retrieve 3prime UTR sequence for refseq genes

Question

[nathanielsaxe]

I've got a list of Refseq gene IDs (NM_007393 etc) and I followed Refseq Mrna To Cds Sequence to get the CDS regions, but is it possible to get another list where it lists the 3 and 5' UTR regions if they are annotated or retrieve the 1kb region flanking regions (I can do it using http://www.informatics.jax.org/marker/MGI:87904, but would have to manually enter each gene in.)

Thanks!

[Ashutosh Pandey]

You may try these posts and see if they help. Let us know if they don't and we can come up with something :-)

Retrieve 3'Utr Sequences For A (Complete) List Of Genes Using Biomart/Ucsc

Easy Way To Get 3' Utr Lengths Of A List Of Genes

How To Get The 3' Utr Given Geneid And Transcriptid In Ensembl Using Python?

[nathanielsaxe]

Hi,

Sorry about the delay in replying, I was having some trouble accessing the website. Anyway, It's exactly what I was looking for.

The only thing is, for some of the genes, it says "sequence unavailable", since its not annotated, is there a way of using that website to get the 1kb downstream instead of utr annotations?

Thanks