primers amplify additional band (!) - (Sep/10/2008 )
I checked my primers for qPCR using regular PCR and ran out the reaction on a gel...and I saw TWO bands! The expected band is much brighter with EtBr staining than the other band. Does that mean the primers are no good for qPCR? I checked for alt splicing on PubMed, but there's no published data on alt splicing for these genes.
Back to the primer design drawing board...?
make sure you are not seeing primers dimers, If the extra band is very low (less than 50bp) just need to add less primer, if higher then rise the anneling temp. If the qPCR is using a probe and you're sure that it is very specific don't worry to much the important thing is the probe signal. If using sybr green then optimized until get one band and if not then design another set.