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

  Statistics of types of functional RNA motifs supported in RegRNA 2.0
RegRNA 2.0 incorporated nurmerous data sources and analytical approaches to identify homologs of functional RNA motifs. The statistics of types of functional RNA motifs supported in RegRNA 2.0 are listed as below:
Types of RNA motifs Incorporated
Data
Incorporated
Tools
Main Focus Species Statistics
Splicing Site   GeneSplicer

Arabidopsis
Drosophila
Human
Pyoelii
Rice

 
Splicing Regulatory Motif Regulatory motifs of
AEDBMotif database
RegRNA 2.0

Adenovirus family
Bos taurus
Drosophila melanogaster
Gallus gallus
Homo sapiens
Mus musculus
Rattus sp.
Rous Sarcoma virus
Unknown

294 splicing regulatory motifs:
124 exon splicing enhancer  (ESE)
  47 exon splicing silencer    (ESS)
  73 intron splicing enhancer (ISE)
  50 intron splicing silencer   (ISS)
Polyadenylation polya_svm Human
Ribosome Binding Site   RBSfinder Prokaryote  
rho-independent Terminator   TransTermHP Bacteria  
UTR Motifs

UTRsite

PatSearch Eukaryotic mRNAs 48 UTRsite motifs
AU-rich Element AU-rich element
patterns of ARED
RegRNA 2.0 Human five ARED cluster patterns
RNA C-to-U Editing Sites   CURE Plants  
Riboswitch RiboSW descriptors RiboSW Bacteria, plants, fungi 12 riboswitches:
Purine, Lysine, FMN, TPP, Glycine,
SAM, Cobalamin, yybP-ykoY,
ykkC-yxkD, SAM_alpha, PreQ1, glmS
RNA Elements ERPIN profiles ERPIN Bacteria, human and etc. 11 RNA elements:
SECIS, IRE uptake, IRE storage,
Polyadenylation site, Tbox,
Rho-independent Terminator,
Hammerhead form I & III,
CRE, IRES, TAR HIV-1
RNA cis-regulatory
Elements
cis-reg families of
Rfam database
INFERNAL Eukaryote
Bacteria
Archaea
209 Rfamcis-reg families
Long Stem   EMBOSS einverted    
BLAST fRNAdb functional RNAs
of fRNAdb
BLAST Homo sapiens
Mus musculus
Rattus norvegicus and etc.
475,318 fRNAdb sequences
 (length less than 500bps)
miRNA Target Sites miRNAs of miRBase miRanda Homo sapiens
Mus musculus, and etc.
 (Total:166 species)
21,643 miRNA sequences
ncRNA Hybridization Sites ncRNAs of
NONCODE
BLAST,
RNAcofold
Arabidopsis thaliana
Caenorhabditis elegans
Drosophila melanogaster
Escherichia_coli
Homo sapiens
Mus musculus
Oryza sativa
Rattus norvegicus
Saccharomyces cerevisiae
      340 A. thaliana ncRNAs
      369 C. elegans ncRNAs
      176 D. melanogaster ncRNAs
        60 E. coli ncRNAs
      648 H. sapiens ncRNAs
101,634 M. musculus ncRNAs
      439 O. sativa ncRNAs
  66,810 R. norvegicus ncRNAs
      105 S. cerevisiae ncRNAs
TRANSFAC motifs TRANSFAC TRANSFAC Match Homo sapiens
Mus musculus
Rattus norvegicus and etc
(Total:134 species)
2,171 transcription factor binding matrices
User defined motif   RNAMotif    
Open Reading Frame   RegRNA 2.0    
GC-content Ratio   RegRNA 2.0    
RNA Accessibility   RNAplfold