3'UTR sequence of a gene - (Jul/01/2011 )
I'm going to the basics. Would appreciate if anyone could let me what is the best way to retrieve the 3'UTR sequence of a gene?
You mightbe able to look at cDNA sequences in a database, but these might not be complete. There may be new ways to do it, but I have used 3' RACE in the past and it does the job well.
Hope this helps.
Yes you can use biomart if you want to retrieve one or many genes. If you are interested in just one gene, the easy way is to obtain the refseq for that gene in the NCIB gene database, in the annotation of the genbank file, the ORF is indicated, anything after the ORF is 3'UTR. For example, the ALDOA gene in NCBI has this refseq http://www.ncbi.nlm.nih.gov/nuccore/NM_000034 the ORF or CD is between 1008 and 2102, 3UTR is after 2102.