hub GCA_000001905.1 genome assembly
shortLabel African savanna elephant (2009 genbank)
longLabel African savanna elephant (2009 genbank)/Loxodonta africana/GCA_000001905.1_Loxafr3.0 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCA_000001905.1_Loxafr3.0.description.html

genome GCA_000001905.1
taxId 9785
groups groups.txt
description African savanna elephant (2009 genbank)
twoBitPath GCA_000001905.1.2bit
twoBitBptUrl GCA_000001905.1.2bit.bpt
chromSizes GCA_000001905.1.chrom.sizes.txt
chromAliasBb GCA_000001905.1.chromAlias.bb
organism Loxafr3.0 Jul. 2009
defaultPos GL010027.1:43253113-43263113
scientificName Loxodonta africana
htmlPath html/GCA_000001905.1_Loxafr3.0.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/001/905/GCA_000001905.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/001/905/GCA_000001905.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/001/905/GCA_000001905.1
liftOver.GCF_001704415.2 liftOver/GCA_000001905.1ToGCF_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_000001905.1_Loxafr3.0.assembly.bb
type bigBed 6
html html/GCA_000001905.1_Loxafr3.0.assembly
searchIndex name
searchTrix ixIxx/GCA_000001905.1_Loxafr3.0.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/GCA_000001905.1_Loxafr3.0.gap.bb
type bigBed 4
group map
html html/GCA_000001905.1_Loxafr3.0.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.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/GCA_000001905.1_Loxafr3.0.gc5Base.bw
html html/GCA_000001905.1_Loxafr3.0.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_000001905.1_Loxafr3.0.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.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/GCA_000001905.1_Loxafr3.0.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.rmsk.bb
maxWindowToDraw 5000000
html html/GCA_000001905.1_Loxafr3.0.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.simpleRepeat.bb
html html/GCA_000001905.1_Loxafr3.0.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 Loxodonta africana Annotation Release 102 (2022-11-30)
html html/GCA_000001905.1_Loxafr3.0.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/GCA_000001905.1_Loxafr3.0.ncbiRefSeq.ix
        bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.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/GCA_000001905.1_Loxafr3.0.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.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/GCA_000001905.1_Loxafr3.0.ncbiRefSeqPredicted.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.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/GCA_000001905.1_Loxafr3.0.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.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/GCA_000001905.1_Loxafr3.0.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/GCA_000001905.1_Loxafr3.0.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/GCA_000001905.1_Loxafr3.0.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/GCA_000001905.1_Loxafr3.0.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.windowMasker.bb
html html/GCA_000001905.1_Loxafr3.0.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/GCA_000001905.1_Loxafr3.0.allGaps.bb
html html/GCA_000001905.1_Loxafr3.0.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.augustus.bb
html html/GCA_000001905.1_Loxafr3.0.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/GCA_000001905.1_Loxafr3.0.xenoRefGene.bb
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
labelFields name,geneName,geneName2
defaultLabelFields geneName
searchIndex name
searchTrix ixIxx/GCA_000001905.1_Loxafr3.0.xenoRefGene.ix
html html/GCA_000001905.1_Loxafr3.0.xenoRefGene

##############################################################################
# GCF_001704415.2 - African savanna elephant - Loxodonta africana - taxId: 9785
##############################################################################
track chainNetGCF_001704415.2
compositeTrack on
shortLabel African savanna elephant Chain/Net
longLabel African savanna elephant (2009-07-15), 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_000001905.1_Loxafr3.0.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 African savanna elephant Chain
        longLabel African savanna elephant (2009-07-15) Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.chainGCF_001704415.2.bb
        linkDataUrl bbi/GCA_000001905.1_Loxafr3.0.chainGCF_001704415.2Link.bb
        priority 1

        track chainSynGCF_001704415.2
        parent chainNetGCF_001704415.2Viewchain
        subGroups view=chain
        shortLabel African savanna elephant synChain
        longLabel African savanna elephant (2009-07-15) Syntenic Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.chainSynGCF_001704415.2.bb
        linkDataUrl bbi/GCA_000001905.1_Loxafr3.0.chainSynGCF_001704415.2Link.bb
        priority 2

        track chainRBestGCF_001704415.2
        parent chainNetGCF_001704415.2Viewchain
        subGroups view=chain
        shortLabel African savanna elephant rbChain
        longLabel African savanna elephant (2009-07-15) Reciprocal Best Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.chainRBestGCF_001704415.2.bb
        linkDataUrl bbi/GCA_000001905.1_Loxafr3.0.chainRBestGCF_001704415.2Link.bb
        priority 3

        track chainLiftOverGCF_001704415.2
        parent chainNetGCF_001704415.2Viewchain
        subGroups view=chain
        shortLabel African savanna elephant loChain
        longLabel African savanna elephant (2009-07-15) Lift Over Chained Alignments
        type bigChain GCF_001704415.2
        bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.chainLiftOverGCF_001704415.2.bb
        linkDataUrl bbi/GCA_000001905.1_Loxafr3.0.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 African savanna elephant net
        longLabel African savanna elephant (2009-07-15) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.GCF_001704415.2.net.bb
        summary bbi/GCA_000001905.1_Loxafr3.0.GCF_001704415.2.net.summary.bb
        speciesOrder GCF_001704415.2
        priority 5

        track synNetGCF_001704415.2
        parent mafNetGCF_001704415.2Viewnet
        subGroups view=net
        shortLabel African savanna elephant synNet
        longLabel African savanna elephant (2009-07-15) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.GCF_001704415.2.synNet.bb
        summary bbi/GCA_000001905.1_Loxafr3.0.GCF_001704415.2.synNet.summary.bb
        speciesOrder GCF_001704415.2
        priority 6

        track rbestNetGCF_001704415.2
        parent mafNetGCF_001704415.2Viewnet
        subGroups view=net
        shortLabel African savanna elephant rbestNet
        longLabel African savanna elephant (2009-07-15) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_000001905.1_Loxafr3.0.GCF_001704415.2.rbestNet.bb
        summary bbi/GCA_000001905.1_Loxafr3.0.GCF_001704415.2.rbestNet.summary.bb
        speciesOrder GCF_001704415.2
        priority 7


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