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

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...

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Veröffentlicht in:	Science (American Association for the Advancement of Science) 2003-07, Vol.301 (5631), p.376-379
Hauptverfasser:	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:	Artikel
Sprache:	eng
Schlagworte:	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
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Beschreibung
Zusammenfassung:	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.
ISSN:	0036-8075 1095-9203
DOI:	10.1126/science.1081288