hub GCF_018350155.1 genome assembly shortLabel Geoffroy's cat longLabel Geoffroy's cat/Leopardus geoffroyi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0 genome assembly useOneFile on email genome-www@soe.ucsc.edu descriptionUrl html/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.description.html genome GCF_018350155.1 taxId 46844 groups groups.txt description Geoffroy's cat twoBitPath GCF_018350155.1.2bit twoBitBptUrl GCF_018350155.1.2bit.bpt chromSizes GCF_018350155.1.chrom.sizes.txt chromAliasBb GCF_018350155.1.chromAlias.bb chromAuthority ucsc organism O.geoffroyi_Oge1_pat1.0 May 2021 defaultPos NC_059326.1:79898129-79908129 scientificName Leopardus geoffroyi htmlPath html/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/018/350/155/GCF_018350155.1 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/018/350/155/GCF_018350155.1 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/018/350/155/GCF_018350155.1 liftOver.GCF_018350175.1 liftOver/GCF_018350155.1ToGCF_018350175.1.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_018350155.1_O.geoffroyi_Oge1_pat1.0.assembly.bb type bigBed 6 html html/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.assembly searchIndex name searchTrix ixIxx/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.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/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.gap.bb type bigBed 4 group map html html/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.gap track cytoBandIdeo shortLabel Chromosome Band (Ideogram) longLabel Ideogram for Orientation group map visibility dense type bigBed 4 + bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.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_018350155.1_O.geoffroyi_Oge1_pat1.0.gc5Base.bw html html/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.tanDups track tandemDups parent tanDups on shortLabel Tandem Dups longLabel Paired exactly identical sequence survey over entire genome assembly bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.tandemDups.bb type bigBed 12 track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.rmsk.bb xrefDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.rmsk.align.bb maxWindowToDraw 5000000 html html/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.repeatMasker track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.simpleRepeat.bb html html/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.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 Leopardus geoffroyi Annotation Release 100 (2021-12-17) html html/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.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_018350155.1_O.geoffroyi_Oge1_pat1.0.ncbiRefSeq.ix bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.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/$$" labelFields name2,geneName,geneName2 defaultLabelFields name2 searchIndex name searchTrix ixIxx/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.ncbiRefSeqCurated.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.ncbiRefSeqCurated.bb baseColorUseCds given baseColorDefault genomicCodons priority 2 track ncbiRefSeqPredicted color 12,12,120 parent refSeqComposite on shortLabel RefSeq Predicted longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*) type bigGenePred urls name2="https://www.ncbi.nlm.nih.gov/gene/?term=$$" 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_018350155.1_O.geoffroyi_Oge1_pat1.0.ncbiRefSeqPredicted.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.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_018350155.1_O.geoffroyi_Oge1_pat1.0.ncbiRefSeqOther.ix bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.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_018350155.1_O.geoffroyi_Oge1_pat1.0.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_018350155.1_O.geoffroyi_Oge1_pat1.0.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_018350155.1_O.geoffroyi_Oge1_pat1.0.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_018350155.1_O.geoffroyi_Oge1_pat1.0.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.windowMasker.bb html html/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.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_018350155.1_O.geoffroyi_Oge1_pat1.0.allGaps.bb html html/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility dense color 180,0,0 type bigGenePred bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.augustus.bb html html/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.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_018350155.1_O.geoffroyi_Oge1_pat1.0.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_018350155.1_O.geoffroyi_Oge1_pat1.0.xenoRefGene.ix html html/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.xenoRefGene track ensGene shortLabel Ensembl genes longLabel Ensembl genes 2021_08 group genes priority 40 visibility pack color 150,0,0 itemRgb on type bigGenePred bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.ensGene.bb searchTrix ixIxx/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.ensGene.ix searchIndex name labelFields name,name2 defaultLabelFields name2 baseColorUseCds given baseColorDefault genomicCodons labelSeparator " " html html/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.ensGene ############################################################################## # GCF_018350175.1 - Geoffroy's cat - Leopardus geoffroyi - taxId: 46844 ############################################################################## track chainNetGCF_018350175.1 compositeTrack on shortLabel Geoffroy's cat Chain/Net longLabel Geoffroy's cat (2021-05-13), 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_018350175.1 html html/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.chainNet track chainNetGCF_018350175.1Viewchain shortLabel Chain view chain visibility pack parent chainNetGCF_018350175.1 spectrum on track chainGCF_018350175.1 parent chainNetGCF_018350175.1Viewchain subGroups view=chain shortLabel Geoffroy's cat Chain longLabel Geoffroy's cat (2021-05-13) Chained Alignments type bigChain GCF_018350175.1 bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.chainGCF_018350175.1.bb linkDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.chainGCF_018350175.1Link.bb priority 1 track chainSynGCF_018350175.1 parent chainNetGCF_018350175.1Viewchain subGroups view=chain shortLabel Geoffroy's cat synChain longLabel Geoffroy's cat (2021-05-13) Syntenic Chained Alignments type bigChain GCF_018350175.1 bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.chainSynGCF_018350175.1.bb linkDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.chainSynGCF_018350175.1Link.bb priority 2 track chainRBestGCF_018350175.1 parent chainNetGCF_018350175.1Viewchain subGroups view=chain shortLabel Geoffroy's cat rbChain longLabel Geoffroy's cat (2021-05-13) Reciprocal Best Chained Alignments type bigChain GCF_018350175.1 bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.chainRBestGCF_018350175.1.bb linkDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.chainRBestGCF_018350175.1Link.bb priority 3 track chainLiftOverGCF_018350175.1 parent chainNetGCF_018350175.1Viewchain subGroups view=chain shortLabel Geoffroy's cat loChain longLabel Geoffroy's cat (2021-05-13) Lift Over Chained Alignments type bigChain GCF_018350175.1 bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.chainLiftOverGCF_018350175.1.bb linkDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.chainLiftOverGCF_018350175.1Link.bb priority 4 track mafNetGCF_018350175.1Viewnet shortLabel Net view net visibility full parent chainNetGCF_018350175.1 track netGCF_018350175.1 parent mafNetGCF_018350175.1Viewnet subGroups view=net shortLabel Geoffroy's cat net longLabel Geoffroy's cat (2021-05-13) Net Alignment type bigMaf bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.GCF_018350175.1.net.bb summary bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.GCF_018350175.1.net.summary.bb speciesOrder GCF_018350175.1 priority 5 track synNetGCF_018350175.1 parent mafNetGCF_018350175.1Viewnet subGroups view=net shortLabel Geoffroy's cat synNet longLabel Geoffroy's cat (2021-05-13) Syntenic Net Alignment type bigMaf bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.GCF_018350175.1.synNet.bb summary bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.GCF_018350175.1.synNet.summary.bb speciesOrder GCF_018350175.1 priority 6 track rbestNetGCF_018350175.1 parent mafNetGCF_018350175.1Viewnet subGroups view=net shortLabel Geoffroy's cat rbestNet longLabel Geoffroy's cat (2021-05-13) Reciprocal Best Net Alignment type bigMaf bigDataUrl bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.GCF_018350175.1.rbestNet.bb summary bbi/GCF_018350155.1_O.geoffroyi_Oge1_pat1.0.GCF_018350175.1.rbestNet.summary.bb speciesOrder GCF_018350175.1 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