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Fig. 2 | Genome Biology

Fig. 2

From: Retrozymes are a unique family of non-autonomous retrotransposons with hammerhead ribozymes that propagate in plants through circular RNAs

Fig. 2

Sequence features of genomic retrozymes and Ty3-gypsy retrotransposons. a Schematic representation of a full genomic retrozyme element. Target site duplications (TSDs) delimiting the retrozyme are shown in grey. The 5′ and 3′ ends of the long terminal repeats (LTRs) are shown in blue and red, respectively, with the small conserved boxes highlighted in darker colors. The positions of the conserved primer binding site (PBS), the polypurine tract (PPT) and the hammerhead ribozymes (HHR) are indicated. The self-cleavage (SC) sites delimiting the retrozyme RNA are indicated with arrows. b Schematic representation of the transcribed and self-cleaved retrozyme RNA. c Alignment of the conserved 3′ and 5′ boxes (PBSs, PPTs and LTR ends) of representative retrozymes (top) and the equivalent regions of Ty3-gypsy retrotransposons (bottom). Consensus sequence of the motif is shown in the middle: totally conserved positions are shown as uppercase letters (either A, C, G, U, Y or R), whereas positions conserved in between 70–100 % of the sequences are shown as lowercase letters, and positions below 70 % in conservation are shown as dots. d Schematic representation of a genomic Ty3-gypsy retrotransposon (top) and its transcribed RNA (bottom). LTRs are shown in light grey. Small conserved 5′ and 3′ boxes are shown in blue and red respectively. Characteristic unique (U5, U3) and repeated (R) domains of the LTRs are indicated. The typical open reading frames of Ty3-gypsy retrotransposons are indicated as gag and pol. e Sequence alignment of selected HHRs from 25 plant species. The helixes and loops of the HHR are depicted at the bottom. Self-cleavage site is indicated with an arrow. Consensus sequences shown at the bottom were obtained as in panel c

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