Reference genes. - (May/25/2011 )

Hi everyone,
I have a question about reference genes. Why when I design assay for some gene the primer sequence are different when I use different reference gene. I thought that primer sequences for my target gene are the same no matter which reference i use.
Cheers!

From the complete lack of provided details about the nature of your primer design application I assumed you are talking about Roche UPL Assay design Center.
In that case the application searches for primers that are compatible with each other when you run a multiplex reaction. So if you change the housekeeping gene, the application tries to find the most compatible primer pair for your target gene. For each reference the optimal "partner" primer pair may be different.