Figure 1.

The sequences of the first five Sμ–Sα junctions derived from A–T patients (Pan et al. 2002). The Sμ and Sα1 or Sα2 sequences are aligned above and below the recombined switch junctional sequences. Microhomology was determined by identifying the longest region at the S junction of perfect uninterrupted donor/acceptor identity (solid-line boxes). Imperfect repeats were determined by identifying the longest overlap region at the S junction by allowing one mismatch on either side of the breakpoint (the extra nucleotide beyond the perfect matched sequence identity is indicated by dotted-line boxes). The Sμ and Sα breakpoints for each S fragment are indicated by a downward arrowhead and an upward arrowhead, respectively, and their positions in the germ-line sequences (X54713, L19121 and AF030305; Mills et al. 1990; Islam et al. 1994; Pan et al. 2001) are indicated above or below the arrowhead. (a) 21 bp microhomology (28/29 bp imperfect repeat), (b) 12 bp microhomology (19/20 bp imperfect repeat), (c) 6 bp microhomology (9/10 bp imperfect repeat), (d) 7 bp microhomology (10/11 bp imperfect repeat), (e) 7 bp microhomology (11/12 bp imperfect repeat).