RRC ID 6977
Author Tsuchimoto S, Hirao Y, Ohtsubo E, Ohtsubo H.
Title New SINE families from rice, OsSN, with poly(A) at the 3' ends.
Journal Genes Genet Syst
Abstract A database search of the sequences flanking a member of rice retrotransposon RIRE7 revealed that a 298-bp sequence in the region downstream of the member is a repetitive sequence interspersed in the genome of Oryza sativa cv. Nipponbare. Most of the repetitive sequences were flanked by a direct repeat of a target-site sequence, about 14 bp in length. The consensus sequence, 293 bp in length, had no regions encoding any proteins but had sequence motifs of an internal promoter of RNA polymerase III. These indicate that the sequence is a retroposon SINE, designated OsSN1 (Oryza sativa SINE1). OsSN1 is a new rice SINE, because it has no homology with any of the three p-SINE families previously identified from rice, and because it has a stretch of A at the 3' end, unlike p-SINE and any other Gramineae SINEs which have a stretch of T at the 3' end. The Nipponbare genome was found to have many members related to OsSN1, forming two additional new SINE families (designated OsSN2 and OsSN3). OsSN2 and OsSN3 are highly homologous to the 3' and 5' regions of OsSN1, respectively. This suggests that OsSN1 has a mosaic structure, which is generated by sequence exchange (or shuffling) between ancestral OsSN2 and OsSN3. Despite the absence of homology in the 3' regions between OsSN1 (or OsSN2) and OsSN3, a sequence, 5'-TTCTC-3', is commonly present in the region preceding the A stretch at the 3' end. This sequence together with the A stretch and a stem-loop structure found in the region near the A stretch are assumed to be important for retroposition. OsSN members were present in strains of Oryza species, as were p-SINE members. Some of the members showed insertion polymorphism at the respective loci among the rice strains. p-SINE had such polymorphic members, which are useful for classification and phylogenetic analysis of various strains of Oryza species. The polymorphic members of OsSN were more frequently found than those of p-SINE, and therefore, such members are likely to be useful for extensive taxonomic and phylogenetic studies on various rice strains.
Volume 83(3)
Pages 227-36
Published 2008-6-1
DOI 10.1266/ggs.83.227
PII JST.JSTAGE/ggs/83.227
PMID 18670134
MeSH 3' Flanking Region Base Sequence Consensus Sequence DNA, Plant / chemistry Genome, Plant Molecular Sequence Data Oryza / genetics* Phylogeny Poly A / analysis* Polymorphism, Genetic RNA, Plant / chemistry Sequence Alignment Sequence Deletion Short Interspersed Nucleotide Elements*
IF 0.917
Times Cited 15
Rice C5924 W0106 W1945 W0108 W1588 W1169=W1165 W1625 W1508