Table 1

Statistics of types of functional RNA motifs supported in RegRNA 2.0

Types of functional RNA motifs

Incorporated data

Incorporated approaches

Number of entries


Splicing sites

GeneSplicer [15]

Splicing regulatory motifs

AEdb [8]

RegRNA 2.0

294 splicing motifs

Polyadenylation Sites

polya_svm [16]

Ribosome binding site

RBSfinder [17]

Rho-independent terminator

TransTermHP [18]

UTR Motifs

UTRsite [1]

PatSearch [22]

48 UTRsite motifs

AU-rich element

ARED [10]

RegRNA 2.0

5 ARE patterns

RNA editing sites

CURE [19]

Riboswitches

RiboSW models

RiboSW [21]

12 riboswitches

RNA elements

ERPIN profiles

ERPIN [23]

11 RNA elements

RNA cis-regulatory elements

Rfam CMs [4]

INFERNAL [24]

209 Rfam cis-reg families

Long stem

einverted [30]

Known functional RNAs

fRNAdb [7]

BLAST [29]

475,318 fRNAdb sequences

miRNA target

miRBase [28]

miRanda [20]

21,643 miRNA sequences

ncRNA hybridization sites

NONCODE [11]

BLAST [29],

RNAcofold [34]

170,581 ncRNA sequences

TRANSFAC motifs

TRANSFAC [14]

Match [25]

2,171 transcription factor binding matrices

User-defined motif

RNAMotif [26]

Open Reading Frame

RegRNA 2.0

GC-content ratio

RegRNA 2.0

RNA accessibility

RNAplfold [34]


Chang et al. BMC Bioinformatics 2013 14(Suppl 2):S4   doi:10.1186/1471-2105-14-S2-S4

Open Data