Dashboard - Overview of the database

Abstract

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

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 target motifs 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.

This database catalogues the motif instances of 223 RBPs in 525, 718 complete coding (UTR and CDS) and non-coding transcripts at various thresholds of motif similarity across the transcriptomes (excluding introns) of human and 4 model organisms. You can search the database for a specific species, gene or group of genes, a particular RBP, or distinct transcript attributes.

All figures 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.

As a result of server changes by the institutes, we had to temporarily disable the option for Excel output in the detailed results of motif instances search tools. We are working hard to correct the issue. In the meantime, you can access the data in CSV format through the “downloadable links”. We appologize for the inconveniance.