NBDC portal site
NBDC handles affairs in integration of life science databases, and funds programs for integration in specific research fields and for technology development. It takes over the challenges of the "MEXT Integrated Database Project", which ended in FY2010, and the "BIRD (BioInformatics R&D) Project", which ended in FY2011.
MHLW: National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) website
NIBIOHN provides eight databases, including those on research resources such as cells and genes and the toxicogenomics database. Additionally, the site provides a cross-searching service Sagace that you can search across databases about drug-discovery/disease researches, including the above eight.
MAFF: AgrID - Agrigenomics Information Database
AgrID is a portal site of genome information of crops and livestock. AgrID links to web sites of genome sequences, genome annotation, gene expression, mutant resources, etc, as products of genome projects in MAFF.
METI: MEDALS - METI Life Science Integrated Database portal site
MEDALS consolidates outcomes from life science projects conducted by METI institutes. Databases valuable for life science study are categorized into DNA, genome, protein and RNA databases, and furthermore, the site provides information on analysis tools and project reports.