< evaSnp | This track contains mappings of single nucleotide variants < evaSnp | and small insertions and deletions (indels) < evaSnp | from the European Variation Archive < evaSnp | (EVA) < evaSnp | Release 3 for the crab-eating macaque macFas5 genome. The dbSNP database at NCBI no longer < evaSnp | hosts non-human variants. < evaSnp |
< evaSnp | < evaSnp |< evaSnp | Variants are shown as single tick marks at most zoom levels. < evaSnp | When viewing the track at or near base-level resolution, the displayed < evaSnp | width of the SNP variant corresponds to the width of the variant in the < evaSnp | reference sequence. Insertions are indicated by a single tick mark displayed < evaSnp | between two nucleotides, single nucleotide polymorphisms are displayed as the < evaSnp | width of a single base, and multiple nucleotide variants are represented by a < evaSnp | block that spans two or more bases. The display is set to automatically collapse to < evaSnp | dense visibility when there are more than 100k variants in the window. < evaSnp | When the window size is more than 250k bp, the display is switched to density graph mode. < evaSnp |
< evaSnp | < evaSnp |< evaSnp | Navigation to an individual variant can be accomplished by typing or copying < evaSnp | the variant identifier (rsID) or the genomic coordinates into the Position/Search box on the < evaSnp | Browser.
< evaSnp | < evaSnp |< evaSnp | A click on an item in the graphical display displays a page with data about < evaSnp | that variant. Data fields include the Reference and Alternate Alleles, the < evaSnp | class of the variant as reported by EVA, the source of the data, the amino acid < evaSnp | change, if any, and the functional class as determined by UCSC's Variant Annotation < evaSnp | Integrator. < evaSnp |
< evaSnp | < evaSnp |Variants can be filtered using the track controls to show subsets of the < evaSnp | data by either EVA Sequence Ontology (SO) term, UCSC-generated functional effect, or < evaSnp | by color, which bins the UCSC functional effects into general classes.
< evaSnp | < evaSnp |< evaSnp | Mousing over an item shows the ucscClass, which is the consequence according to the < evaSnp | Variant Annotation Integrator, and < evaSnp | the aaChange when one is available, which is the change in amino acid in HGVS.p < evaSnp | terms. Items may have multiple ucscClasses, which will all be shown in the mouse-over < evaSnp | in a comma-separated list. Likewise, multiple HGVS.p terms may be shown for each rsID < evaSnp | separated by spaces describing all possible AA changes.
< evaSnp |< evaSnp | Multiple items may appear due to different variant predictions on multiple gene transcripts. < evaSnp | For all organisms the gene models used were ncbiRefSeqCurated, except for mm39 which < evaSnp | used ncbiRefSeqSelect.
< evaSnp | < evaSnp | < evaSnp |< evaSnp | Variants are colored according to the most potentially deleterious functional effect prediction < evaSnp | according to the Variant Annotation Integrator. Specific bins can be seen in the Methods section < evaSnp | below. < evaSnp |
< evaSnp | < evaSnp |< evaSnp |
| Color | < evaSnp |Variant Type | < evaSnp |
|---|---|
| Protein-altering variants and splice site variants | |
| Synonymous codon variants | |
| Non-coding transcript or Untranslated Region (UTR) variants | |
| Intergenic and intronic variants |
< evaSnp | Variants are classified by EVA into one of the following sequence ontology terms: < evaSnp |
< evaSnp | < evaSnp |< evaSnp | Data were downloaded from the European Variation Archive EVA release 3 (2022-02-24) < evaSnp | current_ids.vcf.gz files corresponding to the proper assembly.
< evaSnp |< evaSnp | Chromosome names were converted to UCSC-style, a few problematic variants were removed, < evaSnp | and the variants passed through the < evaSnp | Variant Annotation Integrator to < evaSnp | predict consequence. For every organism the ncbiRefSeqCurated gene models were used to < evaSnp | predict the consequences, except for mm39 which used the ncbiRefSeqSelect models.
