Characterization of promoter regions of DeuSINEs. (A) Six tRNA-like structures of the promoter regions of tRNA-derived DeuSINEs: (a) LmeSINE1a, (b) LmeSINE1b, (c) SacSINE1, (d) EbuSINE1, (e) EbuSINE2, and (f) BflSINE1. Standard base pairs and G-T wobble pairs are shown as black dashes and dots, respectively. Nucleotides conserved in functional tRNAs (8T, 14A, 15G, 18G, 32C, 33T, and 37R) are circled, and the Box B promoter sequences are boxed. The numbering system corresponds with that of general tRNA (Gauss et al. 1979). (B) An alignment of consensus sequences of the 5S rRNA-related regions (red boxes) of AmnSINE1, SINE3, SINE3_IP, and OS-SINE1. Zebrafish 5S rRNA gene sequences were obtained from Kapitonov and Jurka (2003). The 5S rRNA sequences of human and rainbow trout were obtained from GenBank (accession nos. X51545 and J01861, respectively). Box A, Box C, and Intermediate Element of pol III promoters are denoted with black lines. Nucleotides shaded in black are conserved across sequences.
