RNA knockdown by shRNA would not necessarily lead to similar knockdown of the protein. Depending on the cell/tissue type, the protein product could have a much different half-life than the RNA template. Also, changes in other endogenous regulatory factors of protein translation could also affect your results.

Thanks Jake for your reply.

Actually i am getting knock down in protein but not much change is seen at RNA level. So is it possible that without much change in RNA level, precise effect of knock down is seen on protein.

Are you sure that this is RNA that you see and not DNA contamination? Are your primers located on different exons?

Maybe mRNA and protein expression patterns are different. You can detect both mRNA and protein level in different time points. 

RNAi sequences have been known to affect RNA expression (certainly), but protein translation can also blocked. Even epigenetic affects have been suggested.

Another thing to consider is how you are measuring RNA and protein expression. If there are more than one isoform of the gene expressed, RT-PCR may be looking at multiple variants, while the shRNA may be targeting only one. Antibodies for the protein may be similarly specific for a common, or isoform specific region.

Hi Michael, could you please offer me a literature which suggested RNAi can inhibit protein translation? I'm currently nerve-wracked with similar problem too. With shRNA stably expressed, my target protein were almost gone but RNA only showed only 50% deprival. The journal editor asked me to give an explanation for this discrepancy.