< evaSnp4 | This track contains mappings of single nucleotide variants < evaSnp4 | and small insertions and deletions (indels) < evaSnp4 | from the European Variation Archive < evaSnp4 | (EVA) < evaSnp4 | Release 4 for the chimp panTro5 genome. The dbSNP database at NCBI no longer < evaSnp4 | hosts non-human variants. < evaSnp4 |
< evaSnp4 | < evaSnp4 |< evaSnp4 | Variants are shown as single tick marks at most zoom levels. < evaSnp4 | When viewing the track at or near base-level resolution, the displayed < evaSnp4 | width of the SNP variant corresponds to the width of the variant in the < evaSnp4 | reference sequence. Insertions are indicated by a single tick mark displayed < evaSnp4 | between two nucleotides, single nucleotide polymorphisms are displayed as the < evaSnp4 | width of a single base, and multiple nucleotide variants are represented by a < evaSnp4 | block that spans two or more bases. The display is set to automatically collapse to < evaSnp4 | dense visibility when there are more than 100k variants in the window. < evaSnp4 | When the window size is more than 250k bp, the display is switched to density graph mode. < evaSnp4 |
< evaSnp4 | < evaSnp4 |< evaSnp4 | Navigation to an individual variant can be accomplished by typing or copying < evaSnp4 | the variant identifier (rsID) or the genomic coordinates into the Position/Search box on the < evaSnp4 | Browser.
< evaSnp4 | < evaSnp4 |< evaSnp4 | A click on an item in the graphical display displays a page with data about < evaSnp4 | that variant. Data fields include the Reference and Alternate Alleles, the < evaSnp4 | class of the variant as reported by EVA, the source of the data, the amino acid < evaSnp4 | change, if any, and the functional class as determined by UCSC's Variant Annotation < evaSnp4 | Integrator. < evaSnp4 |
< evaSnp4 | < evaSnp4 |Variants can be filtered using the track controls to show subsets of the < evaSnp4 | data by either EVA Sequence Ontology (SO) term, UCSC-generated functional effect, or < evaSnp4 | by color, which bins the UCSC functional effects into general classes.
< evaSnp4 | < evaSnp4 |< evaSnp4 | Mousing over an item shows the ucscClass, which is the consequence according to the < evaSnp4 | Variant Annotation Integrator, and < evaSnp4 | the aaChange when one is available, which is the change in amino acid in HGVS.p < evaSnp4 | terms. Items may have multiple ucscClasses, which will all be shown in the mouse-over < evaSnp4 | in a comma-separated list. Likewise, multiple HGVS.p terms may be shown for each rsID < evaSnp4 | separated by spaces describing all possible AA changes.
< evaSnp4 |< evaSnp4 | Multiple items may appear due to different variant predictions on multiple gene transcripts. < evaSnp4 | For all organisms the gene models used were the NCBI RefSeq curated when available, if not then < evaSnp4 | ensembl genes, or finally UCSC mappings of RefSeq if neither of the previous models was possible. < evaSnp4 |
< evaSnp4 | < evaSnp4 |< evaSnp4 | Variants are colored according to the most potentially deleterious functional effect prediction < evaSnp4 | according to the Variant Annotation Integrator. Specific bins can be seen in the Methods section < evaSnp4 | below. < evaSnp4 |
< evaSnp4 | < evaSnp4 |< evaSnp4 |
| Color | < evaSnp4 |Variant Type | < evaSnp4 |
|---|---|
| Protein-altering variants and splice site variants | |
| Synonymous codon variants | |
| Non-coding transcript or Untranslated Region (UTR) variants | |
| Intergenic and intronic variants |
< evaSnp4 | Variants are classified by EVA into one of the following sequence ontology terms: < evaSnp4 |
< evaSnp4 | < evaSnp4 |< evaSnp4 | Data were downloaded from the European Variation Archive EVA release 4 (2022-11-21) < evaSnp4 | current_ids.vcf.gz files corresponding to the proper assembly.
< evaSnp4 |< evaSnp4 | Chromosome names were converted to UCSC-style < evaSnp4 | and the variants passed through the < evaSnp4 | Variant Annotation Integrator to < evaSnp4 | predict consequence. For every organism the NCBI RefSeq curated models were used when available, < evaSnp4 | followed by ensembl genes, and finally UCSC mapping of RefSeq when neither of the previous models < evaSnp4 | were possible.
< evaSnp4 |< evaSnp4 | Variants were then colored according to their predicted consequence in the following fashion: < evaSnp4 |
< evaSnp4 | Sequence Ontology ("SO:") < evaSnp4 | terms were converted to the variant classes, then the files were converted to BED, < evaSnp4 | and then bigBed format. < evaSnp4 |
< evaSnp4 |< evaSnp4 | No functional annotations were provided by the EVA (e.g., missense, nonsense, etc). < evaSnp4 | These were computed using UCSC's Variant Annotation Integrator (Hinrichs, et al., 2016). < evaSnp4 | Amino-acid substitutions for missense variants are based < evaSnp4 | on RefSeq alignments of mRNA transcripts, which do not always match the amino acids < evaSnp4 | predicted from translating the genomic sequence. Therefore, in some instances, the < evaSnp4 | variant and the genomic nucleotide and associated amino acid may be reversed. < evaSnp4 | E.g., a Pro > Arg change from the perspective of the mRNA would be Arg > Pro from < evaSnp4 | the persepective the genomic sequence. Also, in bosTau9, galGal5, rheMac8, < evaSnp4 | danRer10 and danRer11 the mitochondrial sequence was removed or renamed to match UCSC. < evaSnp4 | For complete documentation of the processing of these tracks, read the < evaSnp4 | < evaSnp4 | EVA Release 4 MakeDoc.
