hub GCF_009806435.1 genome assembly shortLabel rabbit (New Zealand White DNA-2018 2021 refseq) longLabel rabbit (New Zealand White DNA-2018 2021 refseq)/Oryctolagus cuniculus/GCF_009806435.1_UM_NZW_1.0 genome assembly useOneFile on email hclawson@ucsc.edu descriptionUrl html/GCF_009806435.1_UM_NZW_1.0.description.html genome GCF_009806435.1 taxId 9986 groups groups.txt description rabbit (New Zealand White DNA-2018 2021 refseq) twoBitPath GCF_009806435.1.2bit twoBitBptUrl GCF_009806435.1.2bit.bpt chromSizes GCF_009806435.1.chrom.sizes.txt chromAliasBb GCF_009806435.1.chromAlias.bb chromAuthority ucsc organism UM_NZW_1.0 Feb. 2021 defaultPos NC_067374.1:69531604-69541604 scientificName Oryctolagus cuniculus htmlPath html/GCF_009806435.1_UM_NZW_1.0.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/009/806/435/GCF_009806435.1 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/009/806/435/GCF_009806435.1 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/009/806/435/GCF_009806435.1 liftOver.hg38 liftOver/GCF_009806435.1ToHg38.over.chain.gz liftOver.mm39 liftOver/GCF_009806435.1ToMm39.over.chain.gz 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_009806435.1_UM_NZW_1.0.assembly.bb type bigBed 6 html html/GCF_009806435.1_UM_NZW_1.0.assembly searchIndex name searchTrix ixIxx/GCF_009806435.1_UM_NZW_1.0.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_009806435.1_UM_NZW_1.0.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_009806435.1_UM_NZW_1.0.gc5Base.bw html html/GCF_009806435.1_UM_NZW_1.0.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCF_009806435.1_UM_NZW_1.0.tanDups track gapOverlap parent tanDups on shortLabel Gap Overlaps longLabel Paired exactly identical sequence on each side of a gap bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.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_009806435.1_UM_NZW_1.0.tandemDups.bb type bigBed 12 track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.rmsk.bb xrefDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.rmsk.align.bb maxWindowToDraw 5000000 html html/GCF_009806435.1_UM_NZW_1.0.repeatMasker track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.simpleRepeat.bb html html/GCF_009806435.1_UM_NZW_1.0.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 Oryctolagus cuniculus Annotation Release 103 (2022-11-09) html html/GCF_009806435.1_UM_NZW_1.0.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=$$" labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_009806435.1_UM_NZW_1.0.ncbiRefSeq.ix bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.ncbiRefSeq.bb longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given baseColorDefault genomicCodons priority 1 track ncbiRefSeqCurated color 12,12,120 parent refSeqComposite on shortLabel RefSeq Curated longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) type bigGenePred urls geneName="https://www.ncbi.nlm.nih.gov/nuccore/$$?report=genbank" geneName2="https://www.ncbi.nlm.nih.gov/datasets/gene/$D/?search=$$" labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_009806435.1_UM_NZW_1.0.ncbiRefSeqCurated.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.ncbiRefSeqCurated.bb baseColorUseCds given baseColorDefault genomicCodons priority 2 track ncbiRefSeqPredicted color 12,12,120 parent refSeqComposite on shortLabel RefSeq Predicted longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*) type bigGenePred urls geneName="https://www.ncbi.nlm.nih.gov/nuccore/$$?report=genbank" geneName2="https://www.ncbi.nlm.nih.gov/datasets/gene/$D/?search=$$" labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_009806435.1_UM_NZW_1.0.ncbiRefSeqPredicted.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.ncbiRefSeqPredicted.bb baseColorUseCds given baseColorDefault genomicCodons priority 3 track ncbiRefSeqOther color 32,32,32 parent refSeqComposite on shortLabel RefSeq Other longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*) priority 4 searchIndex name searchTrix ixIxx/GCF_009806435.1_UM_NZW_1.0.ncbiRefSeqOther.ix bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.ncbiRefSeqOther.bb type bigBed 12 + labelFields name skipEmptyFields on urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" 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_009806435.1_UM_NZW_1.0.