The quantitatively different responses of the two probe sets were not entirely unexpected. In our prior study, we demonstrated a similar, but less than perfect, correlation between the SLC6A4 expression levels determined by the two probes. Whereas the differences could be artifactual, we strongly believe that they represent true differences in the amount and type of transcript measured because of the following rationale. Our primer probe set for exon 1 was specifically designed to recognize full-length transcripts that are capable of being 5′ capped and thereby stable intracellularly. In contrast, while the commercially available exon 8 probe will also measure these full-length transcripts, it will also recognize partial transcripts that result from promiscuous transcription along the gene. Since this type of transcription is generally not regulated by the promoter [Sipos and Gyurkovics, 2005; ENCODE, 2007] and these incomplete transcripts will not be properly capped or be translated into a functional protein, they, in some respects, may be biologically irrelevant. Still, there is considerable evidence that some of these promiscuous transcripts may serve other functions [ENCODE, 2007].
