hub GCF_000715135.1 genome assembly shortLabel common tobacco longLabel common tobacco/Nicotiana tabacum/GCF_000715135.1_Ntab-TN90 genome assembly useOneFile on email hclawson@ucsc.edu descriptionUrl html/GCF_000715135.1_Ntab-TN90.description.html genome GCF_000715135.1 taxId 4097 groups groups.txt description common tobacco twoBitPath GCF_000715135.1.2bit twoBitBptUrl GCF_000715135.1.2bit.bpt chromSizes GCF_000715135.1.chrom.sizes.txt chromAliasBb GCF_000715135.1.chromAlias.bb organism Ntab-TN90 May 2014 defaultPos NW_015885955.1:196364-206364 scientificName Nicotiana tabacum htmlPath html/GCF_000715135.1_Ntab-TN90.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/715/135/GCF_000715135.1 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/715/135/GCF_000715135.1 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/715/135/GCF_000715135.1 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_000715135.1_Ntab-TN90.assembly.bb type bigBed 6 html html/GCF_000715135.1_Ntab-TN90.assembly searchIndex name searchTrix ixIxx/GCF_000715135.1_Ntab-TN90.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 dense color 0,0,0 bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.gap.bb type bigBed 4 group map html html/GCF_000715135.1_Ntab-TN90.gap track cytoBandIdeo shortLabel Chromosome Band (Ideogram) longLabel Ideogram for Orientation group map visibility dense type bigBed 4 + bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.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_000715135.1_Ntab-TN90.gc5Base.bw html html/GCF_000715135.1_Ntab-TN90.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCF_000715135.1_Ntab-TN90.tanDups track gapOverlap parent tanDups on shortLabel Gap Overlaps longLabel Paired exactly identical sequence on each side of a gap bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.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_000715135.1_Ntab-TN90.tandemDups.bb type bigBed 12 track repeatMasker compositeTrack on shortLabel RepeatMasker longLabel Repeating Elements by RepeatMasker group varRep visibility dense type bigBed 6 + colorByStrand 50,50,150 150,50,50 maxWindowToDraw 10000000 spectrum on html html/GCF_000715135.1_Ntab-TN90.repeatMasker track repeatMaskerSINE parent repeatMasker shortLabel SINE longLabel SINE Repeating Elements by RepeatMasker type bigBed 6 + priority 1 bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.rmsk.SINE.bb track repeatMaskerLTR parent repeatMasker shortLabel LTR longLabel LTR Repeating Elements by RepeatMasker type bigBed 6 + priority 3 bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.rmsk.LTR.bb track repeatMaskerDNA parent repeatMasker shortLabel DNA longLabel DNA Repeating Elements by RepeatMasker type bigBed 6 + priority 4 bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.rmsk.DNA.bb track repeatMaskerSimple parent repeatMasker shortLabel Simple longLabel Simple Repeating Elements by RepeatMasker type bigBed 6 + priority 5 bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.rmsk.Simple.bb track repeatMaskerLowComplexity parent repeatMasker shortLabel Low Complexity longLabel Low Complexity Repeating Elements by RepeatMasker type bigBed 6 + priority 6 bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.rmsk.Low_complexity.bb track repeatMaskerSatellite parent repeatMasker shortLabel Satellite longLabel Satellite Repeating Elements by RepeatMasker type bigBed 6 + priority 7 bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.rmsk.Satellite.bb track repeatMaskerRNA parent repeatMasker shortLabel RNA longLabel RNA Repeating Elements by RepeatMasker type bigBed 6 + priority 8 bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.rmsk.RNA.bb track repeatMaskerOther parent repeatMasker shortLabel Other longLabel Other Repeating Elements by RepeatMasker type bigBed 6 + priority 9 bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.rmsk.Other.bb track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.simpleRepeat.bb html html/GCF_000715135.1_Ntab-TN90.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 Nicotiana tabacum Annotation Release 100 (2019-12-04) html html/GCF_000715135.1_Ntab-TN90.refSeqComposite priority 2 track ncbiRefSeq parent refSeqComposite on color 12,12,120 altColor 120,12,12 shortLabel RefSeq All type bigGenePred labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_000715135.1_Ntab-TN90.ncbiRefSeq.ix bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.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 labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_000715135.1_Ntab-TN90.ncbiRefSeqCurated.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.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 labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_000715135.1_Ntab-TN90.ncbiRefSeqPredicted.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.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_000715135.1_Ntab-TN90.ncbiRefSeqOther.ix bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.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_000715135.1_Ntab-TN90.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_000715135.1_Ntab-TN90.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_000715135.1_Ntab-TN90.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_000715135.1_Ntab-TN90.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.windowMasker.bb html html/GCF_000715135.1_Ntab-TN90.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_000715135.1_Ntab-TN90.allGaps.bb html html/GCF_000715135.1_Ntab-TN90.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility dense color 180,0,0 type bigGenePred bigDataUrl bbi/GCF_000715135.1_Ntab-TN90.augustus.bb html html/GCF_000715135.1_Ntab-TN90.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_000715135.1_Ntab-TN90.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_000715135.1_Ntab-TN90.xenoRefGene.ix html html/GCF_000715135.1_Ntab-TN90.xenoRefGene