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  1. INE (View Publication)
    Full Name of the Resource : Integrated rice genome explorer
    Resource Category : Databases -> Plant Databases -> Rice

    Brief Description : The rice genome database INE (INtegrated rice genome Explorer) is a rice integrated database with a browser for all the genomic information that have been accumulated from the large-scale rice genome analysis including cDNA analysis, genetic mapping, physical mapping and the ongoing rice genome sequencing project. A total of 481 Mbp of rice genomic sequence data (as of Sept. 2004) from 3,454 PAC/BAC and newly constructed fosmid clones has been incorporated in the database as a result of an extensive effort of the International Rice Genome Sequencing Project (IRGSP) to accelerate the completion of gettingthe genome sequence. Since the IRGSP comes very near to the goal ofcompletion, INE, which serves as the central database of IRGSP, currently contains almost 370 Mbp of non-overlapping sequence corresponding to about 95% of the entire rice genome. The sequence data areintegrated with the genetic map, a YAC (yeast artificial chromosome)-based physical map, transcript map, PAC (P1-derived artificial chromosome) / BAC (bacterial artificial chromosome) contigs for each sequenced clone. This map-based information of the sequence data would be very useful in elucidating the structure and function of specific regions of the genome particularly those containing agronomically important genes. In 2002, RGP has finished sequencing of chromosome 1, the longest chromosomein the genome (Sasaki et al. 2002), followed by the analysis of chromosome 4 by the NCGR of Chinese Academy of Sciences (Feng et al. 2002), and chromosome 10 by US rice genome sequencing consortium (2003). At present the remaining nine chromosomes are almost completedand the finished sequences from PAC/BAC/fosmid clones are incorporated in INE. INE is also linked to the sequence annotation information. RGP is assigned for sequencing and annotation of chromosomes 1,2,6,7,8, and 9. In 2003, sequences from the rice full-length cDNAs were presented (The rice full-length cDNA consortium, 2003). The mapped cDNAs are the powerful resources for model construction of the evidenced genes. RGP has revised the system of manual curation ofthe predicted genes with the emphasis on the mapped cDNAs. For almost all the PAC/BAC clones aligned in chromosomes 2, 7, 8, and most part of 9 and half of chromosome 6, results of the manual curationof the genome sequences for the precise prediction of gene domain are presented. The RGP is also proceeding the re- annotation in which the gene models are revised with the updated information. For theclones of other six chromosomes, that are chromosomes 3,4,5,10,11, and 12, results of rice automated annotation system (RiceGAAS, Sakata et al, 2002) are presented with the finished genome sequence. Thus INE will continue to provide a system for consolidating all thegenome sequence data accumulated by the IRGSP as well as all relevant information to be elucidated from analysis of the genome sequence. INE can be accessed at

    Institute/s :
    Rice Genome Research Program (RGP), National Institute of Agrobiological Sciences / Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305, Japan
    Mitsubishi Space Software Co., Ltd., 1-6-1, Takezono, Tsukuba, Ibaraki 305-0032, Japan

    Country : Japan

    Associated Institutes :

    • Rice Genome Research Program (RGP), National Institute of Agrobiological Resources, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
    • Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
    • Mitsubishi Space Software Co., Ltd, 1-17-15 Sengen, Tsukuba, Ibaraki 305-0047, Japan

    Associated Country : Japan

    Authors/Contributors : Sasaki, T.
    Contact Email :
    Year : 2000
    Language : English

    Keywords : Chromosomes, Artificial, Yeast# *Databases, Factual# *Genome, Plant# Oryza sativa / *genetics# User-Computer Interface