I am performing some RT-qPCR with RNA transcripts (HIV-integrase) and as a control (RCAS transcripts). The amplification curve for my HIV int has low y-axis values. To rule out the possibility of template issues. I did the PCR with Plasmid and gDNA, but still the same output (File attached).

To rule out any probe synthesis issue: we ordered the new probe with a different quencher. But still the same results.

The probe sequence is AAAGGTGAAGGGGCAGTAGTAATACA.

Any suggestions to solve the problem will be greatly appreciated. I use the Lightcycler96.