Say I want to design primers for Q-PCR for a gene with exons A, B, and C. My cells are grown in conditions in which skipping of exon B should be increased, so I want to do Q-PCR to confirm. I thought of designing a primer set like this:
Forward primer: spanning the junction of exons A and C.
Reverse primer: somewhere downstream of exon C.
Is there a tool like Primer Blast or Primer3 that automatically allows me to "skip" an exon when designing primers? Or I will have to make the sequence of the alternative RNA product "by hand"?