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Exon recombination, also called exon shuffling, is a process where exons from the same or different genes recombine to produce novel combinations of exon-intron sequences that may evolve into new genes. This mechanism is critical for speciation and has been observed across vertebrates, invertebrates, and some plants. It works alongside gene duplication and divergence to generate genetic diversity and new protein functions.

Exon recombination is mediated by non-homologous recombination and retrotransposition. Non-homologous recombination occurs when DNA strands with no sequence similarity recombine to produce novel gene structures. Retrotransposition involves reverse transcription of mRNA into DNA, which then recombines with exons of other genes to create new genetic combinations.

Illegitimate recombination can cause exon duplication, leading to altered gene function and disease. In chronic granulomatous disease, non-homologous sequences between exons 8 and 11 of the phox gene recombine, duplicating exons 9 and 10. This reduces NADPH oxidase activity, impairing the enzyme's ability to generate reactive oxygen species needed to clear bacterial infections, resulting in granuloma formation.

Splice frame rules govern how exons recombine during exon shuffling. Each exon has three reading frames, and incoming exons can recombine at any of these frames, potentially causing frameshift mutations. Not all recombination events are useful; some create premature stop codons and produce immature proteins, limiting the success of exon shuffling events.

Approximately 2.5 million years ago, a portion of Adh mRNA reverse-transcribed into DNA and recombined with exons of the Ynd gene, creating the new Jingwei gene through retrotransposition. The resulting protein contains two domains: one from Ynd and one from Adh. Jingwei is expressed in the Drosophila testis and functions in hormone and pheromone biosynthesis.

PMCHL1 is a human pseudogene that arose around 25 million years ago when the MCH gene underwent exon recombination by retrotransposition in early primates. This event created new intron-exon boundaries that evolved into the Hominidae-specific PMCHL1. Although a pseudogene, its antisense RNA is expressed in the human brain and likely retains functions related to energy balance.

Illegitimate recombination is a common mechanism of exon duplication in several human genetic disorders. These include Duchenne and Becker muscular dystrophy, familial hypercholesterolemia, Lesch-Nyhan syndrome, hemophilia, and lipoprotein lipase deficiency. Each disease results from exon duplication that disrupts normal gene function and protein production.