\nThis track shows human clinically relevant variants from the \nClinVar database,\nmapped from hg38 to the panTro6 genome. The mapping uses UCSC's whole-genome alignments and the \ntool LiftOver. \nThe annotations are somewhat speculative, \nas LiftOver is not meant to be used for cross-organism mapping. Among others, \nLiftOver has no notion of phylogenetic trees or protein orthology, so the \nexact protein to which they are mapped may not be the annotated ortholog.\nIn areas with protein repeats it may have been mapped to the wrong exon. When the \ngenome nucleotide in panTro6 is different from hg38, the corresponding position \ncould be several basepairs away. Generally, the more different the gene, the harder the\nmapping. Before planning assays on these data, a manual alignment and annotation \nof the human and panTro6 nucleotide or amino acid sequences is recommended.\n\n\n
\nGenomic locations of ClinVar variants are labeled with the human ClinVar variant\ndescriptions. For example, the label \"C>G\" usually means that in human, the cDNA \nnucleotide change is from C>T. On a transcript on the reverse strand, the human\ngenome nucleotide on the forward strand would be G. In panTro6, the genome may not\nbe G at this position. Zoom in to see the nucleotide in panTro6, or click the\nvariant to show the human position and nucleotide and the panTro6 nucleotide.
\n\nAll ClinVar information related to each is variant is shown on that\nvariant's details page. Hold the mouse over a feature\nto show the clinical significance of a variant in humans.\n
\n\nOnly short variants with a length < 10 bp on the human genome were\nlifted. A few variants that after lifting result in panTro6 annotations longer than\n30bp were filtered out, too. This can happen in repetitive regions that are\nhard to align.
\n\n\nAnnotations are shaded by clinical annotation:\nred for pathogenic,\ndark grey for uncertain significance or not provided and\ngreen for benign.\n
\n\n\nThe score of the variants is the number of \"stars\" in ClinVar. On the track configuration \npage (above), you can filter the track to show only variants with more than a certain \nnumber of stars. For more information on the star rating, see the \nClinVar documentation.\n
\n\n\nThe raw data can be explored interactively with the \nTable Browser\nor the Data Integrator.\n\n
\nFor automated download and analysis, the genome annotation is stored in a bigBed file that\ncan be downloaded from\nour download server.\nThe files for this track are called clinvarLift.bb. Individual\nregions or the whole genome annotation can be obtained using our tool bigBedToBed\nwhich can be compiled from the source code or downloaded as a precompiled\nbinary for your system. Instructions for downloading source code and binaries can be found\nhere.\nThe tool can also be used to obtain only features within a given range, e.g. \nbigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/panTro6/bbi/clinvarLift.bb -chrom=chr1 -start=0 -end=100000000 stdout
\n\n\n\nThe hg38 ClinvarMain track was annotated with nucleotides and positions, lifted to panTro6,\nfiltered again for variants < 30bp\nand annotated with nucleotides again. The output was converted to the \nbigBed format.\nThe program that performs the mapping is available on\nGithub.\n
\n\n\nThanks to NCBI for making the ClinVar data available on their FTP site as a tab-separated file.\n
\n\n\nLandrum MJ, Lee JM, Benson M, Brown G, Chao C, Chitipiralla S, Gu B, Hart J, Hoffman D, Hoover J\net al.\n\nClinVar: public archive of interpretations of clinically relevant variants.\nNucleic Acids Res. 2016 Jan 4;44(D1):D862-8.\nPMID: 26582918; PMC:
\nThe GC percent track shows the percentage of G (guanine) and C (cytosine) bases\nin 5-base windows. High GC content is typically associated with\ngene-rich areas.\n
\n\nThis track may be configured in a variety of ways to highlight different\napsects of the displayed information. Click the\n"Graph configuration help"\nlink for an explanation of the configuration options.\n\n
The data and presentation of this graph were prepared by\nHiram Clawson.\n
\n\n", "longLabel": "GC Percent in 5-Base Windows", "maxHeightPixels": "128:36:16", "shortLabel": "GC Percent", "track": "gc5BaseBw", "type": "bigWig 0 100", "viewLimits": "30:70", "visibility": "hide", "windowingFunction": "Mean" } }, "description": "GC Percent in 5-Base Windows", "category": [ "Mapping and Sequencing" ] }, { "trackId": "panTro6-HLTOGAannotvHg38v1", "name": "TOGA vs. hg38", "type": "FeatureTrack", "assemblyNames": [ "panTro6" ], "adapter": { "type": "BigBedAdapter", "uri": "https://hgdownload.soe.ucsc.edu/gbdb/panTro6/TOGAvHg38v1/HLTOGAannotVsHg38v1.bb" }, "metadata": { "ucsc": { "bigDataUrl": "/gbdb/panTro6/TOGAvHg38v1/HLTOGAannotVsHg38v1.bb", "group": "genes", "html": "\nTOGA\n(Tool to infer Orthologs from Genome Alignments)\nis a homology-based method that integrates gene annotation, inferring\northologs and classifying genes as intact or lost.\n
