Fig. 1.

Genome-wide optimal energy RNA configurations for select motifs representative of each HRV species. (A) All HRVs display characteristic 5′UTR CL elements with minimal predicted structural variation (blue boxes). (B) The alignments and predicted structures of the IRES of HRVs reveal a bait-and-switch arrangement for initiation of translation. A stem-pairing AUG (light green box) is found for each species, but a highly variable region of intervening sequence near the initiator AUG (dark green box) was noted. (C) HRV 3′UTRs have a unique unbranched stem motif before the poly-A tail. The left-most codon (red box, white text) is the ORF terminator. Other boxes highlight additional terminators (tan boxes), including a characteristic codon (tan box, red text) found in the apical loop.