# STOCKHOLM 1.0
#=GF ID Flavi_NKV_CRE
#=GF AC RF03540
#=GF DE No-Known-Vector Flavivirus 3' UTR cis-acting replication element (CRE)
#=GF AU Lamkiewicz K; 0000-0002-6375-6441
#=GF GA 50.0
#=GF NC 49.3
#=GF TC 51.7
#=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 GO; 0039694; viral RNA genome replication;
#=GF DR SO; 0000837; UTR_region;
#=GF RN [1]
#=GF RM 9696848
#=GF RT Identification of specific nucleotide sequences within the conserved 3'-SL
#=GF RT in the dengue type 2 virus genome required for replication.
#=GF RA Zeng L, Falgout B, Markoff L
#=GF RL J Virol 1998;72:7510-7522.
#=GF RN [2]
#=GF RM 23760236
#=GF RT Differential RNA sequence requirement for dengue virus replication in
#=GF RT mosquito and mammalian cells.
#=GF RA Villordo SM, Gamarnik AV
#=GF RL J Virol. 2013;87:9365-9372.
#=GF RN [3]
#=GF RM 28421048
#=GF RT Functional Information Stored in the Conserved Structural RNA Domains of
#=GF RT Flavivirus Genomes.
#=GF RA Fernandez-Sanles A, Rios-Marco P, Romero-Lopez C, Berzal-Herranz A
#=GF RL Front Microbiol. 2017;8:546.
#=GF CC Flavi_NKV_CRE is a Flavivirus family were the vector is not known.
#=GF CC Flavivirus 3' UTR cis-acting replication element (CRE) plays a crucial
#=GF CC role in the virus replication and is thought to be needed for the
#=GF CC formation of a "replication complex" [1], it is composed of a small
#=GF CC hairpin (sHP) and a larger structural element (3'SL). It has been shown
#=GF CC that mutations in sHP are lethal for the virus [2]. CRE is involved in the
#=GF CC 5'-3' UTR interation of flaviviruses [3]
#=GF WK Flavivirus_3'_UTR
#=GF SQ 2

NC_003635.1/10505-10600 UCCCGUUACCGGGGGUGG--GGUGAUUAGCCAUGGUCGCACAGAUCAAGCUCAGAUUGCUUACAUGUAAUCUGUGUGGUCAUGAAUAUGACCUCCGCU
NC_004119.1/10598-10690 AUCUUGAAUGGGGGGCGGCGUGGAUAUA--UACUCCAGCCAGAAA-AGACUCAGAUUGUCU-CAUGACUUUCUGACUGGCGUACA-UAGCCAUCCGCU
#=GC SS_cons            :<<<<____>>>><<<<<--<<<-<<----<<<<<<<<<<<<<<<-<<<<_______>>>>------->>>>>>>>>>>>>>>--->>->>>->>>>>
#=GC RF                 acCcguaAucgGggGcGGcGgGgauuUAGccacgcccgcccggaucaggCUCAGAUUGccuACAUGaaauccgggcgggcgugaAUaaGcCcUCCgCu
//