\n\n\nAs input, TOGA uses a gene annotation of a reference species\n(human/hg38 for mammals, chicken/galGal6 for birds) and\na whole genome alignment between the reference and query genome.\n
\n\nTOGA implements a novel paradigm that relies on alignments of intronic\nand intergenic regions and uses machine learning to accurately distinguish\northologs from paralogs or processed pseudogenes.\n
\n\nTo annotate genes,\nCESAR 2.0\nis used to determine the positions and boundaries of coding exons of a\nreference transcript in the orthologous genomic locus in the query species.\n
\n\n\nEach annotated transcript is shown in a color-coded classification as\n
\nClicking on a transcript provides additional information about the orthology\nclassification, inactivating mutations, the protein sequence and protein/exon\nalignments.\n
\n\n\nThis data was prepared by the Michael Hiller Lab\n
\n\n\nThe TOGA software is available from\ngithub.com/hillerlab/TOGA\n
\n\n\nKirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales AE, Ahmed AW, Kontopoulos\nDG, Hilgers L et al.\n\nIntegrating gene annotation with orthology inference at scale.\nScience. 2023 Apr 28;380(6643):eabn3107.\nPMID: 37104600; PMC:
CpG islands are associated with genes, particularly housekeeping\ngenes, in vertebrates. CpG islands are typically common near\ntranscription start sites and may be associated with promoter\nregions. Normally a C (cytosine) base followed immediately by a \nG (guanine) base (a CpG) is rare in\nvertebrate DNA because the Cs in such an arrangement tend to be\nmethylated. This methylation helps distinguish the newly synthesized\nDNA strand from the parent strand, which aids in the final stages of\nDNA proofreading after duplication. However, over evolutionary time,\nmethylated Cs tend to turn into Ts because of spontaneous\ndeamination. The result is that CpGs are relatively rare unless\nthere is selective pressure to keep them or a region is not methylated\nfor some other reason, perhaps having to do with the regulation of gene\nexpression. CpG islands are regions where CpGs are present at\nsignificantly higher levels than is typical for the genome as a whole.
\n\n\nThe unmasked version of the track displays potential CpG islands\nthat exist in repeat regions and would otherwise not be visible\nin the repeat masked version.\n
\n\n\nBy default, only the masked version of the track is displayed. To view the\nunmasked version, change the visibility settings in the track controls at\nthe top of this page.\n
\n\nCpG islands were predicted by searching the sequence one base at a\ntime, scoring each dinucleotide (+17 for CG and -1 for others) and\nidentifying maximally scoring segments. Each segment was then\nevaluated for the following criteria:\n\n
\nThe entire genome sequence, masking areas included, was\nused for the construction of the track Unmasked CpG.\nThe track CpG Islands is constructed on the sequence after\nall masked sequence is removed.\n
\n\nThe CpG count is the number of CG dinucleotides in the island. \nThe Percentage CpG is the ratio of CpG nucleotide bases\n(twice the CpG count) to the length. The ratio of observed to expected \nCpG is calculated according to the formula (cited in \nGardiner-Garden et al. (1987)):\n\n
Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)\n\nwhere N = length of sequence.\n
\nThe calculation of the track data is performed by the following command sequence:\n
\ntwoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \n | cpg_lh /dev/stdin 2> cpg_lh.err \n | awk '{$2 = $2 - 1; width = $3 - $2; printf(\"%s t%d t%s t%s %s t%s t%s t%0.0f t%0.1f t%s t%s n\", $1, $2, $3, $5, $6, width, $6, width*$7*0.01, 100.0*2*$6/width, $7, $9);}' \n | sort -k1,1 -k2,2n > cpgIsland.bed\n\nThe unmasked track data is constructed from\ntwoBitToFa -noMask output for the twoBitToFa command.\n\n\n\nCpG islands and its associated tables can be explored interactively using the\nREST API, the\nTable Browser or the\nData Integrator.\nAll the tables can also be queried directly from our public MySQL\nservers, with more information available on our\nhelp page as well as on\nour blog.
\n\nThe source for the cpg_lh program can be obtained from\nsrc/utils/cpgIslandExt/.\nThe cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose \"save file\")\n
\n\nThis track was generated using a modification of a program developed by G. Miklem and L. Hillier \n(unpublished).
