RiceRBP: A database of experimentally identified RNA-binding proteins in Oryza sativa L

• Published in: Plant science (Limerick) Vol. 180; no. 2; pp. 204 - 211
• Main Authors: Morris, Robert T., Doroshenk, Kelly A., Crofts, Andrew J., Lewis, Nicholas, Okita, Thomas W., Wyrick, John J.
• Format: Journal Article
• Language: English
• Published: Shannon Elsevier Ireland Ltd 01.02.2011; [Ireland]: Elsevier Science Ireland Ltd; Elsevier
• Subjects: bioinformatics; Biological and medical sciences; Computational Biology; data analysis; Databases, Genetic; Databases, Protein; Fundamental and applied biological sciences. Psychology; gene banks; gene expression; Gene Expression Profiling; gene expression regulation; Gene Expression Regulation, Plant; Genome, Plant; glutelins; Hordeum - genetics; Hordeum - metabolism; http://www.bioinformatics2.wsu.edu/RiceRBP; Information Storage and Retrieval - methods; Internet; Mass Spectrometry; messenger RNA; Oligonucleotide Array Sequence Analysis; Oryza - genetics; Oryza - metabolism; Oryza sativa; Phylogeny; Plant Proteins - analysis; Plant Proteins - genetics; Plant Proteins - metabolism; Prolamine; prolamins; Protein Structure, Tertiary; rice; Rice seed; RNA, Plant - metabolism; RNA-binding protein; RNA-binding proteins; RNA-Binding Proteins - analysis; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Seeds - genetics; Seeds - metabolism; Software; Sorghum - genetics; Sorghum - metabolism; storage proteins; translation (genetics); transport proteins; Triticum - genetics; Triticum - metabolism; User-Computer Interface; Zea mays - genetics; Zea mays - metabolism; Database; RBP; Oryza sativa; RNA-binding protein; Rice seed; Prolamine; Monocotyledones; RNA binding protein; Plant biology; Cereal crop; Gramineae; Seed; Angiospermae; Spermatophyta; Prolamin
• ISSN: 0168-9452; 1873-2259
• DOI: 10.1016/j.plantsci.2010.08.004

▶ A novel database of experimentally identified RNA-binding proteins in rice. ▶ Novel tools to analyze the sequence, function, and expression of RNA-binding proteins. ▶ Predicted RNA-binding protein orthologs in other plant species, as well as novel ortholog search and mining tools. RNA-binding proteins play critical roles at multiple steps during gene expression, including mRNA transport and translation. mRNA transport is particularly important in rice ( Oryza sativa L.) in order to ensure the proper localization of the prolamine and glutelin seed storage proteins. However, relatively little information is available about RNA-binding proteins that have been isolated or characterized in plants. The RiceRBP database is a novel resource for the analysis of RNA-binding proteins in rice. RiceRBP contains 257 experimentally identified RNA-binding proteins, which are derived from at least 221 distinct rice genes. Many of the identified proteins catalogued in RiceRBP had not previously been annotated or predicted to bind RNA. RiceRBP provides tools to facilitate the analysis of the identified RNA-binding proteins, including information about predicted protein domains, phylogenetic relationships, and expression patterns of the identified genes. Importantly, RiceRBP also contains tools to search and analyze predicted RNA-binding protein orthologs in other plant species. We anticipate that the data and analysis tools provided by RiceRBP should facilitate the study of plant RNA-binding proteins. RiceRBP is available at http://www.bioinformatics2.wsu.edu/RiceRBP.