hub GCF_002863925.1 genome assembly
shortLabel horse (Twilight 2018)
longLabel horse (Twilight 2018)/Equus caballus/GCF_002863925.1_EquCab3.0 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCF_002863925.1_EquCab3.0.description.html

genome GCF_002863925.1
taxId 9796
groups groups.txt
description horse (Twilight 2018)
twoBitPath GCF_002863925.1.2bit
twoBitBptUrl GCF_002863925.1.2bit.bpt
chromSizes GCF_002863925.1.chrom.sizes.txt
chromAliasBb GCF_002863925.1.chromAlias.bb
chromAuthority ucsc
organism EquCab3.0 Jan. 2018
defaultPos NC_009144.3:62753525-62763525
scientificName Equus caballus
htmlPath html/GCF_002863925.1_EquCab3.0.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/002/863/925/GCF_002863925.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/002/863/925/GCF_002863925.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/002/863/925/GCF_002863925.1
liftOver.GCF_001704415.2 liftOver/GCF_002863925.1ToGCF_001704415.2.over.chain.gz
liftOver.GCF_041296265.1 liftOver/GCF_002863925.1ToGCF_041296265.1.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_002863925.1_EquCab3.0.assembly.bb
type bigBed 6
html html/GCF_002863925.1_EquCab3.0.assembly
searchIndex name
searchTrix ixIxx/GCF_002863925.1_EquCab3.0.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_002863925.1_EquCab3.0.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_002863925.1_EquCab3.0.gc5Base.bw
html html/GCF_002863925.1_EquCab3.0.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_002863925.1_EquCab3.0.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCF_002863925.1_EquCab3.0.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_002863925.1_EquCab3.0.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCF_002863925.1_EquCab3.0.rmsk.bb
maxWindowToDraw 5000000
html html/GCF_002863925.1_EquCab3.0.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_002863925.1_EquCab3.0.simpleRepeat.bb
html html/GCF_002863925.1_EquCab3.0.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_002863925.1-RS_2024_08 (2024-08-07)
html html/GCF_002863925.1_EquCab3.0.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/GCF_002863925.1_EquCab3.0.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_002863925.1_EquCab3.0.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/GCF_002863925.1_EquCab3.0.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_002863925.1_EquCab3.0.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/GCF_002863925.1_EquCab3.0.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_002863925.1_EquCab3.0.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_002863925.1_EquCab3.0.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_002863925.1_EquCab3.0.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_002863925.1_EquCab3.0.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_002863925.1_EquCab3.0.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_002863925.1_EquCab3.0.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_002863925.1_EquCab3.0.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_002863925.1_EquCab3.0.windowMasker.bb
html html/GCF_002863925.1_EquCab3.0.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_002863925.1_EquCab3.0.allGaps.bb
html html/GCF_002863925.1_EquCab3.0.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_002863925.1_EquCab3.0.augustus.bb
html html/GCF_002863925.1_EquCab3.0.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_002863925.1_EquCab3.0.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_002863925.1_EquCab3.0.xenoRefGene.ix
html html/GCF_002863925.1_EquCab3.0.xenoRefGene

track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes 2022_01
group genes
priority 40
visibility pack
color 150,0,0
itemRgb on
type bigGenePred
bigDataUrl bbi/GCF_002863925.1_EquCab3.0.ensGene.bb
searchTrix ixIxx/GCF_002863925.1_EquCab3.0.ensGene.ix
searchIndex name
labelFields name,name2
defaultLabelFields name2
baseColorUseCds given
baseColorDefault genomicCodons
labelSeparator " "
html html/GCF_002863925.1_EquCab3.0.ensGene

