Downloading 3' UTR sequences for miRNA Target Prediction

Question

[yronimuz]

Hello,

I am trying to download all the 3' UTR sequences of the differentially expressed genes through Ensembl (BioMart). It went well as well as the interrogation of the miRNA seed and got some results. My question is, ensembl gave me an output with 138 genes with unavailable 3' UTR sequences. Do you know, other than ensembl, I can find the 3' UTR sequences of these genes?

Thank you.

[benformatics]

How do you know that these genes even have 3'UTRs?

[yronimuz]

These are all protein coding genes.

[i.sudbery]

Not all protein coding genes have an annotated UTR in ensembl. Particularly where these genes were predicted by homology from other species. It would be helpful if you sent an example gene id of one of these genes without a UTR.

[yronimuz]

Thank you for your response. Yes, I understand. Below is an example of an output from ensembl that gave me genes that do not have annotated UTRs; I manually attached the gene name beside the ensembl ID

ENSSSCG00000000645 | GABARAPL1 AGGATAT...[shortened]...CATGTGGGTGG

ENSSSCG00000000477| HELB Sequence unavailable

ENSSSCG00000001457 | SLA-DQB1 Sequence unavailable

Do you think 3' UTRs of the same gene in humans, which is more annotated than pigs, can be used? Thank you.

[kuttibiotech2009]

My species name is Anas platyrhynchos.

Could you please tell me how to download the entire 3' UTR sequence?

Thank you in advance

Answer 1

[i.sudbery]

For both of the genes you posted, the gene has multiple transcripts. Some of those transcripts have UTRs annotated, some don't. At least in these cases you shuold be able to find at least one transcript for the gene that has a UTR sequence.

[yronimuz]

Yes. Now I have extracted them again, together with other transcripts, which clearly shows that some of their transcripts have UTR regions! Thank you!