MOESM1 of Retrotransposon gag-like 1 (RTL1) and the molecular evolution of self-targeting imprinted microRNAs

Additional file 1: Figure S1. Conservation of sequences of (a) miR-136 (b) miR-127 (c) miR-433 (d) miR-432 and (e) mir-431. microRNAs (antisense) shown above mRNA sequences (sense); dots represent nucleotide identical to human RTL1. Homo (human, euarchontoglirean), Ovies (sheep, laurasiatherian), Orycteropus (aardvark, afrotherian), Dasypus (armadillo, xenarthran). Figure S2. Self-complementarity of (a) miR-127-3p and (b) miR-433-3p. Predicted hairpin structures of pre-miR-127 and pre-miR-433 were obtained from miRDB [60]. The mature microRNAs processed from pre-miRNA hairpins are indicated by yellow background. miRNA seed sequences indicated in red. Figure S3. Alignment of seven 33-nucleotide TRB repeats for RTL1 genes (sense strand) of diverse eutherian species. Nucleotides in red and blue are complementary to pre-miR-432. Blue sequences are complementary to the seeds of miR-432-5p and miR-432-3p (miR-432-5p target cuccaag occurs twice; miR-432-3p target ccaucca occurs once within pre-miR-432). The TRB repeats are disrupted in mouse and rat Rtl1 genes (see Additional file 1: Fig. S4). Figure S4. Partial sequence of the mouse RTL1 mRNA showing 12-nucleotide TRA repeats, 66-nucleotide TRB2 repeats, and 24-nucleotide TRC repeats. The TRB2 and TRC repeats have been derived from within the ancestral 33-nucleotide TRB repeats. Sequences in blue are complementary to the seed sequences of miR-432-5p and miR-432-3p. Sequences in red are complementary to the seed sequences of miR-434-5p and miR-434-3p. Figure S5. Autotargets and allotargets of miR-434-5p and miR-434-3p in the sequence of mouse Rtl1 mRNA. These complex relations are a consequence of the 24-nucleotide TRC repeats. Figure S6. (a) The pre-miR-432 hairpin: CUUGGAG is the seed of miR-432-5p (appears twice); UGGAUGG is the seed of miR-432-3p; 33-nucleotide periodicity of TRB repeats indicated by successive arrow heads. (b) The pre-miR-434 hairpin: CUCGACU (appears twice) is the seed of miR-434-5p; UUGAACC (appears thrice) is the seed of miR-434-3p; 24-nucleotide periodicity of TRC repeats is indicated by successive arrow heads. The mature microRNAs processed from the hairpins are indicated by yellow. Structures of pre-miRNA hairpins from miRdb [60]. (PDF 3063 kb)