Fig. 1

Portion of the Clustal alignment of the sd1 exon sequences in TN1, IR8 and Nipponbare. Position 1 is the first nucleotide of exon 1 of the gene. For TN1, IR8 and Nipponbare, position 1 is located at 40,361,934; 39,824,196; and 38,382,466, of chromosome 1, respectively. OsTN1g004133, OsIR8_01G0407900 and Os01g0883800 refer to the sd1 gene IDs of TN1, IR8 and Nipponbare, respectively. Beside the gene IDs are the positions of the first base and last base of the sequence, with the latter representing its total length. The total sequence length as well as the start and end positions of each exon are depicted in Fig. 2. Deleted nucleotides are represented by dashes. The location of the first base of the start codon is indicated by an arrow pointing downwards. Exons are colored whether they are the first, second or third exon. Nucleotides in introns are uncolored, except for the sequence before the start codon of IR8, which was assigned as a 5′ untranslated region in its annotation