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. Author manuscript; available in PMC: 2008 Jul 27.
Published in final edited form as: J Mol Biol. 2007 May 8;370(5):856–869. doi: 10.1016/j.jmb.2007.04.076

Figure 1.

Figure 1

The Dicistroviridae virus genome and IGR IRES secondary structures. (a) The Dicistroviridae genome contains two cistrons on a single positive-sense RNA. The synthesis of the proteins from each cistron is governed by an IRES. The IRES, located between the two cistrons (intergenic region or IGR), is subdivided into two classes. (b) Cartoon representations of the two classes of IGR IRESes, drawn to scale relative to one another. The PSIV IGR IRES represents a typical class 1 IGR IRES while TSV represents a typical class 2 IGR IRES. Here, we use a detailed nomenclature to distinguish between various elements in the IRES structure. Nomenclature used to name the various structural elements follows standard RNA structure usage (J, junction; P, paired/helix; L, loop). SL III, IV, V, and the pseudoknots are also referred to with their traditional names. Furthermore, we reserve the term “domain” for folded into a higher-order structure, and collections of related secondary structures that may or may not adopt a higher-order fold are referred to as “regions.”