preference for region of primer design for qRT-PCR - (Jun/15/2007 )

is there a general rule regarding whether, for example, primers designed from UTRs perform poorer than exon regions? maybe this is the case if UTR regions are more prone to stronger secondary structure and so less efficient with primer annealing during RT of the mRNA, and PCR of the amplicon.

General rule for qRTPCR primer design is that primers should span exon borders as this minimizes the probability of amplification of gDNA contamination. 3'UTR is often not specific enough...