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 pack type bigBed 4 + html html/GCF_009806435.1_UM_NZW_1.0.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_009806435.1_UM_NZW_1.0.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_009806435.1_UM_NZW_1.0.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.windowMasker.bb html html/GCF_009806435.1_UM_NZW_1.0.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_009806435.1_UM_NZW_1.0.allGaps.bb html html/GCF_009806435.1_UM_NZW_1.0.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility dense color 180,0,0 type bigGenePred bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.augustus.bb html html/GCF_009806435.1_UM_NZW_1.0.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_009806435.1_UM_NZW_1.0.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_009806435.1_UM_NZW_1.0.xenoRefGene.ix html html/GCF_009806435.1_UM_NZW_1.0.xenoRefGene track GCF_009806435.1_UM_NZW_1.0ChainNet compositeTrack on shortLabel Chain/Net longLabel Chain alignments to target sequence: GCF_009806435.1_UM_NZW_1.0 subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment subGroup2 species Assembly s000=hg38 s001=mm39 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_009806435.1_UM_NZW_1.0.chainNet track GCF_009806435.1_UM_NZW_1.0ChainNetViewchain shortLabel Chains view chain visibility dense parent GCF_009806435.1_UM_NZW_1.0ChainNet spectrum on track GCF_009806435.1_UM_NZW_1.0ChainNetViewSynTen shortLabel Syntenic view synten visibility hide parent GCF_009806435.1_UM_NZW_1.0ChainNet spectrum on track GCF_009806435.1_UM_NZW_1.0ChainNetViewRBest shortLabel Reciprocal best view rbest visibility hide parent GCF_009806435.1_UM_NZW_1.0ChainNet spectrum on track GCF_009806435.1_UM_NZW_1.0ChainNetViewLiftOver shortLabel Lift over view liftover visibility hide parent GCF_009806435.1_UM_NZW_1.0ChainNet spectrum on track chainHg38 parent GCF_009806435.1_UM_NZW_1.0ChainNetViewchain on subGroups view=chain species=s000 chainType=c00 shortLabel Human/hg38 Chain longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments type bigChain hg38 bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.chainHg38.bb linkDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.chainHg38Link.bb otherDb hg38 html html/GCF_009806435.1_UM_NZW_1.0.chainNet priority 54.081 track chainSynHg38 parent GCF_009806435.1_UM_NZW_1.0ChainNetViewSynTen off subGroups view=synten species=s000 chainType=c01 shortLabel Human/hg38 synChain longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments type bigChain hg38 bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.chainSynHg38.bb linkDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.chainSynHg38Link.bb otherDb hg38 html html/GCF_009806435.1_UM_NZW_1.0.chainNet priority 54.081 track chainRBestHg38 parent GCF_009806435.1_UM_NZW_1.0ChainNetViewRBest off subGroups view=rbest species=s000 chainType=c02 shortLabel Human/hg38 rbChain longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments type bigChain hg38 bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.chainRBestHg38.bb linkDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.chainRBestHg38Link.bb otherDb hg38 html html/GCF_009806435.1_UM_NZW_1.0.chainNet priority 54.081 track chainLiftOverHg38 parent GCF_009806435.1_UM_NZW_1.0ChainNetViewLiftOver off subGroups view=liftover species=s000 chainType=c03 shortLabel Human/hg38 loChain longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments type bigChain hg38 bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.chainLiftOverHg38.bb linkDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.chainLiftOverHg38Link.bb otherDb hg38 html html/GCF_009806435.1_UM_NZW_1.0.chainNet priority 54.081 track chainMm39 parent GCF_009806435.1_UM_NZW_1.0ChainNetViewchain off subGroups view=chain species=s001 chainType=c00 shortLabel Mouse/mm39 Chain longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments type bigChain mm39 bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.chainMm39.bb linkDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.chainMm39Link.bb