FIGURE 6.

Examples of ambiguities between the coding and noncoding nature of three RNAs. (A) The RNA C0343 from E. coli is listed as a noncoding RNA in Rfam. However, it overlaps with an RNAcode-predicted coding segment. While there is no evidence for a RNA secondary structure according to the RNAz classification value, the highly significant RNAcode prediction and MS experiments suggest that C0343 is an mRNA and not an ncRNA. (B) RNAIII of Staphylococcus aureus (Rfam RF00503) contains a short ORF of a hemolysin gene. RNAcode predicts the open reading frame at the correct position, while RNAz clearly detects a structural signal. These results are consistent with the well-established dual nature of this molecule. (C) The Bacillus subtilis RNA SR1 is known to have function on the RNA level by targeting an mRNA. RNAcode detects a short ORF that was shown by Gimpel et al. (2010) to produce a small peptide and is thus another example of a dual-function RNA.