Flavivirus 3' UTR are untranslated regions in the genome of viruses in the genus Flavivirus. Background The Flavivirus positive-oriented, single-stranded RNA genome has a length of 10,000 - 11,000 bases. The genus includes human pathogens like Zika virus, West-Nile virus, Dengue virus, Yellow Fever virus and other. The 3' UTR ranges between 400 and 700 nucleotides in length. Its RNA secondary structure is known to be necessary for the viral replication during infection. In contrast to the structurally conserved 5' UTR of flaviviruses, individual structural elements differ between different viruses, which is associated with the host-adaptation. Flaviviruses are therefore classified into four different groups: Mosquito-borne flaviviruses (MBFV), tick-borne flaviviruses (TBFV), insect-specific flaviviruses (ISFV) and those with no known vector (NKV). Across all groups, three RNA secondary structure elements are conserved within the 3' UTR: the dumbbell element (DB), cis-acting replication element (CRE) and the exoribonuclease-resistant RNA elements (xrRNA). Further, unique elements have been observed for specific groups as well. Subgenomic flavivirus RNA The 3' UTR of flavivirus - and sometimes even a small part of the 3' end of the coding region - is also called subgenomic flavivirus RNA (sfRNA). It has been shown that sfRNA is implied in many different pathways that comprises both, host defenses and viral infection. SfRNA is produced by incomplete degradation of the viral genome by the host cell (via XRN1). Local RNA secondary structures (xrRNA elements) in the 3' UTR and long-range RNA-RNA interactions between 5' UTR and 3' UTR of flaviviruses stall XRN1 and causes the undigested fragment of the genome. xrRNA element The exoribonuclease-resistant RNA elements (xrRNA) are described throughout all groups of flaviviruses. Usually, each virus harbors two xrRNAs, xrRNA1 and xrRNA2, in the beginning of the 3' UTR. The formation of these stem-loops, especially xrRNA1, is vital to ensure resistance against XRN1 activity. The Y-shaped stem-loop is also termed SL II and SL IV, respectively. In order to function as xrRNA, the sequence downstream is needed as well, since the upper loop region forms a pseudoknot (PK) with the single-stranded region directly downstream to its respective hairpin. In some species, the region downstream also forms a small hairpin. In such cases, the PK interactions takes place between the two loop regions. Conserved formation of these structures were observed in mammalian cells but not in mosquito cells, suggesting this region has varying functions in different hosts. In plant-viruses, xrRNA elements have