[Credits]

Life Science Database Archive
KOME

Database Description

General information of database

info Database name KOME
info Alternative name Knowledge-based Oryza Molecular biological Encyclopedia
info DOI 
info Creator 
Creator Name:
Shoshi Kikuchi
Creator Affiliation:
National Institute of Agrobiological Sciences
info Contact address 

2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
National Institute of Agrobiological Sciences
Plant Genome Research Unit
Shoshi Kikuchi
E-mail : kome ad

info Database classification Plant databases - Rice
info Organism 
Taxonomy Name:
Oryza sativa
Taxonomy ID:
info Database description 

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.

info Features and manner of utilization of database 

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.

info License CC BY-SA Detail
info Background and funding 

The information about full-length cDNA clones were collected and completely sequenced by the joint collaboration of National Institute of Agrobiological Sciences (NIAS), Foundation of Advancement of International Science (FAIS), and RIKEN institute, under the supervision of BRAIN (Bio-oriented Technology Research Advancement Institution). This work has been undertaken through the project named "The Rice Full-Length cDNA".

info Background and funding 
Name:
The Rice Full-Length cDNA
info Reference(s) 
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:
 

Original website information

info Database maintenance site 

info URL of the original website (Closed) http://cdna01.dna.affrc.go.jp/cDNA/
info Operation start date 2003/07/18
info Last update date 2010/03/31
info URL of the portal site 
info Whole data download -
info Referenced database 

DDBJ
NCBI-GenBank
TIGR
BGI RIS
Rice Microarray Opening Site (RMOS)
Rice mutant panel database (Tos17)
A Database of Plant Cis-acting Regulatory DNA Elements (PLACE)
PIR
SWISS-PROT
UniProt
InterPro
Blocks
Rice Proteome Database

info Entry list Available
info Query search Available
info Web services Not available
info URL of Web services -
info Need for user registration Not available