\n\n\nGardiner-Garden M, Frommer M.\n\nCpG islands in vertebrate genomes.\nJ Mol Biol. 1987 Jul 20;196(2):261-82.\nPMID: 3656447\n
\n", "longLabel": "CpG Islands (Islands < 300 Bases are Light Green)", "parent": "cpgIslandSuper pack", "priority": "1", "shortLabel": "CpG Islands", "track": "cpgIslandExt" } }, "description": "CpG Islands (Islands < 300 Bases are Light Green)", "category": [ "Regulation" ] }, { "type": "FeatureTrack", "trackId": "panTro6-cpgIslandExtUnmasked", "name": "CpG Islands - Unmasked CpG", "assemblyNames": [ "panTro6" ], "adapter": { "type": "BedTabixAdapter", "bedGzLocation": { "uri": "cpgIslandExtUnmasked.bed.gz" }, "index": { "indexType": "CSI", "location": { "uri": "cpgIslandExtUnmasked.bed.gz.csi" } } }, "metadata": { "ucsc": { "html": "CpG islands are associated with genes, particularly housekeeping\ngenes, in vertebrates. CpG islands are typically common near\ntranscription start sites and may be associated with promoter\nregions. Normally a C (cytosine) base followed immediately by a \nG (guanine) base (a CpG) is rare in\nvertebrate DNA because the Cs in such an arrangement tend to be\nmethylated. This methylation helps distinguish the newly synthesized\nDNA strand from the parent strand, which aids in the final stages of\nDNA proofreading after duplication. However, over evolutionary time,\nmethylated Cs tend to turn into Ts because of spontaneous\ndeamination. The result is that CpGs are relatively rare unless\nthere is selective pressure to keep them or a region is not methylated\nfor some other reason, perhaps having to do with the regulation of gene\nexpression. CpG islands are regions where CpGs are present at\nsignificantly higher levels than is typical for the genome as a whole.
\n\n\nThe unmasked version of the track displays potential CpG islands\nthat exist in repeat regions and would otherwise not be visible\nin the repeat masked version.\n
\n\n\nBy default, only the masked version of the track is displayed. To view the\nunmasked version, change the visibility settings in the track controls at\nthe top of this page.\n
\n\nCpG islands were predicted by searching the sequence one base at a\ntime, scoring each dinucleotide (+17 for CG and -1 for others) and\nidentifying maximally scoring segments. Each segment was then\nevaluated for the following criteria:\n\n
\nThe entire genome sequence, masking areas included, was\nused for the construction of the track Unmasked CpG.\nThe track CpG Islands is constructed on the sequence after\nall masked sequence is removed.\n
\n\nThe CpG count is the number of CG dinucleotides in the island. \nThe Percentage CpG is the ratio of CpG nucleotide bases\n(twice the CpG count) to the length. The ratio of observed to expected \nCpG is calculated according to the formula (cited in \nGardiner-Garden et al. (1987)):\n\n
Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)\n\nwhere N = length of sequence.\n
\nThe calculation of the track data is performed by the following command sequence:\n
\ntwoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \n | cpg_lh /dev/stdin 2> cpg_lh.err \n | awk '{$2 = $2 - 1; width = $3 - $2; printf(\"%s t%d t%s t%s %s t%s t%s t%0.0f t%0.1f t%s t%s n\", $1, $2, $3, $5, $6, width, $6, width*$7*0.01, 100.0*2*$6/width, $7, $9);}' \n | sort -k1,1 -k2,2n > cpgIsland.bed\n\nThe unmasked track data is constructed from\ntwoBitToFa -noMask output for the twoBitToFa command.\n\n\n\nCpG islands and its associated tables can be explored interactively using the\nREST API, the\nTable Browser or the\nData Integrator.\nAll the tables can also be queried directly from our public MySQL\nservers, with more information available on our\nhelp page as well as on\nour blog.
\n\nThe source for the cpg_lh program can be obtained from\nsrc/utils/cpgIslandExt/.\nThe cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose \"save file\")\n
\n\nThis track was generated using a modification of a program developed by G. Miklem and L. Hillier \n(unpublished).
\n\n\nGardiner-Garden M, Frommer M.\n\nCpG islands in vertebrate genomes.\nJ Mol Biol. 1987 Jul 20;196(2):261-82.\nPMID: 3656447\n
\n", "longLabel": "CpG Islands on All Sequence (Islands < 300 Bases are Light Green)", "parent": "cpgIslandSuper hide", "priority": "2", "shortLabel": "Unmasked CpG", "track": "cpgIslandExtUnmasked" } }, "description": "CpG Islands on All Sequence (Islands < 300 Bases are Light Green)", "category": [ "Regulation" ] }, { "type": "FeatureTrack", "trackId": "panTro6-cytoBandIdeo", "name": "Chromosome Band (Ideogram)", "assemblyNames": [ "panTro6" ], "adapter": { "type": "BedTabixAdapter", "bedGzLocation": { "uri": "cytoBandIdeo.bed.gz" }, "index": { "indexType": "CSI", "location": { "uri": "cytoBandIdeo.bed.gz.csi" } } }, "metadata": { "ucsc": { "group": "map", "longLabel": "Ideogram for Orientation", "shortLabel": "Chromosome Band (Ideogram)", "track": "cytoBandIdeo", "type": "bed 4 +", "visibility": "dense", "html": "" } }, "description": "Ideogram for Orientation", "category": [ "Mapping and Sequencing" ] }, { "type": "FeatureTrack", "trackId": "panTro6-gap", "name": "Gap", "assemblyNames": [ "panTro6" ], "adapter": { "type": "BedTabixAdapter", "bedGzLocation": { "uri": "gap.bed.gz" }, "index": { "indexType": "CSI", "location": { "uri": "gap.bed.gz.csi" } } }, "metadata": { "ucsc": { "group": "map", "html": "\nThis track shows the gaps in the Jan. 2018 chimp genome assembly.\n
\n\nGenome assembly procedures are covered in the NCBI\nassembly documentation.