< evaSnp4 | < evaSnp4 |< evaSnp4 | Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies, < evaSnp4 | and more information about how to convert SNPs between assemblies can be found on the following < evaSnp4 | FAQ entry.
< evaSnp4 |< evaSnp4 | The data can be explored interactively with the Table Browser, < evaSnp4 | or the Data Integrator. For automated analysis, the data may be < evaSnp4 | queried from our REST API. Please refer to our < evaSnp4 | mailing list archives < evaSnp4 | for questions, or our Data Access FAQ for more < evaSnp4 | information.
< evaSnp4 | < evaSnp4 |
< evaSnp4 | For automated download and analysis, this annotation is stored in a bigBed file that
< evaSnp4 | can be downloaded from our download server. The file for this track is called evaSnp4.bb.
< evaSnp4 | Individual regions or the whole genome annotation can be obtained using our tool
< evaSnp4 | bigBedToBed which can be compiled from the source code or downloaded as a precompiled
< evaSnp4 | binary for your system. Instructions for downloading source code and binaries can be found
< evaSnp4 | here.
< evaSnp4 | The tool can also be used to obtain only features within a given range, e.g.
< evaSnp4 |
< evaSnp4 | bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/panTro5/bbi/evaSnp4.bb -chrom=chr21 -start=0 -end=100000000 stdout
< evaSnp4 |
< evaSnp4 | This track was produced from the European < evaSnp4 | Variation Archive release 4 data. Consequences were predicted using UCSC's Variant Annotation < evaSnp4 | Integrator and NCBI's RefSeq as well as ensembl gene models. < evaSnp4 |
< evaSnp4 | < evaSnp4 |< evaSnp4 | Cezard T, Cunningham F, Hunt SE, Koylass B, Kumar N, Saunders G, Shen A, Silva AF, < evaSnp4 | Tsukanov K, Venkataraman S et al. The European Variation Archive: a FAIR resource of genomic variation for all < evaSnp4 | species. Nucleic Acids Res. 2021 Oct 28:gkab960. < evaSnp4 | doi:10.1093/nar/gkab960. < evaSnp4 | Epub ahead of print. PMID: 34718739. PMID: PMC8728205. < evaSnp4 |
< evaSnp4 |< evaSnp4 | Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, < evaSnp4 | Haussler D, Kent WJ. < evaSnp4 | UCSC Data Integrator and Variant Annotation Integrator. < evaSnp4 | Bioinformatics. 2016 May 1;32(9):1430-2. < evaSnp4 | PMID: 26740527; PMC: < evaSnp4 | PMC4848401 < evaSnp4 |
< evaSnp4 | < evaSnp5 | html < evaSnp5 |< evaSnp5 | This track contains mappings of single nucleotide variants < evaSnp5 | and small insertions and deletions (indels) < evaSnp5 | from the European Variation Archive < evaSnp5 | (EVA) < evaSnp5 | Release 5 for the chimp panTro5 genome. The dbSNP database at NCBI no longer < evaSnp5 | hosts non-human variants. < evaSnp5 |
< evaSnp5 | < evaSnp5 |< evaSnp5 | Variants are shown as single tick marks at most zoom levels. < evaSnp5 | When viewing the track at or near base-level resolution, the displayed < evaSnp5 | width of the SNP variant corresponds to the width of the variant in the < evaSnp5 | reference sequence. Insertions are indicated by a single tick mark displayed < evaSnp5 | between two nucleotides, single nucleotide polymorphisms are displayed as the < evaSnp5 | width of a single base, and multiple nucleotide variants are represented by a < evaSnp5 | block that spans two or more bases. The display is set to automatically collapse to < evaSnp5 | dense visibility when there are more than 100k variants in the window. < evaSnp5 | When the window size is more than 250k bp, the display is switched to density graph mode. < evaSnp5 |
< evaSnp5 | < evaSnp5 |< evaSnp5 | Navigation to an individual variant can be accomplished by typing or copying < evaSnp5 | the variant identifier (rsID) or the genomic coordinates into the Position/Search box on the < evaSnp5 | Browser.
< evaSnp5 | < evaSnp5 |< evaSnp5 | A click on an item in the graphical display displays a page with data about < evaSnp5 | that variant. Data fields include the Reference and Alternate Alleles, the < evaSnp5 | class of the variant as reported by EVA, the source of the data, the amino acid < evaSnp5 | change, if any, and the functional class as determined by UCSC's Variant Annotation < evaSnp5 | Integrator. < evaSnp5 |
< evaSnp5 | < evaSnp5 |Variants can be filtered using the track controls to show subsets of the < evaSnp5 | data by either EVA Sequence Ontology (SO) term, UCSC-generated functional effect, or < evaSnp5 | by color, which bins the UCSC functional effects into general classes.
< evaSnp5 | < evaSnp5 |< evaSnp5 | Mousing over an item shows the ucscClass, which is the consequence according to the < evaSnp5 | Variant Annotation Integrator, and < evaSnp5 | the aaChange when one is available, which is the change in amino acid in HGVS.p < evaSnp5 | terms. Items may have multiple ucscClasses, which will all be shown in the mouse-over < evaSnp5 | in a comma-separated list. Likewise, multiple HGVS.p terms may be shown for each rsID < evaSnp5 | separated by spaces describing all possible AA changes.
