hub GCF_003957565.2 genome assembly shortLabel zebra finch (Blue55 v1.4 primary hap 2021) longLabel zebra finch (Blue55 v1.4 primary hap 2021)/Taeniopygia guttata/GCF_003957565.2_bTaeGut1.4.pri genome assembly useOneFile on email hclawson@ucsc.edu descriptionUrl html/GCF_003957565.2_bTaeGut1.4.pri.description.html genome GCF_003957565.2 taxId 59729 groups groups.txt description zebra finch (Blue55 v1.4 primary hap 2021) twoBitPath GCF_003957565.2.2bit twoBitBptUrl GCF_003957565.2.2bit.bpt chromSizes GCF_003957565.2.chrom.sizes.txt chromAliasBb GCF_003957565.2.chromAlias.bb chromAuthority ucsc organism bTaeGut1.4.pri May 2021 defaultPos NC_044213.2:50551029-50561029 scientificName Taeniopygia guttata htmlPath html/GCF_003957565.2_bTaeGut1.4.pri.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/003/957/565/GCF_003957565.2 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/003/957/565/GCF_003957565.2 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/003/957/565/GCF_003957565.2 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_003957565.2_bTaeGut1.4.pri.assembly.bb type bigBed 6 html html/GCF_003957565.2_bTaeGut1.4.pri.assembly searchIndex name searchTrix ixIxx/GCF_003957565.2_bTaeGut1.4.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/GCF_003957565.2_bTaeGut1.4.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/GCF_003957565.2_bTaeGut1.4.pri.gc5Base.bw html html/GCF_003957565.2_bTaeGut1.4.pri.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCF_003957565.2_bTaeGut1.4.pri.tanDups track gapOverlap parent tanDups on shortLabel Gap Overlaps longLabel Paired exactly identical sequence on each side of a gap bigDataUrl bbi/GCF_003957565.2_bTaeGut1.4.pri.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_003957565.2_bTaeGut1.4.pri.tandemDups.bb type bigBed 12 track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCF_003957565.2_bTaeGut1.4.pri.rmsk.bb xrefDataUrl bbi/GCF_003957565.2_bTaeGut1.4.pri.rmsk.align.bb maxWindowToDraw 5000000 html html/GCF_003957565.2_bTaeGut1.4.pri.repeatMasker track repeatModeler shortLabel RepeatModeler longLabel RepeatModeler Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCF_003957565.2_bTaeGut1.4.pri.rModel.bb xrefDataUrl bbi/GCF_003957565.2_bTaeGut1.4.pri.rModel.align.bb maxWindowToDraw 5000000 html html/GCF_003957565.2_bTaeGut1.4.pri.repeatModeler track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCF_003957565.2_bTaeGut1.4.pri.simpleRepeat.bb html html/GCF_003957565.2_bTaeGut1.4.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 Taeniopygia guttata Annotation Release 106 (2021-05-26) html html/GCF_003957565.2_bTaeGut1.4.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/GCF_003957565.2_bTaeGut1.4.pri.ncbiRefSeq.ix bigDataUrl bbi/GCF_003957565.2_bTaeGut1.4.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 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_003957565.2_bTaeGut1.4.pri.ncbiRefSeqCurated.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_003957565.2_bTaeGut1.4.pri.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_003957565.2_bTaeGut1.4.pri.ncbiRefSeqPredicted.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_003957565.2_bTaeGut1.4.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/GCF_003957565.2_bTaeGut1.4.pri.ncbiRefSeqOther.ix bigDataUrl bbi/GCF_003957565.2_bTaeGut1.4.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/GCF_003957565.2_bTaeGut1.4.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/GCF_003957565.2_bTaeGut1.4.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/GCF_003957565.2_bTaeGut1.4.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/GCF_003957565.2_bTaeGut1.4.pri.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCF_003957565.2_bTaeGut1.4.pri.windowMasker.bb html html/GCF_003957565.2_bTaeGut1.4.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/GCF_003957565.2_bTaeGut1.4.pri.allGaps.bb html html/GCF_003957565.2_bTaeGut1.4.pri.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility dense color 180,0,0 type bigGenePred bigDataUrl bbi/GCF_003957565.2_bTaeGut1.4.pri.augustus.bb html html/GCF_003957565.2_bTaeGut1.4.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/GCF_003957565.2_bTaeGut1.4.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/GCF_003957565.2_bTaeGut1.4.pri.xenoRefGene.ix html html/GCF_003957565.2_bTaeGut1.4.pri.xenoRefGene