FIG. 4.

Sequence analysis and RNA folding predictions reveal conserved picornavirus features in EV109. RNA secondary structure prediction of the EV109 5′ UTR using pknotsRG (35) and visualized using PseudoViewer, version 3 (7). Previously described type 1 IRES features maintained in EV109 include a 5′ cloverleaf as stem-loop I, a GNRA sequence in stem-loop IV, and a pyrimidine-rich region in stem-loop VI (29). Stem-loops II and III are predicted as one combined stem-loop structure. Other nucleic acid folding software (Mfold and nupack) predicted similar secondary structures (10, 51).