{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T17:14:41Z","timestamp":1779297281951,"version":"3.51.4"},"reference-count":24,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,11,14]],"date-time":"2019-11-14T00:00:00Z","timestamp":1573689600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003151","name":"Fonds de Recherche Qu\u00e9bec \u2013 Nature et Technologies","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003151","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fonds de Recherche Qu\u00e9bec \u2013 Sant\u00e9"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Protein\u2013RNA interactions are essential for controlling most aspects of RNA metabolism, including synthesis, processing, trafficking, stability and degradation. In vitro selection methods, such as RNAcompete and RNA Bind-n-Seq, have defined the consensus target motifs of hundreds of RNA-binding proteins (RBPs). However, readily available information about the distribution features of these motifs across full transcriptomes was hitherto lacking. Here, we introduce oRNAment (o RNA motifs enrichment in transcriptomes), a database that catalogues the putative motif instances of 223 RBPs, encompassing 453 motifs, in a transcriptome-wide fashion. The database covers 525 718 complete coding and non-coding RNA species across the transcriptomes of human and four prominent model organisms: Caenorhabditis elegans, Danio rerio, Drosophila melanogaster\u00a0and Mus musculus. The unique features of oRNAment include: (i) hosting of the most comprehensive mapping of RBP motif instances to date, with 421 133 612 putative binding sites described across five species; (ii) options for the user to filter the data according to a specific threshold; (iii) a user-friendly interface and efficient back-end allowing the rapid querying of the data through multiple angles (i.e. transcript, RBP, or sequence attributes)\u00a0and (iv) generation of several interactive data visualization charts describing the results of user queries. oRNAment is freely available at http:\/\/rnabiology.ircm.qc.ca\/oRNAment\/.<\/jats:p>","DOI":"10.1093\/nar\/gkz986","type":"journal-article","created":{"date-parts":[[2019,10,29]],"date-time":"2019-10-29T04:20:12Z","timestamp":1572322812000},"source":"Crossref","is-referenced-by-count":50,"title":["oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species"],"prefix":"10.1093","author":[{"given":"Louis Philip","family":"Benoit\u00a0Bouvrette","sequence":"first","affiliation":[{"name":"Institut de Recherches Cliniques de Montr\u00e9al (IRCM) Montr\u00e9al, Qu\u00e9bec, Canada"},{"name":"D\u00e9partement de Biochimie et M\u00e9decine Mol\u00e9culaire, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samantha","family":"Bovaird","sequence":"additional","affiliation":[{"name":"Institut de Recherches Cliniques de Montr\u00e9al (IRCM) Montr\u00e9al, Qu\u00e9bec, Canada"},{"name":"Division of Experimental Medicine, McGill University, Montr\u00e9al, Qu\u00e9bec, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9555-860X","authenticated-orcid":false,"given":"Mathieu","family":"Blanchette","sequence":"additional","affiliation":[{"name":"School of Computer Science, McGill University, Montr\u00e9al, Qu\u00e9bec, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"L\u00e9cuyer","sequence":"additional","affiliation":[{"name":"Institut de Recherches Cliniques de Montr\u00e9al (IRCM) Montr\u00e9al, Qu\u00e9bec, Canada"},{"name":"D\u00e9partement de Biochimie et M\u00e9decine Mol\u00e9culaire, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada"},{"name":"Division of Experimental Medicine, McGill University, Montr\u00e9al, Qu\u00e9bec, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,11,14]]},"reference":[{"key":"2019111404590676500_B1","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1038\/nrg3813","article-title":"A census of human RNA-binding proteins","volume":"15","author":"Gerstberger","year":"2014","journal-title":"Nat. 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