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)

RMfam (2015)

CisREgRNA subset of Rfam (2011)

RegRNA (Integrated server for finding motifs in mRNA) v2.0 (2013)

Atlas of UTR Regulatory Activity (AURA) (2018)

AREsite (2016)

Recode (2010)

RBPDB RNA-binding protein specificities (2011) and the data from Ray et al 2013

IRESite (2015)

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)

ERPIN (2009)

Conserved viral RNA secondary structures (2001)

IRESdb (last updated 2002).

SelexDB (2000)

GeneExpress (2000)

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)

Magnolia and Carnac

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.

Vienna RNA

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

Vienna RNA


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. Pubmed

RNAMotifs (Transterm)

Updated 6/5/18 by CMB