\nNCBI also provides\nspecific information about this assembly.\n
\nThe definition of the gaps in this assembly is from the\nAGP file delivered with the sequence. The NCBI document\nAGP Specification describes the format of the AGP file.\n
\n\nGaps are represented as black boxes in this track.\nIf the relative order and orientation of the contigs on either side\nof the gap is supported by read pair data, \nit is a bridged gap and a white line is drawn \nthrough the black box representing the gap. \n
\nThis assembly contains the following principal types of gaps:\n
\nThis track shows the sequences used in the Jan. 2018 chimp genome assembly.\n
\n\nGenome assembly procedures are covered in the NCBI\nassembly documentation.
\nNCBI also provides\nspecific information about this assembly.\n
\nThe definition of this assembly is from the\nAGP file delivered with the sequence. The NCBI document\nAGP Specification describes the format of the AGP file.\n
\n\nIn dense mode, this track depicts the contigs that make up the \ncurrently viewed scaffold. \nContig boundaries are distinguished by the use of alternating gold and brown \ncoloration. Where gaps\nexist between contigs, spaces are shown between the gold and brown\nblocks. The relative order and orientation of the contigs\nwithin a scaffold is always known; therefore, a line is drawn in the graphical\ndisplay to bridge the blocks.
\n\nComponent types found in this track (with counts of that type in parentheses):\n
\nThis track displays regions that are likely to be useful as microsatellite\nmarkers. These are sequences of at least 15 perfect di-nucleotide and \ntri-nucleotide repeats and tend to be highly polymorphic in the\npopulation.\n
\n\n\nThe data shown in this track are a subset of the Simple Repeats track, \nselecting only those \nrepeats of period 2 and 3, with 100% identity and no indels and with\nat least 15 copies of the repeat. The Simple Repeats track is\ncreated using the \nTandem Repeats Finder. For more information about this \nprogram, see Benson (1999).
\n\n\nTandem Repeats Finder was written by \nGary Benson.
\n\n\nBenson G.\n\nTandem repeats finder: a program to analyze DNA sequences.\nNucleic Acids Res. 1999 Jan 15;27(2):573-80.\nPMID: 9862982; PMC:
\nThis track shows joined fragments of interrupted repeats extracted\nfrom the output of the \nRepeatMasker program which screens DNA sequences\nfor interspersed repeats and low complexity DNA sequences using the\n\nRepbase Update library of repeats from the\nGenetic\nInformation Research Institute (GIRI). Repbase Update is described in\nJurka (2000) in the References section below.\n
\n\n\nThe detailed annotations from RepeatMasker are in the RepeatMasker track. This\ntrack shows fragments of original repeat insertions which have been interrupted\nby insertions of younger repeats or through local rearrangements. The fragments\nare joined using the ID column of RepeatMasker output.\n
\n\n\nIn pack or full mode, each interrupted repeat is displayed as boxes\n(fragments) joined by horizontal lines, labeled with the repeat name.\nIf all fragments are on the same strand, arrows are added to the\nhorizontal line to indicate the strand. In dense or squish mode, labels\nand arrows are omitted and in dense mode, all items are collapsed to\nfit on a single row.\n
\n\n\nItems are shaded according to the average identity score of their\nfragments. Usually, the shade of an item is similar to the shades of\nits fragments unless some fragments are much more diverged than\nothers. The score displayed above is the average identity score,\nclipped to a range of 50% - 100% and then mapped to the range\n0 - 1000 for shading in the browser.\n
\n\n\nUCSC has used the most current versions of the RepeatMasker software\nand repeat libraries available to generate these data. Note that these\nversions may be newer than those that are publicly available on the Internet.\n
\n\n\nData are generated using the RepeatMasker -s flag. Additional flags\nmay be used for certain organisms. See the\nFAQ for more information.\n
\n\n\nThanks to Arian Smit, Robert Hubley and GIRI for providing the tools and\nrepeat libraries used to generate this track.\n
\n\n\nSmit AFA, Hubley R, Green P.\nRepeatMasker Open-3.0.\n\nhttp://www.repeatmasker.org. 1996-2010.\n
\n\n\nRepbase Update is described in:\n
\n\n\nJurka J.\n\nRepbase Update: a database and an electronic journal of repetitive elements.\nTrends Genet. 2000 Sep;16(9):418-420.\nPMID: 10973072\n
