Table 1.

The influence of RNA secondary structure on specific splice sites

Splice site	3D structure	Affected enhancers or silencers
A2–D3	Single stem loop	ESSV exposed
A3	Extended stem loop	ESS2 and ESE2 exposed and bound simultaneously by hnRNP A1
D1	Stable stem loop	Role is not established
A7	Three stem loops	Loop 1 contains the ISS Loop 2 contains the A7 site and ESE3 Loop 3 contains ESE3

Notes: This table lists the secondary structural conformations adopted by HIV-1 mRNA and the influence that this secondary structure has on splicing enhancers and silencers. Adapted from Stoltzfus.5

Abbreviations: 3D, three dimensional; ESS, exonic splicing silencer; ESE, exonic splicing enhancer; ESSV, exonic splicing silencer; hnRNP, heterogeneous nuclear ribonucleoprotein; ISS, intronic splicing silencer.