hub GCF_028583685.1 genome assembly shortLabel sugar glider (PSGF00001 2023) longLabel sugar glider (PSGF00001 2023)/Petaurus breviceps papuanus/GCF_028583685.1_PetGlider_PUasm1.0 genome assembly useOneFile on email hclawson@ucsc.edu descriptionUrl html/GCF_028583685.1_PetGlider_PUasm1.0.description.html genome GCF_028583685.1 taxId 3040969 groups groups.txt description sugar glider (PSGF00001 2023) twoBitPath GCF_028583685.1.2bit twoBitBptUrl GCF_028583685.1.2bit.bpt chromSizes GCF_028583685.1.chrom.sizes.txt chromAliasBb GCF_028583685.1.chromAlias.bb organism PetGlider_PUasm1.0 Feb. 2023 defaultPos NW_027186296.1:36534378-36544378 scientificName Petaurus breviceps papuanus htmlPath html/GCF_028583685.1_PetGlider_PUasm1.0.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/028/583/685/GCF_028583685.1 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/028/583/685/GCF_028583685.1 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/028/583/685/GCF_028583685.1 liftOver.GCF_002263795.3 liftOver/GCF_028583685.1ToGCF_002263795.3.over.chain.gz liftOver.hg38 liftOver/GCF_028583685.1ToHg38.over.chain.gz track assembly longLabel Assembly shortLabel Assembly visibility hide colorByStrand 150,100,30 230,170,40 color 150,100,30 altColor 230,170,40 bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.assembly.bb type bigBed 6 html html/GCF_028583685.1_PetGlider_PUasm1.0.assembly searchIndex name searchTrix ixIxx/GCF_028583685.1_PetGlider_PUasm1.0.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_028583685.1_PetGlider_PUasm1.0.cytoBand.bb track gc5Base shortLabel GC Percent longLabel GC Percent in 5-Base Windows group map visibility dense 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_028583685.1_PetGlider_PUasm1.0.gc5Base.bw html html/GCF_028583685.1_PetGlider_PUasm1.0.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCF_028583685.1_PetGlider_PUasm1.0.tanDups track gapOverlap parent tanDups on shortLabel Gap Overlaps longLabel Paired exactly identical sequence on each side of a gap bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.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/GCF_028583685.1_PetGlider_PUasm1.0.tandemDups.bb type bigBed 12 track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.rmsk.bb xrefDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.rmsk.align.bb maxWindowToDraw 5000000 html html/GCF_028583685.1_PetGlider_PUasm1.0.repeatMasker track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.simpleRepeat.bb html html/GCF_028583685.1_PetGlider_PUasm1.0.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_028583685.1-RS_2024_10 (2024-10-13) html html/GCF_028583685.1_PetGlider_PUasm1.0.refSeqComposite priority 2 track ncbiRefSeq parent refSeqComposite on color 12,12,120 shortLabel RefSeq All type bigGenePred urls name2="https://www.ncbi.nlm.nih.gov/gene/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$" labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_028583685.1_PetGlider_PUasm1.0.ncbiRefSeq.ix bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.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 urls name2="https://www.ncbi.nlm.nih.gov/gene/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$" labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_028583685.1_PetGlider_PUasm1.0.ncbiRefSeqCurated.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.ncbiRefSeqCurated.bb baseColorUseCds given baseColorDefault genomicCodons priority 2 track ncbiRefSeqPredicted color 12,12,120 parent refSeqComposite on shortLabel RefSeq Predicted longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*) type bigGenePred urls name2="https://www.ncbi.nlm.nih.gov/gene/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$" labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_028583685.1_PetGlider_PUasm1.0.ncbiRefSeqPredicted.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.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/GCF_028583685.1_PetGlider_PUasm1.0.ncbiRefSeqOther.ix bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.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/GCF_028583685.1_PetGlider_PUasm1.0.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 dense type bigBed 4 + html html/GCF_028583685.1_PetGlider_PUasm1.0.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/GCF_028583685.1_PetGlider_PUasm1.0.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/GCF_028583685.1_PetGlider_PUasm1.0.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.windowMasker.bb html html/GCF_028583685.1_PetGlider_PUasm1.0.windowMasker track allGaps shortLabel All Gaps longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps group map visibility hide type bigBed 3 bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.allGaps.bb html html/GCF_028583685.1_PetGlider_PUasm1.0.