Get the 5'UTR of a set of genes

Question

[IP]

Hi!

I have a list of a acession numbers of NCBI(NM_024837 ...) and I want to get the 5'UTR of those genes, is there a way to get those sequences in an automic manner?

Answer 1

[Carlo Yague]

Go to biomart, and use your accession numbers (refseq mRNA IDs) in Filters -> gene -> Input external references ID list. Then go to Attributes -> Sequences and tick 5'UTR. Retrieve results and done.

[IP]

Great! thank you very much!

[gustavo.borin]

Is there a similar way to get the 5' UTR sequences of several genes from JGI database? I'm working with a filamentous fungus and I know it's possible to take these sequences in JGI, but you have to click in each gene to obtain this data. I have also looked the Biomart tool from Ensembl Fungi, but the strain avaliable is not the same that I study. So, how can I take these sequences automatically from JGI?

Thanks in advance!

[Carlo Yague]

I don't have an account on JGI but you should be able to achieve what you want using the download tools.