Conserved secondary structure elements in DHV-1 5'-UTR and HCV-like IRES RNAs. (A) Predicted secondary structure of the entire DHV-1 IRES. Domains are labeled according to the corresponding domains of the HCV IRES shown in (B) The structure was predicted by comparative sequence analysis and M-fold software to predict the most thermodynamically favourable structures. AUG triplets marked with a solid black bar represent the translation initiation site for the viral polyprotein. Lightly shaded rectangles indicate base pairs that are maintained despite sequence variation between types, strains, and isolates of the virus. Single-site substitutions that do not disrupt base pairing are indicated by asterisks, and base pairs maintained by paired covariant substitutions are indicated by lozenges. Unpaired bases that are conserved in the HCV IRES are indicated by gray shading.
Liu et al. Virology Journal 2011 8:147 doi:10.1186/1743-422X-8-147