Question: retrieve 3prime UTR sequence for refseq genes
0
gravatar for nathanielsaxe
4.0 years ago by
United Kingdom
nathanielsaxe10 wrote:

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!

utr genes refseq sequence • 2.0k views
ADD COMMENTlink written 4.0 years ago by nathanielsaxe10
3

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?

ADD REPLYlink written 4.0 years ago by Ashutosh Pandey11k

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 unavaliable", since its not annotated, is there a way of using that website to get the 1kb downstream instead of utr annotations?

Thanks

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by nathanielsaxe10
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