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. 2014 Apr 1;5:63. doi: 10.3389/fgene.2014.00063

Figure 2.

Figure 2

Distribution of BHB motifs at the junctions of permuted tRNAs in algae and archaea. (A) The tRNA nucleotides are numbered according to Marck and Grosjean (2002) and the arrows indicate the positions of the BHB motifs. The type of BHB motif and the presence or absence of an intron is indicated for each tRNA. For example, “C. merolae Leu(TAA), HBh', +intron, (37/38)” at the position between nucleotides 20 and 21 means that the HBh' is from the junction of the C. merolae permuted tRNALeu(UAA), which contains an intron at 37/38. (B) The BHB motif is classified by one or two 3-nucleotide (nt) bulges (denoted as “B = 3”) separated by a central 4-base pair (bp) helix (denoted as “H = 4”) and flanked by two helices (denoted as h or h′), each with more than two base pairings. “hBHBh′” is the strict form of the BHB motif, which contains two bulges, a central helix and two flanking helices. The relaxed form of the BHB motif (BHL) lacking some of these bulges or helices is denoted as “hBH” or “HBh'.” The term “no H” represents motifs that do not contain a central 4-bp helix.