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. 2015 Jul;21(7):1219–1232. doi: 10.1261/rna.049338.114

FIGURE 2.

FIGURE 2.

(A) Alignment based secondary structure prediction of the 5′ UTR of 86 isolates. The alignment was calculated by LocARNA, the consensus sequence and structure by RNAalifold. The sequence for SLI is contained in only nine isolate sequences and therefore appears here as white. SLII is different from that described in Honda et al. (1999a), but in agreement with Zhao and Wimmer (2001) and SHAPE analysis of Pang et al. (2011) (see Supplemental Fig. 1C). Here, we show an alternative secondary structure for SLIIId with a slightly better MFE and conservation compared with the known structure. (Blue sequences) Forbidden to pair by RNAalifold in order to build the pseudoknot that is essential for the recruitment of the ribosome and therefore for viral protein translation (Berry et al. 2011). (Gray) Secondary structure different from those proposed by Honda et al. (1999a). (B) Consensus sequences and secondary structures of the CRE, VR, and X-tail in two alternative foldings. CRE and VR based on 96 isolates, X-tail based on 19 isolates. Apical regions of 5BSL1, 5BSL2, and 5BSL3.1 show up as described previously (Diviney et al. 2008). Even though it seems that the apical part of the stems can vary between isolates, the consensus secondary structure leaves little variability (see dotplot in Fig. 3). SLIV is present in all tested isolates but appears white since the stem is variable (see supplement, STK file for variable region). (Gray) Differences in secondary structures of 5BSL1 (SL9033), and 5BSL2 (SL9033) compared with data of Diviney et al. (2008), of 5BSL3.1 (SL9132) compared with data of Diviney et al. (2008) and Romero-López et al. (2014), of SLIV (Kolykhalov et al. 1996), of SLII (Kolykhalov et al. 1996; Blight and Rice 1997; Ito and Lai 1997), and of DLS (Ivanyi-Nagy et al. 2006; Shetty et al. 2010; Romero-López et al. 2014). (Rectangle) Consensus of RNAalifold to establish 5BSL3.2, instead of the interaction in Figures 3 (oval) and 7, No. 15 (Diviney et al. 2008). A detailed explanation of the base pair color code is available in the Supplemental Material.