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. 2003 Dec;13(12):2519–2532. doi: 10.1101/gr.1549503

Figure 4.

Figure 4

(A) Positions of GGT, ISGF3, and predicted gene DKFZp434p211 within the block structure of the LCR22s. Each of the LCR22s is ordered with respect to the centromere of chromosome 22q11.2. The block structure of LCR22 was created using miropeats software to detect sequence relationships. The colors of the blocks were chosen to coordinate with the genes within. The GGT (yellow), IGSF3 (orange), and DKFZp434p211 (overlapping with BCR; blue) genes are shown in their proper transcription orientation. The position of the functional GGT locus (LCR22-8) and its unprocessed pseudogene copies within the LCR22 block structure are shown. (B) Recombination events in GGT and IGSF3. GGT exons 3-17 (chr22:21695000-21722900; yellow numbered boxes) became duplicated to LCR22-2 and LCR22-4. IGSF3 (orange; 1p13.1; chr1:117622772-117711984) became juxtaposed to the copies of GGT. R/C, reverse/complement. Both GGT and IGSF3 harbor the Alu S subfamily member (Alu B1, IGSF3; Alu B2, GGT) at the breakpoint junction (Alu B2a1, Alu B2a2, LCR22-2 and LCR22-4, respectively) between the two functional genes (black-filled elements). The products of the recombination are shown (LCR22-2, chr22:15700573-15723288 and LCR22-4, chr22:18260039-18282533). (C) Recombination events in GGT and predicted gene DKFZp434p211. The two substrates, GGT and DKFZp434p211 (overlapping with BCR), are shown. R/C, reverse/complement. Examination of the pattern of exons and high-copy repetitive elements revealed an Alu Y that was present at the junction between the two substrates in the duplicated products of the recombination event (black fill) in LCR22-5, LCR22-7, and LCR20 (Suppl. Fig. 4). The L2 LINE elements upstream of exon 13 in GGT (yellow fill) and the Alu elements upstream exon 1 of DKFZp434p211 (interval) are indicated (blue line). A putative unequal crossover occurred between Alu C1 and Alu C2 in duplicated copies of GGT and DKFZp434p211, resulting in the fusion product shown. Sequences upstream and including Alu C2 in the fusion product were present in the GGT substrate, and sequences distal to the Alu were present in the DKFZp434p211 substrate.