< evaSnp5 |< evaSnp5 | Multiple items may appear due to different variant predictions on multiple gene transcripts. < evaSnp5 | For all organisms the gene models used were the NCBI RefSeq curated when available, if not then < evaSnp5 | ensembl genes, or finally UCSC mappings of RefSeq if neither of the previous models was possible. < evaSnp5 |
< evaSnp5 | < evaSnp5 |< evaSnp5 | Variants are colored according to the most potentially deleterious functional effect prediction < evaSnp5 | according to the Variant Annotation Integrator. Specific bins can be seen in the Methods section < evaSnp5 | below. < evaSnp5 |
< evaSnp5 | < evaSnp5 |< evaSnp5 |
| Color | < evaSnp5 |Variant Type | < evaSnp5 |
|---|---|
| Protein-altering variants and splice site variants | |
| Synonymous codon variants | |
| Non-coding transcript or Untranslated Region (UTR) variants | |
| Intergenic and intronic variants |
< evaSnp5 | Variants are classified by EVA into one of the following sequence ontology terms: < evaSnp5 |
< evaSnp5 | < evaSnp5 |< evaSnp5 | Data were downloaded from the European Variation Archive EVA release 5 (2023-9-7) < evaSnp5 | current_ids.vcf.gz files corresponding to the proper assembly.
< evaSnp5 |< evaSnp5 | Chromosome names were converted to UCSC-style < evaSnp5 | and the variants passed through the < evaSnp5 | Variant Annotation Integrator to < evaSnp5 | predict consequence. For every organism the NCBI RefSeq curated models were used when available, < evaSnp5 | followed by ensembl genes, and finally UCSC mapping of RefSeq when neither of the previous models < evaSnp5 | were possible.
< evaSnp5 |< evaSnp5 | Variants were then colored according to their predicted consequence in the following fashion: < evaSnp5 |
< evaSnp5 | Sequence Ontology ("SO:") < evaSnp5 | terms were converted to the variant classes, then the files were converted to BED, < evaSnp5 | and then bigBed format. < evaSnp5 |
< evaSnp5 |< evaSnp5 | No functional annotations were provided by the EVA (e.g., missense, nonsense, etc). < evaSnp5 | These were computed using UCSC's Variant Annotation Integrator (Hinrichs, et al., 2016). < evaSnp5 | Amino-acid substitutions for missense variants are based < evaSnp5 | on RefSeq alignments of mRNA transcripts, which do not always match the amino acids < evaSnp5 | predicted from translating the genomic sequence. Therefore, in some instances, the < evaSnp5 | variant and the genomic nucleotide and associated amino acid may be reversed. < evaSnp5 | E.g., a Pro > Arg change from the perspective of the mRNA would be Arg > Pro from < evaSnp5 | the persepective the genomic sequence. Also, in bosTau9, galGal5, rheMac8, < evaSnp5 | danRer10 and danRer11 the mitochondrial sequence was removed or renamed to match UCSC. < evaSnp5 | For complete documentation of the processing of these tracks, read the < evaSnp5 | < evaSnp5 | EVA Release 5 MakeDoc.
< evaSnp5 | < evaSnp5 |< evaSnp5 | Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies, < evaSnp5 | and more information about how to convert SNPs between assemblies can be found on the following < evaSnp5 | FAQ entry.
< evaSnp5 |< evaSnp5 | The data can be explored interactively with the Table Browser, < evaSnp5 | or the Data Integrator. For automated analysis, the data may be < evaSnp5 | queried from our REST API. Please refer to our < evaSnp5 | mailing list archives < evaSnp5 | for questions, or our Data Access FAQ for more < evaSnp5 | information.
< evaSnp5 | < evaSnp5 |
< evaSnp5 | For automated download and analysis, this annotation is stored in a bigBed file that
< evaSnp5 | can be downloaded from our download server. The file for this track is called evaSnp5.bb.
< evaSnp5 | Individual regions or the whole genome annotation can be obtained using our tool
< evaSnp5 | bigBedToBed which can be compiled from the source code or downloaded as a precompiled
< evaSnp5 | binary for your system. Instructions for downloading source code and binaries can be found
< evaSnp5 | here.
< evaSnp5 | The tool can also be used to obtain only features within a given range, e.g.
