What major discoveries in modern genetics have disproven the one gene one protein theory?
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The one gene one protein theory assumes that each gene encodes for only one single protein. Considering our knowledge of process such as alternative splicing in which multiple coding regions or exons of each gene can be combine in different ways to make different proteins, the model of a single protein being encoded on each gene is far to simplistic.  Take the example of an imaginary gene with 3 exons, during the RNA splicing process the exons could be reassembled in several different orders. i.e. {1,2,3} , {3,2,1} , {2,1,3}, {3,1,2} , {1,3,2}.  Each of these combinations could result in a different order of bases and ultimately a different mRNA molecule and a different protein.
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