Novel CPuORFs. (A–C) Transcript alignments are shown in miniature followed by all possible ORFs, where the darkness of red indicates the context strength of the AUG. CPuORFs are bordered in blue; the beginning of each associated mORF is bordered in green. Orange vertical lines (“Nucleotide conservation” lane) indicate that all residues are identical in that column. Note gaps in sequence identity between uORF and mORF. The orange horizontal line below each accession indicates sequence coverage or indels relative to the alignment. In the scale bar, 0.5 k = 500 nt. Sequences are ordered, top to bottom, relative to their phylogenetic distance from A. thaliana. (A) Previously confirmed CPuORF-14 (Hayden and Jorgensen 2007). (B) CPuORF-24n. (C) CPuORF-26n. (D) Protein alignments of novel CPuORFs. Color scheme is ClustalX default. Within alignments, sequences are ordered relative to their distance from A. thaliana. Related to Table 3.