< evaSnp5 |
< evaSnp5 | bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/panTro5/bbi/evaSnp5.bb -chrom=chr21 -start=0 -end=100000000 stdout
< evaSnp5 |
< evaSnp5 | This track was produced from the European < evaSnp5 | Variation Archive release 5 data. Consequences were predicted using UCSC's Variant Annotation < evaSnp5 | Integrator and NCBI's RefSeq as well as ensembl gene models. < evaSnp5 |
< evaSnp5 | < evaSnp5 |< evaSnp5 | Cezard T, Cunningham F, Hunt SE, Koylass B, Kumar N, Saunders G, Shen A, Silva AF, < evaSnp5 | Tsukanov K, Venkataraman S et al. The European Variation Archive: a FAIR resource of genomic variation for all < evaSnp5 | species. Nucleic Acids Res. 2021 Oct 28:gkab960. < evaSnp5 | doi:10.1093/nar/gkab960. < evaSnp5 | Epub ahead of print. PMID: 34718739. PMID: PMC8728205. < evaSnp5 |
< evaSnp5 |< evaSnp5 | Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, < evaSnp5 | Haussler D, Kent WJ. < evaSnp5 | UCSC Data Integrator and Variant Annotation Integrator. < evaSnp5 | Bioinformatics. 2016 May 1;32(9):1430-2. < evaSnp5 | PMID: 26740527; PMC: < evaSnp5 | PMC4848401 < evaSnp5 |
< evaSnp5 | 3129,3132d2698 < ncbiRefSeqGenomicDiff | html < ncbiRefSeqGenomicDiff | < ncbiRefSeqOther | html < ncbiRefSeqOther | 4571,5350d4136 < transMapEnsemblV5 | html < transMapEnsemblV5 |< transMapEnsemblV5 | This track contains GENCODE or Ensembl alignments produced by < transMapEnsemblV5 | the TransMap cross-species alignment algorithm from other vertebrate < transMapEnsemblV5 | species in the UCSC Genome Browser. GENCODE is Ensembl for human and mouse, < transMapEnsemblV5 | for other Ensembl sources, only ones with full gene builds are used. < transMapEnsemblV5 | Projection Ensembl gene annotations will not be used as sources. < transMapEnsemblV5 | For closer evolutionary distances, the alignments are created using < transMapEnsemblV5 | syntenically filtered BLASTZ alignment chains, resulting in a prediction of the < transMapEnsemblV5 | orthologous genes in chimp. < transMapEnsemblV5 |
< transMapEnsemblV5 | < transMapEnsemblV5 | < transMapEnsemblV5 |< transMapEnsemblV5 | This track follows the display conventions for < transMapEnsemblV5 | PSL alignment tracks.
< transMapEnsemblV5 |< transMapEnsemblV5 | This track may also be configured to display codon coloring, a feature that < transMapEnsemblV5 | allows the user to quickly compare cDNAs against the genomic sequence. For more < transMapEnsemblV5 | information about this option, click < transMapEnsemblV5 | here. < transMapEnsemblV5 | Several types of alignment gap may also be colored; < transMapEnsemblV5 | for more information, click < transMapEnsemblV5 | here. < transMapEnsemblV5 | < transMapEnsemblV5 |
< transMapEnsemblV5 |
< transMapEnsemblV5 | To ensure unique identifiers for each alignment, cDNA and gene accessions were < transMapEnsemblV5 | made unique by appending a suffix for each location in the source genome and < transMapEnsemblV5 | again for each mapped location in the destination genome. The format is: < transMapEnsemblV5 |
< transMapEnsemblV5 | accession.version-srcUniq.destUniq < transMapEnsemblV5 |< transMapEnsemblV5 | < transMapEnsemblV5 | Where srcUniq is a number added to make each source alignment unique, and < transMapEnsemblV5 | destUniq is added to give the subsequent TransMap alignments unique < transMapEnsemblV5 | identifiers. < transMapEnsemblV5 | < transMapEnsemblV5 |
< transMapEnsemblV5 | For example, in the cow genome, there are two alignments of mRNA BC149621.1. < transMapEnsemblV5 | These are assigned the identifiers BC149621.1-1 and BC149621.1-2. < transMapEnsemblV5 | When these are mapped to the human genome, BC149621.1-1 maps to a single < transMapEnsemblV5 | location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 < transMapEnsemblV5 | maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note < transMapEnsemblV5 | that multiple TransMap mappings are usually the result of tandem duplications, where both < transMapEnsemblV5 | chains are identified as syntenic. < transMapEnsemblV5 |
< transMapEnsemblV5 | < transMapEnsemblV5 |< transMapEnsemblV5 | The raw data for these tracks can be accessed interactively through the < transMapEnsemblV5 | Table Browser or the < transMapEnsemblV5 | Data Integrator. < transMapEnsemblV5 | For automated analysis, the annotations are stored in < transMapEnsemblV5 | bigPsl files (containing a < transMapEnsemblV5 | number of extra columns) and can be downloaded from our < transMapEnsemblV5 | download server, < transMapEnsemblV5 | or queried using our API. For more < transMapEnsemblV5 | information on accessing track data see our < transMapEnsemblV5 | Track Data Access FAQ. < transMapEnsemblV5 | The files are associated with these tracks in the following way: < transMapEnsemblV5 |
< transMapEnsemblV5 | bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/panTro5/transMap/V4/panTro5.refseq.transMapV4.bigPsl < transMapEnsemblV5 | -chrom=chr6 -start=0 -end=1000000 stdout < transMapEnsemblV5 | < transMapEnsemblV5 | < transMapEnsemblV5 |
< transMapEnsemblV5 | This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data < transMapEnsemblV5 | submitted to the international public sequence databases by < transMapEnsemblV5 | scientists worldwide and annotations produced by the RefSeq, < transMapEnsemblV5 | Ensembl, and GENCODE annotations projects.
