Below is a list of resources we have found useful in exploring mRNA sequences. This page is hosted by Transterm.
RNA sequence databases from Nucleic Acids Research Database issue.
fRNAdb Integrates many RNA related 'tracks' on the human genome (2008)
Sites last updated before 2005: The Ancient Conserved Untranslated Sequences database (ACUTS) (1996)
Potential functional regions may be called motifs, elements, Conserved Untranslated Sequences (CUS), Conserved non-coding sequences (CNS), Conserved non-coding regions (CNR), Conserved (or cis) Regulatory Modules (CRM).
UTRsite (last update 2010)
CisREgRNA subset of Rfam (2011)
Atlas of UTR Regulatory Activity (AURA) (2012)
RBPDB RNA-binding protein specificities (2011)
Conserved non-coding potentially RNA structured regions in vertebrate genomes from Siepel et al 2005, Pedersen et al 2006, Washietl et al 2005.
Nucleic acid structure databases from Nucleic Acids Research
3' UTR SIRF (2007)
SelenoDB SECIS elements and Selenoproteins (2008)
IRESdb (last updated 2002).
BRAliBase: Compilation and comparison of many different tools, and Bralibase 2.1 (last update 2006)
Pattern scanner of the yeast S. cerevisiae coding sequences and 5' flanking regions
MACAW, A useful program for prediction of conserved elements by Gibbs sampling.
MEME, A useful program for prediction of conserved elements by expectation maximisation.
RNAMotif, Search for motifs with a defined syntax
SECISearch, Search for SECIS elements.
RNA2Search a pipleline used to search for an RNA localisation element from Drosophila.
FIRE. A system to search for both promoter and 3'UTR regulatory elements
IRE elements prediction (SIRE)
The RNA World Website many links to RNA related sites and tools
LogoPaint (Scheriber and Brown, Bioinformatics 2002)
microRNAs: microRNA registry including targets
Non-coding RNAs: RFam, NONCODE.
RRM domain, part of the RRM clan
KH Domain, part of the KH clan
dsRNA binding domain, part of the DSRM domain part of the DSRM clan
Hamilton, R.S. and Davis, I. (2007) RNA localization signals: Deciphering the message with bioinformatics. Seminars in Cell & Developmental Biology, 18, 178-185. PubMed
Doyle, F., Zaleski, C., George, A.D., Stenson, E.K., Ricciardi, A. and Tenenbaum, S.A. (2008) Bioinformatic tools for studying post-transcriptional gene regulation : The UAlbany 3'UTR collection and other informatic resources. Methods Mol Biol, 419, 39-52. PubMed
Updated 6/5/15 by CMB