Secondary structure models for six structurally conserved elements in the 5' half of HIV-related RNA genomes.

<p>Nucleotides are colored by HIV-1 SHAPE reactivities. Secondary structures are shown for the final constrained HIV-1 secondary structure model. Base pairs are colored by level of structural consensus; black base pairs appear only in constrained HIV-1 predictions. Positions of predicted elements are shown on the HIV-1 (NL4-3) genome; annotations indicate statistical dependence, known RNA elements, major splice sites, and protein reading frames.