Figure 2

Predicted consensus secondary RRE structure: A consensus secondary structure of our RRE sequences were generated from, 20 subtype C (panel A) and B (panel B) and 13 RRE sequences from this study (panel C) which uses multiple sequence alignment program using RNA fold program in the Vienna RNA package (Zuker algorithm) as described in the text. Five (A to E) well defined stem-loop structures including the branched stem-lop B critical for binding Rev protein were identified. In this program the pale colors indicate that a base-pair cannot be formed in some sequences of the alignment.