Question: Finding the transcript with UniProt canonical sequence (or ID)
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gravatar for ajingnk
3.3 years ago by
ajingnk120
United States
ajingnk120 wrote:

I have UniProt canonical sequence and UniProtID. Is there any easy way (like Biopython) to get the transcript sequence for UniProt protein sequence (I also have gene name and UniProtID)? I saw many corresponding Ensemble Transcript for one UniProt entry. I just need the one corresponding to canonical sequence. Is there any easy way to find that?

 

 

Thanks

uniprot sequence • 1.6k views
ADD COMMENTlink modified 3.3 years ago by Elisabeth Gasteiger1.5k • written 3.3 years ago by ajingnk120
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gravatar for Elisabeth Gasteiger
3.3 years ago by
Geneva
Elisabeth Gasteiger1.5k wrote:

This is unfortunately not possible in most cases: The canonical protein sequence is the outcome of thorough curation work, which often involves the merge of various sequences encoded by the same gene (in one species). For more details please have a look at http://www.uniprot.org/help/canonical_nucleotide

ADD COMMENTlink written 3.3 years ago by Elisabeth Gasteiger1.5k

Thanks Elisabeth! I saw that "Sequence databases" are listed as cross-reference. Is that possible to retrieve the nucleotide sequence with sequence databases? I just want to get some rough results, so I may not need all corresponding residues. I want to know the all possible mutations for one protein from a transcript.

ADD REPLYlink written 3.3 years ago by ajingnk120

Sorry for not replying earlier.

You can indeed follow the link to EMBL/GenBank/DDBJ, but the problem is that there can be more than one such link and you may have difficulty choosing one, as described in the help document cited above. But if you do not mind which nucleotide sequence(s) to retrieve, you can of course use the protein_id or nucleotide accession number from the cross-referenced sequence databases to retrieve the sequence from the nucleotide sequence databases. In case of doubt, I suggest that you contact EMBL/GenBank/DDBJ directly about the best way to access their data programmatically.

ADD REPLYlink written 3.3 years ago by Elisabeth Gasteiger1.5k
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