\n\n\nFor a discussion of repeats in mammalian genomes, see:\n
\n\n\nSmit AF.\n\nInterspersed repeats and other mementos of transposable elements in mammalian genomes.\nCurr Opin Genet Dev. 1999 Dec;9(6):657-63.\nPMID: 10607616\n
\n\n\nSmit AF.\n\nThe origin of interspersed repeats in the human genome.\nCurr Opin Genet Dev. 1996 Dec;6(6):743-8.\nPMID: 8994846\n
\n" } }, "description": "Fragments of Interrupted Repeats Joined by RepeatMasker ID", "category": [ "Variation and Repeats" ] }, { "type": "FeatureTrack", "trackId": "panTro6-rmsk", "name": "RepeatMasker", "assemblyNames": [ "panTro6" ], "adapter": { "type": "BedTabixAdapter", "bedGzLocation": { "uri": "rmsk.bed.gz" }, "index": { "indexType": "CSI", "location": { "uri": "rmsk.bed.gz.csi" } } }, "metadata": { "ucsc": { "canPack": "off", "group": "varRep", "longLabel": "Repeating Elements by RepeatMasker", "maxWindowToDraw": "10000000", "priority": "1", "shortLabel": "RepeatMasker", "spectrum": "on", "track": "rmsk", "type": "rmsk", "visibility": "dense", "html": "\nThis track was created by using Arian Smit's\nRepeatMasker\nprogram, which screens DNA sequences\nfor interspersed repeats and low complexity DNA sequences. The program\noutputs a detailed annotation of the repeats that are present in the\nquery sequence (represented by this track), as well as a modified version\nof the query sequence in which all the annotated repeats have been masked\n(generally available on the\nDownloads page). RepeatMasker uses the\nRepbase Update library of repeats from the\nGenetic \nInformation Research Institute (GIRI).\nRepbase Update is described in Jurka (2000) in the References section below.\nSome newer assemblies have been made with Dfam, not Repbase. You can\nfind the details for how we make our database data here in our "makeDb/doc/"\ndirectory.
\n\n\nIn full display mode, this track displays up to ten different classes of repeats:\n
\nThe level of color shading in the graphical display reflects the amount of\nbase mismatch, base deletion, and base insertion associated with a repeat\nelement. The higher the combined number of these, the lighter the shading.\n
\n\n\nA "?" at the end of the "Family" or "Class" (for example, DNA?) signifies that\nthe curator was unsure of the classification. At some point in the future,\neither the "?" will be removed or the classification will be changed.
\n\n\nData are generated using the RepeatMasker -s flag. Additional flags\nmay be used for certain organisms. Repeats are soft-masked. Alignments may\nextend through repeats, but are not permitted to initiate in them.\nSee the FAQ for more information.\n
\n\n\nThanks to Arian Smit, Robert Hubley and GIRI for providing the tools and\nrepeat libraries used to generate this track.\n
\n\n\nSmit AFA, Hubley R, Green P. RepeatMasker Open-3.0.\n\nhttp://www.repeatmasker.org. 1996-2010.\n
\n\n\nRepbase Update is described in:\n
\n\n\nJurka J.\n\nRepbase Update: a database and an electronic journal of repetitive elements.\nTrends Genet. 2000 Sep;16(9):418-420.\nPMID: 10973072\n
\n\n\nFor a discussion of repeats in mammalian genomes, see:\n
\n\n\nSmit AF.\n\nInterspersed repeats and other mementos of transposable elements in mammalian genomes.\nCurr Opin Genet Dev. 1999 Dec;9(6):657-63.\nPMID: 10607616\n
\n\n\nSmit AF.\n\nThe origin of interspersed repeats in the human genome.\nCurr Opin Genet Dev. 1996 Dec;6(6):743-8.\nPMID: 8994846\n
\n" } }, "description": "Repeating Elements by RepeatMasker", "category": [ "Variation and Repeats" ] }, { "type": "FeatureTrack", "trackId": "panTro6-simpleRepeat", "name": "Simple Repeats", "assemblyNames": [ "panTro6" ], "adapter": { "type": "BedTabixAdapter", "bedGzLocation": { "uri": "simpleRepeat.bed.gz" }, "index": { "indexType": "CSI", "location": { "uri": "simpleRepeat.bed.gz.csi" } } }, "metadata": { "ucsc": { "group": "varRep", "longLabel": "Simple Tandem Repeats by TRF", "shortLabel": "Simple Repeats", "track": "simpleRepeat", "type": "bed 4 +", "visibility": "hide", "html": "\nThis track displays simple tandem repeats (possibly imperfect repeats) located\nby Tandem Repeats\nFinder (TRF) which is specialized for this purpose. These repeats can\noccur within coding regions of genes and may be quite\npolymorphic. Repeat expansions are sometimes associated with specific\ndiseases.
\n\n\nFor more information about the TRF program, see Benson (1999).\n
\n\n\nTRF was written by \nGary Benson.
