How to Determinate a Reference Protein Sequence?

Question

[taylorzheng.zz]

Hi, everyone, Now I am working on a genome-wide comparative analysis, and I need one protein sequence for one single HUMAN gene as the reference, which one should I select as there are so many alternative sequences (isoforms resulted from alternative splicing) for a single gene?

Zhizhong

[GenoMax]

Have you tried to look in RefSeqGene and/or RefSeq protein?

Answer 1

[Ram]

I think this is a subjective decision. Although people call certain transcripts the "canonical" transcript, it depends on the context - which tissue you're looking at, for instance.

If you want to pick a generic transcript, I'd probably go for the longest of the coding isoforms and use that, although you'd find better meaning if you could handpick relevant isoforms for at least the important genes.