RBPDB: a database of RNA-binding specificities
Open accessAbstract
The RNA-Binding Protein DataBase (RBPDB) is a collection of experimental observations of RNA-binding sites, both in vitro and in vivo, manually curated from primary literature. To build RBPDB, we performed a literature search for experimental binding data for all RNA-binding proteins (RBPs) with known RNA-binding domains in four metazoan species (human, mouse, fly and worm). In total, RPBDB contains binding data on 272 RBPs, including 71 that have motifs in position weight matrix format, and 36 sets of sequences of in vivo-bound transcripts from immunoprecipitation experiments. The database is accessible by a web interface which allows browsing by domain or by organism, searching and export of records, and bulk data downloads. Users can also use RBPDB to scan sequences for RBP-binding sites. RBPDB is freely available, without registration at http://rbpdb.ccbr.utoronto.ca/.
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Known RNA-binding motifs exist for 15% of human, 8% of Drosophila, and 3% of Caenorhabditis elegans RBD-containing proteins.
“For example, 15% of human, 8% of Drosophila and 3% of Caenorhabditis elegans RBD-containing proteins have known RNA-binding motifs3”
From A compendium of RNA-binding motifs for decoding gene regulation (2013) · cites this paper as [3]
Sequence-specific binding between RBPs and their RNA targets is usually mediated by one or more RNA-binding domains, including RRM and KH domains.
“Sequence-specific associations between RBPs and their RNA targets are typically mediated by one or more RNA-binding domains (RBDs), such as the RNA recognition motif (RRM) and hnRNPK-homology (KH)domains.”
From A compendium of RNA-binding motifs for decoding gene regulation (2013) · cites this paper as [3]
The human genome encodes 239 RRM-domain proteins and 38 KH-domain proteins among 424 known and predicted RBPs.
“The human genome, for example, encodes 239 proteins with RRM domains and 38 with KH domains, among a total of 424 known and predicted RBPs3.”
From A compendium of RNA-binding motifs for decoding gene regulation (2013) · cites this paper as [3]
Canonical RBDs typically bind short single-stranded RNA sequences, but some also recognize structured RNAs.
“Canonical RBDs typically bind short, single-stranded (ss)RNA sequences3,4, but some also recognize structured RNAs5.”
From A compendium of RNA-binding motifs for decoding gene regulation (2013) · cites this paper as [3]
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- Authors
- Cook, K. B., Kazan, H., Zuberi, K., Morris, Q., & Hughes, T. R.
- Affiliations
- University of Toronto (CA)
- Corresponding author
- Hughes, T. R.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-10-29
- Volume
- 39
- Issue
- Database
- Pages
- D301-D308
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3013675
- OpenAlex
- W1995224771
- Cited by
- 638
- References
- 45
- Citations by year
- 2026: 37 · 2025: 63 · 2024: 63 · 2023: 37 · 2022: 44 · 2021: 49 · 2020: 77 · 2019: 39 · 2018: 37 · 2017: 33 · 2016: 36 · 2015: 42 · 2014: 33 · 2013: 25 · 2012: 17
- FWCI
- 6.26
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- Canadian Institutes of Health Research (93671_1, MOP-49451)
- National Human Genome Research Institute (1R01HG00570, R01HG005700)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- RNA-binding proteins, RNA binding sites, RNA-binding domain, position weight matrices, RNA-binding motif, immunoprecipitation, database curation, binding site prediction
- MeSH terms
- Animals, Binding Sites, Humans, RNA, Messenger, RNA-Binding Proteins, Sequence Analysis, RNA, Protein Structure, Tertiary, Drosophila Proteins, Caenorhabditis elegans Proteins, Databases, Protein, Mice
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