hub GCA_011100635.1 genome assembly shortLabel common brushtail (genbank 2020) longLabel common brushtail (genbank 2020)/Trichosurus vulpecula/GCA_011100635.1_mTriVul1.pri genome assembly useOneFile on email hclawson@ucsc.edu descriptionUrl html/GCA_011100635.1_mTriVul1.pri.description.html genome GCA_011100635.1 taxId 9337 groups groups.txt description common brushtail (genbank 2020) twoBitPath GCA_011100635.1.2bit twoBitBptUrl GCA_011100635.1.2bit.bpt chromSizes GCA_011100635.1.chrom.sizes.txt chromAliasBb GCA_011100635.1.chromAlias.bb chromAuthority ucsc organism mTriVul1.pri Mar. 2020 defaultPos CM021905.1:189552068-189562068 scientificName Trichosurus vulpecula htmlPath html/GCA_011100635.1_mTriVul1.pri.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/011/100/635/GCA_011100635.1 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/011/100/635/GCA_011100635.1 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/011/100/635/GCA_011100635.1 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/GCA_011100635.1_mTriVul1.pri.assembly.bb type bigBed 6 html html/GCA_011100635.1_mTriVul1.pri.assembly searchIndex name searchTrix ixIxx/GCA_011100635.1_mTriVul1.pri.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/GCA_011100635.1_mTriVul1.pri.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/GCA_011100635.1_mTriVul1.pri.gc5Base.bw html html/GCA_011100635.1_mTriVul1.pri.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCA_011100635.1_mTriVul1.pri.tanDups track tandemDups parent tanDups on shortLabel Tandem Dups longLabel Paired exactly identical sequence survey over entire genome assembly bigDataUrl bbi/GCA_011100635.1_mTriVul1.pri.tandemDups.bb type bigBed 12 track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCA_011100635.1_mTriVul1.pri.rmsk.bb maxWindowToDraw 5000000 html html/GCA_011100635.1_mTriVul1.pri.repeatMasker track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCA_011100635.1_mTriVul1.pri.simpleRepeat.bb html html/GCA_011100635.1_mTriVul1.pri.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 Trichosurus vulpecula Annotation Release 100 (2022-09-28) html html/GCA_011100635.1_mTriVul1.pri.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/GCA_011100635.1_mTriVul1.pri.ncbiRefSeq.ix bigDataUrl bbi/GCA_011100635.1_mTriVul1.pri.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 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/GCA_011100635.1_mTriVul1.pri.ncbiRefSeqPredicted.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCA_011100635.1_mTriVul1.pri.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_011100635.1_mTriVul1.pri.ncbiRefSeqOther.ix bigDataUrl bbi/GCA_011100635.1_mTriVul1.pri.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_011100635.1_mTriVul1.pri.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/GCA_011100635.1_mTriVul1.pri.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_011100635.1_mTriVul1.pri.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_011100635.1_mTriVul1.pri.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCA_011100635.1_mTriVul1.pri.windowMasker.bb html html/GCA_011100635.1_mTriVul1.pri.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/GCA_011100635.1_mTriVul1.pri.allGaps.bb html html/GCA_011100635.1_mTriVul1.pri.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility dense color 180,0,0 type bigGenePred bigDataUrl bbi/GCA_011100635.1_mTriVul1.pri.augustus.bb html html/GCA_011100635.1_mTriVul1.pri.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_011100635.1_mTriVul1.pri.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_011100635.1_mTriVul1.pri.xenoRefGene.ix html html/GCA_011100635.1_mTriVul1.pri.xenoRefGene track HLTOGAannotvHg38v1 bigDataUrl bbi/HLTOGAannotVsHg38v1.bb shortLabel TOGA vs. hg38 longLabel TOGA annotations using human/hg38 as reference group genes visibility pack itemRgb on type bigBed 12 searchIndex name searchTrix ixIxx/HLTOGAannotVsHg38v1.ix html html/TOGAannotation