hub GCF_963662255.1 genome assembly shortLabel white-throated dipper (primary hap 2023) longLabel white-throated dipper (primary hap 2023)/Cinclus cinclus/GCF_963662255.1_bCinCin1.1 genome assembly useOneFile on email hclawson@ucsc.edu descriptionUrl html/GCF_963662255.1_bCinCin1.1.description.html genome GCF_963662255.1 taxId 127875 groups groups.txt description white-throated dipper (primary hap 2023) twoBitPath GCF_963662255.1.2bit twoBitBptUrl GCF_963662255.1.2bit.bpt chromSizes GCF_963662255.1.chrom.sizes.txt chromAliasBb GCF_963662255.1.chromAlias.bb chromAuthority ucsc organism bCinCin1.1 Dec. 2023 defaultPos NC_085046.1:50788178-50798178 scientificName Cinclus cinclus htmlPath html/GCF_963662255.1_bCinCin1.1.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/963/662/255/GCF_963662255.1 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/963/662/255/GCF_963662255.1 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/963/662/255/GCF_963662255.1 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_963662255.1_bCinCin1.1.assembly.bb type bigBed 6 html html/GCF_963662255.1_bCinCin1.1.assembly searchIndex name searchTrix ixIxx/GCF_963662255.1_bCinCin1.1.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_963662255.1_bCinCin1.1.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_963662255.1_bCinCin1.1.gc5Base.bw html html/GCF_963662255.1_bCinCin1.1.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCF_963662255.1_bCinCin1.1.tanDups track gapOverlap parent tanDups on shortLabel Gap Overlaps longLabel Paired exactly identical sequence on each side of a gap bigDataUrl bbi/GCF_963662255.1_bCinCin1.1.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_963662255.1_bCinCin1.1.tandemDups.bb type bigBed 12 track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCF_963662255.1_bCinCin1.1.rmsk.bb xrefDataUrl bbi/GCF_963662255.1_bCinCin1.1.rmsk.align.bb maxWindowToDraw 5000000 html html/GCF_963662255.1_bCinCin1.1.repeatMasker track repeatModeler shortLabel RepeatModeler longLabel RepeatModeler Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCF_963662255.1_bCinCin1.1.rModel.bb xrefDataUrl bbi/GCF_963662255.1_bCinCin1.1.rModel.align.bb maxWindowToDraw 5000000 html html/GCF_963662255.1_bCinCin1.1.repeatModeler track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCF_963662255.1_bCinCin1.1.simpleRepeat.bb html html/GCF_963662255.1_bCinCin1.1.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_963662255.1-RS_2024_01 (2024-01-26) html html/GCF_963662255.1_bCinCin1.1.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=$$" labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_963662255.1_bCinCin1.1.ncbiRefSeq.ix bigDataUrl bbi/GCF_963662255.1_bCinCin1.1.ncbiRefSeq.bb longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given baseColorDefault genomicCodons priority 1 track ncbiRefSeqPredicted color 12,12,120 parent refSeqComposite on shortLabel RefSeq Predicted longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*) type bigGenePred urls geneName="https://www.ncbi.nlm.nih.gov/nuccore/$$?report=genbank" geneName2="https://www.ncbi.nlm.nih.gov/datasets/gene/$D/?search=$$" labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_963662255.1_bCinCin1.1.ncbiRefSeqPredicted.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_963662255.1_bCinCin1.1.ncbiRefSeqPredicted.bb baseColorUseCds given baseColorDefault genomicCodons priority 3 track ncbiRefSeqOther color 32,32,32 parent refSeqComposite on shortLabel RefSeq Other longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*) priority 4 searchIndex name searchTrix ixIxx/GCF_963662255.1_bCinCin1.1.ncbiRefSeqOther.ix bigDataUrl bbi/GCF_963662255.1_bCinCin1.1.ncbiRefSeqOther.bb type bigBed 12 + labelFields name skipEmptyFields on urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" 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_963662255.1_bCinCin1.1.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_963662255.1_bCinCin1.1.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_963662255.1_bCinCin1.1.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_963662255.1_bCinCin1.1.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCF_963662255.1_bCinCin1.1.windowMasker.bb html html/GCF_963662255.1_bCinCin1.1.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_963662255.1_bCinCin1.1.allGaps.bb html html/GCF_963662255.1_bCinCin1.1.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility dense color 180,0,0 type bigGenePred bigDataUrl bbi/GCF_963662255.1_bCinCin1.1.augustus.bb html html/GCF_963662255.1_bCinCin1.1.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_963662255.1_bCinCin1.1.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_963662255.1_bCinCin1.1.xenoRefGene.ix html html/GCF_963662255.1_bCinCin1.1.xenoRefGene