< evaSnp |< evaSnp | Variants were then colored according to their predicted consequence in the following fashion: < evaSnp |
< evaSnp | Sequence Ontology ("SO:") < evaSnp | terms were converted to the variant classes, then the files were converted to BED, < evaSnp | and then bigBed format. < evaSnp |
< evaSnp |< evaSnp | No functional annotations were provided by the EVA (e.g., missense, nonsense, etc). < evaSnp | These were computed using UCSC's Variant Annotation Integrator (Hinrichs, et al., 2016). < evaSnp | Amino-acid substitutions for missense variants are based < evaSnp | on RefSeq alignments of mRNA transcripts, which do not always match the amino acids < evaSnp | predicted from translating the genomic sequence. Therefore, in some instances, the < evaSnp | variant and the genomic nucleotide and associated amino acid may be reversed. < evaSnp | E.g., a Pro > Arg change from the perspective of the mRNA would be Arg > Pro from < evaSnp | the persepective the genomic sequence. < evaSnp | For complete documentation of the processing of these tracks, read the < evaSnp | < evaSnp | EVA Release 3 MakeDoc.
< evaSnp | < evaSnp |< evaSnp | Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies, < evaSnp | and more information about how to convert SNPs between assemblies can be found on the following < evaSnp | FAQ entry.
< evaSnp |< evaSnp | The data can be explored interactively with the Table Browser, < evaSnp | or the Data Integrator. For automated analysis, the data may be < evaSnp | queried from our REST API. Please refer to our < evaSnp | mailing list archives < evaSnp | for questions, or our Data Access FAQ for more < evaSnp | information.
< evaSnp | < evaSnp |
< evaSnp | For automated download and analysis, this annotation is stored in a bigBed file that
< evaSnp | can be downloaded from our download server. The file for this track is called evaSnp.bb.
< evaSnp | Individual regions or the whole genome annotation can be obtained using our tool
< evaSnp | bigBedToBed which can be compiled from the source code or downloaded as a precompiled
< evaSnp | binary for your system. Instructions for downloading source code and binaries can be found
< evaSnp | here.
< evaSnp | The tool can also be used to obtain only features within a given range, e.g.
< evaSnp |
< evaSnp | bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/macFas5/bbi/evaSnp.bb -chrom=chr21 -start=0 -end=100000000 stdout
< evaSnp |
< evaSnp | This track was produced from the European < evaSnp | Variation Archive release 3 data. Consequences were predicted using UCSC's Variant Annotation < evaSnp | Integrator and NCBI's RefSeq gene models. < evaSnp |
< evaSnp | < evaSnp |< evaSnp | Cezard T, Cunningham F, Hunt SE, Koylass B, Kumar N, Saunders G, Shen A, Silva AF, < evaSnp | Tsukanov K, Venkataraman S et al. The European Variation Archive: a FAIR resource of genomic variation for all < evaSnp | species. Nucleic Acids Res. 2021 Oct 28:gkab960. < evaSnp | doi:10.1093/nar/gkab960. < evaSnp | Epub ahead of print. PMID: 34718739. PMID: PMC8728205. < evaSnp |
< evaSnp |< evaSnp | Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, < evaSnp | Haussler D, Kent WJ. < evaSnp | UCSC Data Integrator and Variant Annotation Integrator. < evaSnp | Bioinformatics. 2016 May 1;32(9):1430-2. < evaSnp | PMID: 26740527; PMC: < evaSnp | PMC4848401 < evaSnp |
< evaSnp | < evaSnp4 | html < evaSnp4 |< 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 crab-eating macaque macFas5 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/macFas5/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 crab-eating macaque macFas5 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/macFas5/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 | 3740,3743d3096 < ncbiRefSeqGenomicDiff | html < ncbiRefSeqGenomicDiff | < ncbiRefSeqOther | html < ncbiRefSeqOther | 5276,6055d4628 < 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 crab-eating macaque. < 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/macFas5/transMap/V4/macFas5.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 crab-eating macaque. < 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/macFas5/transMap/V4/macFas5.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 crab-eating macaque. < 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/macFas5/transMap/V4/macFas5.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 crab-eating macaque. < 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/macFas5/transMap/V4/macFas5.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 crab-eating macaque. 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/macFas5/transMap/V5/macFas5.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 | 6093,6458d4665 < unipAliSwissprot | html < unipAliSwissprot | < unipAliTrembl | html < unipAliTrembl | < unipChain | html < unipChain | < unipConflict | html < unipConflict | < unipDisulfBond | html < unipDisulfBond | < unipDomain | html < unipDomain | < unipInterest | html < unipInterest | < unipLocCytopl | html < unipLocCytopl | < unipLocExtra | html < unipLocExtra | < unipLocSignal | html < unipLocSignal | < unipLocTransMemb | html < unipLocTransMemb | < unipModif | html < unipModif | < unipMut | html < unipMut | < unipOther | html < unipOther | < unipRepeat | html < unipRepeat | < uniprot | html < uniprot |< uniprot | This track shows protein sequences and annotations on them from the UniProt/SwissProt database, < uniprot | mapped to genomic coordinates. < uniprot |
