A Regulatory RNA Motifs and Elements Finder
  Release 1.0, Jan 2006

Accession R0004
Feature Type RegRNA in 5'-UTR
Name Selenocysteine Insertion Sequence (SECIS) - type 2
Regulatory Motif


p2=2...9 a


p3=8...12  p3:(((^rr | ^mc) | ^su) 6...10 )

p4=0...3 p5=aav p6=11...14 p6:(0...1 p7=2...7 3...6 r1~p7 0...3$)

(((r1~p3[1,0,0] | r1~p3[1,1,0]) | r1~p3[1,0,1]) | r1~p3[0,1,1])



Description Specific incorporation of selenocysteine in selenoproteins is directed by UGA codons residing within the coding sequence of the corresponding mRNAs. Translation of UGA, usually a termination codon, as selenocysteine requires a conserved stem-loop structure called "SElenoCysteine Insertion Sequence" (SECIS) lying in the 3'UTR region of selenoprotein mRNAs. The consensus structure of SECIS element determined by comparative analysis of several selenoprotein mRNAs as well as on both RNase and chemical probing is shown below: N N N R N A N A N NN NN NN NN NN NN NN RY RY NB AG GA UN A N N N N N N N NN NN NN NN The minimal consensus pattern is shown below (r1 represents pairing rules) where one mismatch is allowed in Helix I and 2 mismatches and/or one insertion/deletion in Helix II. More recent studies have shown that two forms of SECIS may exist: type 1 with short apical loop; and type 2 with large apical loops carrying intra-loop base pairings.
References Fagegaltier D, Lescure A, Walczak R, Carbon P, and Krol A
Structural analysis of new local features in SECIS RNA hairpins.
Nucleic Acids Res 2000; 28(14), 2679-89   PubMed 

Walczak R, Westhof E, Carbon P, and Krol A
A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs.
RNA 1996; 2(4), 367-79   PubMed 

Walczak R, Carbon P, and Krol A
An essential non-Watson-Crick base pair motif in 3 UTR to mediate selenoprotein translation.
RNA 1998; 4(1), 74-84   PubMed 

Department of Biological Science and Technology, Institute of Bioinformatics, National Chiao Tung University, Taiwan
Contact with Dr. Hsien-Da Huang