Alternative splicing or non-optimal PCR conditions?

[Montojo]

Hello,

I have performed a PCR on genomic DNA and after electrophoresis I obtained just one band. However, when I performed a PCR on cDNA (after retrotranscription) with the same primers I obtained 2 or three bands, depending on the sample. How can I know if such different bands result from "alternative splicing" of the mRNA or if it is just an artifact due to non-optimal PCR conditions? Is it possible to clone these PCR products (from cDNA) even if there is no a single band? I have tried to sequence after extracting each band from the gel, but not enought DNA...

Thanks in advance for your help!

[Jon Moulton]

You could try a Northern blot to see if you also get the three bands -- that would eliminate the possibility that the three bands are due to a PCR artifact.