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Antisense transcripts with rice full-length cDNAs

Naoki Osato1, Hitomi Yamada2, Kouji Satoh2, Hisako Ooka2, Makoto Yamamoto3, Kohji Suzuki3, Jun Kawai14, Piero Carninci14, Yasuhiro Ohtomo5, Kazuo Murakami5, Kenichi Matsubara5, Shoshi Kikuchi2 and Yoshihide Hayashizaki14*

Author Affiliations

1 Laboratory for Genome Exploration Research Group, RIKEN Genomic Science Center (GSC), RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan 230-0045

2 Department of Molecular Biology, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki, Japan 305-8602

3 Hitachi Software Engineering Company Ltd, Naka-ku, Yokohama, Kanagawa, Japan 231-0015

4 Genome Science Laboratory, RIKEN Wako Main Campus, Wako, Saitama, Japan 351-0198

5 Laboratory of Genome Sequencing and Analysis Group, Foundation of Advancement of International Science (FAIS), Tsukuba, Ibaraki, Japan 305-0062

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Genome Biology 2003, 5:R5  doi:

Published: 11 December 2003



Natural antisense transcripts control gene expression through post-transcriptional gene silencing by annealing to the complementary sequence of the sense transcript. Because many genome and mRNA sequences have become available recently, genome-wide searches for sense-antisense transcripts have been reported, but few plant sense-antisense transcript pairs have been studied. The Rice Full-Length cDNA Sequencing Project has enabled computational searching of a large number of plant sense-antisense transcript pairs.


We identified sense-antisense transcript pairs from 32,127 full-length rice cDNA sequences produced by this project and public rice mRNA sequences by aligning the cDNA sequences with rice genome sequences. We discovered 687 bidirectional transcript pairs in rice, including sense-antisense transcript pairs. Both sense and antisense strands of 342 pairs (50%) showed homology to at least one expressed sequence tag other than that of the pair. Microarray analysis showed 82 pairs (32%) out of 258 pairs on the microarray were more highly expressed than the median expression intensity of 21,938 rice transcriptional units. Both sense and antisense strands of 594 pairs (86%) had coding potential.


The large number of plant sense-antisense transcript pairs suggests that gene regulation by antisense transcripts occurs in plants and not only in animals. On the basis of our results, experiments should be carried out to analyze the function of plant antisense transcripts.