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PMID: 21036867 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

RBPDB: a database of RNA-binding specificities.

Nucleic acids research ·Vol. 39 ·No. Database issue ·2011-01-00 ·Pages D301-8

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/.

MeSH Terms
Animals Binding Sites Caenorhabditis elegans Proteins/chemistry,metabolism Databases, Protein Drosophila Proteins/chemistry,metabolism Humans Mice Protein Structure, Tertiary RNA, Messenger/chemistry,metabolism RNA-Binding Proteins/chemistry,metabolism Sequence Analysis, RNA
Chemicals
Caenorhabditis elegans Proteins Drosophila Proteins RNA, Messenger RNA-Binding Proteins
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Cook Kate B
Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
Kazan Hilal
Zuberi Khalid
Morris Quaid
Hughes Timothy R
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkq1069
Published
2011-01-00
Epub
2010-00-29
Pages
D301-8
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3013675
Subset
IM
Grants
NHGRI NIH HHS · R01 HG005700 · United States
CIHR · MOP-93671 · Canada
CIHR · MOP-49451 · Canada
NHGRI NIH HHS · 1R01HG00570 · United States
External Links
PubMed source DOI: 10.1093/nar/gkq1069 PMC Full Text View journal details
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