Two new SINE elements, p-SINE2 and p-SINE3, from rice

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<i>p-SINE1</i> was the first plant SINE element identified in the <i>Waxy</i> gene in <i>Oryza sativa</i>, and since then a large number of <i>p-SINE1</i>-family members have been identified from rice species with the AA or non-AA genome. In this paper, we report two new rice SINE elements, designated <i>p-SINE2</i> and <i>p-SINE3</i>, which form distinct families from that of <i>p-SINE1</i>. Each of the two new elements is significantly homologous to <i>p-SINE1</i> in their 5’-end regions with that of the polymerase III promoter (A box and B box), but not significantly homologous in the 3’-end regions, although they all have a T-rich tail at the 3’ terminus. Despite the three elements sharing minimal homology in their 3’-end regions, the deduced RNA secondary structures of <i>p-SINE1</i>, <i>p-SINE2</i> and <i>p-SINE3</i> were found to be similar to one another, such that a stem-loop structure seen in the 3’-end region of each element is well conserved, suggesting that the structure has an important role on the <i>p-SINE</i> retroposition. These findings suggest that the three <i>p-SINE</i> elements originated from a common ancestor. Similar to members of the <i>p-SINE1</i> family, the members of <i>p-SINE2</i> or <i>p-SINE3</i> are almost randomly dispersed in each of the 12 rice chromosomes, but appear to be preferentially inserted into gene-rich regions. The <i>p-SINE2</i> members were present at respective loci not only in the strains of the species with the AA genome in the <i>O. sativa</i> complex, but also in those of other species with the BB, CC, DD, or EE genome in the <i>O. officinalis</i> complex. The <i>p-SINE3</i> members were, however, only present in strains of species in the <i>O. sativa</i> complex. These findings suggest that <i>p-SINE2</i> originated in an ancestral species with the AA, BB, CC, DD and EE genomes, like <i>p-SINE1</i>, whereas <i>p-SINE3</i> originated in an ancestral strain of the species with the AA genome. The nucleotide sequences of <i>p-SINE1</i> members are more divergent than those of <i>p-SINE2</i> or <i>p-SINE3</i>, indicating that <i>p-SINE1</i> is likely to be older than <i>p-SINE2</i> and <i>p-SINE3</i>. This suggests that <i>p-SINE2</i> and <i>p-SINE3</i> have been derived from <i>p-SINE1</i>.<br>


  • Genes & Genetic Systems

    Genes & Genetic Systems 80(3), 161-171, 2005

    The Genetics Society of Japan

Cited by:  3


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