hi

The primers bind to sequences or other transcripts is because they have limited bases (A,T,G.C)and replicated these in genome . Primer design should be based on need: for example, you should select exon and coding regions if you need to express a protein. To check for gene expression level, you should preferably use the exon junction method in the design of the primer.

good luck

Yes, the primer blast shows exact targets as well as intended targets . However, the intended targets don't give the perfect match (please confirm in your case). Interestingly, you may come across a situation I faced once when your primer binds to your GOI and intended target is a nearby sequence cis to the gene, which gives evidence of segmental duplication frequently found in genome (although you rarely see this happening unless you work with some kind of duplicated gene family).

A Possible solution:

Make sure your primer covers exon exon junction (if possible).

Try designing primers across exon boundaries so they are transcript specific