The JEV genome is approximately 11 kb in length that carries a single long open reading frame (ORF) flanked by a 95-neucleotide 59 untranslated region (59 UTR) and a 585-neucleotide 39 UTR. The ORF encodes a polyprotein which is processed by viral and cellular proteases into three structural and seven non structural proteins [5, 6] . The 59 and 39 UTRs of the JEV genome contain conserved sequence elements and can form conserved stem loop structure. 59 UTR contain secondary structures which are required for the formation of translation pre-initiation complex [7] . JEV requires long range RNA-RNA interaction between 59 and 39 regions of its genome for efficient replication; one such interaction occurs between a pair of 10 complementary nucleotides, located in coding sequence for the capsid protein at 136-146 nucleotides from 59 end of the genome, and 39 cyclization sequence, commonly denoted as 39CSI (39 conserved sequence I) located at 104-114 nucleotides from 39 end of the genome [8, 9] . The 39CSI is highly conserved across members of JEV serocomplex, indicating the possibility that RNA elements within the 59 and 39 UTRs in JEV genome are essential for its replication.