Schema for UniProt Variants - UniProt/SwissProt Amino Acid Substitutions |
|---|
| |
Database: dm6 Primary Table: spMut Data last updated: 2017-10-10
Big Bed File: /gbdb/dm6/bbi/uniprot/unipMut.bb
Item Count: 2,561
Format description: Browser extensible data (12 fields) plus information about uniProt mutation
| field | example | description |
|---|
| chrom | chr2L | Chromosome (or contig, scaffold, etc.) | | chromStart | 16045891 | Start position in chromosome | | chromEnd | 16045894 | End position in chromosome | | name | G296R | Name of item | | score | 1000 | Score from 0-1000 | | strand | + | + or - | | thickStart | 16045891 | Start of where display should be thick (start codon) | | thickEnd | 16045894 | End of where display should be thick (stop codon) | | reserved | 0 | Used as itemRgb as of 2004-11-22 | | blockCount | 1 | Number of blocks | | blockSizes | 3 | Comma separated list of block sizes | | chromStarts | 0 | Start positions relative to chromStart | | status | Manually reviewed (Swiss-Prot) | Status | | varType | Experimental mutation of amino acids | Variant Type | | diseases | | Diseases | | mutation | position 296, Gly changed to Arg | Coding seq. mutation | | comments | In allele RU-35; bicaudal phenotype; lowers RNA-binding | Comment | | variationId | | UniProt variant | | dbSnpId | | dbSNP | | uniProtId | Q24009 | UniProt record | | pmids | 9671494 | Source articles |
|
| |
|
|
|
Sample Rows
|
|---|
| |
| chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | status | varType | diseases | mutation | comments | variationId | dbSnpId | uniProtId | pmids |
|---|
| chr2L | 16045891 | 16045894 | G296R | 1000 | + | 16045891 | 16045894 | 0 | 1 | 3 | 0 | Manually reviewed (Swiss-Prot) | Experimental mutation of amino acids | | position 296, Gly changed to Arg | In allele RU-35; bicaudal phenotype; lowers RNA-binding | | | Q24009 | 9671494 |
| chr2L | 16173757 | 16173760 | C629Y | 1000 | + | 16173757 | 16173760 | 0 | 1 | 3 | 0 | Manually reviewed (Swiss-Prot) | Experimental mutation of amino acids | | position 629, Cys changed to Tyr | In AR66; slower channel activation and reduction of peak current | | | Q24270 | 9502794,9539432 |
| chr2L | 16445349 | 16445352 | I8L | 1000 | + | 16445349 | 16445352 | 0 | 1 | 3 | 0 | Manually reviewed (Swiss-Prot) | Naturally occurring sequence variant | strain: MB15b,MB25a | position 8, Ile changed to Leu | strain: MB15b,MB25a; | | | Q8MM24 | |
| chr2L | 16445457 | 16445460 | N44S | 1000 | + | 16445457 | 16445460 | 0 | 1 | 3 | 0 | Manually reviewed (Swiss-Prot) | Naturally occurring sequence variant | strain: MB13a, MB15b, MB25a, MB34a, MB37a,MB63a | position 44, Asn changed to Ser | strain: MB13a, MB15b, MB25a, MB34a, MB37a,MB63a; | | | Q8MM24 | |
| chr2L | 16445625 | 16445628 | S100G | 1000 | + | 16445625 | 16445628 | 0 | 1 | 3 | 0 | Manually reviewed (Swiss-Prot) | Naturally occurring sequence variant | strain: MB01a,MB33a | position 100, Ser changed to Gly | strain: MB01a,MB33a; | | | Q8MM24 | |
| chr2L | 16445673 | 16445676 | V116I | 1000 | + | 16445673 | 16445676 | 0 | 1 | 3 | 0 | Manually reviewed (Swiss-Prot) | Naturally occurring sequence variant | strain: MB08b, MB29b, MB36a, MB40b, MB47a, MB48b, MB52b,MB58b | position 116, Val changed to Ile | strain: MB08b, MB29b, MB36a, MB40b, MB47a, MB48b, MB52b,MB58b; | | | Q8MM24 | |
| chr2L | 16445883 | 16445886 | E186Q | 1000 | + | 16445883 | 16445886 | 0 | 1 | 3 | 0 | Manually reviewed (Swiss-Prot) | Naturally occurring sequence variant | strain: MB08b, MB29b, MB40b, MB45b, MB47a, MB48b, MB52b,MB80b | position 186, Glu changed to Gln | strain: MB08b, MB29b, MB40b, MB45b, MB47a, MB48b, MB52b,MB80b; | | | Q8MM24 | |
| chr2L | 16446311 | 16446314 | G305E | 1000 | + | 16446311 | 16446314 | 0 | 1 | 3 | 0 | Manually reviewed (Swiss-Prot) | Naturally occurring sequence variant | strain: MB01a, MB08b, MB29b, MB36a, MB45b, MB47a, MB48b,MB52b,MB80b | position 305, Gly changed to Glu | strain: MB01a, MB08b, MB29b, MB36a, MB45b, MB47a, MB48b,MB52b,MB80b; | | | Q8MM24 | |