< transMapEnsemblV5 | < transMapEnsemblV5 |< transMapEnsemblV5 | Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, < transMapEnsemblV5 | Lau C et al. < transMapEnsemblV5 | < transMapEnsemblV5 | Targeted discovery of novel human exons by comparative genomics. < transMapEnsemblV5 | Genome Res. 2007 Dec;17(12):1763-73. < transMapEnsemblV5 | PMID: 17989246; PMC: PMC2099585 < transMapEnsemblV5 |
< transMapEnsemblV5 | < transMapEnsemblV5 |< transMapEnsemblV5 | Stanke M, Diekhans M, Baertsch R, Haussler D. < transMapEnsemblV5 | < transMapEnsemblV5 | Using native and syntenically mapped cDNA alignments to improve de novo gene finding. < transMapEnsemblV5 | Bioinformatics. 2008 Mar 1;24(5):637-44. < transMapEnsemblV5 | PMID: 18218656 < transMapEnsemblV5 |
< transMapEnsemblV5 | < transMapEnsemblV5 |< transMapEnsemblV5 | Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. < transMapEnsemblV5 | < transMapEnsemblV5 | Comparative genomics search for losses of long-established genes on the human lineage. < transMapEnsemblV5 | PLoS Comput Biol. 2007 Dec;3(12):e247. < transMapEnsemblV5 | PMID: 18085818; PMC: PMC2134963 < transMapEnsemblV5 |
< transMapEnsemblV5 | < transMapEnsemblV5 | < transMapEstV5 | html < transMapEstV5 |< transMapEstV5 | This track contains GenBank spliced EST alignments produced by < transMapEstV5 | the TransMap cross-species alignment algorithm < transMapEstV5 | from other vertebrate species in the UCSC Genome Browser. < transMapEstV5 | For closer evolutionary distances, the alignments are created using < transMapEstV5 | syntenically filtered BLASTZ alignment chains, resulting in a prediction of the < transMapEstV5 | orthologous genes in chimp. < transMapEstV5 |
< transMapEstV5 | < transMapEstV5 | < transMapEstV5 |< transMapEstV5 | This track follows the display conventions for < transMapEstV5 | PSL alignment tracks.
< transMapEstV5 |< transMapEstV5 | This track may also be configured to display codon coloring, a feature that < transMapEstV5 | allows the user to quickly compare cDNAs against the genomic sequence. For more < transMapEstV5 | information about this option, click < transMapEstV5 | here. < transMapEstV5 | Several types of alignment gap may also be colored; < transMapEstV5 | for more information, click < transMapEstV5 | here. < transMapEstV5 | < transMapEstV5 |
< transMapEstV5 |
< transMapEstV5 | To ensure unique identifiers for each alignment, cDNA and gene accessions were < transMapEstV5 | made unique by appending a suffix for each location in the source genome and < transMapEstV5 | again for each mapped location in the destination genome. The format is: < transMapEstV5 |
< transMapEstV5 | accession.version-srcUniq.destUniq < transMapEstV5 |< transMapEstV5 | < transMapEstV5 | Where srcUniq is a number added to make each source alignment unique, and < transMapEstV5 | destUniq is added to give the subsequent TransMap alignments unique < transMapEstV5 | identifiers. < transMapEstV5 | < transMapEstV5 |
< transMapEstV5 | For example, in the cow genome, there are two alignments of mRNA BC149621.1. < transMapEstV5 | These are assigned the identifiers BC149621.1-1 and BC149621.1-2. < transMapEstV5 | When these are mapped to the human genome, BC149621.1-1 maps to a single < transMapEstV5 | location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 < transMapEstV5 | maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note < transMapEstV5 | that multiple TransMap mappings are usually the result of tandem duplications, where both < transMapEstV5 | chains are identified as syntenic. < transMapEstV5 |
< transMapEstV5 | < transMapEstV5 |< transMapEstV5 | The raw data for these tracks can be accessed interactively through the < transMapEstV5 | Table Browser or the < transMapEstV5 | Data Integrator. < transMapEstV5 | For automated analysis, the annotations are stored in < transMapEstV5 | bigPsl files (containing a < transMapEstV5 | number of extra columns) and can be downloaded from our < transMapEstV5 | download server, < transMapEstV5 | or queried using our API. For more < transMapEstV5 | information on accessing track data see our < transMapEstV5 | Track Data Access FAQ. < transMapEstV5 | The files are associated with these tracks in the following way: < transMapEstV5 |
< transMapEstV5 | bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/panTro5/transMap/V4/panTro5.refseq.transMapV4.bigPsl < transMapEstV5 | -chrom=chr6 -start=0 -end=1000000 stdout < transMapEstV5 | < transMapEstV5 | < transMapEstV5 |
< transMapEstV5 | This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data < transMapEstV5 | submitted to the international public sequence databases by < transMapEstV5 | scientists worldwide and annotations produced by the RefSeq, < transMapEstV5 | Ensembl, and GENCODE annotations projects.
