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_009870125.1_UCI_Dpse_MV25.assembly.bb type bigBed 6 html html/GCF_009870125.1_UCI_Dpse_MV25.assembly searchIndex name searchTrix ixIxx/GCF_009870125.1_UCI_Dpse_MV25.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_009870125.1_UCI_Dpse_MV25.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_009870125.1_UCI_Dpse_MV25.gc5Base.bw html html/GCF_009870125.1_UCI_Dpse_MV25.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCF_009870125.1_UCI_Dpse_MV25.tanDups track tandemDups parent tanDups on shortLabel Tandem Dups longLabel Paired exactly identical sequence survey over entire genome assembly bigDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.tandemDups.bb type bigBed 12 track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.rmsk.bb maxWindowToDraw 5000000 html html/GCF_009870125.1_UCI_Dpse_MV25.repeatMasker track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.simpleRepeat.bb html html/GCF_009870125.1_UCI_Dpse_MV25.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 Drosophila pseudoobscura Annotation Release 104 (2020-04-14) html html/GCF_009870125.1_UCI_Dpse_MV25.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_009870125.1_UCI_Dpse_MV25.ncbiRefSeq.ix bigDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.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_009870125.1_UCI_Dpse_MV25.ncbiRefSeqCurated.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.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_009870125.1_UCI_Dpse_MV25.ncbiRefSeqPredicted.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.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_009870125.1_UCI_Dpse_MV25.ncbiRefSeqOther.ix bigDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.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_009870125.1_UCI_Dpse_MV25.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_009870125.1_UCI_Dpse_MV25.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_009870125.1_UCI_Dpse_MV25.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_009870125.1_UCI_Dpse_MV25.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.windowMasker.bb html html/GCF_009870125.1_UCI_Dpse_MV25.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_009870125.1_UCI_Dpse_MV25.allGaps.bb html html/GCF_009870125.1_UCI_Dpse_MV25.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility dense color 180,0,0 type bigGenePred bigDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.augustus.bb html html/GCF_009870125.1_UCI_Dpse_MV25.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_009870125.1_UCI_Dpse_MV25.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_009870125.1_UCI_Dpse_MV25.xenoRefGene.ix html html/GCF_009870125.1_UCI_Dpse_MV25.xenoRefGene ############################################################################## # dm6 - D. melanogaster - Drosophila melanogaster - taxId: 7227 ############################################################################## track chainNetDm6 compositeTrack on shortLabel D. melanogaster Chain/Net longLabel D. melanogaster (Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno priority 100.1 color 0,0,0 altColor 100,50,0 type bed 3 sortOrder view=+ matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 chainMinScore 5000 chainLinearGap loose matrixHeader A, C, G, T otherDb dm6 html html/GCF_009870125.1_UCI_Dpse_MV25.chainNet track chainNetDm6Viewchain shortLabel Chain view chain visibility pack parent chainNetDm6 spectrum on track chainDm6 parent chainNetDm6Viewchain subGroups view=chain shortLabel D. melanogaster Chain longLabel D. melanogaster (Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)) Chained Alignments type bigChain dm6 bigDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.chainDm6.bb linkDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.chainDm6Link.bb priority 1 track chainSynDm6 parent chainNetDm6Viewchain subGroups view=chain shortLabel D. melanogaster synChain longLabel D. melanogaster (Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)) Syntenic Chained Alignments type bigChain dm6 bigDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.chainSynDm6.bb linkDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.chainSynDm6Link.bb priority 2 track chainRBestDm6 parent chainNetDm6Viewchain subGroups view=chain shortLabel D. melanogaster rbChain longLabel D. melanogaster (Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)) Reciprocal Best Chained Alignments type bigChain dm6 bigDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.chainRBestDm6.bb linkDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.chainRBestDm6Link.bb priority 3 track mafNetDm6Viewnet shortLabel Net view net visibility full parent chainNetDm6 track netDm6 parent mafNetDm6Viewnet subGroups view=net shortLabel D. melanogaster net longLabel D. melanogaster (Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)) Net Alignment type bigMaf bigDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.dm6.net.bb summary bbi/GCF_009870125.1_UCI_Dpse_MV25.dm6.net.summary.bb speciesOrder dm6 priority 4 track synNetDm6 parent mafNetDm6Viewnet subGroups view=net shortLabel D. melanogaster synNet longLabel D. melanogaster (Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)) Syntenic Net Alignment type bigMaf bigDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.dm6.synNet.bb summary bbi/GCF_009870125.1_UCI_Dpse_MV25.dm6.synNet.summary.bb speciesOrder dm6 priority 5 track rbestNetDm6 parent mafNetDm6Viewnet subGroups view=net shortLabel D. melanogaster rbestNet longLabel D. melanogaster (Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)) Reciprocal Best Net Alignment type bigMaf bigDataUrl bbi/GCF_009870125.1_UCI_Dpse_MV25.dm6.rbestNet.bb summary bbi/GCF_009870125.1_UCI_Dpse_MV25.dm6.rbestNet.summary.bb speciesOrder dm6 priority 6