If you want to quantify an uknown quantity of a known target via the use of a standard curve, then you should try to make your standard curve on exactly the target you are trying to quantify (the closer the better). If on the other hand, you are trying to see the validity of the primers by checking their efficiency, I think you could use it as a general indicator.

Three problems that would worry me are:

1) If you are quantifying with Sybr green, the signal depends on the length of the amplicon. So longer amplicons lead to smaller Cqs

2) Polymerases amplify smaller amplicons more efficiently

3) There is a possibility that intervening sequences affect either primer binding or polymerase extension through secondary structures.

As an alternative, I would run a standard curve on:

1) genomic DNA from a target organism

2) amplicon isolated from the use of said primers

3) synthetic DNA

And as always, since I don't know your project, take all this with a grain of salt and ask your supervisor for guidance. Hope this helped.