Figure 3

Schematic alignment of p1 and p2 alleles. P1-wr[B73], p1-ww[4Co63], P1-rw1077 and P1-rr4B2 alleles are represented as dark red and their corresponding p2 alleles as light green pentagons with their apex pointing in the direction of transcription. The retrotransposon cluster downstream of p2 that was only entirely sequenced in P1-wr[B73] is 68 kb in size. In all remaining lines only the end sequences of the cluster that consist of Eninu (E), Ji (J) and Opie (O) retroelement fragments were determined. Downstream flanking genes, which encode a calmodulin-binding protein (here labeled as cbp) and an expressed protein (ep), are illustrated as pink pentagons. Both genes are conserved in grasses and arranged in opposite transcriptional orientation to p alleles. Purple rectangles refer to a sequence that most likely originated as the 3' intergenic region of an ancestral p gene. Due to the duplication event that gave rise to p1 and p2, this region also became present upstream of p1 alleles (see Figure 2 for details). The triangles on top of some purple rectangles stand for retrotransposon (Shadowspawn) insertions. The coding regions of p2/p1[B73], p1/p2[B73] and P1-rw1077 consists of p2 and p1 sequences. In P1-rw1077, the 5' end of exon 1 can be attributed to p1 while the 3' end of exon 1, exon 2 and 3 and flanking retrotransposon sequences are derived from p2 [13]. Interestingly, the retroelements are followed by a truncated P1-wr[B73] exon 3. Note that the drawing is not in scale.