hub GCA_000243295.1 genome assembly shortLabel Florida manatee (Lorelei 2012 genbank) longLabel Florida manatee (Lorelei 2012 genbank)/Trichechus manatus latirostris/GCA_000243295.1_TriManLat1.0 genome assembly useOneFile on email hclawson@ucsc.edu descriptionUrl html/GCA_000243295.1_TriManLat1.0.description.html genome GCA_000243295.1 taxId 127582 groups groups.txt description Florida manatee (Lorelei 2012 genbank) twoBitPath GCA_000243295.1.2bit twoBitBptUrl GCA_000243295.1.2bit.bpt chromSizes GCA_000243295.1.chrom.sizes.txt chromAliasBb GCA_000243295.1.chromAlias.bb organism TriManLat1.0 Jan. 2012 defaultPos JH594607.1:15314155-15324155 scientificName Trichechus manatus latirostris htmlPath html/GCA_000243295.1_TriManLat1.0.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/243/295/GCA_000243295.1 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/243/295/GCA_000243295.1 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/243/295/GCA_000243295.1 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_000243295.1_TriManLat1.0.assembly.bb type bigBed 6 html html/GCA_000243295.1_TriManLat1.0.assembly searchIndex name searchTrix ixIxx/GCA_000243295.1_TriManLat1.0.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 dense color 0,0,0 bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.gap.bb type bigBed 4 group map html html/GCA_000243295.1_TriManLat1.0.gap track cytoBandIdeo shortLabel Chromosome Band (Ideogram) longLabel Ideogram for Orientation group map visibility dense type bigBed 4 + bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.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/GCA_000243295.1_TriManLat1.0.gc5Base.bw html html/GCA_000243295.1_TriManLat1.0.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCA_000243295.1_TriManLat1.0.tanDups track gapOverlap parent tanDups on shortLabel Gap Overlaps longLabel Paired exactly identical sequence on each side of a gap bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.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/GCA_000243295.1_TriManLat1.0.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/GCA_000243295.1_TriManLat1.0.repeatMasker track repeatMaskerSINE parent repeatMasker shortLabel SINE longLabel SINE Repeating Elements by RepeatMasker type bigBed 6 + priority 1 bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.rmsk.SINE.bb track repeatMaskerLINE parent repeatMasker shortLabel LINE longLabel LINE Repeating Elements by RepeatMasker type bigBed 6 + priority 2 bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.rmsk.LINE.bb track repeatMaskerLTR parent repeatMasker shortLabel LTR longLabel LTR Repeating Elements by RepeatMasker type bigBed 6 + priority 3 bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.rmsk.LTR.bb track repeatMaskerDNA parent repeatMasker shortLabel DNA longLabel DNA Repeating Elements by RepeatMasker type bigBed 6 + priority 4 bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.rmsk.DNA.bb track repeatMaskerSimple parent repeatMasker shortLabel Simple longLabel Simple Repeating Elements by RepeatMasker type bigBed 6 + priority 5 bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.rmsk.Simple.bb track repeatMaskerLowComplexity parent repeatMasker shortLabel Low Complexity longLabel Low Complexity Repeating Elements by RepeatMasker type bigBed 6 + priority 6 bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.rmsk.Low_complexity.bb track repeatMaskerSatellite parent repeatMasker shortLabel Satellite longLabel Satellite Repeating Elements by RepeatMasker type bigBed 6 + priority 7 bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.rmsk.Satellite.bb track repeatMaskerRNA parent repeatMasker shortLabel RNA longLabel RNA Repeating Elements by RepeatMasker type bigBed 6 + priority 8 bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.rmsk.RNA.bb track repeatMaskerOther parent repeatMasker shortLabel Other longLabel Other Repeating Elements by RepeatMasker type bigBed 6 + priority 9 bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.rmsk.Other.bb track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.simpleRepeat.bb html html/GCA_000243295.1_TriManLat1.0.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 GCF_000243295.1-RS_2024_01 (2024-01-29) html html/GCA_000243295.1_TriManLat1.0.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_000243295.1_TriManLat1.0.ncbiRefSeq.ix bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.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 labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCA_000243295.1_TriManLat1.0.ncbiRefSeqCurated.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.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 labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCA_000243295.1_TriManLat1.0.ncbiRefSeqPredicted.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.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/GCA_000243295.1_TriManLat1.0.ncbiRefSeqOther.ix bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.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/GCA_000243295.1_TriManLat1.0.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/GCA_000243295.1_TriManLat1.0.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/GCA_000243295.1_TriManLat1.0.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/GCA_000243295.1_TriManLat1.0.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.windowMasker.bb html html/GCA_000243295.1_TriManLat1.0.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/GCA_000243295.1_TriManLat1.0.allGaps.bb html html/GCA_000243295.1_TriManLat1.0.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility dense color 180,0,0 type bigGenePred bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.augustus.bb html html/GCA_000243295.1_TriManLat1.0.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/GCA_000243295.1_TriManLat1.0.xenoRefGene.bb url https://www.ncbi.nlm.nih.gov/nuccore/$$ urlLabel NCBI Nucleotide database: labelFields name,geneName,geneName2 defaultLabelFields geneName searchIndex name searchTrix ixIxx/GCA_000243295.1_TriManLat1.0.xenoRefGene.ix html html/GCA_000243295.1_TriManLat1.0.xenoRefGene track ensGene shortLabel Ensembl genes longLabel Ensembl genes 2020_05 group genes priority 40 visibility pack color 150,0,0 itemRgb on type bigGenePred bigDataUrl bbi/GCA_000243295.1_TriManLat1.0.ensGene.bb searchTrix ixIxx/GCA_000243295.1_TriManLat1.0.ensGene.ix searchIndex name labelFields name,name2 defaultLabelFields name2 baseColorUseCds given baseColorDefault genomicCodons labelSeperator " " html html/GCA_000243295.1_TriManLat1.0.ensGene