RIRE2 is a LTR retrotransposon described in the genome of Oryza sativa (Ohtsubo, Kumekawa and Ohtsubo 1999). This element belongs to a lineage of plant LTR retrotransposons (Tat), sibling of other lineage of putative plant endogenous retroviruses (Athila), providing evidence of a shared ancestral lineage originally described as class A by Wright and Voytas (1998). The genomic structure of RIRE2 is 11.2 Kb in size including LTRs of 441 nt. The internal region displays a Primer Binding Site (PBS) complementary to a tRNAArg, two Open Reading Frames (ORFs) for gag and pol genes, as well as three complementary ORFs named ORF5, ORF4, and ORF3 displayed between the integrase domain, and also, a Polypurine Tract (PPT) adjacent to the 3´LTR (Ohtsubo, Kumekawa and Ohtsubo 1999).
Figure not to scale. If present, long terminal repeats (LTRs) have been highlighted in blue. Amino acid motifs noted with lines indicate the conserved residues in each protein domain, abbreviations below mean:
||DU or DUT=dUTPase
||TAV or IBMP=transactivator/viroplasmin or inclusion body matrix protein
||PBS=primer binding site
||ATF=aphid transmission factor
||VAP=virion associated protein