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   About RISe

Rice is a major food staple for the world's population and serves as a model species in cereal genome research. The Beijing Genomics Institute (BGI) has long been devoting itself to sequencing, information analysis, and biological research of the rice genome. Our Rice Information System (BGI-RIS) is targeted to be the most up-to-date integrated information resource for rice genomes as well as a workbench for comparative genomic analysis among cereal crops.

In addition to the comprehensive data of Oryza sativa L. ssp. indica sequenced by BGI, BGI-RIS will host carefully curated genome information of Oryza sativa L. ssp. japonica (Syngenta) since we have obtained permission from Syngenta to release their data as soon as related paper is published.

In BGI-RIS, sequence contigs of Beijing indica and Syngenta japonica have been further assembled and anchored onto the rice chromosomes. We have annotated the rice genomes for gene content, repetitive elements, and SNPs. Sequence polymorphisms between different rice subspecies have also been identified. Designed as a basic platform for rice study, BGI-RIS presents the sequenced genomes and related information in systematic and graphical ways for the convenience of in-depth comparative studies.

   Tools&Services
   

RePS The first bioinformaitcs software developed by BGI, which masks exact repeats identified from the shotgun data and plays an essential role in rice genome assembling.

   
BGF (Beijing Gene Finding), developed by the Gene Finding Team at BGI, is a program for gene identification in eukaryotic genomic DNA sequences. It is based on Dynamic Programming and HSMM (Hidden Semi-Markov Model) algorithm with a special emphasis on rice genomes.(Mirror in Fudan University)
   
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Assembled genome sequences of indica (93-11) and japonica (Syngenta)
   
Genomic information of Markers, BAC ends, cDNAs, genes and repeats
   
Serial analysis of gene expression study of an elite hybrid rice
   
All these data will be timely updated and new types of biological data, such as tRNA, mRNA and microarray data will be added soon.

   MapView
chromosome 1 chromosome 2 chromosome 3 chromosome 4 chromosome 5 chromosome 6 chromosome 7 chromosome 8 chromosome 9 chromosome 10 chromosome 11 chromosome 12
Beijing indica Syngenta japonica

   What's New
   
The quality genome sequences for both parental lines (93-11 and PA64s) were presented and updated, and a high resolution map of genome-wide graphic genotypes was constructed by deep resequencing a core population of 132Liang-You-Pei-Jiu recombinant inbred lines. The study provided an ideal platform for molecular breeding by quantitative trait loci cloning in rice.pdf
 
Latest gene annotation updated (2008-10-28) on the ftp site, according to pre-published paper "Improved annotation of the rice (Oryza sativa) genomes"
 
Latest genes updated(2006-12-28), both the graphical view and the ftp site, according to pre-published paper "Re-annotation of the rice genome(s) by selective pre-masking of intergenic transposable elements"
 
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics
Latest version of Sequence Assembly of Rice Genome(Beijing indica) (149 SuperScaffolds, 39,922 Scaffolds, 50,231 Contigs )
13,613 full length cDNA mapped to Beijing indica.
38,861 BGF and 39,578 FgeneSH predicted genes of Beijing Indica .
 
Latest version of Sequence Assembly of Rice Genome( Syngenta japonica) (119 SuperScaffolds, 26,160 Scaffolds, 35,047 Contigs )
14,827 full length cDNA mapped to Syngenta japonica.
36,038 BGF and 36,757 FgeneSH predicted genes of Syngenta japonica.
 
Up to 4,723,468 SNPs identified between Beijing Indica and Syngenta Japonica.
A draft sequence of the rice (Oryza sativa ssp. indica) genome 2002.1

   Document & Help
   
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Citing the BGI-RISe Database

   CompView

CompView is an interactive visualization tool that is being developed for identifying and visualizing conserved syntenic blocks (homoeologous chromosome segments and homologs) across multiple related genomes simultaneously.

Users can switch between CompView and MapView and start with a gene or region of interest in searching for related information. Once fully implemented, CompView will provide users with timely genomic information across species beyond genera and families.
    BGI Last Modified 28 Oct, 2008     Feedback_
    Supported by China National Grid Project 2002AA104250