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Putative Orthologous Groups |
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Putative Orthologous Groups |
PlantRBP/POGS is a relational database that integrates data from rice, maize, and Arabidopsis by placing the complete Arabidopsis and rice proteomes, and the available maize sequences into "putative orthologous groups" (POGS). Annotation efforts are now beginning and will focus on predicted RNA binding proteins (e.g. those with known RNA binding domains or known to influence RNA function).
Putative Orthologous Groups (POGs) form the heart of the database, and were assigned using a mutual best hit strategy after performing BLAST comparisons of the predicted Arabidopsis and rice proteomes. Each POG entry includes cross-referenced orthologs and paralogs in Arabidopsis and rice, annotated with domain organization, gene models, phylogenetic trees showing closely-related proteins, and intracellular targeting predictions. The database can be queried to identify POGs with specific domain combinations and predicted intracellular locations.
The method used for POG assignments and other features of the database are described in:
Walker, N., Stiffler, N. and Barkan, A. (2007) POGs/PlantRBP: a resource for comparative genomics in plants Nucleic Acids Res, 35, D852-D856.
Please cite this paper if you use this database in published work.
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Search(multiple terms in the same or different field will be linked with "AND".) |
UpdatesAnnotation Tool Now Available
A tool for community annotation is now available. We welcome your input about POG assignments, literature
citations, experimentally-verified protein function and localization, etc. To suggest annotations, click on
"Annotate" on the relevant POG page.
Most Recent Sequence Updates
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Disclaimer: The current version of PlantRBP is a working draft. Work in progress includes the refinement of methods for POG assignments and phylogenetic analysis to improve the number of "well-supported" POGs, addition of gene models, and annotation of POGs for RBPs with experimental data and literature citations.
We encourage user feedback regarding the functionality of the database, suggestions for additional proteins that should be included, gene model corrections, experimental data, references, etc.
Contact:
Nicholas Stiffler stiffler@molbio.uoregon.edu
Alice Barkan abarkan@molbio.uoregon.edu
Links:
PlantRBP Project
Photosynthetic Mutant Library (PML)
Plastid Proteome Database
Development and maintenance of this database is funded by grant DBI-0421799 from the National Science Foundation Plant Genome Research Program.