Welcome to RBP2GO (version 2.0)
RBP2GO is a comprehensive database dedicated to the analysis of RNA-binding proteins, their interactions and functions. RBP2GO offers three search options for each species, which can be accessed via the sidebar under SEARCH SPECIES. Information on RNA-binding domains (RBDs) and RNA-related family IDs (Rfam IDs) is also available under SEARCH DOMAINS. More details can be found in the HELP menu.
RBP candidates
22526
RBP aspirants
7738
RNA-binding domains
977
RNA-related family IDs (Rfam IDs)
672
Species
13
References
RBP2GO: A comprehensive, pan-species database on RNA-binding proteins, their interactions and functions. Caudron-Herger et al. Nucleic Acids Research 2021.
R-DeeP: Proteome-wide and Quantitative Identification of RNA-Dependent Proteins by Density Gradient Ultracentrifugation. Caudron-Herger et al. Molecular Cell 2019.
Identification, quantification and bioinformatic analysis of RNA-dependent proteins by RNase treatment and density gradient ultracentrifugation using R-DeeP. Caudron-Herger et al. Nature Protocols 2020.
A database on RNA-dependent proteins (R-DeeP) is also available here.
RBP candidates
6099
Homo sapiens
Human Protein of Interest
Enter a protein ID, gene name or protein name into the search field:
Gene Ontology
Enter a Gene Ontology (GO) term or a keyword into the search field:
Advanced search option including search for list of proteins or GO terms.
Protein List
GO List
InterPro ID List
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RBP candidates
2897
Mus musculus
Mouse Protein of Interest
Enter a protein ID, gene name or protein name into the search field:
Gene Ontology
Enter a Gene Ontology (GO) term or a keyword into the search field:
Advanced search option including search for list of proteins or GO terms.
Protein List
GO List
InterPro ID List
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RBP candidates
311
Danio rerio
Zebrafish Protein of Interest
Enter a protein ID, gene name or protein name into the search field:
Gene Ontology
Enter a Gene Ontology (GO) term or a keyword into the search field:
Advanced search option including search for list of proteins or GO terms.
Protein List
GO List
InterPro ID List
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RBP candidates
2979
Drosophila melanogaster
Fly Protein of Interest
Enter a protein ID, gene name or protein name into the search field:
Gene Ontology
Enter a Gene Ontology (GO) term or a keyword into the search field:
Advanced search option including search for list of proteins or GO terms.
Protein List
GO List
InterPro ID List
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RBP candidates
1861
Caenorhabditis elegans
C. elegans Protein of Interest
Enter a protein ID, gene name or protein name into the search field:
Gene Ontology
Enter a Gene Ontology (GO) term or a keyword into the search field:
Advanced search option including search for list of proteins or GO terms.
Protein List
GO List
InterPro ID List
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RBP candidates
2155
Saccharomyces cerevisiae
S. cerevisiae Protein of Interest
Enter a protein ID, gene name or protein name into the search field:
Gene Ontology
Enter a Gene Ontology (GO) term or a keyword into the search field:
Advanced search option including search for list of proteins or GO terms.
Protein List
GO List
InterPro ID List
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RBP candidates
2352
Arabidopsis thaliana
A. thaliana Protein of Interest
Enter a protein ID, gene name or protein name into the search field:
Gene Ontology
Enter a Gene Ontology (GO) term or a keyword into the search field:
Advanced search option including search for list of proteins or GO terms.
Protein List
GO List
InterPro ID List
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RBP candidates
169
Trypanosoma brucei
T. brucei Protein of Interest
Enter a protein ID, gene name or protein name into the search field:
Gene Ontology
Enter a Gene Ontology (GO) term or a keyword into the search field:
Advanced search option including search for list of proteins or GO terms.
Protein List
GO List
InterPro ID List
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RBP candidates
79
Leishmania donovani
L. donovani Protein of Interest
Enter a protein ID, gene name or protein name into the search field:
Gene Ontology
Enter a Gene Ontology (GO) term or a keyword into the search field:
Advanced search option including search for list of proteins or GO terms.
Protein List
GO List
InterPro ID List
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RBP candidates
1162
Leishmania mexicana
L. mexicana Protein of Interest
Enter a protein ID, gene name or protein name into the search field:
Gene Ontology
Enter a Gene Ontology (GO) term or a keyword into the search field:
Advanced search option including search for list of proteins or GO terms.
Protein List
GO List
InterPro ID List
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RBP candidates
1020
Plasmodium falciparum
P. falciparum Protein of Interest
Enter a protein ID, gene name or protein name into the search field:
Gene Ontology
Enter a Gene Ontology (GO) term or a keyword into the search field:
Advanced search option including search for list of proteins or GO terms.
Protein List
GO List
InterPro ID List
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RBP candidates
226
Salmonella enterica subsp. enterica ser. Typhimurium
S. enterica Protein of Interest
Enter a protein ID, gene name or protein name into the search field:
Gene Ontology
Enter a Gene Ontology (GO) term or a keyword into the search field:
Advanced search option including search for list of proteins or GO terms.
Protein List
GO List
InterPro ID List
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RBP candidates
1216
Escherichia coli
E. coli Protein of Interest
Enter a protein ID, gene name or protein name into the search field:
Gene Ontology
Enter a Gene Ontology (GO) term or a keyword into the search field:
Advanced search option including search for list of proteins or GO terms.
Protein List
GO List
InterPro ID List
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- RNA-binding domains (RBDs) have been known for 20 years as consensus sequences allowing RBPs to bind to RNA, constituting canonical domains such as the RNA recognition motif (RRM) or the K-homology (KH) domain. In the last decade, this idea has been challenged by the discovery of non-canonical RBDs, harboring other functions than RNA binding. Here, we provide an updated list of RBDs, including the more recently discovered ones.
