Your superior's hypothesis may be correct. There is no change in the coding region of pitx1, since the cDNA's show no change in sequence, so it should be a regulatory issue. However, this experiment does not give positive proof of that (meaning, your superior's hypothesis.)
Work Step by Step
Changes in the effects of genes have to do either with changes in coding region or in gene regulation. Since the evidence shows no change in coding region, the change must be regulation.