A Gene cassette is a type of mobile genetic element that contains a gene and a recombination site. They may exist incorporated into an integron or freely as circular DNA. Gene cassettes often carry antibiotic resistance genes. An example would be the kanMX cassette which confers kanamycin (an antibiotic) resistance upon bacteria.
Integrons are genetic structures in bacteria which express and are capable of acquiring and exchanging gene cassettes. These cassettes typically carry a single gene without a promoter. The entire series of cassettes is transcribed from an adjacent promoter. The gene cassettes are speculated to be inserted and excised via a circular intermediate. This would involve recombination between short sequences found at their termini and known as 59 base elements (59-be) - which may not be 59 bases long. The 59-be are a diverse family of sequences that function as recognition sites for the site-specific integrase (enzyme responsible for integrating the gene cassette into an integron).
In genetic engineering, a gene cassette refers to a manipulable fragment of DNA carrying, and capable of expressing, one or more genes of interest between one or more sets of restriction sites. It can be transferred from one DNA sequence (usually on a vector) to another by 'cutting' the fragment out using restriction enzymes and 'pasting' it back into the new context.
- Stokes, H.W. et al., Structure and function of 59-base element recombination sites associated with mobile gene cassettes. Mol Microbiol. 1997 Nov;26(4):731-45. 
- Partridge S, Tsafnat G, Coiera E, Iredell J. Gene cassettes and cassette arrays in mobile resistance integrons. FEMS Microbiology Reviews 2009;33(4),757-784. 
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