< uniprot |< uniprot | UniProt/SwissProt data has been curated from scientific publications by the UniProt staff, < uniprot | UniProt/TrEMBL data has been predicted by various computational algorithms. < uniprot | The annotations are divided into multiple subtracks, based on their "feature type" in UniProt. < uniprot | The first two subtracks below - one for SwissProt, one for TrEMBL - show the < uniprot | alignments of protein sequences to the genome, all other tracks below are the protein annotations < uniprot | mapped through these alignments to the genome. < uniprot |
< uniprot | < uniprot || Track Name | < uniprot |Description | < uniprot |
|---|---|
| UCSC Alignment, SwissProt = curated protein sequences | < uniprot |Protein sequences from SwissProt mapped to the genome. All other < uniprot | tracks are (start,end) SwissProt annotations on these sequences mapped < uniprot | through this alignment. Even protein sequences without a single curated < uniprot | annotation (splice isoforms) are visible in this track. Each UniProt protein < uniprot | has one main isoform, which is colored in dark. Alternative isoforms are < uniprot | sequences that do not have annotations on them and are colored in light-blue. < uniprot | They can be hidden with the TrEMBL/Isoform filter (see below). |
| UCSC Alignment, TrEMBL = predicted protein sequences | < uniprot |Protein sequences from TrEMBL mapped to the genome. All other tracks < uniprot | below are (start,end) TrEMBL annotations mapped to the genome using < uniprot | this track. This track is hidden by default. To show it, click its < uniprot | checkbox on the track configuration page. |
| UniProt Signal Peptides | < uniprot |Regions found in proteins destined to be secreted, generally cleaved from mature protein. | < uniprot |
| UniProt Extracellular Domains | < uniprot |Protein domains with the comment "Extracellular". | < uniprot |
| UniProt Transmembrane Domains | < uniprot |Protein domains of the type "Transmembrane". | < uniprot |
| UniProt Cytoplasmic Domains | < uniprot |Protein domains with the comment "Cytoplasmic". | < uniprot |
| UniProt Polypeptide Chains | < uniprot |Polypeptide chain in mature protein after post-processing. | < uniprot |
| UniProt Regions of Interest | < uniprot |Regions that have been experimentally defined, such as the role of a region in mediating protein-protein interactions or some other biological process. | < uniprot |
| UniProt Domains | < uniprot |Protein domains, zinc finger regions and topological domains. | < uniprot |
| UniProt Disulfide Bonds | < uniprot |Disulfide bonds. | < uniprot |
| UniProt Amino Acid Modifications | < uniprot |Glycosylation sites, modified residues and lipid moiety-binding regions. | < uniprot |
| UniProt Amino Acid Mutations | < uniprot |Mutagenesis sites and sequence variants. | < uniprot |
| UniProt Protein Primary/Secondary Structure Annotations | < uniprot |Beta strands, helices, coiled-coil regions and turns. | < uniprot |
| UniProt Sequence Conflicts | < uniprot |Differences between Genbank sequences and the UniProt sequence. | < uniprot |
| UniProt Repeats | < uniprot |Regions of repeated sequence motifs or repeated domains. | < uniprot |
| UniProt Other Annotations | < uniprot |All other annotations, e.g. compositional bias | < uniprot |
< uniprot | For consistency and convenience for users of mutation-related tracks, < uniprot | the subtrack "UniProt/SwissProt Variants" is a copy of the track < uniprot | "UniProt Variants" in the track group "Phenotype and Literature", or < uniprot | "Variation and Repeats", depending on the assembly. < uniprot |
< uniprot | < uniprot |< uniprot | Genomic locations of UniProt/SwissProt annotations are labeled with a short name for < uniprot | the type of annotation (e.g. "glyco", "disulf bond", "Signal peptide" < uniprot | etc.). A click on them shows the full annotation and provides a link to the UniProt/SwissProt < uniprot | record for more details. TrEMBL annotations are always shown in < uniprot | light blue, except in the Signal Peptides, < uniprot | Extracellular Domains, Transmembrane Domains, and Cytoplamsic domains subtracks.
