hub GCA_964188545.1 genome assembly shortLabel Southeastern Asian house mouse (T2T 2024) longLabel Southeastern Asian house mouse (T2T 2024)/Mus musculus castaneus/GCA_964188545.1_CAST_EiJ_T2T_v1 genome assembly useOneFile on email hclawson@ucsc.edu descriptionUrl html/GCA_964188545.1_CAST_EiJ_T2T_v1.description.html genome GCA_964188545.1 taxId 10091 groups groups.txt description Southeastern Asian house mouse (T2T 2024) twoBitPath GCA_964188545.1.2bit twoBitBptUrl GCA_964188545.1.2bit.bpt chromSizes GCA_964188545.1.chrom.sizes.txt chromAliasBb GCA_964188545.1.chromAlias.bb organism CAST_EiJ_T2T_v1 Jun. 2024 defaultPos OZ077261.1:73319489-73329489 scientificName Mus musculus castaneus htmlPath html/GCA_964188545.1_CAST_EiJ_T2T_v1.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/964/188/545/GCA_964188545.1 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/964/188/545/GCA_964188545.1 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/964/188/545/GCA_964188545.1 liftOver.mm39 liftOver/GCA_964188545.1ToMm39.over.chain.gz 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_964188545.1_CAST_EiJ_T2T_v1.assembly.bb type bigBed 6 html html/GCA_964188545.1_CAST_EiJ_T2T_v1.assembly searchIndex name searchTrix ixIxx/GCA_964188545.1_CAST_EiJ_T2T_v1.assembly.ix url https://www.ncbi.nlm.nih.gov/nuccore/$$ urlLabel NCBI Nucleotide database: group map track gap longLabel AGP gap shortLabel Gap (AGP defined) visibility dense color 0,0,0 bigDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.gap.bb type bigBed 4 group map html html/GCA_964188545.1_CAST_EiJ_T2T_v1.gap track cytoBandIdeo shortLabel Chromosome Band (Ideogram) longLabel Ideogram for Orientation group map visibility dense type bigBed 4 + bigDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.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_964188545.1_CAST_EiJ_T2T_v1.gc5Base.bw html html/GCA_964188545.1_CAST_EiJ_T2T_v1.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCA_964188545.1_CAST_EiJ_T2T_v1.tanDups track gapOverlap parent tanDups on shortLabel Gap Overlaps longLabel Paired exactly identical sequence on each side of a gap bigDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.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/GCA_964188545.1_CAST_EiJ_T2T_v1.tandemDups.bb type bigBed 12 track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.rmsk.bb xrefDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.rmsk.align.bb maxWindowToDraw 5000000 html html/GCA_964188545.1_CAST_EiJ_T2T_v1.repeatMasker track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.simpleRepeat.bb html html/GCA_964188545.1_CAST_EiJ_T2T_v1.simpleRepeat 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_964188545.1_CAST_EiJ_T2T_v1.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_964188545.1_CAST_EiJ_T2T_v1.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_964188545.1_CAST_EiJ_T2T_v1.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.windowMasker.bb html html/GCA_964188545.1_CAST_EiJ_T2T_v1.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_964188545.1_CAST_EiJ_T2T_v1.allGaps.bb html html/GCA_964188545.1_CAST_EiJ_T2T_v1.allGaps track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility pack color 180,0,0 type bigGenePred bigDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.augustus.bb html html/GCA_964188545.1_CAST_EiJ_T2T_v1.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_964188545.1_CAST_EiJ_T2T_v1.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_964188545.1_CAST_EiJ_T2T_v1.xenoRefGene.ix html html/GCA_964188545.1_CAST_EiJ_T2T_v1.xenoRefGene ############################################################################## # mm39 - Mouse - Mus musculus - taxId: 10090 ############################################################################## track chainNetMm39 compositeTrack on shortLabel Mouse Chain/Net longLabel Mouse (Jun. 2020 (GRCm39/mm39)), 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 3000 chainLinearGap medium matrixHeader A, C, G, T otherDb mm39 html html/GCA_964188545.1_CAST_EiJ_T2T_v1.chainNet track chainNetMm39Viewchain shortLabel Chain view chain visibility pack parent chainNetMm39 spectrum on track chainMm39 parent chainNetMm39Viewchain subGroups view=chain shortLabel Mouse Chain longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Chained Alignments type bigChain mm39 bigDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.chainMm39.bb linkDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.chainMm39Link.bb priority 1 track chainSynMm39 parent chainNetMm39Viewchain subGroups view=chain shortLabel Mouse synChain longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Syntenic Chained Alignments type bigChain mm39 bigDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.chainSynMm39.bb linkDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.chainSynMm39Link.bb priority 2 track chainRBestMm39 parent chainNetMm39Viewchain subGroups view=chain shortLabel Mouse rbChain longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Reciprocal Best Chained Alignments type bigChain mm39 bigDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.chainRBestMm39.bb linkDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.chainRBestMm39Link.bb priority 3 track chainLiftOverMm39 parent chainNetMm39Viewchain subGroups view=chain shortLabel Mouse loChain longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Lift Over Chained Alignments type bigChain mm39 bigDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.chainLiftOverMm39.bb linkDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.chainLiftOverMm39Link.bb priority 4 track mafNetMm39Viewnet shortLabel Net view net visibility full parent chainNetMm39 track netMm39 parent mafNetMm39Viewnet subGroups view=net shortLabel Mouse net longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Net Alignment type bigMaf bigDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.mm39.net.bb summary bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.mm39.net.summary.bb speciesOrder mm39 priority 5 track synNetMm39 parent mafNetMm39Viewnet subGroups view=net shortLabel Mouse synNet longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Syntenic Net Alignment type bigMaf bigDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.mm39.synNet.bb summary bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.mm39.synNet.summary.bb speciesOrder mm39 priority 6 track rbestNetMm39 parent mafNetMm39Viewnet subGroups view=net shortLabel Mouse rbestNet longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Reciprocal Best Net Alignment type bigMaf bigDataUrl bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.mm39.rbestNet.bb summary bbi/GCA_964188545.1_CAST_EiJ_T2T_v1.mm39.rbestNet.summary.bb speciesOrder mm39 priority 7