Figure 2

Schematic alignment of p non-coding sequences. p non-coding regions, which include regulatory elements (distal and proximal enhancer and promoter), can be located upstream, downstream or on both sides of p coding sequences. However, only cis-elements in the upstream non-coding regions have been shown to have regulatory function. P1-wr[B73] is the only p1 allele shown with a multi-gene structure, as indicated by exon 3 stemming from a neighboring P1-wr[B73] repeat. Due to the tandem array, each P1-wr[B73] coding region is flanked by this non-coding sequence. The p1/p2[B73] 5' end (not shown) is identical to the P1-wr[B73] 5' end. The p1/p2[B73] 3' end is detached from the p1/p2[B73] coding region due to retrotransposon insertions. Opie (light turquoise rectangle), Eninu (light yellow rectangle) and the displaced former 3' UTR of p1/p2[B73] (red bar) are displayed. A shadowspawn retroelement (not drawn to scale) is inserted further downstream. p1-ww[4Co63] is virtually identical to the displaced p1/p2[B73] 3' end. P1-rw1077 and P1-rr coding regions are bordered by large direct repeats (blue rectangles). Both 5' and 3' repeats are depicted with their adjacent exons indicating the omitted coding region. p1-ww[4Co63] and the p1/p2[B73] 3' end are flanked by the same 5' sequences as P1-rr and P1-rw1077 (namely Opie, Eninu and the displaced 3' UTR). In addition, p1-ww[4Co63] and p1/p2[B73] share the 3' flanking sequences with P1-rr and P1-rw1077 as indicated by the downstream gene coding for a calmodulin-binding protein (cbp, pink pentagon). Notice that P1-wr[B73], P1-rw1077 and P1-rr vary mainly in a region that contains a fragmented MULE insertion (purple rectangle) and a sequence specified by light blue rectangles, which is partially and completely duplicated in P1-rw1077 and P1-rr, respectively. The orange bar stands for the MULE TIR that is missing in the 5' P1-rr repeat. Regulatory elements, i.e. distal and proximal enhancer and basal promoter, depicted in shades of green, were only determined for P1-rr. In other p genes or alleles, green rectangles merely refer to sequence similarity with P1-rr. Functional homology has not been investigated. The dark yellow rectangle represents a further Mu-like transposon that overlaps with the proximal enhancer and promoter region. A Heartbreaker MITE (blue bar) is part of the proximal enhancer region. Transposable elements of various families are shown as triangles above the schematic sequences. Notice the missing Tourist MITE in p1-ww[4Co63] and the displaced 3' end of p1/p2[B73]. Exons (red rectangles) are added with the intention to facilitate orientation. The Eco RI cloning sites and the hybridization site of probe 15 used to screen the lambda library for p1-ww[4Co63] sequencing are marked.