prime_UTR_variant|3 prime UTR variant,missense_variant|Missense variant,synonymous_variant|Synonymous variant,non_coding_transcript_exon_variant|Non-coding transcript exon variant,no_sequence_alteration|No sequence alteration,splice_region_variant|Splice region variant,frameshift_variant|Frameshift variant,stop_gained|Stop gained,splice_acceptor_variant|Splice acceptor variant,inframe_deletion|Inframe deletion,inframe_insertion|Inframe insertion,splice_donor_variant|Splice donor variant,coding_sequence_variant|Coding sequence variant,initiator_codon_variant|Initiator codon variant,stop_lost|Stop lost,stop_retained_variant|Stop retained variant,intergenic_variant|Intergenic variant
filterType.ucscClass multipleListOnlyOr
filterValues.itemRgb 255,,0,,0|Protein-altering and splice variants,0,,128,,0|Synonymous variants,0,,0,,255|Non-coding transcripts or UTR variants,0,,0,,0|Intergenic and intronic variants
filterLabel.itemRgb General variant types by color grouping
maxWindowCoverage 250000
maxItems 1000000
html contrib/evaSnp8/description

track Tiberius
bigDataUrl contrib/tiberius/tiberius.bigGenePred.bb
shortLabel Tiberius genes
longLabel Tiberius ab initio gene prediction
type bigGenePred
visibility pack
color 0,102,204
noScoreFilter on
html contrib/tiberius/Tiberius.html
group genes
dataVersion Tiberius version 2025-01-07
baseColorDefault genomicCodons