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_002263795.2_ARS-UCD1.3.assembly.bb type bigBed 6 html html/GCF_002263795.2_ARS-UCD1.3.assembly searchIndex name searchTrix ixIxx/GCF_002263795.2_ARS-UCD1.3.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_002263795.2_ARS-UCD1.3.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_002263795.2_ARS-UCD1.3.gc5Base.bw html html/GCF_002263795.2_ARS-UCD1.3.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCF_002263795.2_ARS-UCD1.3.tanDups track gapOverlap parent tanDups on shortLabel Gap Overlaps longLabel Paired exactly identical sequence on each side of a gap bigDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.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_002263795.2_ARS-UCD1.3.tandemDups.bb type bigBed 12 track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.rmsk.bb xrefDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.rmsk.align.bb maxWindowToDraw 5000000 html html/GCF_002263795.2_ARS-UCD1.3.repeatMasker track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.simpleRepeat.bb html html/GCF_002263795.2_ARS-UCD1.3.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 Bos taurus Annotation Release 106 (2022-05-20) html html/GCF_002263795.2_ARS-UCD1.3.refSeqComposite priority 2 track ncbiRefSeq parent refSeqComposite on color 12,12,120 shortLabel RefSeq All type bigGenePred urls geneName="https://www.ncbi.nlm.nih.gov/nuccore/$$?report=genbank" geneName2="https://www.ncbi.nlm.nih.gov/datasets/gene/$D/?search=$$" labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_002263795.2_ARS-UCD1.3.ncbiRefSeq.ix bigDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.ncbiRefSeq.bb longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given baseColorDefault genomicCodons priority 1 track ncbiRefSeqCurated color 12,12,120 parent refSeqComposite on shortLabel RefSeq Curated longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) type bigGenePred urls geneName="https://www.ncbi.nlm.nih.gov/nuccore/$$?report=genbank" geneName2="https://www.ncbi.nlm.nih.gov/datasets/gene/$D/?search=$$" labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_002263795.2_ARS-UCD1.3.ncbiRefSeqCurated.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.ncbiRefSeqCurated.bb baseColorUseCds given baseColorDefault genomicCodons priority 2 track ncbiRefSeqPredicted color 12,12,120 parent refSeqComposite on shortLabel RefSeq Predicted longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*) type bigGenePred urls geneName="https://www.ncbi.nlm.nih.gov/nuccore/$$?report=genbank" geneName2="https://www.ncbi.nlm.nih.gov/datasets/gene/$D/?search=$$" labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_002263795.2_ARS-UCD1.3.ncbiRefSeqPredicted.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.ncbiRefSeqPredicted.bb baseColorUseCds given baseColorDefault genomicCodons priority 3 track ncbiRefSeqOther color 32,32,32 parent refSeqComposite on shortLabel RefSeq Other longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*) priority 4 searchIndex name searchTrix ixIxx/GCF_002263795.2_ARS-UCD1.3.ncbiRefSeqOther.ix bigDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.ncbiRefSeqOther.bb type bigBed 12 + labelFields name skipEmptyFields on urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" 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_002263795.2_ARS-UCD1.3.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_002263795.2_ARS-UCD1.3.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_002263795.2_ARS-UCD1.3.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_002263795.2_ARS-UCD1.3.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.windowMasker.bb html html/GCF_002263795.2_ARS-UCD1.3.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_002263795.2_ARS-UCD1.3.allGaps.bb html html/GCF_002263795.2_ARS-UCD1.3.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility dense color 180,0,0 type bigGenePred bigDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.augustus.bb html html/GCF_002263795.2_ARS-UCD1.3.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_002263795.2_ARS-UCD1.3.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_002263795.2_ARS-UCD1.3.xenoRefGene.ix html html/GCF_002263795.2_ARS-UCD1.3.xenoRefGene ############################################################################## # GCF_002263795.3 - cattle - Bos taurus - taxId: 9913 ############################################################################## track chainNetGCF_002263795.3 compositeTrack on shortLabel cattle Chain/Net longLabel cattle (2018-04-11), 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_002263795.3 html html/GCF_002263795.2_ARS-UCD1.3.chainNet track chainNetGCF_002263795.3Viewchain shortLabel Chain view chain visibility pack parent chainNetGCF_002263795.3 spectrum on track chainGCF_002263795.3 parent chainNetGCF_002263795.3Viewchain subGroups view=chain shortLabel cattle Chain longLabel cattle (2018-04-11) Chained Alignments type bigChain GCF_002263795.3 bigDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.chainGCF_002263795.3.bb linkDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.chainGCF_002263795.3Link.bb priority 1 track chainSynGCF_002263795.3 parent chainNetGCF_002263795.3Viewchain subGroups view=chain shortLabel cattle synChain longLabel cattle (2018-04-11) Syntenic Chained Alignments type bigChain GCF_002263795.3 bigDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.chainSynGCF_002263795.3.bb linkDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.chainSynGCF_002263795.3Link.bb priority 2 track chainRBestGCF_002263795.3 parent chainNetGCF_002263795.3Viewchain subGroups view=chain shortLabel cattle rbChain longLabel cattle (2018-04-11) Reciprocal Best Chained Alignments type bigChain GCF_002263795.3 bigDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.chainRBestGCF_002263795.3.bb linkDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.chainRBestGCF_002263795.3Link.bb priority 3 track chainLiftOverGCF_002263795.3 parent chainNetGCF_002263795.3Viewchain subGroups view=chain shortLabel cattle loChain longLabel cattle (2018-04-11) Lift Over Chained Alignments type bigChain GCF_002263795.3 bigDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.chainLiftOverGCF_002263795.3.bb linkDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.chainLiftOverGCF_002263795.3Link.bb priority 4 track mafNetGCF_002263795.3Viewnet shortLabel Net view net visibility full parent chainNetGCF_002263795.3 track netGCF_002263795.3 parent mafNetGCF_002263795.3Viewnet subGroups view=net shortLabel cattle net longLabel cattle (2018-04-11) Net Alignment type bigMaf bigDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.GCF_002263795.3.net.bb summary bbi/GCF_002263795.2_ARS-UCD1.3.GCF_002263795.3.net.summary.bb speciesOrder GCF_002263795.3 priority 5 track synNetGCF_002263795.3 parent mafNetGCF_002263795.3Viewnet subGroups view=net shortLabel cattle synNet longLabel cattle (2018-04-11) Syntenic Net Alignment type bigMaf bigDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.GCF_002263795.3.synNet.bb summary bbi/GCF_002263795.2_ARS-UCD1.3.GCF_002263795.3.synNet.summary.bb speciesOrder GCF_002263795.3 priority 6 track rbestNetGCF_002263795.3 parent mafNetGCF_002263795.3Viewnet subGroups view=net shortLabel cattle rbestNet longLabel cattle (2018-04-11) Reciprocal Best Net Alignment type bigMaf bigDataUrl bbi/GCF_002263795.2_ARS-UCD1.3.GCF_002263795.3.rbestNet.bb summary bbi/GCF_002263795.2_ARS-UCD1.3.GCF_002263795.3.rbestNet.summary.bb speciesOrder GCF_002263795.3 priority 7