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Exon shuffling is a molecular mechanism for the formation of new genes. It is a process through which two or more exons from different genes can be brought together ectopically, or the same exon can be duplicated, to create a new exon-intron structure. There are different mechanisms through which exon shuffling occurs: transposon mediated exon shuffling, crossover during sexual recombination of parental genomes and illegitimate recombination.

Exon shuffling follows certain splice frame rules. Introns can interrupt the reading frame of a gene by inserting a sequence between two consecutive codons , between the first and second nucleotide of a codon , or between the second and third nucleotide of a codon. Additionally exons can be classified into nine different groups based on the phase of the flanking introns Symmetric exons are the only ones that can be inserted into introns, undergo duplication, or be deleted without changing the reading frame.

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