Figure 3

Potential downstream RNA secondary structures in all sequences analysed. (Continued in Figure 4.) As of 20 April 2008, there were 357 alphavirus sequences in GenBank with coverage of the U UUU UUA motif in the 6K cistron. The 100 nt region starting from the U UUU UUA motif, and including the first 93 nt of 3'-adjacent sequence, was extracted from all 357 sequences (although in 26 sequences a shorter region had to be used due to incomplete sequence data). Shown here are the 108 unique ≤100-nt sequences, plus an additional seven duplicate sequences also included since they have different species/strain annotations. The total number of duplicate sequences represented by each sequence shown is given in column 1, while column 2 gives an example GenBank accession number for the sequence, and column 3 gives the virus name abbreviation. Potential RNA secondary structures were identified using a combination of RNAfold and alidot [36], pknots [37], and manual inspection. Bases within potential stems are indicated either in colour or with underlines (if overlapping other potential stems) and potential base-pairings are indicated with brackets – '()', '[]' or '<>'. '<>' signify more dubious base-pairings, including stems that were experimentally shown not to affect frameshifting efficiency (dual luciferase assays with inserts comprising the U UUU UUA motif and 3'-adjacent sequence; B Chung et al, in preparation). Base variations that maintain base-pairings are marked in bold. Note that not all sequences in GenBank represent functional (infectious) viruses and it is possible that certain sequences whose shift site and/or predicted RNA structure do not conform with the majority of isolates for the same species may represent defective viruses – for example the non-standard slippery heptanucleotide in the SPDV sequence AJ012631 is due to a 36-codon deletion in 6K relative to other SPDV sequences.