ARC Centre of Excellence for Plant Energy Biology

Pre-release edition

Rice DB • Oryza Information Portal

Rice DB’s Oryza sativa database, lets you search and display gene identifiers, functional & proteomic annotations, subcellular localisation, phenotypes and upstream transcription motifs.

Enter identifiers, keywords, upstream 1 kb DNA motifs (up to 2 wildcards), paste FASTA format IDs, or advanced syntax in the blue box for Oryza sativa japonica (rice) data search. Spreadsheet results can be downloaded as TSV (tab-separated values). Nucleotide & peptide sequences can be downloaded in multi-FASTA format. View tutorial online or PDF. Click to choose data fields >
Rice DB searches sequenced Oryza sativa ssp. japonica cultivar Nipponbare nuclear gene loci. The database matches over 1.1 million identifiers in 40 formats including systematic gene identifiers (e.g., MSU/TIGR LOC IDs), published gene names, miRNA names and Arabidopsis thaliana orthologues (TAIR AGIs). It can also search 1kb of upstream DNA motif sequences and a full text index of annotated locus and domain keywords.
Use simple phrases ("MAP kinase") to find words adjacent in a field. The AND keyword finds words across multiple fields ("nucleus and kinase"). Use OR keyword to combine alternatives ("phosphatase or MAP kinase"). Spelling suggestions are provided where possible. Keywords and wildcard searches can be limited to certain fields, for example * in miRNA. Find out more about Rice DB with screenshots, syntax & data or click to choose data fields now >.

Your recent queries are shown on the right and can be easily re-run or edited. All queries may be copied and reproduced using advanced syntax.
Rice DB can help you validate and clean up identifier lists. Click ‘Templates’ below to access advanced queries for finding syntax errors, finding duplicates, or converting your own bulk lists. Results will show your original row numbers so you can relate the results to your source file.

Open tutorial online Tutorial

Narsai R, Devenish J, Castleden I, Narsai K, Xu L, Shou H, Whelan J (2013) Rice DB: An Oryza Information Portal linking annotation, sub-cellular location, function, expression, regulation and evolutionary information for rice and Arabidopsis. Plant J, Accepted Article, DOI: 10.1111/tpj.12357

Where relevant, reference original data sources (last updated 2013-02-27) in addition to RiceDB 0.60. All RiceDB queries can be published and reproduced as plain text queries.

1. Point to orange Field options and tick desired Field(s) for spreadsheet output, OR
2. Type an item from each row to help make advanced syntax from scratch.

count  show  find syntax errors in  find duplicates in  get unique sorted list of 
IDs >  location predictors >  data >   Hover on orange for data fields 
grouped  with  related to   for IDs like  for  
lists >  More info about lists


predicted locations 

get  predicted locations  for  LOC_Os04g01590.1 


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Tutorial Examples

Note: Include references to relevant data sources when citing Rice DB.