(A) Detailed structures of P1-ovov454 (progenitor) and RET-generated P1-rr-twin/p1-ww-twin (TDDCI/Deletion) alleles deduced from Figure 1. The horizontal blue lines are p1 gene sequence while the green lines are p1 proximal sequences, including the p2 gene sequence (a p1 paralog, ∼70 kb proximal to p1); the blue and green boxes are exons 1, 2, and 3 (right to left) of p1 and p2, respectively. The small horizontal arrows indicate the orientation and the approximate position of the PCR primers. The gray boxes indicate probe 8B used in DNA gel blot analysis, the short vertical black lines are SacI sites, and the numbers between the SacI sites indicate the lengths of those fragments detected by probe 8B. The hatched boxes represent the distal (black) and proximal (green) 5248 bp repeats flanking the p1 locus. These repeats are identical except for six SNPs, indicated by short red vertical lines inside the green hatched box (SNPs 3 and 4 are only 43 bp apart). Other symbols have the same meaning as in Figure 1. (B) PCR products obtained using primers 1 + Ac5 (upper) or 2 + Ac3 (lower). Lane 1, 1 kb DNA ladder; lane 2, P1-ovov454; lane 3, P1-rr-T22; 4, p1-ww-T22; lane 5, P1-ovov454; lane 6, P1-rr-T24; 7, p1-ww-T24; lane 8, P1-ovov454; lane 9, P1-rr-E17; lane10, P1-ovov454; lane 11, P1-rr-E340; lane 12, P1-ovov454; lane 13, P1-rr-T21; 14, p1-ww-T21; lane 15, P1-ovov454; lane 16, P1-rr-E5; lane 17, P1-ovov454; lane 18, P1-rr-E311. Note: the sequences of primers 1 and 2 are specific for each allele. (C) DNA gel blot analysis of the TDDCI/deletion alleles. Genomic DNA was digested with SacI and the blot was hybridized with probe 8B (see Figure 2A for the position of the probe). Lane 1: p1-ww[4Co63], lane 2: P1-ovov454/p1-ww[4Co63], lane 3: P1-rr-T22/p1-ww[4Co63], lane 4: p1-ww-T22/p1-ww[4Co63], lane 5: P1-rr-T24/p1-ww[4Co63], lane 6: p1-ww-T24/p1-ww[4Co63], lane 7: P1-rr-E17/p1-ww[4Co63], lane 8: P1-rr-E340/p1-ww[4Co63], lane 9: P1-rr-T21/p1-ww[4Co63], lane 10: p1-ww-T21/p1-ww[4Co63], lane 11: P1-rr-E311/p1-ww[4Co63], lane 12: P1-rr-E5/p1-ww[4Co63].