gene duplication - affected by siRNA? (Mar/10/2008 )
i'll try to explain the situation here. first of all i'm not an expert on siRNA. there's this gene, which is at least duplicated (maybe more copies, the maize genome is not sequenced completely yet), and one of the copies has an insertion (apparently a transposon, it is like 6 kb long). i have done some bioinformatic analysis regarding the formation of siRNA and there appears to be a possibility of happening in the insertion. rt-pcr has been made and this gene appears but there is no way to determine which copy it is. is there any way to test that the gene with the insertion is being affected? i have also thought it could be silenced by RdDM but can't think of a way to prove it. any ideas welcome. thanks.
How long is the siRNA sequence you have inserted? as long as your sequenceis complementary to a common region in all the endogenous copies of the gene it should be working. I just thought that both, the gene and the siRNA should be expressed in the same tissue.