hub GCA_028858705.1 genome assembly shortLabel whooping crane (maternal hap 2023 genbank) longLabel whooping crane (maternal hap 2023 genbank)/Grus americana/GCA_028858705.1_bGruAme1.mat genome assembly useOneFile on email hclawson@ucsc.edu descriptionUrl html/GCA_028858705.1_bGruAme1.mat.description.html genome GCA_028858705.1 taxId 9117 groups groups.txt description whooping crane (maternal hap 2023 genbank) twoBitPath GCA_028858705.1.2bit twoBitBptUrl GCA_028858705.1.2bit.bpt chromSizes GCA_028858705.1.chrom.sizes.txt chromAliasBb GCA_028858705.1.chromAlias.bb chromAuthority ucsc organism bGruAme1.mat Feb. 2023 defaultPos CM054305.1:73289446-73299446 scientificName Grus americana htmlPath html/GCA_028858705.1_bGruAme1.mat.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/028/858/705/GCA_028858705.1 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/028/858/705/GCA_028858705.1 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/028/858/705/GCA_028858705.1 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_028858705.1_bGruAme1.mat.assembly.bb type bigBed 6 html html/GCA_028858705.1_bGruAme1.mat.assembly searchIndex name searchTrix ixIxx/GCA_028858705.1_bGruAme1.mat.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_028858705.1_bGruAme1.mat.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_028858705.1_bGruAme1.mat.gc5Base.bw html html/GCA_028858705.1_bGruAme1.mat.gc5Base track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCA_028858705.1_bGruAme1.mat.rmsk.bb xrefDataUrl bbi/GCA_028858705.1_bGruAme1.mat.rmsk.align.bb maxWindowToDraw 5000000 html html/GCA_028858705.1_bGruAme1.mat.repeatMasker track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCA_028858705.1_bGruAme1.mat.simpleRepeat.bb html html/GCA_028858705.1_bGruAme1.mat.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_028858705.1-RS_2023_03 (2023-04-02) html html/GCA_028858705.1_bGruAme1.mat.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_028858705.1_bGruAme1.mat.ncbiRefSeq.ix bigDataUrl bbi/GCA_028858705.1_bGruAme1.mat.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_028858705.1_bGruAme1.mat.ncbiRefSeqPredicted.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCA_028858705.1_bGruAme1.mat.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_028858705.1_bGruAme1.mat.ncbiRefSeqOther.ix bigDataUrl bbi/GCA_028858705.1_bGruAme1.mat.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_028858705.1_bGruAme1.mat.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_028858705.1_bGruAme1.mat.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_028858705.1_bGruAme1.mat.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_028858705.1_bGruAme1.mat.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCA_028858705.1_bGruAme1.mat.windowMasker.bb html html/GCA_028858705.1_bGruAme1.mat.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_028858705.1_bGruAme1.mat.allGaps.bb html html/GCA_028858705.1_bGruAme1.mat.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility dense color 180,0,0 type bigGenePred bigDataUrl bbi/GCA_028858705.1_bGruAme1.mat.augustus.bb html html/GCA_028858705.1_bGruAme1.mat.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_028858705.1_bGruAme1.mat.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_028858705.1_bGruAme1.mat.xenoRefGene.ix html html/GCA_028858705.1_bGruAme1.mat.xenoRefGene