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  Rice Metabolic Pathways: RiceCyc Home  

Pathway Database
RiceCyc ver 3.3
Organism: Oryza sativa (rice)
Genome data: O. sativa japonica strain/cv. Nipponbare
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Pathways  |  Enzyme function  |  Compounds  |  Genes
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Developed and curated by
Gramene database
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Developed and curated by the Gramene Database, RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project on the release 5 of the TIGR-assembly of Oryza sativa japonica cv. Nipponbare genome sequenced by IRGSP. The database was created using the Pathway Tools PathoLogic module developed by Peter D. Karp and coworkers at the Bioinformatics Research Group at SRI International. RiceCyc undergoes regular rounds of curation in order to integrate exciting new discoveries on biochemical pathways in rice as well as to promote the plant researchers to use the novel pathways discovered by our prediction protcols for their research programs. The computationally generated pathways are subjected to manual curation based on published literature.

Since the functions of many of the rice genes are either provided by homology and/or HMM based predictions, many of the pathways might be incomplete or may contain errors. The manual curation of pathways is an ongoing process at Gramene and we welcome feedback from the research community.

If you notice any problems or errors on the pathways, please send a message to RiceCyc curators or by clicking the 'Feedback' button at the top right corner of this page  or on the bottom of the respective pathway display page.

Publication(s):

Gramene: a bird's eye view of cereal genomes. Jaiswal et al. Nucleic Acids Research, 2006 Jan 1;34(Database issue):D717-23. [Abstract / Full Text]

Useful Links:

KEGG pathways
KEGG rice pathways
IUBMB Enzyme nomenclature
Brenda enzyme database
BioCyc
ENZYME at Expasy
Reactome
Cellular Expression Profiling of Rice
Rice oligonucleotide array project