I am designing primers to amplify gene of approx 6kb length. I am testing gene families which are located adjacent to each other on the genome with high similarity (63-83%). How do I design specific primers?
Do you need to be certain to get all of the coding region (e.g. promotor through 5'UTR)? Or is there some flexibility in exactly which parts of the gene you need to amplify?
The fact that the genes are adjacent won't matter, not with several kb of sequence distance.
Do an alignment of the genes in the gene family to find regions that flank your gene of interest that are divergent. Use a primer design program & limit primer choice to those regions. You don't need much of a mismatch to get specificity.