Dashboard - Overview of the database

Welcome to oRNAment - o RNA motifs enrichment in complete transcriptomes

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.

Content of database

Species Biotype Number of transcripts Number of species-specific motif instances Number of total motif instances
Homo sapiens Coding 185,299 124,151,929 143,894,604
Non-coding 38,068 21,062,656 24,575,566
Caenorhabditis elegans Coding 35,863 2,251,756 26,556,716
Non-coding 25,247 181,075 2,050,393
Danio rerio Coding 57,775 44,992,635 64,298,342
Non-coding 8115 2,320,758 3,340,611
Drosophila melanogaster Coding 30,827 8,285,643 37,925,214
Non-coding 3943 392,876 1,889,209
Mus musculus Coding 118,489 84,496,835 101,078,407
Non-coding 22,092 12,893,010 15,524,550
Source Number of RBP Number of motifs
RNAcompete 172 218
RBNS 78 235
Total unique in database 223 453

Distribution of motifs instances observed by biotype

Number of motifs instances observed per RBP