- The list of RBDs used in this study was compiled using published lists of domains as well as domains related to RNA binding from the InterPro database. The domains enriched in RNA-binding proteins were selected using the procedure as illustrated below. New RBDs discovered through an enrichment analysis were also appended to this list.
- The full list of RBDs can be downloaded from the Download section.
- The domain information used in RBP2GO was downloaded from the InterPro database (May 2022).
- To select a list of RNA-related InterPro family IDs or Rfam IDs, we applied the same procedure as for the RBDs.
- The full list of Rfam IDs can be downloaded from the Download section.
- The family ID information used in this database was downloaded from the InterPro database (May 2022).
In this panel, it is possible to search for protein domains in order to determine whether or not they are RBDs.
InterPro ID List
The RNA-binding status is only available for the Domain, Repeat and Family types of InterPro IDs.
If it is intended to search for proteins with specific domains, please use the Advanced Search in the respective species and use the InterPro ID List field.
Data Download
- In this section, all datasets used in the RBP2GO database are available for download.
- IMPORTANTLY, the datasets contain a large amount of information, in particular, the complete GO trees are included, so that the datasets are not displayed properly e.g. in Excel. Therefore, we recommend to work with these datasets using for example RStudio or other suitable programs of your choice.
- The dataset sizes range from about 100 KB to 100 MB (species specific files) up to 500 MB (scripts).
Homo sapiens
Mus musculus
Danio rerio
Drosophila melanogaster
Caenorhabditis elegans
Saccharomyces cerevisiae
Arabidopsis thaliana
Trypanosoma brucei
Leishmania donovani
Leishmania mexicana
Plasmodium falciparum
Salmonella Typhimurium
Escherichia coli
All species
Domains
R scripts
References and Links
Reference Table
R-DeeP and RBP Studies
Species Specific Databases
Proteins and Protein-Protein Interactions Databases
Intrinsically Disordered Proteins and Low Complexity Domains
Coiled-coil Prediction
Gene Ontology
Diseases
Isoelectric point
Databases Collections
Literature Search
Icons and Webpage
Help and Documentation
- RBP2GO is a comprehensive database dedicated to the analysis of RNA-binding proteins, their interactions and functions. RBP2GO offers three search options for each species, which can be accessed via the sidebar under SEARCH SPECIES.
- The Protein Search and the GO Search options can be used to search the database for single proteins and GO terms respectively. The button About the Format gives more details about the possible input formats.
- The Advanced Search offers the possibility to search simultaneously for a list of proteins and/or a list of GO terms. In addition, a range of isoelectric points (pI) can be selected when available. For Homo sapiens the search can even be limited to the CGC genes.
- The RBP2GO score reflects the likelihood of a protein binding to RNA on a scale from 0 to 100 and is derived from the total number of listings of this protein in proteome-wide RBP/R-DeeP studies of the respective species as well as the average number of listings of its top ten interaction partners according to the String interaction score. Next to the RBP2GO score, the listing score of the proteins (number of times the each protein is listed as RBP) is indicated as well as the average listing score of the top ten interactors according to the STRING database.
- In Version 2.0, the SEARCH DOMAINS menu is dedicated to the protein domains and families. Users can determine whether an InterPro ID is linked to RNA or not and accordingly sort the InterPro IDs of interest.
- In Version 2.0, the RBP2GO composite score is calculated with the frequency of detection of the respective protein (component 1) and of its top 10 protein interactors in the reference studies (component 2), as well as the presence of RBDs or RNA-related family IDs (Rfam IDs) in the protein (domain score or component 3). Hence, this score indicates the likelihood of both RBP candidates and non-listed proteins to be an RBP.
- The search results can be downloaded depending on the content as CSV or TXT files for further processing.
- the DOWNLOAD menu contains all the species-specific datasets included in the database, which can be downloaded by clicking on the corresponding button. In addition, the DOWNLOAD menu offers the possibility to access the RBD list, the Rfam ID list and a high-confidence list of human RBP candidates. Finally, the script of the current database (in RShiny App format) and the whole analysis script (Version 2.0) are available in this section for download.
- The full reference table is available for download under the menu REFERENCES.
- The sidebar is dynamic and can be removed by clicking on the list icon next to the RBP2GO logo at the top left corner of the screen.
A detailed and user-friendly documentation can be downloaded here (Version 2.0, 2023):
A short tutorial video is also available (Version 1.0, 2021):
About RBP2GO
RBP2GO versions
- RBP2GO Version 2.0, release date August 2023 (current version), manuscript submitted
Main change: addition of the RNA-binding domain information and domain search. Creation of the RBP2GO composite score, based on the RBP2GO score with the inclusion of the RNA-binding domain and RNA-related InterPro family knowledge.
- RBP2GO Version 1.0, release date July 2020
How to cite
Manuscript published: January 2021
RBP2GO: A comprehensive, pan-species database on RNA-binding proteins, their interactions and functions. Caudron-Herger et al. Nucleic Acids Research 2021.
Related publications
R-DeeP: Proteome-wide and Quantitative Identification of RNA-Dependent Proteins by Density Gradient Ultracentrifugation. Caudron-Herger et al. Molecular Cell 2019.
Identification, quantification and bioinformatic analysis of RNA-dependent proteins by RNase treatment and density gradient ultracentrifugation using R-DeeP. Caudron-Herger et al. Nature Protocols 2020.
Related database
Contact
The authors of the RBP2GO database can be contacted at the following email address
© 2023 - RBP2GO Version 2.0 - Released August 2023
