RT-PCR-Multiple bands-unusual problem

[Paul Mozdziak]

I'm doing some RT-PCR to see if a particular factor is expressed in 
muscle. First I am using previously published primers. Second my 
positive control is a small amount of a cDNA probe for my factor of 
interest. The probe samples amplify beautifully. However, when I run 
my rt-pcr stuff from muscle out on a 3% gel (sigma agarose (50-1000 
bp) I get two bands (one at 150 bp--what I should get and one a few base 
pairs smaller)--they just barely resolve. I ran these samples out 
shortly after I finished the pcr. 

Any ideas to explain my problem and too solve it?

My RNA was not DNAsed--and it's just total RNA. There was alot of RNA at 
the beginning of the procedure in my muscle samples ~1 microgram.

Thanks much

Paul