These two genes share almost the same sequence and have only three to four different amino acids.
You only have the AA sequence or also the gene sequence.. If you have the gene sequence you should design primers with a high binding temperature which are very specific for the genes..
You have to check that the primers bind at the same temperature (and the best would be same GC Content) ,the primers have the same length, that the PCR product has the same length... I now its some work but than i see no problem for that.. And for sure you still have to check efficiency before you do your Experiment. I wouild suggest same Forward or reverse primers and then design different ones for the site where there is the difference in AA sequence ...
Align the sequences of the genes so that you can easily visualize where the differences are between them--use ClustalW for example. If you plan to do SYBR green detection, you will need to design primers where the 3' terminal nucleotides (or as close to the 3' end as possible) are different between the two paralogs. (Tms of these primers should NOT be any higher than normal--that would just make non-specific binding more stable! So, if anything, the primer Tms should be on the low side.) If you design TaqMan primers and probe, try to find a region where you can have mismatches as near the 3' ends of the amplification primers as possible as well as having a mismatch in the central region where you can design probes that distinguish the two genes. I don't agree with Norbert that you can try to use the same primers for both genes and just rely on probe specificity. That's a potentially noisy approach--useful for detecting two alleles presence/absence--but probably not for accurate quantitation. I did something very like this in this paper http://www.ncbi.nlm.nih.gov/pubmed/18799802 with three similar genes, and in that case, much specificity was provided by using reverse primers located in the much less conserved 3'UTR.
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