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STRING has protein (amino acid sequences) mapped to a single gene ID. I have these doubts with respect to STRING ID. I find that

1.All alleles of a single gene share the same STRING ID and

2.Especially in Eukaryotes, splice variants of the single gene(which might translate to different proteins) share the same STRING ID.

Does STRING take into account these two things like UniProt and have different IDs based on allelic differences and splice variants?If so,how?

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  • $\begingroup$ At this moment the STRING database is not accessible. Can you give an example? $\endgroup$ – WYSIWYG Dec 17 '14 at 6:32
  • $\begingroup$ Rvxxxx is a gene id. $\endgroup$ – WYSIWYG Dec 17 '14 at 13:49
  • $\begingroup$ STRING uses only gene ID to map protein sequences $\endgroup$ – Raghavakrishna Dec 17 '14 at 13:54
  • $\begingroup$ STRING is now working.Another example STRING ID:4932.Q0010 (Saccharomyces cerevisiae) AA sequence:MYYIMFLYNMLLIIILIFYSIVGVPIIIFNNNYYWDPDIFLFIIYYFIKFIIIFNLYLYYMINYIVYTPSGSPPGRGTYI LLYNMLYSYNMFIDYVMKFITCVTYMYLMFWLLSPTPSPYYVSEVPVS $\endgroup$ – Raghavakrishna Dec 18 '14 at 6:23
  • $\begingroup$ please don't use (non-biological) acronyms such as w.r.t - it makes things unnecessarily hard to read (meta.biology.stackexchange.com/questions/104/…) $\endgroup$ – rg255 Dec 18 '14 at 9:58
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STRING does not distinguish between different products of the same gene. E.g. for human, the protein identifier you see (ENSP...) corresponds to the longest splice form for each gene (ENSG...). Therefore, STRING won't help you if you need to distinguish between splice forms.

Splice forms are merged because for most sources of evidence, there is little data for the interactions of individual splice forms.

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  • $\begingroup$ What about allelic differences? $\endgroup$ – Raghavakrishna Dec 18 '14 at 16:21
  • $\begingroup$ we also don't distinguish alleles at all, we don't even retrieve them from Ensembl $\endgroup$ – Michael Kuhn Dec 19 '14 at 11:26

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