FIG. 6.

Evolutionary relationship between CTE and TBE. (A) Conservation of neutral sequences between TBE and individual CTEs. Different portions of TBE secondary structure model are shown. The portions of the secondary structure models of CTEs from SRV-1, ERA-IAP, intracisternal A-particle-related retroelement ORG-IAP, and IAPE-related CTE-like sequence (CTE IAPE-10, accession no. U53819) (37) are shown, as indicated. Red letters denote the conserved TAP-binding motifs in CTEs, as shown in Fig. 1 and 2. The recurrent Stem1 structure of TBE and similar stem regions of CTEs are indicated by green shading. Shadings in the hairpin loop regions show the residues that are conserved between TBE and CTEs of SRV-1 (yellow) and ORG-IAP (blue). Italics show the conserved primary structure. Dashes indicate virtual gaps in RNA folding; the downward-pointing arrow indicates the start of stem 1. (B) TBE-related tandem repeats in ERA-IAP retroelement. At the right, the alignment of TBE and a region of the ERA-IAP LTR is shown. Arrows show the 15-nt tandem repeat units in ERA-IAP (R1 through R4). At the left, the alignment of the ERA-IAP repeat units and the consensus TBE repeat unit is shown. The conserved residues are shaded.