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Transcription start site determination - (Feb/13/2006 )

I am trying to determine the transcription start site for my gene. I have performed 5' RACE PCR and was wondering if it is a fairly safe assumption that if the 5' end of my sequence obtained from 5' RACE lines up with the 5' end of 3 different EST sequences after a BLAST search, do I have the true end of the 5' UTR?

-archie-

I tend to think that this gives a pretty good indication but is not confirmation... you could still be looking at a strong stop region in the mRNA (due to secondary structure or high GC content etc) that is reproduced in other ests because it is such a strong stop...

the ways to confirm experimentally are to use the cap-dependent RACE kits (RLM-RACE from ambion) that require that mRNAs be capped (confirming full-length 5' end) or to do high temperature primer extensions (denatures secondary strucutre/strong stops) and get the same sized band... In my opinon, the cap-dependent technique is best because presumably only full length mRNAs can be amplified...may still have problems with strong stops in primer extensions...

HTH

-beccaf22-

I've used the GeneRacer kit from Invitrogen to map transcription start sites. The kit provides a method for making cDNA only from full-length capped mRNA, so that you don't get false start sites from truncated transcripts.

-benchoholic-