Databases and tools related to finding cis regulatory RNA elements in mRNA sequences
Below is a list of resources we have found useful in exploring mRNA sequences. This page is hosted by Transterm.
1. mRNA sequence databases, with or without conserved regulatory elements.
fRNAdb Integrates many RNA related 'tracks' on the human genome and rtools which integrates tools
The UTR database (UTRdb) (last update 2010)
Selected species specific databases: human (UCSC, ENCODE), mouse, thale cress, fruitfly, yeast.
Sites last updated before 2005 (but might be useful): The Ancient Conserved Untranslated Sequences database (ACUTS) (1996)
2. RNA element compilations which contain mRNA elements, curated, or from high throughput studies.
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)
Rfam RNA families and covariance models, contains some mRNA elements (IRE, SECIS, GAIT) etc (2015)
CisREgRNA subset of Rfam (2011)
RegRNA (Integrated server for finding motifs in mRNA) v2.0 (2013)
Atlas of UTR Regulatory Activity (AURA) (2018)
RBPDB RNA-binding protein specificities (2011) and the data from Ray et al 2013
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
Nested MICA and MotifExplorer
SelenoDB 2.0 SECIS elements and Selenoproteins (2014)
Conserved viral RNA secondary structures (2001)
IRESdb (last updated 2002).
3. Some tools that can be used for motif and/or RNA structure discovery.
BRAliBase: Compilation and comparison of many different tools, and Bralibase 2.1 (last update 2006)
PatScan or Scan for Matches
Pattern scanner of the yeast S. cerevisiae coding sequences and 5' flanking regions
Three tools to predict the expression level from analysis of a 5' UTR for mammals, monocot and dicot plants.
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
RNABob, QRNA, COVE, PKnots, Infernal from Washington University and the Rfam project
SECISearch, Search for SECIS elements.
RNA2Search a pipleline used to search for an RNA localisation element from Drosophila.
ncRNA integrated suite (SCARNA, Murlet, MXSCARNA, RNAmine, PHMMTS and PSTAG ) from the ncRNA software tools
FIRE. A system to search for both promoter and 3'UTR regulatory elements
IRE elements prediction (SIRE)
Integration of several methods for regulatory element prediction for RNA (Recrit) and for DNA, transcription factor binding sites (MotifVoter)
List of RNA structure prediction software
4. Tools to find novel elements overlapping coding sequences
Mlogd2 virus database
5. General RNA structure and element prediction suites
The RNA World Website many links to RNA related sites and tools
LogoPaint (Scheriber and Brown, Bioinformatics 2002)
6. Non-coding RNAs.
microRNAs: microRNA registry including targets
Tarbase experimentally confirmed microRNA targets in mRNAs and the RNA paper describing it.
Non-coding RNAs: RFam, NONCODE.
7. RNA-binding proteins- major classes in the human genome
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
8. Other translation related databases
The Codon Usage database (CUTG)
9. Reviews on bioinformatic analysis of mRNAs
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
Lim, C. S., & Brown, C. M. (2017). Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs. Frontiers in Microbiology, 8, 2582. http://doi.org/10.3389/fmicb.2017.02582 Pubmed
Updated 6/5/18 by CMB