Fig. 5

Predicted coding and amino acid sequences of Nipponbare, TN1 and IR8 sd1 gene sequences. Position 1 is 40,361,934; 39,824,196; and 38,382,466 in chromosome 1 of TN1, IR8 and Nipponbare, respectively. The IR8 sd1 sequence illustrated here is based on its gff annotation dated May 10, 2020 and not yet corrected. TN1 and IR8 CDS and protein sequences were aligned to the Nipponbare CDS via Clustal to see the similarity of the sequences per position. The same Nipponbare CDS was translated and the mapping of its amino acids per codon became the basis of this diagram, such that all nucleotides and amino acid translations were the same for the three cultivars unless indicated. The nucleotides with amino acid translation that are colored light blue and not italicized are the deleted CDS region in TN1 sd1, which is the exon gap in Fig. 2a. The italicized nucleotides (including the violet shaded adenine) is intron 1 of TN1 sd1. The colored codon tat (TN1 and IR8) is the synonymous codon of tac of Nipponbare, while codon cgg (TN1 and IR8) is a mutation for codon cag (Nipponbare), which changes amino acid Q (Nipponbare) to R (TN1 and IR8). The violet shaded adenine in codon 1 is the extra nucleotide that caused the 1 bp difference of the genomic deletion of TN1 and IR8 against the sd1 sequence of Monna et al. (2002)