| chr2L | 16446335 | 16446338 | I313V | 1000 | + | 16446335 | 16446338 | 0 | 1 | 3 | 0 | Manually reviewed (Swiss-Prot) | Naturally occurring sequence variant | strain: MB48b,MB52b | position 313, Ile changed to Val | strain: MB48b,MB52b; | | | Q8MM24 | |
| chr2L | 16446593 | 16446596 | V399E | 1000 | + | 16446593 | 16446596 | 0 | 1 | 3 | 0 | Manually reviewed (Swiss-Prot) | Naturally occurring sequence variant | strain: MB34a,MB39b | position 399, Val changed to Glu | strain: MB34a,MB39b; | | | Q8MM24 | |
|
| |
|
|
|
UniProt Variants (spMut) Track Description
|
|---|
| |
Description
NOTE:
This track is intended for use primarily by physicians and other
professionals concerned with genetic disorders, by genetics researchers, and
by advanced students in science and medicine. While the genome browser database
is open to the public, users seeking information about a personal medical or
genetic condition are urged to consult with a qualified physician for
diagnosis and for answers to personal questions.
This track shows the genomic positions of natural and artifical amino acid variants
in the UniProt/SwissProt database.
The data has been curated from scientific publications by the UniProt staff.
Display Conventions and Configuration
Genomic locations of UniProt/SwissProt variants are labeled with the amino acid
change at a given position and, if known, the abbreviated disease name. A
"?" is used if there is no disease annotated at this location, but the
protein is described as being linked to only a single disease in UniProt.
Mouse over a mutation to see the UniProt comments.
Artificially-introduced mutations are colored green and naturally-occurring variants are colored
red. For full information about a particular variant, click the "UniProt variant" linkout.
The "UniProt record" linkout lists all variants of a particular protein sequence.
The "Source articles" linkout lists the articles in PubMed that originally described
the variant(s) and were used as evidence by the UniProt curators.
Methods
UniProt sequences were aligned to RefSeq sequences first with BLAT, then lifted
to genome positions with pslMap. UniProt variants were parsed from the UniProt
XML file. The variants were then mapped to the genome through the alignment
using the pslMap program. This mapping approach
draws heavily on the LS-SNP pipeline by Mark Diekhans. The complete script is
part of the kent source tree and is located in src/hg/utils/uniprotMutations.
Data Access
The raw data can be explored interactively with the
Table Browser, or the
Data Integrator.
For automated analysis, the genome annotation is stored in a bigBed file that
can be downloaded from the
download server.
The underlying data file for this track is called spMut.bb. Individual
regions or the whole genome annotation can be obtained using our tool bigBedToBed
which can be compiled from the source code or downloaded as a precompiled binary
for your system. Instructions for downloading source code and binaries can be found
here.
The tool can also be used to obtain only features within a given range, for example:
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/dm6/bbi/uniprot/spMut.bb -chrom=chr6 -start=0 -end=1000000 stdout
Please refer to our
mailing list archives
for questions, or our
Data Access FAQ
for more information.
Credits
This track was created by Maximilian Haeussler, with advice from Mark Diekhans and Brian Raney.
References
UniProt Consortium.
Reorganizing the protein space at the Universal Protein Resource (UniProt).
Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5.
PMID: 22102590; PMC: PMC3245120
Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E, Bairoch A.
The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure
information on human protein variants.
Hum Mutat. 2004 May;23(5):464-70.
PMID: 15108278
| |
|
|
|