< uniprot | < uniprot |< uniprot | Mouse over a feature to see the full UniProt annotation comment. For variants, the mouse over will < uniprot | show the full name of the UniProt disease acronym. < uniprot |
< uniprot | < uniprot |< uniprot | The subtracks for domains related to subcellular location are sorted from outside to inside of < uniprot | the cell: Signal peptide, < uniprot | extracellular, < uniprot | transmembrane, and cytoplasmic. < uniprot |
< uniprot | < uniprot |< uniprot | Features in the "UniProt Modifications" (modified residues) track are drawn in < uniprot | light green. Disulfide bonds are shown in < uniprot | dark grey. Topological domains < uniprot | in maroon and zinc finger regions in < uniprot | olive green. < uniprot |
< uniprot | < uniprot |< uniprot | Duplicate annotations are removed as far as possible: if a TrEMBL annotation < uniprot | has the same genome position and same feature type, comment, disease and < uniprot | mutated amino acids as a SwissProt annotation, it is not shown again. Two < uniprot | annotations mapped through different protein sequence alignments but with the same genome < uniprot | coordinates are only shown once.
< uniprot | < uniprot |On the configuration page of this track, you can choose to hide any TrEMBL annotations. < uniprot | This filter will also hide the UniProt alternative isoform protein sequences because < uniprot | both types of information are less relevant to most users. Please contact us if you < uniprot | want more detailed filtering features.
< uniprot | < uniprot |Note that for the human hg38 assembly and SwissProt annotations, there < uniprot | also is a public < uniprot | track hub prepared by UniProt itself, with < uniprot | genome annotations maintained by UniProt using their own mapping < uniprot | method based on those Gencode/Ensembl gene models that are annotated in UniProt < uniprot | for a given protein. For proteins that differ from the genome, UniProt's mapping method < uniprot | will, in most cases, map a protein and its annotations to an unexpected location < uniprot | (see below for details on UCSC's mapping method).
< uniprot | < uniprot |< uniprot | Briefly, UniProt protein sequences were aligned to the transcripts associated < uniprot | with the protein, the top-scoring alignments were retained, and the result was < uniprot | projected to the genome through a transcript-to-genome alignment. < uniprot | Depending on the genome, the transcript-genome alignments was either < uniprot | provided by the source database (NBCI RefSeq), created at UCSC (UCSC RefSeq) or < uniprot | derived from the transcripts (Ensembl/Augustus). The transcript set is NCBI < uniprot | RefSeq for hg38, UCSC RefSeq for hg19 (due to alt/fix haplotype misplacements < uniprot | in the NCBI RefSeq set on hg19). For other genomes, RefSeq, Ensembl and Augustus < uniprot | are tried, in this order. The resulting protein-genome alignments of this process < uniprot | are available in the file formats for liftOver or pslMap from our data archive < uniprot | (see "Data Access" section below). < uniprot |
< uniprot | < uniprot |An important step of the mapping process protein -> transcript -> < uniprot | genome is filtering the alignment from protein to transcript. Due to < uniprot | differences between the UniProt proteins and the transcripts (proteins were < uniprot | made many years before the transcripts were made, and human genomes have < uniprot | variants), the transcript with the highest BLAST score when aligning the < uniprot | protein to all transcripts is not always the correct transcript for a protein < uniprot | sequence. Therefore, the protein sequence is aligned to only a very short list < uniprot | of one or sometimes more transcripts, selected by a three-step procedure: < uniprot |
< uniprot | For strategy 2 and 3, many of the transcripts found do not differ in coding < uniprot | sequence, so the resulting alignments on the genome will be identical. < uniprot | Therefore, any identical alignments are removed in a final filtering step. The < uniprot | details page of these alignments will contain a list of all transcripts that < uniprot | result in the same protein-genome alignment. On hg38, only a handful of edge < uniprot | cases (pseudogenes, very recently added proteins) remain in 2023 where strategy < uniprot | 3 has to be used.
< uniprot | < uniprot |In other words, when an NCBI or UCSC RefSeq track is used for the mapping and to align a < uniprot | protein sequence to the correct transcript, we use a three stage process: < uniprot |
This system was designed to resolve the problem of incorrect mappings of < uniprot | proteins, mostly on hg38, due to differences between the SwissProt < uniprot | sequences and the genome reference sequence, which has changed since the < uniprot | proteins were defined. The problem is most pronounced for gene families < uniprot | composed of either very repetitive or very similar proteins. To make sure that < uniprot | the alignments always go to the best chromosome location, all _alt and _fix < uniprot | reference patch sequences are ignored for the alignment, so the patches are < uniprot | entirely free of UniProt annotations. Please contact us if you have feedback on < uniprot | this process or example edge cases. We are not aware of a way to evaluate the < uniprot | results completely and in an automated manner.
