‒ an integrated web server for identifying functional RNA motifs and sites
Home Scan Statistics Documentation Tutorial Release 2.0, Jun. 2012

Chang TH, Huang HY, Hsu JB, Weng SL, Horng JT, Huang HD: An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. BMC bioinformatics 2013, 14 Suppl 2:S4

RegRNA1.0 (old version): Link

RegRNA 2.0 is an integrated web server for identifying functional RNA motifs in an input RNA sequence. RegRNA 2.0 extends our previvous work, RegRNA which is a widely used regulatory RNA motifs identification tool (times cited: 47#) by incoporating more analytical methods and updated data sources. Through our integrated user-friendly interface, user can conveniently use these analytical approaches and observe results with good graphical visualization. Serveral kinds of functional RNA motifs and sites can be identified by RegRNA 2.0:
  ▪ Splicing sites (donor site, acceptor site)
  ▪ Splicing regulatory motifs(ESE, ESS, ISE, ISS elements)
  ▪ Polyadenylation sites
  ▪ Transcriptional motifs (rho-independent terminator, TRANSFAC)
  ▪ Translational motifs (ribosome binding sites)
  ▪ UTR motifs (UTRsite patterns)
  ▪ mRNA degradation elements (AU-rich elements)
  ▪ RNA editing sites (C-to-U editing sites)
  ▪ Riboswitches (RiboSW)
  ▪ RNA cis-regulatory elements (Rfam, ERPIN)
  ▪ Similar funcitonal RNA sequences (fRNAdb)
  ▪ RNA-RNA interaction regions (miRNA, ncRNA)
  ▪ User defined Motif (RNAMotif)
  ▪ Miscellaneous information (open reading frame, GC-ratio, RNA accessibility and etc.)

   Improvements of RegRNA 2.0

As compared with RegRNA, RegRNA 2.0 integrates more data and is capable of identifying more types of functional RNA motifs (as shown in Table below). In addition, RegRNA 2.0 provides further analysis and related information for predictive results, and presents results with good graphical visualization.



RegRNA 2.0

Polyadenylation sites


Yes (polya_svm)

Ribosome binding sites


Yes (RBSfinder)

Rho-independent terminator


Yes (TransTermHP)

RNA editing sites


Yes (CURE)

AU-rich elements


Yes (ARED 5 patterns)

RNA cis-elements


Yes (Rfam & ERPIN 220 cis-elements)

similar functional RNAs


Yes (BLAST+fRNAdb 475,318 fRNAs)

ncRNA hybridization region


Yes (BLAST+RNAcofold+NONCODE 170,581 ncRNAs)

Open reading frame


Yes (RegRNA 2.0)

Motif region structure


Yes (RNAfold)

RNALogo displaying


Yes (RNALogo)

GC-content Ratio


Yes (RegRNA 2.0)

RNA accessibility


Yes (RNAplfold)

DNA motifs

Yes (TRANSFAC 7.4)

Yes & Updated (TRANSFAC 2012.1)

Splicing regulatory motifs

Yes (AEDB 278 motifs)

Yes & Updated (AEDB 294 motifs)

UTR motifs

Yes (UTRSite 40 motifs)

Yes & Updated (UTRSite 48 motifs)


Yes (RNAMotif descriptor)

Yes & Updated (RiboSW, Rfam models)

miRNA target sites

Yes (miRBase 744 miRNAs)

Yes & Updated (miRBase 21,643 miRNAs)

Splicing sites

Yes (GeneSplicer)

Yes (GeneSplicer)

Long stems

Yes (EMBOSS einverted)

Yes (EMBOSS einverted)

User defined Motifs

Yes (RNAMotif)

Yes (RNAMotif)

  Example of predicted result: