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

Accession R0021
Feature Type RegRNA in 5'-UTR
Name Barley yellow dwarf virus translation control element (BYDV_TE)
Regulatory Motif

p1=7...7 3...3 p2=ggauccug[1,0,0] p2:(4...4 p3=4...4) gnrna ~p3

2...2 p4=4...4 4...4 ~p4 4...4 p5=nn nnn (p6=6...6 c (u | c) a[0,1,0]

guc a[0,1,0] (a | c) r1~p6 | p8=5...5 n p9=3...3 nn

p10=6...6  c (u | c) a[0,1,0] guc a[0,1,0] (a | c) r1~p10 n ~p9 nn ~p8)

nnn r1~p5 6...6 r1~p1[1,0,1]
Description Efficient translation of Barley yellow dwarf virus (BYDV) RNA, lacking both a 5'cap and a poly(A) tail, is mediated by a cap-independent translation element (TE) located in the 3'UTR whose minimum length is obout 90 nt. Nuclease probing and structure directed mutagenesis has shown that TE is able to fold into a specific cruciform secondary structure containing four helices. Cap-independent translation requires all secondary structure elements and most primary sequences. Recent data suggest that TE base pairs to the 5'UTR unless the TE itself is located in the 5'UTR. Similar structures appear to be present in soybean dwarf luteovirus (SDV), and tobacco necrosis necrovirus (TNE). The TNV TE lacks a stem-loop present the BYDV TE. All have conserved loops that can base-pair to a stem-loop in the 5' UTR. TE mediates translation initiation at the AUG closest to the mRNA 5' end, possibly facilitating ribosome recruiting and 3'-5' communication.
References Guo L, Allen E, and Miller WA
Structure and function of a cap-independent translation element that functions in either the 3 or the 5 untranslated region.
RNA 2000; 6(12), 1808-20   PubMed 

Guo L, Allen EM, and Miller WA
Base-pairing between untranslated regions facilitates translation of uncapped, nonpolyadenylated viral RNA.
Mol Cell 2001; 7(5), 1103-9   PubMed 

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