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. 2022 Apr 5;19(1):496–506. doi: 10.1080/15476286.2022.2058818

Figure 1.

Figure 1.

The secondary structure model of BVDV IRES RNA derived from SHAPE-MaP probing. The three main domains are labelled (I–III) with outlined individual RNA motifs: SL Ia, SL Ib, SL Ic, SL II, SL IIIa, SL IIIb, SL IIIc, SL IIId1, SL IIId2, SL IIIe, SL IIIf, SL IIIg. The H-type pseudoknot has been manually inserted within the single-stranded residues at positions 381–387 and 410–416 of domain III. The residues lacking reactivity values correspond to the sites of primer annealing (light grey). The secondary structure is colour-coded according to the SHAPE reactivity values represented by low (< 0.25), medium (0.25–0.80), high reactivity (0.8–2), and hyperreactivity (>2).