RBPDB

e.g., human; SARS-CoV-2; lncRNA; single cell; spatial omics; immune; Oryza sativa; European Bioinformatics Institute;China

Database Profile

General information

URL:	http://rbpdb.ccbr.utoronto.ca/
Full name:	The Database of RNA-binding Protein Specificities
Description:	RBPDB is a collection of experimental observations of RNA-binding sites
Year founded:	2011
Last update:	2012-11-21
Version:	v1.3
Accessibility:	Accessible
Country/Region:	Canada

Classification & Tag

Data type:	Protein
Data object:	Animal
Database category:	Interaction
Major species:	Caenorhabditis elegans Drosophila melanogaster Homo sapiens Mus musculus
Keywords:	RNA-binding sites

Contact information

University/Institution:	University of Toronto
Address:	Toronto,Ontario M5S 3E1,Canada
City:	Toronto
Province/State:	Ontario
Country/Region:	Canada
Contact name (PI/Team):	Timothy R. Hughes
Contact email (PI/Helpdesk):	t.hughes@utoronto.ca

Publications


21036867	RBPDB: a database of RNA-binding specificities. [PMID: 21036867] Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR. Abstract 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/. Nucleic Acids Res. 2011:39(Database issue) \| 339 Citations (from Europe PMC, 2025-03-22)

RBPDB: a database of RNA-binding specificities. [PMID: 21036867]

Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR.

Abstract

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/.

Nucleic Acids Res. 2011:39(Database issue) | 339 Citations (from Europe PMC, 2025-03-22)

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All databases:

470/6275 (92.526%)

Interaction:

80/1052 (92.49%)

470

Total Rank

313

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24.077

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Cited by


ATtRACT
AURA
CLIPdb
ENPD
EuRBPDB
Molecular Biology Database Collection
MSGP
POSTAR
RBP Image Database
RBP-Var
RBP2GO
READDB
RNAInter
SpliceAid-F
ViRBase

Record metadata

Created on: 2015-06-20

Curated by:

Lina Ma [2018-06-11]

Lin Xia [2016-04-01]

Lin Xia [2015-11-20]

Lin Xia [2015-06-26]

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Database Commons a catalog of worldwide biological databases

a catalog of worldwide biological databases

Database Profile

RBPDB

General information

Classification & Tag

Contact information

Publications

Ranking

Community reviews

Word cloud

Tags

Related Databases

Record metadata

Database Commons
a catalog of worldwide biological databases