# STOCKHOLM 1.0
#=GF ID Flavi_NKV_xrRNA
#=GF AC RF03539
#=GF DE No-known vector Flavivirus exoribonuclease-resistant RNA element
#=GF AU Lamkiewicz K; 0000-0002-6375-6441
#=GF GA 50.0
#=GF NC 38.4
#=GF TC 82.8
#=GF SE Lamkiewicz K
#=GF SS Predicted; LocARNA 2.0.0RC8
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
#=GF DR SO; 0000837; UTR_region;
#=GF RN [1]
#=GF RM 19064258
#=GF RT A highly structured, nuclease-resistant, noncoding RNA produced by
#=GF RT flaviviruses is required for pathogenicity.
#=GF RA Pijlman GP, Funk A, Kondratieva N, Leung J, Torres S, van der Aa L, Liu
#=GF RA WJ, Palmenberg AC, Shi PY, Hall RA, Khromykh AA
#=GF RL Cell Host Microbe. 2008;4:579-591.
#=GF RN [2]
#=GF RM 23006624
#=GF RT A noncoding RNA produced by arthropod-borne flaviviruses inhibits the
#=GF RT cellular exoribonuclease XRN1 and alters host mRNA stability.
#=GF RA Moon SL, Anderson JR, Kumagai Y, Wilusz CJ, Akira S, Khromykh AA, Wilusz J
#=GF RL RNA. 2012;18:2029-2040.
#=GF RN [3]
#=GF RM 25635835
#=GF RT Dengue virus RNA structure specialization facilitates host adaptation.
#=GF RA Villordo SM, Filomatori CV, Sanchez-Vargas I, Blair CD, Gamarnik AV
#=GF RL PLoS Pathog. 2015;11:e1004604.
#=GF RN [4]
#=GF RM 28587300
#=GF RT The 5' and 3' Untranslated Regions of the Flaviviral Genome.
#=GF RA Ng WC, Soto-Acosta R, Bradrick SS, Garcia-Blanco MA, Ooi EE
#=GF RL Viruses. 2017; [Epub ahead of print]
#=GF RN [5]
#=GF RM 18701589
#=GF RT A viral noncoding RNA generated by cis-element-mediated protection against
#=GF RT 5'->3' RNA decay represses both cap-independent and cap-dependent
#=GF RT translation.
#=GF RA Iwakawa HO, Mizumoto H, Nagano H, Imoto Y, Takigawa K, Sarawaneeyaruk S,
#=GF RA Kaido M, Mise K, Okuno T
#=GF RL J Virol. 2008;82:10162-10174.
#=GF RN [6]
#=GF RM 29866852
#=GF RT A folded viral noncoding RNA blocks host cell exoribonucleases through a
#=GF RT conformationally dynamic RNA structure.
#=GF RA Steckelberg AL, Akiyama BM, Costantino DA, Sit TL, Nix JC, Kieft JS
#=GF RL Proc Natl Acad Sci U S A. 2018;115:6404-6409.
#=GF RN [7]
#=GF RM 32848042
#=GF RT The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows
#=GF RT how diverse sequences are integrated into a conserved fold.
#=GF RA Steckelberg AL, Vicens Q, Costantino DA, Nix JC, Kieft JS
#=GF RL RNA. 2020; [Epub ahead of print]
#=GF CC The exoribonuclease-resistant RNA elements (xrRNA) are described
#=GF CC throughout all groups of flaviviruses. Usually, each virus harbors two
#=GF CC xrRNAs, xrRNA1 and xrRNA2, in the beginning of the 3' UTR [1]. The
#=GF CC formation of these stem-loops, especially xrRNA1, is vital to ensure
#=GF CC resistance against XRN1 activity [2]. The Y-shaped stem-loop is also
#=GF CC termed SL II and SL IV, respectively. In order to function as xrRNA, the
#=GF CC sequence downstream is needed as well, since the upper loop region forms a
#=GF CC pseudoknot (PK) with the single-stranded region directly downstream to its
#=GF CC respective hairpin. In some species, the region downstream also forms a
#=GF CC small hairpin. In such cases, the PK interactions takes place between the
#=GF CC two loop regions. Conserved formation of these structures were observed in
#=GF CC mammalian cells but not in mosquito cells, suggesting this region has
#=GF CC varying functions in different hosts[3][4]. In plant-viruses, xrRNA
#=GF CC elements have been observed as well, showing some similarities to
#=GF CC flaviviral xrRNAs[5][6]. However, plant-virus xrRNA and flaviviral xrRNA
#=GF CC are distinguishable by their underlying three-dimensional folds[7].
#=GF WK Flavivirus_3'_UTR
#=GF SQ 3

NC_003635.1/10257-10338 GAGUGUUGAGGGCAACCAGUGGGCUAGCCACA----UGGGUAUGACGCACCCA---CCCUCUGCAUUC-UUGUAAAUACUUUGGCCAGUC-
NC_004119.1/10281-10362 UGCGAGUGAGGGCAACUCUGGGAUUAGCUCAA----UGGGUGUGACGACCCUA---CCCUU--CCGCAUUUGUAAAUAAUUGAGCCAGUCA
NC_005039.1/10454-10530 AA-GUGUCAGGCCAA---GAUUGAGAAAAUCUUGCCACAGCUUGGCAGACUGUGCAGCCUGCAGCCCUAGAGGGAG----------ACUGA
#=GC SS_cons            (((((--(((((,,,,,,<<<<_____>>>>,....<<<<-<<____>>>>>>...)))))--))))):::::::::::::::::::::::
#=GC RF                 ggcgggUgAGGgCAACuaggggGuuAgcccca....ugGGUguGACgacCCca...cCCUcuaccgccauuGuAAAUAaUUuaGCCAgUcA
//