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility dense color 180,0,0 type bigGenePred bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.augustus.bb html html/GCF_028583685.1_PetGlider_PUasm1.0.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/GCF_028583685.1_PetGlider_PUasm1.0.xenoRefGene.bb url https://www.ncbi.nlm.nih.gov/nuccore/$$ urlLabel NCBI Nucleotide database: labelFields name,geneName,geneName2 defaultLabelFields geneName searchIndex name searchTrix ixIxx/GCF_028583685.1_PetGlider_PUasm1.0.xenoRefGene.ix html html/GCF_028583685.1_PetGlider_PUasm1.0.xenoRefGene track GCF_028583685.1_PetGlider_PUasm1.0ChainNet compositeTrack on shortLabel Chain/Net longLabel Chain alignments to target sequence: GCF_028583685.1_PetGlider_PUasm1.0 subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment subGroup2 species Assembly s000=GCF_002263795.3 s001=hg38 subGroup3 chainType chain_type c00=chain c01=syntenic c02=reciprocal_best c03=lift_over c04=chain_align c05=syntenic_align c06=reciprocal_align c07=lift_over_align dragAndDrop subTracks visibility hide group compGeno color 0,0,0 altColor 255,255,0 type bed 3 chainLinearGap loose chainMinScore 5000 dimensions dimensionX=chainType dimensionY=species sortOrder species=+ view=+ chainType=+ configurable on html html/GCF_028583685.1_PetGlider_PUasm1.0.chainNet track GCF_028583685.1_PetGlider_PUasm1.0ChainNetViewchain shortLabel Chains view chain visibility dense parent GCF_028583685.1_PetGlider_PUasm1.0ChainNet spectrum on track GCF_028583685.1_PetGlider_PUasm1.0ChainNetViewSynTen shortLabel Syntenic view synten visibility hide parent GCF_028583685.1_PetGlider_PUasm1.0ChainNet spectrum on track GCF_028583685.1_PetGlider_PUasm1.0ChainNetViewRBest shortLabel Reciprocal best view rbest visibility hide parent GCF_028583685.1_PetGlider_PUasm1.0ChainNet spectrum on track GCF_028583685.1_PetGlider_PUasm1.0ChainNetViewLiftOver shortLabel Lift over view liftover visibility hide parent GCF_028583685.1_PetGlider_PUasm1.0ChainNet spectrum on track chainGCF_002263795.3 parent GCF_028583685.1_PetGlider_PUasm1.0ChainNetViewchain on subGroups view=chain species=s000 chainType=c00 shortLabel cattle Chain longLabel cattle/GCF_002263795.3_ARS-UCD2.0 (2023-07-01) Chained Alignments type bigChain GCF_002263795.3 bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.chainGCF_002263795.3.bb linkDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.chainGCF_002263795.3Link.bb otherDb GCF_002263795.3 html html/GCF_028583685.1_PetGlider_PUasm1.0.chainNet priority 92.620 track chainSynGCF_002263795.3 parent GCF_028583685.1_PetGlider_PUasm1.0ChainNetViewSynTen off subGroups view=synten species=s000 chainType=c01 shortLabel cattle synChain longLabel cattle/GCF_002263795.3_ARS-UCD2.0 (2023-07-01) Chained Alignments type bigChain GCF_002263795.3 bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.chainSynGCF_002263795.3.bb linkDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.chainSynGCF_002263795.3Link.bb otherDb GCF_002263795.3 html html/GCF_028583685.1_PetGlider_PUasm1.0.chainNet priority 92.620 track chainRBestGCF_002263795.3 parent GCF_028583685.1_PetGlider_PUasm1.0ChainNetViewRBest off subGroups view=rbest species=s000 chainType=c02 shortLabel cattle rbChain longLabel cattle/GCF_002263795.3_ARS-UCD2.0 (2023-07-01) Chained Alignments type bigChain GCF_002263795.3 bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.chainRBestGCF_002263795.3.bb linkDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.chainRBestGCF_002263795.3Link.bb otherDb GCF_002263795.3 html html/GCF_028583685.1_PetGlider_PUasm1.0.chainNet priority 92.620 track chainLiftOverGCF_002263795.3 parent GCF_028583685.1_PetGlider_PUasm1.0ChainNetViewLiftOver off subGroups view=liftover species=s000 chainType=c03 shortLabel cattle loChain longLabel cattle/GCF_002263795.3_ARS-UCD2.0 (2023-07-01) Chained Alignments type bigChain GCF_002263795.3 bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.chainLiftOverGCF_002263795.3.bb linkDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.chainLiftOverGCF_002263795.3Link.bb otherDb GCF_002263795.3 html html/GCF_028583685.1_PetGlider_PUasm1.0.chainNet priority 92.620 track chainHg38 parent GCF_028583685.1_PetGlider_PUasm1.0ChainNetViewchain off subGroups view=chain species=s001 chainType=c00 shortLabel Human/hg38 Chain longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments type bigChain hg38 bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.chainHg38.bb linkDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.chainHg38Link.bb otherDb hg38 html html/GCF_028583685.1_PetGlider_PUasm1.0.chainNet priority 92.848 track chainSynHg38 parent GCF_028583685.1_PetGlider_PUasm1.0ChainNetViewSynTen