What is the worm 3'UTRome?

3'UTRs are important portions of mRNAs required for post-transcriptional regulation by interacting with proteins or non-coding RNAs (e.g. microRNAs). To study the role of 3'UTRs we are building a 3'UTR database for C. elegans.

The UTRome.org database is intended as a comprehensive resource for 3'UTR biology in C. elegans. The database provides detailed information on 3'UTR structures and alternative polyadenylation for all protein-coding mRNAs, and includes annotations extracted from other databases (such as WormBase and PicTar) as well as new annotations generated by others.

Examples of functional elements within 3'UTRs include predicted and validated microRNA (miRNA) binding sites (responsible for post-transcriptional gene regulation), putative consensus signals for polyA addition, and predicted secondary structures (which may influence the biological activity of 3'UTRs).

For questions, please contact Marco Mangone at mangone@asu.edu
Please cite Blazie et al., 2017 Genetics

The New 3'UTRome V3 is now live in GBrowse!

Past publications: The UTRome website has been described in:

Alternative polyadenylation directs tissue specific miRNA targeting in Caenorhabditis elegans somatic tissues
Blazie S, Geissel H, Wilky H, Joshi R, Newbern J and Mangone M
Genetics (2017) https://doi.org/10.1534/genetics.116.196774 - RAW DATA

Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles
Blazie S, Babb C, Wilky H, Rawls A, Park J and Mangone M
BMC Biology (2015) 13:4 doi:10.1186/s12915-015-0116-6 - RAW DATA

The Landscape of C. elegans 3'UTRs.
Mangone M, Manoharan AP, Thierry-Mieg D, Thierry-Mieg J, Han T, Mackowiak S, Mis E, Zegar C, Gutwein MR, Khivansara V, Attie O, Chen K, Salehi-Ashtiani K, Vidal M, Harkins TT, Bouffard P, Suzuki Y, Sugano S, Kohara Y, Rajewsky N, Piano F, Gunsalus KC, Kim JK.
Science (2010) DOI: 10.1126/science.1191244

UTRome.org: a platform for 3'UTR biology in C. elegans.
Mangone M, Macmenamin P, Zegar C, Piano F, Gunsalus KC.
Nucleic Acids Res. (2008) 36, D57

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