Collection, Mapping, and Annotation of over 28,000 cDNA Clones from Japonica Rice

• Published in: Science (American Association for the Advancement of Science) Vol. 301; no. 5631; pp. 376 - 379
• Main Authors: Kikuchi, Shoshi, Satoh, Kouji, Nagata, Toshifumi, Kawagashira, Nobuyuki, Doi, Koji, Kishimoto, Naoki, Yazaki, Junshi, Ishikawa, Masahiro, Yamada, Hitomi, Ooka, Hisako, Hotta, Isamu, Kojima, Keiichi, Namiki, Takahiro, Ohneda, Eisuke, Yahagi, Wataru, Suzuki, Kohji, Li, Chao Jie, Ohtsuki, Kenji, Shishiki, Toru, Otomo, Yasuhiro, Murakami, Kazuo, Lida, Yoshiharu, Sugano, Sumio, Fujimura, Tatsuto, Suzuki, Yutaka, Tsunoda, Yuki, Kurosaki, Takashi, Kodama, Takeko, Masuda, Hiromi, Kobayashi, Michie, Xie, Quihong, Lu, Min, Narikawa, Ryuya, Sugiyama, Akio, Mizuno, Kouichi, Yokomizo, Satoko, Niikura, Junko, Ikeda, Rieko, Ishibiki, Junya, Kawamata, Midori, Yoshimura, Akemi, Miura, Junichirou, Kusumegi, Takahiro, Oka, Mitsuru, Ryu, Risa, Ueda, Mariko, Matsubara, Kenichi, Kawai, Jun, Carninci, Piero, Adachi, Jun, Aizawa, Katsunori, Arakawa, Takahiro, Fukuda, Shiro, Hara, Ayako, Hashidume, Wataru, Hashizume, Wataru, Hayatsu, Norihito, Imotani, Koichi, Ishii, Yoshiki, Ishii, Yoshiyuki, Itoh, Masayoshi, Kagawa, Ikuko, Kondo, Shinji, Konno, Hedeaki, Konno, Hideaki, Miyazaki, Ai, Osato, Naoki, Ota, Yoshimi, Saito, Rintaro, Sasaki, Daisuke, Sato, Kenjiro, Shibata, Kazuhiro, Shinagawa, Akira, Shiraki, Toshiyuki, Yoshino, Masayasu, Hayashizaki, Yoshihide, Yasunishi, Ayako
• Format: Journal Article
• Language: English
• Published: Washington, DC American Association for the Advancement of Science 18.07.2003; The American Association for the Advancement of Science
• Subjects: Agronomy. Soil science and plant productions; Alternative Splicing; Amino Acid Sequence; Arabidopsis; Biological and medical sciences; Classical and quantitative genetics. Population genetics. Molecular genetics; Cloning; Cloning, Molecular; Coding; Comparative Analysis; Complementary DNA; Computational Biology; Cultivars: description, identification, tests, catalogs; Databases, Nucleic Acid; Databases, Protein; Deoxyribonucleic acid; DNA; DNA, Complementary; Donors; Exons; Freshwater; Fundamental and applied biological sciences. Psychology; Generalities. Genetics. Plant material; Genes; Genes, Plant; Genetic loci; Genetics and breeding of economic plants; Genome, Plant; Genomes; Genomics; Molecular genetics; Molecular Sequence Data; Open Reading Frames; Oryza - genetics; Oryza sativa japonica; Plant Proteins - chemistry; Plant Proteins - genetics; Plant Proteins - physiology; Protein Structure, Tertiary; Proteins; Rice; RNA, Antisense - genetics; Sequence Analysis, DNA; Sequence Homology, Amino Acid; Sequence Homology, Nucleic Acid; Sequencing; Transcription factors; Transcription Factors - chemistry; Transcription Factors - genetics; Transcription, Genetic; Transcripts (Written Records); Varietal selection. Specialized plant breeding, plant breeding aims; Asia; Japan; Genetic mapping; Monocotyledones; Nucleotide sequence; Genomics; Sequence alignment; Homology; Experimental study; Structure function relationship; Cereal crop; Oryza sativa; Complementary DNA; Gramineae; Angiospermae; Database; Plant protein; Collection; Spermatophyta; Chemical composition; Molecular cloning; Genome; Bioinformatics; Cultivar
• ISSN: 0036-8075; 1095-9203
• DOI: 10.1126/science.1081288

We collected and completely sequenced 28,469 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. Nipponbare. Through homology searches of publicly available sequence data, we assigned tentative protein functions to 21,596 clones (75.86%). Mapping of the cDNA clones to genomic DNA revealed that there are 19,000 to 20,500 transcription units in the rice genome. Protein informatics analysis against the InterPro database revealed the existence of proteins presented in rice but not in Arabidopsis. Sixty-four percent of our cDNAs are homologous to Arabidopsis proteins.