NAR Molecular Biology Database Collection entry number 860
Ohyanagi H.1,2, Tanaka T.3, Sakai H.3, Shigemoto Y.1,4, Yamaguchi K.5, Habara T.5,6, Fujii Y.5,6, Antonio B.A.3, Nagamura Y.3, Imanishi T.6, Ikeo K.1, Itoh T.3,6, Gojobori T.1,6 and Sasaki T.3
1Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
2Tsukuba Division, Mitsubishi Space Software Co., Ltd., 1-6-1 Takezono, Tsukuba, Ibaraki 305-0032, Japan
3Genome Research Department, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
4Life Science Systems Division, Fujitsu Limited, 1-17-25 Shinkamata, Ota-ku, Tokyo 144-8588, Japan
5Japan Biological Information Research Center, Japan Biological Informatics Consortium, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
6Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan

Database Description

With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was held in Japan with the aim of annotating and manually curating all the genes in the rice genome. Here we present the Rice Annotation Project Database (RAP-DB), which has been developed to provide access to the annotation data. The RAP-DB has two different types of annotation viewers, BLAST and BLAT search, and other useful features. By connecting the annotations to other rice genomics data, such as full-length cDNAs and Tos17 mutant lines, the RAP-DB serves as a hub for rice genomics. All of the resources can be accessed through http://rapdb.lab.nig.ac.jp/.


We thank the IRGSP and RAP members for their supports. This work was supported in part by a grant from the special Coordination Funds for Promoting Science and Technology of the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan. Funding to pay the Open Access publication charges for this article was provided by a grant from the NIAS Genebank Project.


1. Moore,G., Devos,K.M., Wang,Z. and Gale,M.D. (1995) Cereal genome evolution. Grasses, line up and form a circle. Curr. Biol., 5, 737-739.
2. Sasaki,T. and Burr,B. (2000) International Rice Genome Sequencing Project: the effort to completely sequence the rice genome. Curr. Opin. Plant Biol., 3, 138-141.
3. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature, 436, 793-800.
4. Yuan,Q., Ouyang,S., Wang,A., Zhu,W., Maiti,R., Lin,H., Hamilton,J., Haas,B., Sultana,R., Cheung,F. et al. (2005) The institute for genomic research Osa1 rice genome annotation database. Plant Physiol., 138, 18-26.
5. Kikuchi,S., Satoh,K., Nagata,T., Kawagashira,N., Doi,K., Kishimoto,N., Yazaki,J., Ishikawa,M., Yamada,H., Ooka,H. et al. (2003) Collection, mapping, and annotation of over 28 000 cDNA clones from japonica rice. Science, 301, 376-379.
6. Miyao,A., Tanaka,K., Murata,K., Sawaki,H., Takeda,S., Abe,K., Shinozuka,Y., Onosato,K. and Hirochika,H. (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell, 15, 1771-1780.
7. Stein,L.D., Mungall,C., Shu,S., Caudy,M., Mangone,M., Day,A., Nickerson,E., Stajich,J.E., Harris,T.W., Arva,A. et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res., 12, 1599-1610.
8. Imanishi,T., Itoh,T., Suzuki,Y., O'Donovan,C., Fukuchi,S., Koyanagi,K.O., Barrero,R.A., Tamura,T., Yamaguchi-Kabata,Y., Tanino,M. et al. (2004) Integrative annotation of 21 037 human genes validated by full-length cDNA clones. PLoS Biol., 2, e162.
9. Kent,W.J. (2002) BLAT--the BLAST-like alignment tool. Genome Res., 12, 656-664.
10. Altschul,S.F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
11. Dowell,R.D., Jokerst,R.M., Day,A., Eddy,S.R. and Stein,L. (2001) The distributed annotation system. BMC Bioinformatics, 2, 7.

Category: Plant databases
Subcategory: Rice

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