I'm making a comparison between proteomics and RNAseq data. When I try to align Uniprot proteins with their Ensembl transcripts I find that some Uniprot proteins have more than one reference to a transcript. The implication is that more than one transcript from the same gene can code for an identical protein. This doesn't make much sense to me and I'm hoping someone can provide some insight. Thanks!
-Jeremy
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jacobsen.jeremy •
Further on what Devon Ryan said above:
The relationship between Ensembl IDs is:
1 ENSG -> n ENST
1 ENST -> 1 ENSP
1 ENSP -> 1 ESNT -> 1 ENSG
i.e. it is possible that a gene gives rise to 2 different transcripts which result in the same protein, but in that case there would still be 2 different Ensembl protein identifiers assigned if the UTR are different.
example: UniProt Q810A1 is mapped to
ENSMUST00000018491; ENSMUSP00000018491; ENSMUSG00000018347. ENSMUST00000071465; ENSMUSP00000071406; ENSMUSG00000018347.
There are 2 ENSP because UTR are different, and therefore generate 2 ENST which results in 2 ENSP whose protein sequence is identical.
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Elisabeth Gasteiger
You can have transcripts that differ only in their UTRs (untranslated regions), meaning that they'll produce identical proteins. This sort of situation will be common in any of the better annotated organisms.
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Devon Ryan
Thanks Devon. One more related question.. Are the proteins identical after translation? I assume they are but I'm not a Biologist.
Thanks again!
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jacobsen.jeremy •
In general I would say yes, they're identical. Theoretically one could conceive of a difference in RNA editing, but if that occurs then it's really obscure.
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Devon Ryan
That a gene can have multiple transcripts is a major source of headaches for me. For the reason why this is so, look into alternative splicing
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Katie D'Aco
oops, I misread your question. I didn't realize you were comparing proteins and transcripts. I was thinking genes and transcripts.
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Katie D'Aco
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I've noticed that the opposite can happen as well, you can see several transcripts map to the same uniprot id.
Are you differentiating between isoforms? Uniprot groups multiple protein isoforms under the same general identifier.