Does mRNA RefSeq of a gene differs from transcript to transcript for the same species?

Question

[varsha]

I am not expert in this field, Please help me. I am compiling RefSeq (NM) for multiple genes in our panel. I have found different NM_ accession number for the same gene associated with different gene transcript. For example APC gene has NM_001127511.2 for Transcript 1 NM_000038.5 for Transcript 3 Now which one should I use as RefSeq of the gene? Do we have to give preference to the accession number associated with canonical transcript? If yes, which one is canonical transcript? and how to find that out? Thanks Regards

Answer 1

[Kristoffer Vitting-Seerup]

Unfortunatly RefSeq does not have gene ids that group transcript ids together. The NM_xxxxx should be viewed as a transcript id so you will have to use the gene name or all transcript ids as a refrence.

On a sidenote unless you have a very specific reason I would suggest that you use another database. A very large fraction of the Bioinformatics now uses the Gencode annotaion which you can find here.