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_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.assembly.bb type bigBed 6 html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.assembly searchIndex name searchTrix ixIxx/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_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_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_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_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.gc5Base.bw html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.tanDups track tandemDups parent tanDups on shortLabel Tandem Dups longLabel Paired exactly identical sequence survey over entire genome assembly bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.tandemDups.bb type bigBed 12 track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.rmsk.bb xrefDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.rmsk.align.bb maxWindowToDraw 5000000 html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.repeatMasker track repeatModeler shortLabel RepeatModeler longLabel RepeatModeler Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.rModel.bb xrefDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.rModel.align.bb maxWindowToDraw 5000000 html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.repeatModeler track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.simpleRepeat.bb html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_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 RefSeq GCF_029289425.1-RS_2023_04 (2023-04-20) html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.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=$$" labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.ncbiRefSeq.ix bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.ncbiRefSeq.bb longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given baseColorDefault genomicCodons priority 1 track ncbiRefSeqCurated color 12,12,120 parent refSeqComposite on shortLabel RefSeq Curated longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) type bigGenePred urls geneName="https://www.ncbi.nlm.nih.gov/nuccore/$$?report=genbank" geneName2="https://www.ncbi.nlm.nih.gov/datasets/gene/$D/?search=$$" labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.ncbiRefSeqCurated.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.ncbiRefSeqCurated.bb baseColorUseCds given baseColorDefault genomicCodons priority 2 track ncbiRefSeqPredicted color 12,12,120 parent refSeqComposite on shortLabel RefSeq Predicted longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*) type bigGenePred urls geneName="https://www.ncbi.nlm.nih.gov/nuccore/$$?report=genbank" geneName2="https://www.ncbi.nlm.nih.gov/datasets/gene/$D/?search=$$" labelFields name,geneName,geneName2 defaultLabelFields geneName2 searchIndex name searchTrix ixIxx/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.ncbiRefSeqPredicted.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.ncbiRefSeqPredicted.bb baseColorUseCds given baseColorDefault genomicCodons priority 3 track ncbiRefSeqOther color 32,32,32 parent refSeqComposite on shortLabel RefSeq Other longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*) priority 4 searchIndex name searchTrix ixIxx/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.ncbiRefSeqOther.ix bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.ncbiRefSeqOther.bb type bigBed 12 + labelFields name skipEmptyFields on urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" 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_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_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_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_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_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_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_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_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_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.windowMasker.bb html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_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_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.allGaps.bb html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility dense color 180,0,0 type bigGenePred bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.augustus.bb html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_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_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_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_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.xenoRefGene.ix html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.xenoRefGene track GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priChainNet compositeTrack on shortLabel Chain/Net longLabel Chain alignments to target sequence: GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri subGroup1 view Views chain=Chains synten=Syntenic rbest=Reciprocal_best liftover=Lift_over align=Alignment subGroup2 species Assembly s000=hs1 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_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainNet track GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priChainNetViewchain shortLabel Chains view chain visibility dense parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priChainNet spectrum on track GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priChainNetViewSynTen shortLabel Syntenic view synten visibility hide parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priChainNet spectrum on track GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priChainNetViewRBest shortLabel Reciprocal best view rbest visibility hide parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priChainNet spectrum on track GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priChainNetViewLiftOver shortLabel Lift over view liftover visibility hide parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priChainNet spectrum on track chainHs1 parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priChainNetViewchain on subGroups view=chain species=s000 chainType=c00 shortLabel hs1 Chain longLabel hs1/hs1 () Chained Alignments type bigChain hs1 bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainHs1.bb linkDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainHs1Link.bb otherDb hs1 html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainNet priority 13.055 track chainSynHs1 parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priChainNetViewSynTen off subGroups view=synten species=s000 chainType=c01 shortLabel hs1 synChain longLabel hs1/hs1 () Chained Alignments type bigChain hs1 bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainSynHs1.bb linkDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainSynHs1Link.bb otherDb hs1 html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainNet priority 13.055 track chainRBestHs1 parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priChainNetViewRBest off subGroups view=rbest species=s000 chainType=c02 shortLabel hs1 rbChain longLabel hs1/hs1 () Chained Alignments type bigChain hs1 bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainRBestHs1.bb linkDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainRBestHs1Link.bb otherDb hs1 html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainNet priority 13.055 track chainHg38 parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priChainNetViewchain off subGroups view=chain species=s001 chainType=c00 shortLabel hg38 Chain longLabel hg38/hg38 () Chained Alignments type bigChain hg38 bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainHg38.bb linkDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainHg38Link.bb otherDb hg38 html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainNet priority 13.123 track chainSynHg38 parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priChainNetViewSynTen off subGroups view=synten species=s001 chainType=c01 shortLabel hg38 synChain longLabel hg38/hg38 () Chained Alignments type bigChain hg38 bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainSynHg38.bb linkDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainSynHg38Link.bb otherDb hg38 html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainNet priority 13.123 track chainRBestHg38 parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priChainNetViewRBest off subGroups view=rbest species=s001 chainType=c02 shortLabel hg38 rbChain longLabel hg38/hg38 () Chained Alignments type bigChain hg38 bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainRBestHg38.bb linkDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainRBestHg38Link.bb otherDb hg38 html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainNet priority 13.123 track GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priMafNetViewnet shortLabel Nets view align visibility hide parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priChainNet track netHs1 parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priMafNetViewnet off subGroups view=align species=s000 chainType=c04 shortLabel hs1 mafNet longLabel hs1/hs1 () Chained Alignments type bigMaf bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.hs1.net.bb summary bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.hs1.net.summary.bb speciesOrder hs1 html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainNet priority 13.055 track synNetHs1 parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priMafNetViewnet off subGroups view=align species=s000 chainType=c05 shortLabel hs1 synNet longLabel hs1/hs1 () Chained Alignments type bigMaf bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.hs1.synNet.bb summary bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.hs1.synNet.summary.bb speciesOrder hs1 html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainNet priority 13.055 track rbestNetHs1 parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priMafNetViewnet off subGroups view=align species=s000 chainType=c06 shortLabel hs1 rbestNet longLabel hs1/hs1 () Chained Alignments type bigMaf bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.hs1.rbestNet.bb summary bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.hs1.rbestNet.summary.bb speciesOrder hs1 html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainNet priority 13.055 track netHg38 parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priMafNetViewnet off subGroups view=align species=s001 chainType=c04 shortLabel hg38 mafNet longLabel hg38/hg38 () Chained Alignments type bigMaf bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.hg38.net.bb summary bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.hg38.net.summary.bb speciesOrder hg38 html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainNet priority 13.123 track synNetHg38 parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priMafNetViewnet off subGroups view=align species=s001 chainType=c05 shortLabel hg38 synNet longLabel hg38/hg38 () Chained Alignments type bigMaf bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.hg38.synNet.bb summary bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.hg38.synNet.summary.bb speciesOrder hg38 html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainNet priority 13.123 track rbestNetHg38 parent GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_priMafNetViewnet off subGroups view=align species=s001 chainType=c06 shortLabel hg38 rbestNet longLabel hg38/hg38 () Chained Alignments type bigMaf bigDataUrl bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.hg38.rbestNet.bb summary bbi/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.hg38.rbestNet.summary.bb speciesOrder hg38 html html/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri.chainNet priority 13.123