How To Obtain Protein Or Uniprot Coordinates From Chromosomal Coordinates?

Question

[riknro]

Hi,

I have chromosomal coordinates for a particular Positions in a gene.How I obtain the corresponding position in protein???

Thanks

Answer 1

[Elisabeth Gasteiger]

Have you seen ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/variants/ as announced for UniProt release 2013_12? http://www.uniprot.org/news/2013/12/11/release

This directory contains the following files:

humsavar.txt: Index of manually curated Human polymorphisms and disease mutations from UniProtKB/Swiss-Prot.

homo_sapiens_variation.txt.gz: Index of variants from the 1000 Genomes Project www.1000genome.org) that are not in UniProtKB/Swiss-Prot and that modify the protein sequence, including nonynonymous or missense variants and initiator codon variants. These variants are currently not available in the corresponding UniProtKB entries. There are 2 columns that might be interesting for you: "Cytogenetic Band" and "Chromosome Coordinate ".

[Christof Winter]

How do you handle multiple transcripts that produce different isoforms when assigning an amino acid position to a genomic position?

[Elisabeth Gasteiger]

Apologies, I hadn't noticed your question. The new file, homo_sapiens_variation.txt contains alternative isoforms, e.g. for gene A1CF

A1CF    Q9NQ94-2    p.Ile73Val    rs192585176    missense variant    -    -    -    10q11.23    10:g.52603765T>C    ENSG00000148584    ENST00000373997    ENSP00000363109

A1CF    Q9NQ94-2    p.Lys114Asn    rs181537708    missense variant    -    -    -    10q11.23    10:g.52601645C>G    ENSG00000148584    ENST00000373997    ENSP00000363109
..

A1CF    Q9NQ94-4    p.Ile81Val    rs192585176    missense variant    -    -    -    10q11.23    10:g.52603765T>C    ENSG00000148584    ENST00000373995    ENSP00000363107

A1CF    Q9NQ94-4    p.Lys122Asn    rs181537708    missense variant    -    -    -    10q11.23    10:g.52601645C>G    ENSG00000148584    ENST00000373995    ENSP00000363107

A1CF    Q9NQ94-4    p.Ser162Pro    rs143123872    missense variant    -    -    -    10q11.23    10:g.52595978A>G    ENSG00000148584    ENST00000373995    ENSP00000363107
...

A1CF    Q9NQ94-6    p.Ile73Val    rs192585176    missense variant    -    -    -    10q11.23    10:g.52603765T>C    ENSG00000148584    ENST00000395495    ENSP00000378873

A1CF    Q9NQ94-6    p.Lys114Asn    rs181537708    missense variant    -    -    -    10q11.23    10:g.52601645C>G    ENSG00000148584    ENST00000395495    ENSP00000378873


Isoform sequences are mapped to Ensembl, just like canonical sequences are. Does this answer your question?

Answer 2

[Christof Winter]

ANNOVAR is your friend. If it's human, you could also try the web server at http://wannovar.usc.edu/.