Primer Design

[rishcaar]

I need to design a load of primers for a number of human genes which have several isoforms. My supervisor wants me to design them so they can also be used for rodents, but she does not want them to be degenerate.

I am having difficulty finding regions with sufficient homology and was wondering what number of mismatches if any would be acceptable, or would it be better to just design them separately.

Thanks for your advice

[mmustafa]

It's better to design them separately. Mismatches will result in amplification of something other than what you have in mind.