I would like to quantify a transcript that has different splicing variants. In order to be able to quantify all of them, I cannot design my primers or my probes across a junction but I need to have all of them in the same exon of the transcript. I know that in this case I have the risk of amplifying genomic DNA. Is this in your experience a big confounder? Do you think that my assay will still be reliable? Or is better for me to design primers across a junction even if in this way I will not be able to quantify all my variants?

Thanks.