I found a gene in my plant sample through a homology search. I only got the CDS region though from our RNA database. How can I know the extent of the boundaries of the 5' and 3' regions of this gene? Any bioinformatics tool to do this? Any help is appreciated.
Dear Nomar,
If you go to the ENSEMBL database website (www.ensembl.org) and search for the gene of interest in your organism of interest, it will give you transcript details, including the UTR regions which are color coded. Hope this helps.
Greets,
Appie
A common approach is to obtain cDNA sequence and use a sequence translation software program (e.g. ExPASy) to find the longest ORF. In most cases, the sequence between the 5'end and the start codon of the longest ORF will be the 5'UTR. The sequence between the stop codon and the poly(A) will be the 3'UTR.
You can use these databases given below that might help you...
http://itbtools.ba.itb.cnr.it/utrscan
http://utrdb.ba.itb.cnr.it/search
https://www.ba.itb.cnr.it/BIG/Blast/BlastUTR.html
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