RBPDB: a database of RNA-binding specificities

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/.

Figure 1.

Example of searching RBPDB by gene name. Shown are results generated by using the advanced search form to search experiments. The query ‘HNRNPA1’ was entered in the gene name field and ‘human’ selected for species. Navigation links and links to view detailed information are indicated, as are the icons to export data in text, CSV, Excel, HTML and Word formats.

Figure 2.

Download page of RBPDB. This screenshot shows the bulk data set downloads available.

Figure 3.

Example of scanning input sequence for potential RBP-binding sites. The 3′-UTR of human c-fos was downloaded from GENBANK (Accession no. NM_005252, nucleotides 1349–2158) and submitted to the sequence scan form on the RBPDB home page.