(A) Position of Alu elements involved in USP18 copies in LCR22-2, -3a, and -4. The USP18 gene (light red shapes; exonic orientation shown) within the block structure of LCR22-2, -3a, and -4 is shown. Alu elements A1 (black), A2 (gray), and A3(white) are illustrated in the “+” or “-” orientation. The duplicated copies of the Alu elements within their respective copies of USP18 are illustrated. (B) LCR22 breakpoints occurred within Alu elements. The position of the Alus (A1, black; A4, light gray; A2, dark gray; A3, white) at the breakpoints (dotted line) in the USP18 functional locus (light red) and copies are shown. (C) Alus involved in breakpoints with respect to the genomic organization of USP18. The genomic organization of USP18 was determined by comparing the cDNA sequence with the human genomic sequence by BLAST analysis. The position of Alus A1, A2, A3, and A4 with respect to genomic organization of USP18 is illustrated (dotted line). (D) Structure of Alu elements A1, A2, A3, and A4, and their duplicated copies. Each Alu monomer (red, pink) is illustrated on either side of the A-rich spacer (blue). The 3′ poly A tail is shown (black). Alu A1 and its copy, A1b in LCR22-3a, contain the first monomer and spacer only, and both are part of the Alu Sq family. Alu A2, Alu Jo, and its copy in LCR22-3a, A2b are shown. The 5′ part of the Alu is not part of the Alu Jo subclass (yellow box). Alu A4 is a member of the Alu Sc subclass. The duplicated copies, A4a1 and A4a2, are chimeric, composed in part with sequences from A4 and part from another Alu (yellow box). Alu A3 and its copies, A3b1, A3b2, A3a1, and A3a2 are illustrated. Alus A3b1 and A3b2 contain only the second monomer and poly A site from Alu A3 and the rest from another Alu element (yellow). More details are provided in the Supplemental Figures 1-3.
