How To Obtain Protein Or Uniprot Coordinates From Chromosomal Coordinates?
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8.7 years ago
riknro • 0

Hi,

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

Thanks

uniprot coordinates • 3.1k views
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8.7 years ago

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 ".

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

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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?

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8.7 years ago
Christof Winter ★ 1.0k

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

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