ArticlePlant & cell physiology2013
Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.
Article in Plant & cell physiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 462 papers, 3 of them syntheses that pooled it.
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Who cites it
462 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Transcriptomic Landscape and Regulatory Pathways of Drought Response in Rice (International journal of molecular sciences · 2026Pooled it
- Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.Journal of proteome research · 2024Pooled it
- Meta-QTL s and haplotypes for efficient zinc biofortification of rice.The plant genome · 2023Pooled it
- An IRAT109 NAM population: Genetic characterization and mapping utility for trait dissection in japonica rice (Oryza sativa L.).The plant genome · 2026Article
- Drought and salinity stress remodel Asian rice (Oryza sativa) leaf development through cell-type-specific regulatory programs.The New phytologist · 2026Article
- De novo genome assembly of Texas wintergrass [Nassella leucotricha {Trin. & Rupr.} Pohl] supports diagnostic marker development and phylogenetic analysis of species within the family Poaceae.G3 (Bethesda, Md.) · 2026Article
- A grass-specific structural myosin VIII regulates protoxylem development and hydraulic conductance in sorghum.Plant physiology · 2026Article
- Integrative genomics resolves rice loci associated with acidic soil-related aluminum, cadmium, and manganese stress responses.Plant cell reports · 2026Article
- Identification and characterization of low-sulfur-inducible genes and pathways in roots of upland and lowland rice grown under hydroponic and soil conditions.Journal of experimental botany · 2026Article
- Genomic Footprints of Historical Introgression Between Ancient Lineages of Wild Oryza AA-Genome Species With Widely Separated Contemporary Distributions.Genome biology and evolution · 2026Article
- Genome-wide association mapping of distinctness, uniformity and stability traits and varietal identification in rice (Oryza sativa L.).Journal of the science of food and agriculture · 2026Article
- Fine-tuning quantitative agronomic traits by manipulating gene copy number in rice.The New phytologist · 2026Article
- A portable recalibration workflow for reference-based variant calling in non-human genomes.PLoS computational biology · 2026Article
- Rice EMF3 Alleles Adjust Flower Opening Time to Enhance the Seed Setting Rate Under High Temperature Stress.Plant biotechnology journal · 2026Article
- Article
- Class I TCP transcription factor OsTCP4 suppresses plant height via negatively regulating the green revolution genePlant diversity · 2026Article
- Subfamily-level comparative transcriptomics of key immune regulators in plants and suspension cells reveals novel rice blast resistance genes.Plant & cell physiology · 2026Article
- Annotating genomes at increased scale and resolution.Nature reviews. Genetics · 2026Review
- High-Contiguity Haplotype-Resolved Genome Assembly of the Hexaploid Actinidia valvata Rootstock Sheds Light on Waterlogging Resistance Gene.Plant biotechnology journal · 2026Article
- Rice Annotation Project Database (RAP-DB): Literature-Curated Gene Annotation and Integrated Omics Resources for Rice Functional Genomics and Molecular Breeding.Rice (New York, N.Y.) · 2026Article
402 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.