pre mRNA after total mRNA isolation? - (Nov/21/2012 )

I am studying different spliced isoforms from a particular gene by RT-qPCR. I get amplification from a particular intron. How can I know whether the amplification is coming from pre mRNA? Can one 'clean' somehow the mRNA from the pre mRNA?

Thank you.

pre-mrna is processed so quickly that it is highly unlikely to be present in sufficient quantities to interfere.

It can also come from the traces of DNA, that is far more likely. You can use DNAse to clen your sample.