Gene Analysis Results 2

The ab initio program FGENESH predicted that the mRNA is 2229 nucleotides spanning 7 exons (Fig. 1-A).  The homology-based program Phytozome predicted that the mRNA is 3193 nucleotides spanning 9 exons (Fig. 1-B).  FGENESH predicted that the protein is 742 amino acids long (Fig. 2-A). Phytozome predicted the protein is 847 amino acids long (Fig. 2-B).  In both gene maps, exons 1, 2, and 3 cover the exact same regions.  Exons 4 and 5 in the Phytozome prediction are predicted introns in the FGENESH output.  Exon 6 of the Phytozome output begins 14 bases after the beginning of exon 4 of the FGENESH output and they end at the same place.  Phytozome predicted exons 5, 6, and 7 are identical to FGENESH predicted exons 7, 8, and 9 respectively.  In the FGENESH and Phytozome predicted protein sequences, amino acid positions 1-437 are exactly homologous.  FGENESH positions 442-742 are exactly homologous to Phytozome positions 547-847. The discrepancy between the two peptide is that the FGENESH amino acid contains ‘KSLQ’ at positions 438-441, which is replaced in the Phytozome output by a set of 109 amino acids occupying positions 438-546.  Nowhere does this sequence of 109 amino acids contain ‘KSLQ.’