Genetically engineered crops are digested by animals in the same way as conventional crops. Numerous scientific studies have examined the digestive fate of genetically engineered DNA and protein introduced intro genetically engineered feed (see the Federation of Animal Science Societies Communications website for a comprehensive listing.) Genetically engineered DNA, or the novel proteins encoded therein, have never been detected in the milk, meat or eggs derived from animals fed genetically engineered feedstuffs.
Nutrients in meat, milk and eggs from livestock fed genetically engineered feeds have been found to be the same as the nutrients from livestock fed conventional feeds. The metabolic processes involved in digestion, absorption and the use of feed proteins by livestock species make it very unlikely for a protein of any plant gene to be found intact in food of animal origin, and none have been detected.
For more information, see this article on genetic engineering and animal feed.