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FRT3 is an engineered recombination target site derived from the wild-type FRT site (the target site for the FLP recombinase encoded by the Saccharomyces cerevisiae 2μ plasmid). It is composed of two 13bp inverted repeats flanking an 8bp asymmetric spacer sequence (5'-GAAGTTCCTATTCttcaaataGTATAGGAACTTC-3') and contains mutations in the spacer sequence compared to FRT (PMID:7947678). Recombination occurs between a pair of target sites oriented in the same direction; the 13bp repeats each act as binding sites for the recombinase (PMID:3047402), while the asymmetric 8bp spacer is the site of DNA strand exchange and determines the orientation of the target site (PMID:3711092). Since the recombinase binding sites are not altered compared to FRT, FRT3 is a target site for the native FLP recombinase (and any engineered FLP derivative which retains the native target-site specificity). Sequence homology between the spacer sequence of the two target sites is required for efficient FLP-mediated recombination to occur (PMID:3711092). Thus, a FRT3 'spacer variant' site will recombine with an identical FRT3 site, but is not expected to recombine with the native FRT site or other engineered derivatives (PMID:7947678).

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