(A) Position of Alu elements involved in GGTLA rearrangements. The GGTLA gene (green shapes; exonic orientation shown) within the block structure of the LCR22s is shown. Alu elements D4 (gray) and D5 (white) are illustrated in the “+” or “-” orientation, associated with their GGTLA and gene copies. (B) Alus involved in breakpoints with respect to the genomic organization of GGTLA. The genomic organization of GGTLA was determined by comparing the cDNA sequence with the human genomic sequence by BLAST analysis. The position of Alus D4 and D5 with respect to the genomic organization of GGTLA is illustrated (dotted line). (C) Structure of Alu element D5 including its duplicated copies. A breakpoint in Alu D5 resulted in two reciprocal copies, D5c and D5e. For more details, see Supplemental Figure 7.
