Biomart issue, why so few 3'utrs?
1
0
Entering edit mode
15 days ago
RNAseqer ▴ 270

I have previously used the biomart webportal to dow nload fastas for the 3'utrs of a gene-stable ensemble id list. Typically I limit my output to "MANE Select" as I am trying to get just one 3'utr for each gene. However, I recently provided a list of ~2000 ensemble ids and only got 3'utrs for only ~125 of these. I know there are more than 125 protein coding genes in this list. Has biomart recently undergone changes that could explain why I am getting so few 3'utrs? If the problem lies in there being relatively few 3'utrs classified by Mane Select is there another set of parameters I could use to get a non-redundant list ? If so, what criteria would be used to select a single 3'utr when there are multiple annotated for a given gene?

Any help would be appreciated.

utr biomart • 249 views
ADD COMMENT
0
Entering edit mode

Which species is this?

ADD REPLY
0
Entering edit mode

AFAIK "MANE" project is only for human protein-coding genes.

One potential explanation. Out of the 2000 ID's only 125 may be MANE.

RNAseqer : You could post a few examples of ID's where you are and are not able to find UTR.

ADD REPLY
0
Entering edit mode
15 days ago

The MANE-select transcripts are pairs of identically annotated transcripts in ReqSeq and Ensembl. The 3' UTR is the region where otherwise similar transcripts are likely to differ between Ensembl and RefSeq. I know that a lot of work has recently gone in to harmonising the 3' UTRs, but I don't know how far this has gone.

ADD COMMENT

Login before adding your answer.

Traffic: 2654 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6