How do the amplification curves look like?

It is hard to suggest anything without more details about your setup and observed curves. But you should keep in mind that the gel can be more sensitive than the qPCR. Unless the band you see in the gel is really bright, my guess would be that the RNA you are trying to quantify is at a very low starting concentration. You just have to increase your starting ammount or adjust primer concentration. Or maybe try 45 cycles of PCR, which would be my last choice.

I wish you luck with your experiments. Let us know when you find out what the problem is.

agree with @ Thiago Jacomasso

regards

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