\n\n\nBenson G.\n\nTandem repeats finder: a program to analyze DNA sequences.\nNucleic Acids Res. 1999 Jan 15;27(2):573-80.\nPMID: 9862982; PMC:
\nThis track associates UCSC Genome Browser chromosome names to accession\nnames from the International Nucleotide Sequence Database Collaboration (INSDC).\n
\n\n\nThe data were downloaded from the NCBI assembly database.\n
\n\nThe data for this track was prepared by\nHiram Clawson.\n\n" } }, "description": "Accession at INSDC - International Nucleotide Sequence Database Collaboration", "category": [ "Mapping and Sequencing" ] }, { "type": "FeatureTrack", "trackId": "panTro6-ucscToRefSeq", "name": "RefSeq Acc", "assemblyNames": [ "panTro6" ], "adapter": { "type": "BedTabixAdapter", "bedGzLocation": { "uri": "ucscToRefSeq.bed.gz" }, "index": { "indexType": "CSI", "location": { "uri": "ucscToRefSeq.bed.gz.csi" } } }, "metadata": { "ucsc": { "group": "map", "longLabel": "RefSeq Accession", "shortLabel": "RefSeq Acc", "track": "ucscToRefSeq", "type": "bed 4", "url": "https://www.ncbi.nlm.nih.gov/nuccore/$$", "urlLabel": "RefSeq accession:", "visibility": "hide", "html": "
\nThis track associates UCSC Genome Browser chromosome names to accession\nidentifiers from the NCBI Reference Sequence Database (RefSeq).\n
\n\n\nThe data were downloaded from the NCBI assembly database.\n
\n\nThe data for this track was prepared by\nHiram Clawson.\n" } }, "description": "RefSeq Accession", "category": [ "Mapping and Sequencing" ] }, { "type": "FeatureTrack", "trackId": "panTro6-windowmaskerSdust", "name": "WM + SDust", "assemblyNames": [ "panTro6" ], "adapter": { "type": "BedTabixAdapter", "bedGzLocation": { "uri": "windowmaskerSdust.bed.gz" }, "index": { "indexType": "CSI", "location": { "uri": "windowmaskerSdust.bed.gz.csi" } } }, "metadata": { "ucsc": { "group": "varRep", "longLabel": "Genomic Intervals Masked by WindowMasker + SDust", "shortLabel": "WM + SDust", "track": "windowmaskerSdust", "type": "bed 3", "visibility": "hide", "html": "
\nThis track depicts masked sequence as determined by\nWindowMasker. The\nWindowMasker tool is included in the NCBI C++ toolkit. The source code\nfor the entire toolkit is available from the NCBI\n\nFTP site.\n
\n\n\nTo create this track, WindowMasker was run with the following parameters:\n
\nwindowmasker -mk_counts true -input panTro6.fa -output wm_counts\nwindowmasker -ustat wm_counts -sdust true -input panTro6.fa -output repeats.bed\n\nThe repeats.bed (BED3) file was loaded into the "windowmaskerSdust" table for\nthis track.\n\n\n
\nMorgulis A, Gertz EM, Schäffer AA, Agarwala R.\nWindowMasker: window-based masker for sequenced genomes.\nBioinformatics. 2006 Jan 15;22(2):134-41.\nPMID: 16287941\n
\n" } }, "description": "Genomic Intervals Masked by WindowMasker + SDust", "category": [ "Variation and Repeats" ] }, { "type": "FeatureTrack", "trackId": "panTro6-augustusGene", "name": "AUGUSTUS", "assemblyNames": [ "panTro6" ], "adapter": { "type": "Gff3TabixAdapter", "gffGzLocation": { "uri": "augustusGene.gff.gz" }, "index": { "indexType": "CSI", "location": { "uri": "augustusGene.gff.gz.csi" } } }, "metadata": { "ucsc": { "baseColorDefault": "genomicCodons", "baseColorUseCds": "given", "color": "12,105,0", "group": "genes", "longLabel": "AUGUSTUS ab initio gene predictions v3.1", "shortLabel": "AUGUSTUS", "track": "augustusGene", "type": "genePred", "visibility": "hide", "html": "\n This track shows ab initio predictions from the program\n AUGUSTUS (version 3.1).\n The predictions are based on the genome sequence alone.\n
\n\n\nFor more information on the different gene tracks, see our Genes FAQ.
