An alignment of the junction sequence with a schematic representation of the 100-kb deletion in the gibbon genome. The junction sequence isolated from H. lar (middle line) and homologous sequences extracted from human genomic contings AL035458.35 and AL356299.16 (upper and lower line, respectively) are shown. Asterisks above and below the alignment indicate identical nucleotides between the H. lar junction sequence and the human homologous sequences. (–) Alignment gap, (shaded region) the AluSx elements that were involved in the unequal homologous recombination, (closed arrow) the chromosomal break point located near the 26-bp Alu core sequence containing χ-like element (open box), which is considered to be a center of homologous and non-homologous recombination (Rudiger et al. 1995). Poly(A) tails of AluSx elements are also indicated. Note all these features of AluSx elements are represented in complementary sequence.