< transMapEstV5 | < transMapEstV5 |< transMapEstV5 | Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, < transMapEstV5 | Lau C et al. < transMapEstV5 | < transMapEstV5 | Targeted discovery of novel human exons by comparative genomics. < transMapEstV5 | Genome Res. 2007 Dec;17(12):1763-73. < transMapEstV5 | PMID: 17989246; PMC: PMC2099585 < transMapEstV5 |
< transMapEstV5 | < transMapEstV5 |< transMapEstV5 | Stanke M, Diekhans M, Baertsch R, Haussler D. < transMapEstV5 | < transMapEstV5 | Using native and syntenically mapped cDNA alignments to improve de novo gene finding. < transMapEstV5 | Bioinformatics. 2008 Mar 1;24(5):637-44. < transMapEstV5 | PMID: 18218656 < transMapEstV5 |
< transMapEstV5 | < transMapEstV5 |< transMapEstV5 | Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. < transMapEstV5 | < transMapEstV5 | Comparative genomics search for losses of long-established genes on the human lineage. < transMapEstV5 | PLoS Comput Biol. 2007 Dec;3(12):e247. < transMapEstV5 | PMID: 18085818; PMC: PMC2134963 < transMapEstV5 |
< transMapEstV5 | < transMapEstV5 | < transMapRefSeqV5 | html < transMapRefSeqV5 |< transMapRefSeqV5 | This track contains RefSeq Gene alignments produced by < transMapRefSeqV5 | the TransMap cross-species alignment algorithm < transMapRefSeqV5 | from other vertebrate species in the UCSC Genome Browser. < transMapRefSeqV5 | For closer evolutionary distances, the alignments are created using < transMapRefSeqV5 | syntenically filtered BLASTZ alignment chains, resulting in a prediction of the < transMapRefSeqV5 | orthologous genes in chimp. < transMapRefSeqV5 |
< transMapRefSeqV5 | < transMapRefSeqV5 | < transMapRefSeqV5 |< transMapRefSeqV5 | This track follows the display conventions for < transMapRefSeqV5 | PSL alignment tracks.
< transMapRefSeqV5 |< transMapRefSeqV5 | This track may also be configured to display codon coloring, a feature that < transMapRefSeqV5 | allows the user to quickly compare cDNAs against the genomic sequence. For more < transMapRefSeqV5 | information about this option, click < transMapRefSeqV5 | here. < transMapRefSeqV5 | Several types of alignment gap may also be colored; < transMapRefSeqV5 | for more information, click < transMapRefSeqV5 | here. < transMapRefSeqV5 | < transMapRefSeqV5 |
< transMapRefSeqV5 |
< transMapRefSeqV5 | To ensure unique identifiers for each alignment, cDNA and gene accessions were < transMapRefSeqV5 | made unique by appending a suffix for each location in the source genome and < transMapRefSeqV5 | again for each mapped location in the destination genome. The format is: < transMapRefSeqV5 |
< transMapRefSeqV5 | accession.version-srcUniq.destUniq < transMapRefSeqV5 |< transMapRefSeqV5 | < transMapRefSeqV5 | Where srcUniq is a number added to make each source alignment unique, and < transMapRefSeqV5 | destUniq is added to give the subsequent TransMap alignments unique < transMapRefSeqV5 | identifiers. < transMapRefSeqV5 | < transMapRefSeqV5 |
< transMapRefSeqV5 | For example, in the cow genome, there are two alignments of mRNA BC149621.1. < transMapRefSeqV5 | These are assigned the identifiers BC149621.1-1 and BC149621.1-2. < transMapRefSeqV5 | When these are mapped to the human genome, BC149621.1-1 maps to a single < transMapRefSeqV5 | location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 < transMapRefSeqV5 | maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note < transMapRefSeqV5 | that multiple TransMap mappings are usually the result of tandem duplications, where both < transMapRefSeqV5 | chains are identified as syntenic. < transMapRefSeqV5 |
< transMapRefSeqV5 | < transMapRefSeqV5 |< transMapRefSeqV5 | The raw data for these tracks can be accessed interactively through the < transMapRefSeqV5 | Table Browser or the < transMapRefSeqV5 | Data Integrator. < transMapRefSeqV5 | For automated analysis, the annotations are stored in < transMapRefSeqV5 | bigPsl files (containing a < transMapRefSeqV5 | number of extra columns) and can be downloaded from our < transMapRefSeqV5 | download server, < transMapRefSeqV5 | or queried using our API. For more < transMapRefSeqV5 | information on accessing track data see our < transMapRefSeqV5 | Track Data Access FAQ. < transMapRefSeqV5 | The files are associated with these tracks in the following way: < transMapRefSeqV5 |
< transMapRefSeqV5 | bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/panTro5/transMap/V4/panTro5.refseq.transMapV4.bigPsl < transMapRefSeqV5 | -chrom=chr6 -start=0 -end=1000000 stdout < transMapRefSeqV5 | < transMapRefSeqV5 | < transMapRefSeqV5 |
< transMapRefSeqV5 | This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data < transMapRefSeqV5 | submitted to the international public sequence databases by < transMapRefSeqV5 | scientists worldwide and annotations produced by the RefSeq, < transMapRefSeqV5 | Ensembl, and GENCODE annotations projects.