< uniprot |< uniprot | Proteins were aligned to transcripts with TBLASTN, converted to PSL, filtered < uniprot | with pslReps (93% query coverage, keep alignments within top 1% score), lifted to genome < uniprot | positions with pslMap and filtered again with pslReps. UniProt annotations were < uniprot | obtained from the UniProt XML file. The UniProt annotations were then mapped to the < uniprot | genome through the alignment described above using the pslMap program. This approach < uniprot | draws heavily on the LS-SNP pipeline by Mark Diekhans. < uniprot | Like all Genome Browser source code, the main script used to build this track < uniprot | can be found on Github. < uniprot |
< uniprot | < uniprot |< uniprot | This track is automatically updated on an ongoing basis, every 2-3 months. < uniprot | The current version name is always shown on the track details page, it includes the < uniprot | release of UniProt, the version of the transcript set and a unique MD5 that is < uniprot | based on the protein sequences, the transcript sequences, the mapping file < uniprot | between both and the transcript-genome alignment. The exact transcript < uniprot | that was used for the alignment is shown when clicking a protein alignment < uniprot | in one of the two alignment tracks. < uniprot |
< uniprot | < uniprot |< uniprot | For reproducibility of older analysis results and for manual inspection, previous versions of this track < uniprot | are available for browsing in the form of the UCSC UniProt Archive Track Hub (click this link to connect the hub now). The underlying data of < uniprot | all releases of this track (past and current) can be obtained from our downloads server, including the UniProt < uniprot | protein-to-genome alignment.
< uniprot | < uniprot |< uniprot | The raw data of the current track can be explored interactively with the < uniprot | Table Browser, or the < uniprot | Data Integrator. < uniprot | For automated analysis, the genome annotation is stored in a bigBed file that < uniprot | can be downloaded from the < uniprot | download server. < uniprot | The exact filenames can be found in the < uniprot | track configuration file. < uniprot | Annotations can be converted to ASCII text by our tool bigBedToBed < uniprot | which can be compiled from the source code or downloaded as a precompiled < uniprot | binary for your system. Instructions for downloading source code and binaries can be found < uniprot | here. < uniprot | The tool can also be used to obtain only features within a given range, for example: < uniprot |
< uniprot | bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/macFas5/uniprot/unipStruct.bb -chrom=chr6 -start=0 -end=1000000 stdout < uniprot |
< uniprot | Please refer to our < uniprot | mailing list archives < uniprot | for questions, or our < uniprot | Data Access FAQ < uniprot | for more information. < uniprot | < uniprot | < uniprot |< uniprot | < uniprot |
To facilitate mapping protein coordinates to the genome, we provide the < uniprot | alignment files in formats that are suitable for our command line tools. Our < uniprot | command line programs liftOver or pslMap can be used to map < uniprot | coordinates on protein sequences to genome coordinates. The filenames are < uniprot | unipToGenome.over.chain.gz (liftOver) and unipToGenomeLift.psl.gz (pslMap).
< uniprot | < uniprot |Example commands: < uniprot |
< uniprot | wget -q https://hgdownload.soe.ucsc.edu/goldenPath/archive/hg38/uniprot/2022_03/unipToGenome.over.chain.gz < uniprot | wget -q https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver < uniprot | chmod a+x liftOver < uniprot | echo 'Q99697 1 10 annotationOnProtein' > prot.bed < uniprot | liftOver prot.bed unipToGenome.over.chain.gz genome.bed < uniprot | cat genome.bed < uniprot |< uniprot | < uniprot | < uniprot |
< uniprot | This track was created by Maximilian Haeussler at UCSC, with a lot of input from Chris < uniprot | Lee, Mark Diekhans and Brian Raney, feedback from the UniProt staff, Alejo < uniprot | Mujica, Regeneron Pharmaceuticals and Pia Riestra, GeneDx. Thanks to UniProt for making all data < uniprot | available for download. < uniprot |
< uniprot | < uniprot |< uniprot | UniProt Consortium. < uniprot | < uniprot | Reorganizing the protein space at the Universal Protein Resource (UniProt). < uniprot | Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5. < uniprot | PMID: 22102590; PMC: PMC3245120 < uniprot |
< uniprot | < uniprot |< uniprot | Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E, Bairoch A. < uniprot | < uniprot | The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure < uniprot | information on human protein variants. < uniprot | Hum Mutat. 2004 May;23(5):464-70. < uniprot | PMID: 15108278 < uniprot |
< uniprot | < unipStruct | html < unipStruct |