Alignment of the ycf68 region in 14 representative angiosperms. Amborella, Nuphar, Zea, and Spinacia represent the form that includes intervening sequence. Codons highlighted in green represent start codons as annotated in the published grass genomes (Zea, Saccharum, Oryza and Triticum) and Nymphaea. Gorymekin et al identified a later start codon in their annotation of the Nymphaea ycf68 in order to maintain an open reading frame. Codons highlighted in red represent in frame stop codons (in frame with the grass start codon in the initial part of the alignment and in frame with the Nymphaea start codon once that point is reached). In either frame, these sequences, although largely conserved at the nucleotide level, are not open in most taxa.
Raubeson et al. BMC Genomics 2007 8:174 doi:10.1186/1471-2164-8-174