Dashboard - Overview of the database

Abstract

oRNAment is a database of putative RBP binding sites in both coding and non-coding RNA in various species.

In oRNAment V2 we improved our database in the following aspects:

• Motif instances are now predicted using the recent Ensembl release 115 (September 2025).
• Ten new species have been added, including non-human primates, rat, and other key model organisms, bringing the total to 15 species covered in the database.
• Expanded RBP and motif coverage: the database now includes 2,089 RBPs across 15 species and 492 motifs. Homologous RBPs from different species are counted separately, though they typically share the same motif.
• Extended scan regions to include up to 150 nt of intronic sequence flanking exons, enabling coverage of splicing regulatory signals and other functions dependent on exon–intron boundaries.
• Added search function to table views of motif instances.

Protein-RNA interactions play important roles in most aspects of RNA metabolism. Several in vitro selection methods, in particular RNAcompete and RNA Bind-n-Seq (RBNS), have defined the consensus target motifs of hundreds of RBPs. However, information about the distribution features of these motifs across the transcriptome is lacking.

Here, we developed a computational tool to enable the global mapping of putative RBP binding sites across full transcriptomes, including messenger RNAs (mRNAs) and non-coding RNAs, in multiple species. The oRNAment database provides a user-friendly interface to parse the motif scan data. See tutorial for further detail.

You can search the database for a specific species, gene or group of genes, a particular RBP, or distinct transcript attributes.

All figures in the result pages are interactive. Click on any figure legend to include/exclude specific items them from the graph, scroll to zoom in/out or hover for more detail.

This database was developed and is maintained by the Lecuyer Lab. Please email us for any comments, suggestions or bug reports. Please include all information you deem relevent in the message including the type and parameters of query, and proximate time of submission.