Database Description
| General information of database | |
Database name
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KOME
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Alternative name
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Knowledge-based Oryza Molecular biological Encyclopedia |
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DOI
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10.18908/lsdba.nbdc00120-000 |
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Creator
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Creator Name
Shoshi Kikuchi
Creator Affiliation
National Institute of Agrobiological Sciences
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Contact address
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2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan National Institute of Agrobiological Sciences Plant Genome Research Unit Shoshi Kikuchi E-mail : 
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Database classification
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Plant databases - Rice |
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Organism
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Database description
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Information about approximately 38,000 full-length cDNA clones that were completely sequenced in the Rice full-length cDNA project is shown in the database. The full-length cDNA clones were collected from various tissues treated under various stress conditions. The database contains not only information about complete nucleotide sequences and encoded amino acid sequences, but also results of homology searches against public databases, mapping information, information about patterns of alternative splicing, protein domains and transmembrane structures, and information about cellular localizations and gene functions annotated with Gene Ontology. |
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Features and manner of utilization of database
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The full-length cDNA libraries were constructed from randomly picked 170,000 clones derived from twenty types of stressed tissues of japonica rice. The clones were grouped into 28,000 independent classes according to their 3' terminal single-pass sequences. All of the representative clones were completely sequenced. |
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License
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CC BY-SA Detail |
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Background and funding
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Name
The Rice Full-Length cDNA
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Reference(s)
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Article title
Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice
Author name(s)
Rice Full-Length cDNA Consortium; National Institute of Agrobiological Sciences Rice Full-Length cDNA Project Team, Kikuchi S*, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, Ohneda E, Yahagi W, Suzuki K, Li CJ, Ohtsuki K, Shishiki T; Foundation of Advancement of International Science Genome Sequencing & Analysis Group, Otomo Y, Murakami K, Iida Y, Sugano S, Fujimura T, Suzuki Y, Tsunoda Y, Kurosaki T, Kodama T, Masuda H, Kobayashi M, Xie Q, Lu M, Narikawa R, Sugiyama A, Mizuno K, Yokomizo S, Niikura J, Ikeda R, Ishibiki J, Kawamata M, Yoshimura A, Miura J, Kusumegi T, Oka M, Ryu R, Ueda M, Matsubara K; RIKEN, Kawai J, Carninci P, Adachi J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Hayatsu N, Imotani K, Ishii Y, Itoh M, Kagawa I, Kondo S, Konno H, Miyazaki A, Osato N, Ota Y, Saito R, Sasaki D, Sato K, Shibata K, Shinagawa A, Shiraki T, Yoshino M, Hayashizaki Y, Yasunishi A.
Journal
Science 2003 July 18; Vol.301 no.5631: pp.376-379
External Links
 
Article title
Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray
Author name(s)
Satoh K, Doi K, Nagata T, Kishimoto N, Suzuki K, Otomo Y, Kawai J, Nakamura M, Hirozane-Kishikawa T, Kanagawa S, Arakawa T, Takahashi-Iida J, Murata M, Ninomiya N, Sasaki D, Fukuda S, Tagami M, Yamagata H, Kurita K, Kamiya K, Yamamoto M, Kikuta A, Bito T, Fujitsuka N, Ito K, Kanamori H, Choi IR, Nagamura Y, Matsumoto T, Murakami K, Matsubara K, Carninci P, Hayashizaki Y, Kikuchi S.
Journal
PLoS One. 2007 Nov 28; 2(11):e1235.
External Links
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| Original website information | |
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Database maintenance site
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URL of the original website
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(Closed) http://cdna01.dna.affrc.go.jp/cDNA/ |
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Operation start date
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2003/07/18 |
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Last update date
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2010/03/31 |
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URL of the portal site
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http://agrid.dna.affrc.go.jp/cgi-bin/sogo.cgi?class=719&lang=en |
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Whole data download
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- |
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Referenced database
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DDBJ |
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Entry list
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Not available |
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Query search
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Not available |
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Web services
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Not available |
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URL of Web services
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- |
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Need for user registration
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Not available |