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

 ► Step1: Input an RNA Sequence (fasta format, up to 10k bps)


   or upload from:  

 ► Step 2: Select RNA Motifs

Transcriptional motifs:

TRANSFAC TFBS ( ,
     score ≥ score ≥ default matrix value)
Rho-independent Terminator
Pre-mRNA motifs:
Splicing Site (species: )
Splicing Regulatory Motif ( )
Polyadenylation Site
Translational motifs:
Ribosome Binding Site
UTR motifs:
UTRsite Motifs
mRNA degradation elements:
AU-rich Elements
RNA editing sites:
C-to-U Editing Sites
Riboswitches:
RiboSW
RNA cis-regulatory elements:
ERPIN
Rfam cis-reg families
RNA structural patterns:
Long Stem (stem_length ≥ )
Functional RNA sequences:
BLAST fRNAdb (similarity or match_length ≥ )
RNA-RNA interaction region:
miRNA Target Sites ( , score ≥ & free_energy ≤ )
ncRNA Hybridization Sites ( , length ≥ & free_energy ≤ )
User defined motif:
RNAMotif descriptor
Miscellaneous:

GC-content Ratio (window_size: )
RNA Accessibility (max_pair_distance: , consecutive_unpair_size: )
Open Reading Frame Prediction :(Start Codon AUG AUG + GUG + UUG )

Ouput settings:
Draw Position Lines on the Map (interval length: )
 Map Width
:
pixel