ArticleNucleic acids research2013
The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Genomics and transcriptomics to protect rice (Frontiers in plant science · 2022Review
- Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Current status of genomic resources on wild relatives of rice.Breeding science · 2020Article
- Article
- Rice Genomics: over the Past Two Decades and into the Future.Genomics, proteomics & bioinformatics · 2018Review
- RicyerDB: A Database For Collecting Rice Yield-related Genes with Biological Analysis.International journal of biological sciences · 2018Article
- Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Origin and Functional Prediction of Pollen Allergens in Plants.Plant physiology · 2016Article
- LCGserver: A Webserver for Exploring Evolutionary Trajectory of Gene Orders in a Large Number of Genomes.Omics : a journal of integrative biology · 2015Article
- Dwarf Tiller1, a Wuschel-related homeobox transcription factor, is required for tiller growth in rice.PLoS genetics · 2014Article
- RiceWiki: a wiki-based database for community curation of rice genes.Nucleic acids research · 2014Article
- A multistep screening method to identify genes using evolutionary transcriptome of plants.Evolutionary bioinformatics online · 2014Article
- Manually curated database of rice proteins.Nucleic acids research · 2014Article
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5 authors.
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Abstract
Over the past 10 years, genomes of cultivated rice cultivars and their wild counterparts have been sequenced although most efforts are focused on genome assembly and annotation of two major cultivated rice (Oryza sativa L.) subspecies, 93-11 (indica) and Nipponbare (japonica). To integrate information from genome assemblies and annotations for better analysis and application, we now introduce a comparative rice genome database, the Rice Genome Knowledgebase (RGKbase, http://rgkbase.big.ac.cn/RGKbase/). RGKbase is built to have three major components: (i) integrated data curation for rice genomics and molecular biology, which includes genome sequence assemblies, transcriptomic and epigenomic data, genetic variations, quantitative trait loci (QTLs) and the relevant literature; (ii) User-friendly viewers, such as Gbrowse, GeneBrowse and Circos, for genome annotations and evolutionary dynamics and (iii) Bioinformatic tools for compositional and synteny analyses, gene family classifications, gene ontology terms and pathways and gene co-expression networks. RGKbase current includes data from five rice cultivars and species: Nipponbare (japonica), 93-11 (indica), PA64s (indica), the African rice (Oryza glaberrima) and a wild rice species (Oryza brachyantha). We are also constantly introducing new datasets from variety of public efforts, such as two recent releases-sequence data from ∼1000 rice varieties, which are mapped into the reference genome, yielding ample high-quality single-nucleotide polymorphisms and insertions-deletions.
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