\n\n\nStatistical signal models were built for splice sites, branch-point\npatterns, translation start sites, and the poly-A signal.\nFurthermore, models were built for the sequence content of\nprotein-coding and non-coding regions as well as for the length distributions\nof different exon and intron types. Detailed descriptions of most of these different models\ncan be found in Mario Stanke's\ndissertation.\nThis track shows the most likely gene structure according to a\nSemi-Markov Conditional Random Field model.\nAlternative splicing transcripts were obtained with\na sampling algorithm (--alternatives-from-sampling=true --sample=100 --minexonintronprob=0.2\n--minmeanexonintronprob=0.5 --maxtracks=3 --temperature=2).\n
\n\n\nThe different models used by Augustus were trained on a number of different species-specific\ngene sets, which included 1000-2000 training gene structures. The --species option allows\none to choose the species used for training the models. Different training species were used\nfor the --species option when generating these predictions for different groups of\nassemblies.\n
| Assembly Group | \nTraining Species | \n
| Fish | \nzebrafish\n |
| Birds | \nchicken\n |
| Human and all other vertebrates | \nhuman\n |
| Nematodes | \ncaenorhabditis | \n
| Drosophila | \nfly | \n
| A. mellifera | \nhoneybee1 | \n
| A. gambiae | \nculex | \n
| S. cerevisiae | \nsaccharomyces | \n
\nThis table describes which training species was used for a particular group of assemblies.\nWhen available, the closest related training species was used.\n
\n\n\nStanke M, Diekhans M, Baertsch R, Haussler D.\n\nUsing native and syntenically mapped cDNA alignments to improve de novo gene finding.\nBioinformatics. 2008 Mar 1;24(5):637-44.\nPMID: 18218656\n
\n\n\nStanke M, Waack S.\n\nGene prediction with a hidden Markov model and a new intron submodel.\nBioinformatics. 2003 Oct;19 Suppl 2:ii215-25.\nPMID: 14534192\n
\n" } }, "description": "AUGUSTUS ab initio gene predictions v3.1", "category": [ "Genes and Gene Predictions" ] }, { "type": "FeatureTrack", "trackId": "panTro6-genscan", "name": "Genscan Genes", "assemblyNames": [ "panTro6" ], "adapter": { "type": "Gff3TabixAdapter", "gffGzLocation": { "uri": "genscan.gff.gz" }, "index": { "indexType": "CSI", "location": { "uri": "genscan.gff.gz.csi" } } }, "metadata": { "ucsc": { "color": "170,100,0", "group": "genes", "longLabel": "Genscan Gene Predictions", "shortLabel": "Genscan Genes", "track": "genscan", "type": "genePred genscanPep", "visibility": "hide", "html": "\nThis track shows predictions from the\nGenscan program\nwritten by Chris Burge.\nThe predictions are based on transcriptional, translational and donor/acceptor\nsplicing signals as well as the length and compositional distributions of exons,\nintrons and intergenic regions.\n
\n\n\nFor more information on the different gene tracks, see our Genes FAQ.
\n\n\nThis track follows the display conventions for\ngene prediction\ntracks.\n
\n\n\nThe track description page offers the following filter and configuration\noptions:\n
\nFor a description of the Genscan program and the model that underlies it,\nrefer to Burge and Karlin (1997) in the References section below.\nThe splice site models used are described in more detail in Burge (1998)\nbelow.\n
\n\n\nBurge C.\nModeling Dependencies in Pre-mRNA Splicing Signals.\nIn: Salzberg S, Searls D, Kasif S, editors.\nComputational Methods in Molecular Biology.\nAmsterdam: Elsevier Science; 1998. p. 127-163.\n
\n\n\nBurge C, Karlin S.\n\nPrediction of complete gene structures in human genomic DNA.\nJ. Mol. Biol. 1997 Apr 25;268(1):78-94.\nPMID: 9149143\n
\n" } }, "description": "Genscan Gene Predictions", "category": [ "Genes and Gene Predictions" ] }, { "type": "FeatureTrack", "trackId": "panTro6-ncbiRefSeq", "name": "NCBI RefSeq - RefSeq All", "assemblyNames": [ "panTro6" ], "adapter": { "type": "Gff3TabixAdapter", "gffGzLocation": { "uri": "ncbiRefSeq.gff.gz" }, "index": { "indexType": "CSI", "location": { "uri": "ncbiRefSeq.gff.gz.csi" } } }, "metadata": { "ucsc": { "baseColorDefault": "genomicCodons", "baseColorUseCds": "given", "color": "12,12,120", "idXref": "ncbiRefSeqLink mrnaAcc name", "longLabel": "NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, YP_*)", "parent": "refSeqComposite on", "priority": "1", "shortLabel": "RefSeq All", "track": "ncbiRefSeq", "html": "" } }, "description": "NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, YP_*)", "category": [ "Genes and Gene Predictions" ] }, { "type": "FeatureTrack", "trackId": "panTro6-ncbiRefSeqCurated", "name": "NCBI RefSeq - RefSeq Curated", "assemblyNames": [ "panTro6" ], "adapter": { "type": "Gff3TabixAdapter", "gffGzLocation": { "uri": "ncbiRefSeqCurated.gff.gz" }, "index": { "indexType": "CSI", "location": { "uri": "ncbiRefSeqCurated.gff.gz.csi" } } }, "metadata": { "ucsc": { "baseColorDefault": "genomicCodons", "baseColorUseCds": "given", "color": "12,12,120", "idXref": "ncbiRefSeqLink mrnaAcc name", "longLabel": "NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*)", "parent": "refSeqComposite on", "priority": "2", "shortLabel": "RefSeq