Question: Get the 5'UTR of a set of genes
0
gravatar for IP
4.5 years ago by
IP710
Denmark/University of Copenagen
IP710 wrote:

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?

5'utr sequence gene • 2.1k views
ADD COMMENTlink modified 4.5 years ago by Carlo Yague5.5k • written 4.5 years ago by IP710
3
gravatar for Carlo Yague
4.5 years ago by
Carlo Yague5.5k
Canada
Carlo Yague5.5k wrote:

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.

ADD COMMENTlink written 4.5 years ago by Carlo Yague5.5k

Great! thank you very much!

ADD REPLYlink written 4.5 years ago by IP710

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!

ADD REPLYlink written 4.4 years ago by gustavo.borin0
1

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

ADD REPLYlink written 4.4 years ago by Carlo Yague5.5k
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