off subGroups view=synten species=s001 chainType=c01 shortLabel Human/hg38 synChain longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments type bigChain hg38 bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.chainSynHg38.bb linkDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.chainSynHg38Link.bb otherDb hg38 html html/GCF_028583685.1_PetGlider_PUasm1.0.chainNet priority 92.848 track chainRBestHg38 parent GCF_028583685.1_PetGlider_PUasm1.0ChainNetViewRBest off subGroups view=rbest species=s001 chainType=c02 shortLabel Human/hg38 rbChain longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments type bigChain hg38 bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.chainRBestHg38.bb linkDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.chainRBestHg38Link.bb otherDb hg38 html html/GCF_028583685.1_PetGlider_PUasm1.0.chainNet priority 92.848 track chainLiftOverHg38 parent GCF_028583685.1_PetGlider_PUasm1.0ChainNetViewLiftOver off subGroups view=liftover species=s001 chainType=c03 shortLabel Human/hg38 loChain longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments type bigChain hg38 bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.chainLiftOverHg38.bb linkDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.chainLiftOverHg38Link.bb otherDb hg38 html html/GCF_028583685.1_PetGlider_PUasm1.0.chainNet priority 92.848 track GCF_028583685.1_PetGlider_PUasm1.0MafNetViewnet shortLabel Nets view align visibility hide parent GCF_028583685.1_PetGlider_PUasm1.0ChainNet track netGCF_002263795.3 parent GCF_028583685.1_PetGlider_PUasm1.0MafNetViewnet off subGroups view=align species=s000 chainType=c04 shortLabel cattle mafNet longLabel cattle/GCF_002263795.3_ARS-UCD2.0 (2023-07-01) Chained Alignments type bigMaf bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.GCF_002263795.3.net.bb summary bbi/GCF_028583685.1_PetGlider_PUasm1.0.GCF_002263795.3.net.summary.bb speciesOrder GCF_002263795.3 html html/GCF_028583685.1_PetGlider_PUasm1.0.chainNet priority 92.620 track synNetGCF_002263795.3 parent GCF_028583685.1_PetGlider_PUasm1.0MafNetViewnet off subGroups view=align species=s000 chainType=c05 shortLabel cattle synNet longLabel cattle/GCF_002263795.3_ARS-UCD2.0 (2023-07-01) Chained Alignments type bigMaf bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.GCF_002263795.3.synNet.bb summary bbi/GCF_028583685.1_PetGlider_PUasm1.0.GCF_002263795.3.synNet.summary.bb speciesOrder GCF_002263795.3 html html/GCF_028583685.1_PetGlider_PUasm1.0.chainNet priority 92.620 track rbestNetGCF_002263795.3 parent GCF_028583685.1_PetGlider_PUasm1.0MafNetViewnet off subGroups view=align species=s000 chainType=c06 shortLabel cattle rbestNet longLabel cattle/GCF_002263795.3_ARS-UCD2.0 (2023-07-01) Chained Alignments type bigMaf bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.GCF_002263795.3.rbestNet.bb summary bbi/GCF_028583685.1_PetGlider_PUasm1.0.GCF_002263795.3.rbestNet.summary.bb speciesOrder GCF_002263795.3 html html/GCF_028583685.1_PetGlider_PUasm1.0.chainNet priority 92.620 track netHg38 parent GCF_028583685.1_PetGlider_PUasm1.0MafNetViewnet off subGroups view=align species=s001 chainType=c04 shortLabel Human/hg38 mafNet longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments type bigMaf bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.hg38.net.bb summary bbi/GCF_028583685.1_PetGlider_PUasm1.0.hg38.net.summary.bb speciesOrder hg38 html html/GCF_028583685.1_PetGlider_PUasm1.0.chainNet priority 92.848 track synNetHg38 parent GCF_028583685.1_PetGlider_PUasm1.0MafNetViewnet off subGroups view=align species=s001 chainType=c05 shortLabel Human/hg38 synNet longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments type bigMaf bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.hg38.synNet.bb summary bbi/GCF_028583685.1_PetGlider_PUasm1.0.hg38.synNet.summary.bb speciesOrder hg38 html html/GCF_028583685.1_PetGlider_PUasm1.0.chainNet priority 92.848 track rbestNetHg38 parent GCF_028583685.1_PetGlider_PUasm1.0MafNetViewnet off subGroups view=align species=s001 chainType=c06 shortLabel Human/hg38 rbestNet longLabel Human/hg38/hg38 (Dec. 2013) Chained Alignments type bigMaf bigDataUrl bbi/GCF_028583685.1_PetGlider_PUasm1.0.hg38.rbestNet.bb summary bbi/GCF_028583685.1_PetGlider_PUasm1.0.hg38.rbestNet.summary.bb speciesOrder hg38 html html/GCF_028583685.1_PetGlider_PUasm1.0.chainNet priority 92.848 track Tiberius bigDataUrl contrib/tiberius/tiberius.bigGenePred.bb shortLabel Tiberius genes longLabel Tiberius ab initio gene prediction type bigGenePred visibility pack color 0,102,204 noScoreFilter on type bigGenePred html contrib/tiberius/Tiberius.html group genes dataVersion Tiberius version 2025-01-07 baseColorDefault genomicCodons