Recombining sequences in site-specific reactions are usually short and occur at a single target site within the recombining sequence. For this to occur there is typically one or more cofactors (to name a few: DNA-binding proteins and the presence or absence of DNA binding sites) and a site specific recombinase. There is a change in orientation of the DNA that will affect gene expression or the structure of the gene product. This is done by changing the spatial arrangement of the promoter or the regulatory elements.
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