Schematic representation of the wp recessive allele and the novel exon combinations generated in its transcribed RNAs. (A) Represents the genomic sequence of the mutant wp allele obtained from the line LN89-5322-2 (iiRtW1wp). The introns are indicated and their length given in bp. The 5,725 bp Tgm-Express insertion in Intron 2 is drawn at top with the arrow heads representing inverted repeats and the five captured gene fragments color coded. The full length of the mutant gene is 9,251 bp. The three Exons in purple represent the cDNA of the proper spliced wild type gene 1,422 bp in size. The 7F and 1428R primers used in the PCR reactions that generated the chimeric cDNA clones shown in Figure 3B and C map at the 5' end of Exon 1 (7F) and the 3' end of Exon 3 (1428R) respectively. (B) Graphic representation of six chimeric, multi-exon cDNA clones (wp-25s, -22s, -28s, -9s, 12s, -4s) derived from seed coat RNAs of the wp mutant line via RT-PCR. These clones contained besides the F3H three Exons (1, 2, 3) varying numbers of alternatively spliced exons (solid color boxes) and introns (dashed narrower boxes) from 3 or 5 of the Tgm-Express1 captured gene fragments (UP, CDC2, FPK, M and CS). A seventh cDNA clone, wp-15s, also derived from the mutant wp line is composed only of the wild type gene (Wp) Exons 1, 2 and 3. (C) Six chimeric cDNA clones (wp-9c, -8c, -2c, -13c, -12c, -6c) derived from cotyledon RNAs of the wp mutant line via RT-PCR. All clones contained the F3H Exons (1, 2,3) with varying numbers of alternatively spliced exonic and intronic regions from the Tgm-Express1 acquired host-gene fragments separating the Exon 2-Exon 3 junction. Abbreviations: UP, unknown protein; CDC2, cell division cycle 2; FPK, fructose-6-phosphate 2-kinase/fructose-2-6-biphosphatase; M, malate dehydrogenase; CS, cysteine synthase. Two CDC2 intronic regions captured by the transposon element and sandwished between the three exonic regions (C, D and C2, Figure 2A) were spliced out to form the CDC2 exon in the chimeric transcripts (Figure 2B and C). One FPK intronic fragment captured by the transposon between two flanking exons (F and PK, Figure 2A) was also spliced out to form the FPK exon in the chimeric transcripts (Figure 2B and C). A smaller FPK intron flanked by 15 bp exon fragment (narrow orange block not named) at the 5'end (Figure 2A) is not always spliced out (Figure 2B and C).