Database Description

General information of database
Database name	RPD
Alternative name	Rice Proteome Database
DOI	10.18908/lsdba.nbdc00191-000
Creator	Creator Name Setsuko Komatsu Creator Affiliation National Institute of Crop Science, National Agriculture and Food Research Organization Literature Search
Contact address	2-1-18 Kannondai Tsukuba, Ibaraki 305-8634, Japan National Institute of Crop Science, National Agriculture and Food Research Organization Setsuko Komatsu E-mail:
Database classification	Proteomics Resources Plant databases - Rice
Organism	Taxonomy Name Oryza sativa Taxonomy ID 4530
Database description	Rice Proteome Database contains information on proteins identified from several organs and organelles on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) reference maps.
Features and manner of utilization of database	Proteins extracted from organs and subcellular compartments in rice on various growing stages were separated by 2D-PAGE. Based on 23 reference maps of 2D-PAGE, each of the proteins was purified and sequenced by gas-phase protein sequencer or mass spectrometry. 14724 identified proteins were mapped by 2D-PAGE. The information on 6011 proteins (e.g. Mw, pI, expression, the amino acid sequence and the result of homology searches) was cataloged and entered in the Rice Proteome Database. The database is searchable by keyword, accession number, protein name, pI, Mw and amino acid sequence, or by selection of a spot on one of the 2D-PAGE maps. Cross-references are provided to tools for proteomics and to other databases.
License	CC BY-SA Detail
Background and funding	Name Analysis and database construction for tissue-specific and subcellular-localized proteins from rice.
Reference(s)	Article title Rice proteome database: a step toward functional analysis of the rice genome. Author name(s) Komatsu S. Journal Plant Mol Biol. 2005 Sep;59(1):179-90. External Links Article title Rice proteomics: a step toward functional analysis of the rice genome. Author name(s) Komatsu S, Konishi H, Shen S, Yang G. Journal Mol Cell Proteomics. 2003 Jan;2(1):2-10. External Links Article title Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003. Author name(s) Komatsu S, Kojima K, Suzuki K, Ozaki K, Higo K. Journal Nucleic Acids Res. 2004 Jan 1;32(Database issue):D388-92. External Links Article title Proteomics of the rice cell: systematic identification of the protein populations in subcellular compartments. Author name(s) Tanaka N, Fujita M, Handa H, Murayama S, Uemura M, Kawamura Y, Mitsui T, Mikami S, Tozawa Y, Yoshinaga T, Komatsu S. Journal Mol Genet Genomics. 2004 Jun;271(5):566-76. Epub 2004 Apr 7. External Links Article title Proteome analysis of rice tissues by two-dimensional electrophoresis: an approach to the investigation of gibberellin regulated proteins. Author name(s) Tanaka N, Konishi H, Khan MM, Komatsu S. Journal Mol Genet Genomics. 2004 Jan;270(6):485-96. Epub 2003 Nov 21. External Links Article title Update and challenges on proteomics in rice. Author name(s) Komatsu S, Yano H. Journal Proteomics. 2006 Jul;6(14):4057-68. External Links
Original website information
Database maintenance site	National Institute of Agrobiological Sciences
URL of the original website	(Closed) http://gene64.dna.affrc.go.jp/RPD/
Operation start date	2003/01/07
Last update date	2004/04/01
URL of the portal site	http://agrid.dna.affrc.go.jp/
Whole data download	-
Referenced database	KOME, NCBI
Entry list	Not available
Query search	Not available
Web services	Not available
URL of Web services	-
Need for user registration	Not available