track GCF_002863925.1_EquCab3.0ChainNet
compositeTrack on
shortLabel Chain/Net
longLabel Chain alignments to target sequence: GCF_002863925.1_EquCab3.0
subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment
subGroup2 species Assembly s000=GCF_041296265.1 s001=GCF_001704415.2
subGroup3 chainType chain_type c00=chain c01=syntenic c02=reciprocal_best c03=lift_over c04=chain_align c05=syntenic_align c06=reciprocal_align c07=lift_over_align
dragAndDrop subTracks
visibility hide
group compGeno
color 0,0,0
altColor 255,255,0
type bed 3
chainLinearGap loose
chainMinScore 5000
dimensions dimensionX=chainType dimensionY=species
sortOrder species=+ view=+ chainType=+
configurable on
html html/GCF_002863925.1_EquCab3.0.chainNet

    track GCF_002863925.1_EquCab3.0ChainNetViewchain
    shortLabel Chains
    view chain
    visibility dense
    parent GCF_002863925.1_EquCab3.0ChainNet
    spectrum on

        track chainGCF_041296265.1
        parent GCF_002863925.1_EquCab3.0ChainNetViewchain on
        subGroups view=chain species=s000 chainType=c00
        shortLabel GCF_041296265.1 Chain
        longLabel GCF_041296265.1/GCF_041296265.1_TB-T2T (2024-08-16) Chained Alignments
        type bigChain GCF_041296265.1
        bigDataUrl bbi/GCF_002863925.1_EquCab3.0.chainGCF_041296265.1.bb
        linkDataUrl bbi/GCF_002863925.1_EquCab3.0.chainGCF_041296265.1Link.bb
        otherDb GCF_041296265.1
        html html/GCF_002863925.1_EquCab3.0.chainNet
        priority 1.564

        track chainGCF_001704415.2
        parent GCF_002863925.1_EquCab3.0ChainNetViewchain off
        subGroups view=chain species=s001 chainType=c00
        shortLabel GCF_001704415.2 Chain
        longLabel GCF_001704415.2/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCF_002863925.1_EquCab3.0.chainGCF_001704415.2.bb
        linkDataUrl bbi/GCF_002863925.1_EquCab3.0.chainGCF_001704415.2Link.bb
        otherDb GCF_001704415.2
        html html/GCF_002863925.1_EquCab3.0.chainNet
        priority 36.621

    track GCF_002863925.1_EquCab3.0ChainNetViewSynTen
    shortLabel Syntenic
    view synten
    visibility hide
    parent GCF_002863925.1_EquCab3.0ChainNet
    spectrum on

        track chainSynGCF_041296265.1
        parent GCF_002863925.1_EquCab3.0ChainNetViewSynTen off
        subGroups view=synten species=s000 chainType=c01
        shortLabel GCF_041296265.1 synChain
        longLabel GCF_041296265.1/GCF_041296265.1_TB-T2T (2024-08-16) Chained Alignments
        type bigChain GCF_041296265.1
        bigDataUrl bbi/GCF_002863925.1_EquCab3.0.chainSynGCF_041296265.1.bb
        linkDataUrl bbi/GCF_002863925.1_EquCab3.0.chainSynGCF_041296265.1Link.bb
        otherDb GCF_041296265.1
        html html/GCF_002863925.1_EquCab3.0.chainNet
        priority 1.564

    track GCF_002863925.1_EquCab3.0ChainNetViewRBest
    shortLabel Reciprocal best
    view rbest
    visibility hide
    parent GCF_002863925.1_EquCab3.0ChainNet
    spectrum on

        track chainRBestGCF_041296265.1
        parent GCF_002863925.1_EquCab3.0ChainNetViewRBest off
        subGroups view=rbest species=s000 chainType=c02
        shortLabel GCF_041296265.1 rbChain
        longLabel GCF_041296265.1/GCF_041296265.1_TB-T2T (2024-08-16) Chained Alignments
        type bigChain GCF_041296265.1
        bigDataUrl bbi/GCF_002863925.1_EquCab3.0.chainRBestGCF_041296265.1.bb
        linkDataUrl bbi/GCF_002863925.1_EquCab3.0.chainRBestGCF_041296265.1Link.bb
        otherDb GCF_041296265.1
        html html/GCF_002863925.1_EquCab3.0.chainNet
        priority 1.564

