RRC ID 6968
Author Xu JH, Osawa I, Tsuchimoto S, Ohtsubo E, Ohtsubo H.
Title Two new SINE elements, p-SINE2 and p-SINE3, from rice.
Journal Genes Genet Syst
Abstract p-SINE1 was the first plant SINE element identified in the Waxy gene in Oryza sativa, and since then a large number of p-SINE1-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 p-SINE2 and p-SINE3, which form distinct families from that of p-SINE1. Each of the two new elements is significantly homologous to p-SINE1 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 p-SINE1, p-SINE2 and p-SINE3 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 p-SINE retroposition. These findings suggest that the three p-SINE elements originated from a common ancestor. Similar to members of the p-SINE1 family, the members of p-SINE2 or p-SINE3 are almost randomly dispersed in each of the 12 rice chromosomes, but appear to be preferentially inserted into gene-rich regions. The p-SINE2 members were present at respective loci not only in the strains of the species with the AA genome in the O. sativa complex, but also in those of other species with the BB, CC, DD, or EE genome in the O. officinalis complex. The p-SINE3 members were, however, only present in strains of species in the O. sativa complex. These findings suggest that p-SINE2 originated in an ancestral species with the AA, BB, CC, DD and EE genomes, like p-SINE1, whereas p-SINE3 originated in an ancestral strain of the species with the AA genome. The nucleotide sequences of p-SINE1 members are more divergent than those of p-SINE2 or p-SINE3, indicating that p-SINE1 is likely to be older than p-SINE2 and p-SINE3. This suggests that p-SINE2 and p-SINE3 have been derived from p-SINE1.
Volume 80(3)
Pages 161-71
Published 2005-6-1
DOI 10.1266/ggs.80.161
PII JST.JSTAGE/ggs/80.161
PMID 16172529
MeSH Base Sequence Chromosome Mapping Cluster Analysis Computational Biology Japan Molecular Sequence Data Oryza / genetics* Phylogeny* Sequence Analysis, DNA Sequence Homology Short Interspersed Nucleotide Elements / genetics* Species Specificity
IF 0.917
Times Cited 13
Rice W1514 W1023 W1323 W1519 W0002 W1166 W0017 W0613 W0008 W1401 W0067(B) W0001 W1681 W0107 W0610 W1943 W1945 W0120 W0593 W0596 W2007 W0440(=C0440) W1581 W0698 W1410 W1588 W1605 W1191 W1192 W1186 W1196 W1183 W1444 W1004 W1052 W1508 W1540 W1625 W1635 W2069 W2077 W2079 W1582 W0006 C5924 W0025(=>C0025) C7599 C8527(B) C8538(B)