< transMapRefSeqV5 | < transMapRefSeqV5 |< transMapRefSeqV5 | Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, < transMapRefSeqV5 | Lau C et al. < transMapRefSeqV5 | < transMapRefSeqV5 | Targeted discovery of novel human exons by comparative genomics. < transMapRefSeqV5 | Genome Res. 2007 Dec;17(12):1763-73. < transMapRefSeqV5 | PMID: 17989246; PMC: PMC2099585 < transMapRefSeqV5 |
< transMapRefSeqV5 | < transMapRefSeqV5 |< transMapRefSeqV5 | Stanke M, Diekhans M, Baertsch R, Haussler D. < transMapRefSeqV5 | < transMapRefSeqV5 | Using native and syntenically mapped cDNA alignments to improve de novo gene finding. < transMapRefSeqV5 | Bioinformatics. 2008 Mar 1;24(5):637-44. < transMapRefSeqV5 | PMID: 18218656 < transMapRefSeqV5 |
< transMapRefSeqV5 | < transMapRefSeqV5 |< transMapRefSeqV5 | Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. < transMapRefSeqV5 | < transMapRefSeqV5 | Comparative genomics search for losses of long-established genes on the human lineage. < transMapRefSeqV5 | PLoS Comput Biol. 2007 Dec;3(12):e247. < transMapRefSeqV5 | PMID: 18085818; PMC: PMC2134963 < transMapRefSeqV5 |
< transMapRefSeqV5 | < transMapRefSeqV5 | < transMapRnaV5 | html < transMapRnaV5 |< transMapRnaV5 | This track contains GenBank mRNA alignments produced by < transMapRnaV5 | the TransMap cross-species alignment algorithm < transMapRnaV5 | from other vertebrate species in the UCSC Genome Browser. < transMapRnaV5 | For closer evolutionary distances, the alignments are created using < transMapRnaV5 | syntenically filtered BLASTZ alignment chains, resulting in a prediction of the < transMapRnaV5 | orthologous genes in chimp. < transMapRnaV5 |
< transMapRnaV5 | < transMapRnaV5 | < transMapRnaV5 |< transMapRnaV5 | This track follows the display conventions for < transMapRnaV5 | PSL alignment tracks.
< transMapRnaV5 |< transMapRnaV5 | This track may also be configured to display codon coloring, a feature that < transMapRnaV5 | allows the user to quickly compare cDNAs against the genomic sequence. For more < transMapRnaV5 | information about this option, click < transMapRnaV5 | here. < transMapRnaV5 | Several types of alignment gap may also be colored; < transMapRnaV5 | for more information, click < transMapRnaV5 | here. < transMapRnaV5 | < transMapRnaV5 |
< transMapRnaV5 |
< transMapRnaV5 | To ensure unique identifiers for each alignment, cDNA and gene accessions were < transMapRnaV5 | made unique by appending a suffix for each location in the source genome and < transMapRnaV5 | again for each mapped location in the destination genome. The format is: < transMapRnaV5 |
< transMapRnaV5 | accession.version-srcUniq.destUniq < transMapRnaV5 |< transMapRnaV5 | < transMapRnaV5 | Where srcUniq is a number added to make each source alignment unique, and < transMapRnaV5 | destUniq is added to give the subsequent TransMap alignments unique < transMapRnaV5 | identifiers. < transMapRnaV5 | < transMapRnaV5 |
< transMapRnaV5 | For example, in the cow genome, there are two alignments of mRNA BC149621.1. < transMapRnaV5 | These are assigned the identifiers BC149621.1-1 and BC149621.1-2. < transMapRnaV5 | When these are mapped to the human genome, BC149621.1-1 maps to a single < transMapRnaV5 | location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 < transMapRnaV5 | maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note < transMapRnaV5 | that multiple TransMap mappings are usually the result of tandem duplications, where both < transMapRnaV5 | chains are identified as syntenic. < transMapRnaV5 |
< transMapRnaV5 | < transMapRnaV5 |< transMapRnaV5 | The raw data for these tracks can be accessed interactively through the < transMapRnaV5 | Table Browser or the < transMapRnaV5 | Data Integrator. < transMapRnaV5 | For automated analysis, the annotations are stored in < transMapRnaV5 | bigPsl files (containing a < transMapRnaV5 | number of extra columns) and can be downloaded from our < transMapRnaV5 | download server, < transMapRnaV5 | or queried using our API. For more < transMapRnaV5 | information on accessing track data see our < transMapRnaV5 | Track Data Access FAQ. < transMapRnaV5 | The files are associated with these tracks in the following way: < transMapRnaV5 |
< transMapRnaV5 | bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/panTro5/transMap/V4/panTro5.refseq.transMapV4.bigPsl < transMapRnaV5 | -chrom=chr6 -start=0 -end=1000000 stdout < transMapRnaV5 | < transMapRnaV5 | < transMapRnaV5 |
< transMapRnaV5 | This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data < transMapRnaV5 | submitted to the international public sequence databases by < transMapRnaV5 | scientists worldwide and annotations produced by the RefSeq, < transMapRnaV5 | Ensembl, and GENCODE annotations projects.
