The mutation occurred within a portion of DNA called ZRS (the Zone of Polarizing Activity Regulatory Sequence). This portion of DNA is known to be associated with the embryonic development of limbs. The only problem is, like all other vertebrates, snakes contain this DNA portion, which seemed to be a normal functional sequence of DNA. It was discovered that this section of DNA had the mutation within it when it was replaced in a mouse embryo. The mouse was born with no limbs and had similar limb development to that of snakes. The following image depicts the normal mouse, cobra, and python limb development within embryos.
It is very interesting to think that the only reason all snakes, with only rare exceptions, don't have legs is because of a mutation that occurred in one small portion of their DNA 150 million years ago. One small switch being turned off had such a great impact that an entire group of reptiles lost their limbs, and adapted to the change. This makes me wonder if it would ever be possible to "un-mutate" the gene back to an active version of itself, and see if limbs can be regrown onto snakes.