Trof, on 14 October 2010 - 06:05 AM, said:
Unresolved secondary structure in mRNA would IMHO prevent amplification at all, not create a smaller product.
I don't know details of your kit, but in my kit 5' RACE oligo is ligated only to a intact GTP head (if I remember it right) so fragmented mRNA wouldn't amplify.
So if your kit wirks the same and all steps were done right, there still remains possibility, that apart from your expected 1kb transcript there is another one, which is smaller and so your PCR is correct.
Thanks for replying. But i really doubt that the smaller transcript exist. Are you using Clontech kit as well?
Edited by hianghao, 14 October 2010 - 03:52 PM.