Curated", "track": "ncbiRefSeqCurated", "html": "" } }, "description": "NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*)", "category": [ "Genes and Gene Predictions" ] }, { "type": "FeatureTrack", "trackId": "panTro6-ncbiRefSeqPredicted", "name": "NCBI RefSeq - RefSeq Predicted", "assemblyNames": [ "panTro6" ], "adapter": { "type": "Gff3TabixAdapter", "gffGzLocation": { "uri": "ncbiRefSeqPredicted.gff.gz" }, "index": { "indexType": "CSI", "location": { "uri": "ncbiRefSeqPredicted.gff.gz.csi" } } }, "metadata": { "ucsc": { "baseColorDefault": "genomicCodons", "baseColorUseCds": "given", "color": "12,12,120", "idXref": "ncbiRefSeqLink mrnaAcc name", "longLabel": "NCBI RefSeq genes, predicted subset (XM_* or XR_*)", "parent": "refSeqComposite off", "priority": "3", "shortLabel": "RefSeq Predicted", "track": "ncbiRefSeqPredicted", "html": "" } }, "description": "NCBI RefSeq genes, predicted subset (XM_* or XR_*)", "category": [ "Genes and Gene Predictions" ] }, { "type": "FeatureTrack", "trackId": "panTro6-refGene", "name": "NCBI RefSeq - UCSC RefSeq", "assemblyNames": [ "panTro6" ], "adapter": { "type": "Gff3TabixAdapter", "gffGzLocation": { "uri": "refGene.gff.gz" }, "index": { "indexType": "CSI", "location": { "uri": "refGene.gff.gz.csi" } } }, "metadata": { "ucsc": { "baseColorDefault": "genomicCodons", "baseColorUseCds": "given", "color": "12,12,120", "dataVersion": "", "group": "genes", "idXref": "hgFixed.refLink mrnaAcc name", "longLabel": "UCSC annotations of RefSeq RNAs (NM_* and NR_*)", "parent": "refSeqComposite off", "priority": "7", "shortLabel": "UCSC RefSeq", "track": "refGene", "type": "genePred refPep refMrna", "visibility": "dense", "html": "\nThe RefSeq Genes track shows known chimp protein-coding and\nnon-protein-coding genes taken from the NCBI RNA reference sequences\ncollection (RefSeq). The data underlying this track are updated weekly.
\n\n\nPlease visit the Feedback for Gene and Reference Sequences (RefSeq) page to\nmake suggestions, submit additions and corrections, or ask for help concerning\nRefSeq records.\n
\n\n\nFor more information on the different gene tracks, see our Genes FAQ.
\n\n\nThis track follows the display conventions for\n\ngene prediction tracks.\nThe color shading indicates the level of review the RefSeq record has\nundergone: predicted (light), provisional (medium), reviewed (dark).\n
\n\n\nThe item labels and display colors of features within this track can be\nconfigured through the controls at the top of the track description page.\n
\nRefSeq RNAs were aligned against the chimp genome using BLAT. Those\nwith an alignment of less than 15% were discarded. When a single RNA\naligned in multiple places, the alignment having the highest base identity\nwas identified. Only alignments having a base identity level within 0.1% of\nthe best and at least 96% base identity with the genomic sequence were kept.\n
\n\n\nThis track was produced at UCSC from RNA sequence data generated by scientists\nworldwide and curated by the NCBI\nRefSeq project.\n
\n\n\nKent WJ.\n\nBLAT - the BLAST-like alignment tool.\nGenome Res. 2002 Apr;12(4):656-64.\nPMID: 11932250; PMC:
\nPruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J,\nLandrum MJ, McGarvey KM et al.\n\nRefSeq: an update on mammalian reference sequences.\nNucleic Acids Res. 2014 Jan;42(Database issue):D756-63.\nPMID: 24259432; PMC:
\nPruitt KD, Tatusova T, Maglott DR.\n\nNCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.\nNucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4.\nPMID: 15608248; PMC:
\nThis track shows known protein-coding and non-protein-coding genes \nfor organisms other than chimp, taken from the NCBI RNA reference \nsequences collection (RefSeq). The data underlying this track are \nupdated weekly.
\n\n\nThis track follows the display conventions for \ngene prediction \ntracks.\nThe color shading indicates the level of review the RefSeq record has \nundergone: predicted (light), provisional (medium), reviewed (dark).
\n\nThe item labels and display colors of features within this track can be\nconfigured through the controls at the top of the track description page. \n
\nThe RNAs were aligned against the chimp genome using blat; those\nwith an alignment of less than 15% were discarded. When a single RNA aligned \nin multiple places, the alignment having the highest base identity was \nidentified. Only alignments having a base identity level within 0.5% of \nthe best and at least 25% base identity with the genomic sequence were kept.\n
\n\n\nThis track was produced at UCSC from RNA sequence data\ngenerated by scientists worldwide and curated by the \nNCBI RefSeq project.
\n\n\nKent WJ.\n\nBLAT--the BLAST-like alignment tool.\nGenome Res. 2002 Apr;12(4):656-64.\nPMID: 11932250; PMC:
\nPruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J,\nLandrum MJ, McGarvey KM et al.\n\nRefSeq: an update on mammalian reference sequences.\nNucleic Acids Res. 2014 Jan;42(Database issue):D756-63.\nPMID: 24259432; PMC:
\nPruitt KD, Tatusova T, Maglott DR.\n\nNCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.\nNucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4.\nPMID: 15608248; PMC: