Retrieve isoform sequences for a protein from UniProt
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sgupt46 • 0
@sgupt46-13716
Last seen 12 days ago
Canada

Hi, I am trying to get amino acid sequence for a protein-isoform from UniProt but not able to find a solution. I can get canonical sequence but the method to obtain isoform sequence is not available.

library(UniProt.ws)
up <- UniProt.ws(taxId=9606)
select(up, keys = "Q2V2M9", columns = c("SEQUENCE"), keytype = "UNIPROTKB")
# select(up, keys = "Q2V2M9-4", columns = c("SEQUENCE"), keytype = "UNIPROTKB")
# Isoform id doesn't work. Because it is also not a key in the UniProt object.

Does anyone know if there is a way to get isoform sequence?

UniProt.ws biomaRt • 127 views
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Entering edit mode
Mike Smith ★ 5.1k
@mike-smith
Last seen 37 minutes ago
EMBL Heidelberg / de.NBI

I'm not sure how to approach this with UniProt.ws, but does this get you what you're looking for via biomaRt ?

library(biomaRt)

ensembl <- useEnsembl(biomart = 'genes', dataset = 'hsapiens_gene_ensembl', mirror = "www")
getBM(attributes = c("peptide", "ensembl_gene_id", "ensembl_transcript_id", "uniprotswissprot"),
      filters = c("uniprot_gn_id"), 
      values = "Q2V2M9", 
      mart = ensembl) |>
  tibble::as_tibble()
#> # A tibble: 7 × 4
#>   peptide                     ensembl_gene_id ensembl_transcri… uniprotswissprot
#>   <chr>                       <chr>           <chr>             <chr>           
#> 1 MAMRPRSHPPVGAGTGGGPACVPVAE… ENSG00000134775 ENST00000591635   ""              
#> 2 RLFWNEVRPFDWPCKNNRRCREFLWS… ENSG00000134775 ENST00000592128   ""              
#> 3 MATLACRVQFLDDTDPFNSTNFPEPS… ENSG00000134775 ENST00000590592   "Q2V2M9"        
#> 4 XAINIGLTVLPPPRTIKIAILNFDEY… ENSG00000134775 ENST00000585579   ""              
#> 5 MATLACRVQFLDDTDPFNSTNFPEPS… ENSG00000134775 ENST00000257209   "Q2V2M9"        
#> 6 MATLACRVQFLDDTDPFNSTNFPEPS… ENSG00000134775 ENST00000359247   "Q2V2M9"        
#> 7 XFRLVVKTALKLLLVFVEYSESNAPL… ENSG00000134775 ENST00000592930   ""

That should be the peptide sequence for each transcript listed in Ensembl. I guess the 3 results that have an entry in the uniprotswissprot column are those that can found on https://www.uniprot.org/uniprot/Q2V2M9; It's not clear to me where the fourth isoform listed on that page has gone.

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