Alu structure and Alu/Alu-mediated rearrangement (AAMR) event formation. (A) A consensus Alu element is depicted, with both left and right 7SL monomers indicated. A Box, B Box, and A′ Box are internal Pol III promoter elements; the linker is an A-rich sequence; and the element ends in a poly(A) tail. (B) A diagram of an AAMR event is shown: A genomic rearrangement is mediated by a substrate pair of Alu elements followed by the formation of a relatively complete chimeric Alu. Block arrows represent Alu elements on the + (forward arrow) and − (reverse arrow) strand. The 5′ CNV-Alu is colored maroon, and the 3′ CNV-Alu is pink. Ctrl-Alu elements not involved in AAMR are in blue. The microhomology generated at the breakpoint junction after the AAMR event is shown in green.