    track GCF_002863925.1_EquCab3.0ChainNetViewLiftOver
    shortLabel Lift over
    view liftover
    visibility hide
    parent GCF_002863925.1_EquCab3.0ChainNet
    spectrum on

        track chainLiftOverGCF_041296265.1
        parent GCF_002863925.1_EquCab3.0ChainNetViewLiftOver off
        subGroups view=liftover species=s000 chainType=c03
        shortLabel GCF_041296265.1 loChain
        longLabel GCF_041296265.1/GCF_041296265.1_TB-T2T (2024-08-16) Chained Alignments
        type bigChain GCF_041296265.1
        bigDataUrl bbi/GCF_002863925.1_EquCab3.0.chainLiftOverGCF_041296265.1.bb
        linkDataUrl bbi/GCF_002863925.1_EquCab3.0.chainLiftOverGCF_041296265.1Link.bb
        otherDb GCF_041296265.1
        html html/GCF_002863925.1_EquCab3.0.chainNet
        priority 1.564

        track chainLiftOverGCF_001704415.2
        parent GCF_002863925.1_EquCab3.0ChainNetViewLiftOver off
        subGroups view=liftover species=s001 chainType=c03
        shortLabel GCF_001704415.2 loChain
        longLabel GCF_001704415.2/GCF_001704415.2_ARS1.2 (2016-08-24) Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCF_002863925.1_EquCab3.0.chainLiftOverGCF_001704415.2.bb
        linkDataUrl bbi/GCF_002863925.1_EquCab3.0.chainLiftOverGCF_001704415.2Link.bb
        otherDb GCF_001704415.2
        html html/GCF_002863925.1_EquCab3.0.chainNet
        priority 36.621

    track GCF_002863925.1_EquCab3.0MafNetViewnet
    shortLabel Nets
    view align
    visibility hide
    parent GCF_002863925.1_EquCab3.0ChainNet

        track netGCF_041296265.1
        parent GCF_002863925.1_EquCab3.0MafNetViewnet off
        subGroups view=align species=s000 chainType=c04
        shortLabel GCF_041296265.1 mafNet
        longLabel GCF_041296265.1/GCF_041296265.1_TB-T2T (2024-08-16) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_002863925.1_EquCab3.0.GCF_041296265.1.net.bb
        summary bbi/GCF_002863925.1_EquCab3.0.GCF_041296265.1.net.summary.bb
        speciesOrder GCF_041296265.1
        html html/GCF_002863925.1_EquCab3.0.chainNet
        priority 1.564

        track synNetGCF_041296265.1
        parent GCF_002863925.1_EquCab3.0MafNetViewnet off
        subGroups view=align species=s000 chainType=c05
        shortLabel GCF_041296265.1 synNet
        longLabel GCF_041296265.1/GCF_041296265.1_TB-T2T (2024-08-16) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_002863925.1_EquCab3.0.GCF_041296265.1.synNet.bb
        summary bbi/GCF_002863925.1_EquCab3.0.GCF_041296265.1.synNet.summary.bb
        speciesOrder GCF_041296265.1
        html html/GCF_002863925.1_EquCab3.0.chainNet
        priority 1.564

        track rbestNetGCF_041296265.1
        parent GCF_002863925.1_EquCab3.0MafNetViewnet off
        subGroups view=align species=s000 chainType=c06
        shortLabel GCF_041296265.1 rbestNet
        longLabel GCF_041296265.1/GCF_041296265.1_TB-T2T (2024-08-16) Chained Alignments
        type bigMaf
        bigDataUrl bbi/GCF_002863925.1_EquCab3.0.GCF_041296265.1.rbestNet.bb
        summary bbi/GCF_002863925.1_EquCab3.0.GCF_041296265.1.rbestNet.summary.bb
        speciesOrder GCF_041296265.1
        html html/GCF_002863925.1_EquCab3.0.chainNet
        priority 1.564


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