I am new to primer design, so my question might sound kind of silly!!
I need to detect expression of a target gene in my cells. the gene has several variants and I want to detect expression of all of them with one pair of primers (otherwise I will need to design variant specific primers). so I need to find identical sequences in all variant. my question is do I need to use the CDS (start ATG to stop codon) of the mRNAs or I can use the UTR containing sequences?
If I use the immature mRNA I might have a better chance of finding identical regions.