The RIKEN Arabidopsis Genome Encyclopedia (RARGE) database houses information on biological resources ranging from transcriptome to phenome, including RIKEN Arabidopsis full-length (RAFL) complementary DNAs (cDNAs), their promoter regions, Dissociation (Ds) transposon-tagged lines and expression data from microarray experiments.

The RARGE II database integrated information for a total of 66,209 Arabidopsis mutant lines, including loss-of-function (RIKEN Arabidopsis Ds mutant and CSHL TARAPPER) and gain-of-function (AtFOX and OsFOX) lines, and organized the phenotype data by mapping the descriptions onto Plant Ontology (PO) and Phenotypic Quality Ontology (PATO) terms.

RAPID is a searchable site of phenotypic data in the selected 4,000 Ds transposon-insertional mutant lines which have the Ds transposon in gene coding region, and observed visible phenotypes systematically depend on growth stage.

Chloroplast Function Database provides easy access to all-inclusive knowledge data, including the information of Arabidopsis knockout mutant resources and their phenotypes for nuclear-encoded chloroplast proteins.

PRIMe is a tool assembly for metabolomics and transcriptomics in plants. To facilitate the identification of phytochemicals, standard metabolites measured by multi-dimensional NMR spectroscopy, GC/MS, LC/MS, and CE/MS, the MS/MS spectral tag (MS2T) library, AtMetExpress LC-MS, ReSpect (RIKEN tandem mass spectral database), PRIMeLink and etc. were implemented on PRIMe.

o achieve functional genomics and annotation of unknown metabolites, we established the following PRIMe contents:MS2T, a library comprising over 1 million entries of un-targeted MS/MS data of plant metabolites; AtMetExpress, a database of transcriptomics and metabolomics approaches in Arabidopsis developmental stages; and ReSpect, hybrid reference MS/MS data resources (acquisitions and literature). PRIMeLink integrates the 3 above databases and provides a bi-directional searchable function from the gene or metabolite perspective.

The ReSpect database is a collection of literature and in-house MSn spectra data for research on plant metabolomics.Now, a total of 9017 spectra records are available.

UniVIO provides hormone-metabolome (hormonome) and transcriptome data in a single formatted (uniformed) heat map from 14 organ parts of rice plants at the reproductive stage and seedling shoots of three gibberellin signaling mutants.

In this study we estimated multiple physicochemical and secondary structural properties of protein sequences, the predicted presence of post-translational modification (PTM) sites, and subcellular localization using a total of 510,123 protein sequences from the proteomes of 31 algal and three plant species. Algal species were broadly selected from green and red algae, glaucophytes, oomycetes, diatoms and other microalgal groups. The results were organizeed in the Algal Protein Annotation Suite database (Alga-PrAS; http://alga-pras.riken.jp/)

The amount of annotation information such as gene-coding regions and structures is steadily growing in the field of plant research. In contrast to the genomics resource of animals and microorganisms, there are still some difficulties with characterization of some gene functions in the plant genomics studies. Acquisition of information on protein structure can help to elucidate the corresponding gene function because proteins encoded in the genome possess highly specific structures and functions. Thus, we calculated multiple physicochemical and secondary structural parameters of protein sequences, using protein sequences from the genomes of six representative plant species.

The Cassava Online Archive provides the information of cassava mRNA sequences and ESTs currently available from NCBI (Genbank/EMBL/DDBJ), their annotations, custom oligo-microarray probes and DNA polymorphisms.

The RARTF provides classified transcription factor encoding genes in the Arabidopsis genome sequence via PSI-BLAST.

The RSOY database provides the information of RIKEN soybean full-length cDNAs.