Analysis of the long-range PCR product andSlgenomic sequences. (A) The amplified long-range PCR product comprises partial sequences of intron 3 and intron 2, as well as a 141-bp junction sequence that is an inversion of a downstream sequence in intron 2. (B) Possible mechanism of insertion of 141 bp mediated by hairpin loop formation in intron 2 (templating fragment shown in bold; inserted DNA sequence denoted by lowercase letters). (C) The position of the 2 copies of a direct repeat T(AC)₁₄ in introns 2 and 3 are presented as black bars. Slipped mispairing between direct repeats would result in duplication of exon 3 and flanking intronic regions in the KitlSl-20J allele as shown in panel A. (D) Occurrence of known site-specific recombination motifs in intron 3 within 50 bp upstream and downstream of the breakpoint. (E) Occurrence of known site-specific recombination motifs in intron 2 within 50 bp upstream and downstream of the breakpoint (see “Discussion” for references).