Note : this part is under construction.


The rice genome allow to access tools developed around rice genomes and omics data generated from them.

Main menu


Here you can find a general description for each and every genome integrated into the hub, along with related information, such as publication or description.


The dataset part contains the list of all the datasets that have been integrated into the hub. From there You can access datasets description pages, which contain a bunch of information about the dataset, and allow you to download related data, when relevant. These data can be, for example, gene count and differentially expressed genes list for RNA-seq data, or variant lists for Whole genome sequencing analysis.

Genome browser

Each genome has its own genome browser, based on jbrowse. You can use them to look at genomic regions and display data from different datasets that may have been integrated, like SNP data, RNA-seq expression density, gwas information, annotation…


the tool part contains a lot of tools that allow to perform various operations on the data that have been integrated into the hub. They have been sorted by different categories.


Gene search : advanced search for genes. You can search for genes using different filtering criteria, like his name, location, annotation… Genes are associated to complete description pages.

ID converter : Allow you to convert MSU/Rapdb annotations to each others. This app also include many informations about the different genes, along with informations taken from the best hit from Arabidopsis, like the pmid, detailed description…

Sequences download : download gene sequences (Gene, mRNA, CDS, protein) from a list of genes, in various formats (Fasta, GenBank, EMBL), with the possibility to download flanquing sequences up to 10Kb.

Go Enrichment : perform GO enrichment from a list of genes.


RNA-seq count display : display RNA-seq normalized gene count from a list of genes. Can display an heatmap of a gene list for a specific dataset, as well as show count data from many datasets for specific genes.

DIANE : RNA-seq data analysis tool, from raw count data to gene regulatory network. Can perform normalization, count visualization, differential expression analyses, clustering, GO enrichment… 

Research comparison

Blast : allow to perform blast search on all the included genomes and their respective transcriptomes, CDS and transcriptome.

Primer designer : Allow to design PCR primers

Primer blaster : Allow to blast previously designed primers on the different integrated genomes to check for their specificity

Synteny viewer : Allow to visualize Synteny blocs on the different integrated genomes using Synvisio


Gigwa : Explore genotyping data, by performing a large panel of actions. 


All the data that are displayed on the hub, like Fasta genomes, annotation in GFF format, and RNA-seq count matrix, are available to download in this section. Each genome have a specific directory containing all the related data.


Information about the development team and the term of service.