Could you please add some more detail? Does you cloning procedure result in an in frame Cre-GFP fusion product? are there any sort of "IRES" or "2A peptide" sequences located between the CRE and GFP coding sequences? Is the CRE expression induced conditionally?

For your cloning experiment if you used a commercial Cre-GFP expression plasmid, use it first as a control of Cre-GFP expression and check what Farbod said.

Hello, thanks for your response I used a product called GeneJammer and got it to work.