RT-PCR primer design: Over introns and exons? - (Oct/16/2006 )
Why would you want to see if your primers for RT-PCR will anneal across a region that contains intron and exon?
So that you amplify your mRNA and NOT the gene, which will skew your results. mRNA sequence will have intron/exon junctions continuous and so the sites at which they meet will be next to each other, and present on mRNA; which means primers specific for this will amplify mRNa and not the gene,which will have intron sequence separating the intron/exon junctions.
Sorry about the poor English; its first thing in the morning for me! Hope this helps
Please check this thread RT-PCR primer design guide.