otherDb mm39 html html/GCF_009806435.1_UM_NZW_1.0.chainNet priority 75.360 track chainSynMm39 parent GCF_009806435.1_UM_NZW_1.0ChainNetViewSynTen off subGroups view=synten species=s001 chainType=c01 shortLabel Mouse/mm39 synChain longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments type bigChain mm39 bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.chainSynMm39.bb linkDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.chainSynMm39Link.bb otherDb mm39 html html/GCF_009806435.1_UM_NZW_1.0.chainNet priority 75.360 track chainRBestMm39 parent GCF_009806435.1_UM_NZW_1.0ChainNetViewRBest off subGroups view=rbest species=s001 chainType=c02 shortLabel Mouse/mm39 rbChain longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments type bigChain mm39 bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.chainRBestMm39.bb linkDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.chainRBestMm39Link.bb otherDb mm39 html html/GCF_009806435.1_UM_NZW_1.0.chainNet priority 75.360 track chainLiftOverMm39 parent GCF_009806435.1_UM_NZW_1.0ChainNetViewLiftOver off subGroups view=liftover species=s001 chainType=c03 shortLabel Mouse/mm39 loChain longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments type bigChain mm39 bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.chainLiftOverMm39.bb linkDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.chainLiftOverMm39Link.bb otherDb mm39 html html/GCF_009806435.1_UM_NZW_1.0.chainNet priority 75.360 track GCF_009806435.1_UM_NZW_1.0MafNetViewnet shortLabel Nets view align visibility hide parent GCF_009806435.1_UM_NZW_1.0ChainNet track netHg38 parent GCF_009806435.1_UM_NZW_1.0MafNetViewnet off subGroups view=align species=s000 chainType=c04 shortLabel Human/hg38 mafNet longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments type bigMaf bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.hg38.net.bb summary bbi/GCF_009806435.1_UM_NZW_1.0.hg38.net.summary.bb speciesOrder hg38 html html/GCF_009806435.1_UM_NZW_1.0.chainNet priority 54.081 track synNetHg38 parent GCF_009806435.1_UM_NZW_1.0MafNetViewnet off subGroups view=align species=s000 chainType=c05 shortLabel Human/hg38 synNet longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments type bigMaf bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.hg38.synNet.bb summary bbi/GCF_009806435.1_UM_NZW_1.0.hg38.synNet.summary.bb speciesOrder hg38 html html/GCF_009806435.1_UM_NZW_1.0.chainNet priority 54.081 track rbestNetHg38 parent GCF_009806435.1_UM_NZW_1.0MafNetViewnet off subGroups view=align species=s000 chainType=c06 shortLabel Human/hg38 rbestNet longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments type bigMaf bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.hg38.rbestNet.bb summary bbi/GCF_009806435.1_UM_NZW_1.0.hg38.rbestNet.summary.bb speciesOrder hg38 html html/GCF_009806435.1_UM_NZW_1.0.chainNet priority 54.081 track netMm39 parent GCF_009806435.1_UM_NZW_1.0MafNetViewnet off subGroups view=align species=s001 chainType=c04 shortLabel Mouse/mm39 mafNet longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments type bigMaf bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.mm39.net.bb summary bbi/GCF_009806435.1_UM_NZW_1.0.mm39.net.summary.bb speciesOrder mm39 html html/GCF_009806435.1_UM_NZW_1.0.chainNet priority 75.360 track synNetMm39 parent GCF_009806435.1_UM_NZW_1.0MafNetViewnet off subGroups view=align species=s001 chainType=c05 shortLabel Mouse/mm39 synNet longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments type bigMaf bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.mm39.synNet.bb summary bbi/GCF_009806435.1_UM_NZW_1.0.mm39.synNet.summary.bb speciesOrder mm39 html html/GCF_009806435.1_UM_NZW_1.0.chainNet priority 75.360 track rbestNetMm39 parent GCF_009806435.1_UM_NZW_1.0MafNetViewnet off subGroups view=align species=s001 chainType=c06 shortLabel Mouse/mm39 rbestNet longLabel Mouse/mm39/mm39 (Jun. 2020) Chained Alignments type bigMaf bigDataUrl bbi/GCF_009806435.1_UM_NZW_1.0.mm39.rbestNet.bb summary bbi/GCF_009806435.1_UM_NZW_1.0.mm39.rbestNet.summary.bb speciesOrder mm39 html html/GCF_009806435.1_UM_NZW_1.0.chainNet priority 75.360