< transMapRnaV5 | < transMapRnaV5 |< transMapRnaV5 | Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, < transMapRnaV5 | Lau C et al. < transMapRnaV5 | < transMapRnaV5 | Targeted discovery of novel human exons by comparative genomics. < transMapRnaV5 | Genome Res. 2007 Dec;17(12):1763-73. < transMapRnaV5 | PMID: 17989246; PMC: PMC2099585 < transMapRnaV5 |
< transMapRnaV5 | < transMapRnaV5 |< transMapRnaV5 | Stanke M, Diekhans M, Baertsch R, Haussler D. < transMapRnaV5 | < transMapRnaV5 | Using native and syntenically mapped cDNA alignments to improve de novo gene finding. < transMapRnaV5 | Bioinformatics. 2008 Mar 1;24(5):637-44. < transMapRnaV5 | PMID: 18218656 < transMapRnaV5 |
< transMapRnaV5 | < transMapRnaV5 |< transMapRnaV5 | Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. < transMapRnaV5 | < transMapRnaV5 | Comparative genomics search for losses of long-established genes on the human lineage. < transMapRnaV5 | PLoS Comput Biol. 2007 Dec;3(12):e247. < transMapRnaV5 | PMID: 18085818; PMC: PMC2134963 < transMapRnaV5 |
< transMapRnaV5 | < transMapRnaV5 | < transMapV5 | html < transMapV5 |< transMapV5 | These tracks contain cDNA and gene alignments produced by < transMapV5 | the TransMap cross-species alignment algorithm < transMapV5 | from other vertebrate species in the UCSC Genome Browser. < transMapV5 | For closer evolutionary distances, the alignments are created using < transMapV5 | syntenically filtered LASTZ or BLASTZ alignment chains, resulting < transMapV5 | in a prediction of the orthologous genes in chimp. For more distant < transMapV5 | organisms, reciprocal best alignments are used. < transMapV5 |
< transMapV5 | < transMapV5 | TransMap maps genes and related annotations in one species to another < transMapV5 | using synteny-filtered pairwise genome alignments (chains and nets) to < transMapV5 | determine the most likely orthologs. For example, for the mRNA TransMap track < transMapV5 | on the human assembly, more than 400,000 mRNAs from 25 vertebrate species were < transMapV5 | aligned at high stringency to the native assembly using BLAT. The alignments < transMapV5 | were then mapped to the human assembly using the chain and net alignments < transMapV5 | produced using BLASTZ, which has higher sensitivity than BLAT for diverged < transMapV5 | organisms. < transMapV5 |< transMapV5 | Compared to translated BLAT, TransMap finds fewer paralogs and aligns more UTR < transMapV5 | bases. < transMapV5 |
< transMapV5 | < transMapV5 |< transMapV5 | This track follows the display conventions for < transMapV5 | PSL alignment tracks.
< transMapV5 |< transMapV5 | This track may also be configured to display codon coloring, a feature that < transMapV5 | allows the user to quickly compare cDNAs against the genomic sequence. For more < transMapV5 | information about this option, click < transMapV5 | here. < transMapV5 | Several types of alignment gap may also be colored; < transMapV5 | for more information, click < transMapV5 | here. < transMapV5 | < transMapV5 |
< transMapV5 |
< transMapV5 | To ensure unique identifiers for each alignment, cDNA and gene accessions were < transMapV5 | made unique by appending a suffix for each location in the source genome and < transMapV5 | again for each mapped location in the destination genome. The format is: < transMapV5 |
< transMapV5 | accession.version-srcUniq.destUniq < transMapV5 |< transMapV5 | < transMapV5 | Where srcUniq is a number added to make each source alignment unique, and < transMapV5 | destUniq is added to give the subsequent TransMap alignments unique < transMapV5 | identifiers. < transMapV5 | < transMapV5 |
< transMapV5 | For example, in the cow genome, there are two alignments of mRNA BC149621.1. < transMapV5 | These are assigned the identifiers BC149621.1-1 and BC149621.1-2. < transMapV5 | When these are mapped to the human genome, BC149621.1-1 maps to a single < transMapV5 | location and is given the identifier BC149621.1-1.1. However, BC149621.1-2 < transMapV5 | maps to two locations, resulting in BC149621.1-2.1 and BC149621.1-2.2. Note < transMapV5 | that multiple TransMap mappings are usually the result of tandem duplications, where both < transMapV5 | chains are identified as syntenic. < transMapV5 |
< transMapV5 | < transMapV5 |< transMapV5 | The raw data for these tracks can be accessed interactively through the < transMapV5 | Table Browser or the < transMapV5 | Data Integrator. < transMapV5 | For automated analysis, the annotations are stored in < transMapV5 | bigPsl files (containing a < transMapV5 | number of extra columns) and can be downloaded from our < transMapV5 | download server, < transMapV5 | or queried using our API. For more < transMapV5 | information on accessing track data see our < transMapV5 | Track Data Access FAQ. < transMapV5 | The files are associated with these tracks in the following way: < transMapV5 |
< transMapV5 | bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/panTro5/transMap/V5/panTro5.refseq.transMapV5.bigPsl < transMapV5 | -chrom=chr6 -start=0 -end=1000000 stdout < transMapV5 | < transMapV5 | < transMapV5 |
< transMapV5 | This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data < transMapV5 | submitted to the international public sequence databases by < transMapV5 | scientists worldwide and annotations produced by the RefSeq, < transMapV5 | Ensembl, and GENCODE annotations projects.
< transMapV5 | < transMapV5 |< transMapV5 | Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, < transMapV5 | Lau C et al. < transMapV5 | < transMapV5 | Targeted discovery of novel human exons by comparative genomics. < transMapV5 | Genome Res. 2007 Dec;17(12):1763-73. < transMapV5 | PMID: 17989246; PMC: PMC2099585 < transMapV5 |
< transMapV5 | < transMapV5 |< transMapV5 | Stanke M, Diekhans M, Baertsch R, Haussler D. < transMapV5 | < transMapV5 | Using native and syntenically mapped cDNA alignments to improve de novo gene finding. < transMapV5 | Bioinformatics. 2008 Mar 1;24(5):637-44. < transMapV5 | PMID: 18218656 < transMapV5 |
< transMapV5 | < transMapV5 |< transMapV5 | Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. < transMapV5 | < transMapV5 | Comparative genomics search for losses of long-established genes on the human lineage. < transMapV5 | PLoS Comput Biol. 2007 Dec;3(12):e247. < transMapV5 | PMID: 18085818; PMC: PMC2134963 < transMapV5 |
< transMapV5 | < transMapV5 |