# STOCKHOLM 1.0
#=GF ID Alfamo_CPB
#=GF AC RF00252
#=GF DE Alfalfa mosaic virus coat protein binding (CPB) RNA
#=GF AU Moxon SJ; 0000-0003-4644-1816
#=GF GA 70.0
#=GF NC 69.9
#=GF TC 70.0
#=GF SE PMID:14718638
#=GF SS Published; PMID:14718638
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 21.38 -Z 2958934 CM SEQDB
#=GF DR GO; 0045727; positive regulation of translation;
#=GF DR SO; 0000655; ncRNA;
#=GF RN [1]
#=GF RM 14718638
#=GF RT Efficient translation of alfamovirus RNAs requires the binding of coat
#=GF RT protein dimers to the 3' termini of the viral RNAs.
#=GF RA Neeleman L, Linthorst HJ, Bol JF
#=GF RL J Gen Virol 2004;85:231-240.
#=GF CC This family represents the Alfalfa mosaic virus (AMV) coat protein (CP)
#=GF CC binding RNA which is found in the 3' UTR. AMV CP can stimulate the
#=GF CC translation of AMV RNA by between 50 and 100-fold. This family contains at
#=GF CC least two CP binding sites which are thought to be essential for efficient
#=GF CC RNA translation [1].
#=GF WK Alfalfa_mosaic_virus_coat_protein_binding_(CPB)_RNA
#=GF SQ 18

U12510.1/700-876     UGAUGUACCCCAUUAUUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAACGACUUCAUAUUGCUUAUA-UGUGUGCUGAUGCACACAUAUAAAUGCUCAUGCGAAACU-GCAUGAAUGCCCCUAAGG-----
V00048.1/700-881     UGAUUUACCCCAUUAAUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAUCGACUUCAUAUUGCUUAUA-UAUGUGCUAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
K03542.1/1961-2142   UGAUUUACCCCAUUAAUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAUCGACUUCAUAUUGCUUAUA-UAUGUGCUAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
V00049.1/42-226      GGAGCUAUAAUACUAAUUUCUGAAUUAGUCAUUGGUAAUUCAA--UGCCAACCUCCACAGGGUGGACUAAGGUUGAGGUAUAGAAUCCUAUUCGCUCCUGGUAGGAGAAAUUCUAUAUUGCUUAUA-UACGUGCUUGUGCACGUAUAUAAAUGCUCAUGCAAAAUU-GCAUGAAUGCCCCUAAGGGA-GC
M59241.1/2007-2188   UGAUGUACCCCAUUAAUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGAAACAACUUCAUAUUGCUUAUA-UAUGUGCUAGUGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
X01572.1/2408-2593   CAAGGGCACGCCGAGCUUGAUGUUUUCUUGACA--UAAGUCAAAUUGCCAACCUCCACUGGGUGGGUCAAGGUUGAGGUAUAGAAUCCUAUUCGCUCCUGAUAGGAGAAAUUCUAUAUUGCUUAUA-UAUGUGCUUACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
AF015716.1/1857-2038 UGAUGUACCCCAUUAAUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGAGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAACGACUUCAUAUUGCUUAUA-UAUGUGCUAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
L00162.1/783-964     UGAUUUACCCCAUUAAUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAUCGACUUCAUAUUGCUUAUA-UAUGUGCUAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
V00050.1/43-228      CAAGGGCACGACGAGCUUGAUGUUUUCUUGACA--UAAGUCAAAUUGCCAACCUCCACUGGGUGGAUUAAGGUUGAGGUAUAGAAUCCUAUUCGCUCCUGAUAGGAGAAAUUCUAUAUUGCUUAUA-UAUGUGCUUAUGCACAUAUAUAAAUGCUCAUGCAAAACUUGCAUGAAUGCCCCUAAGGGA-GC
AF015717.1/1857-2038 UGAUGUACCCCAUUAAUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAACGACUUCAUAUUGCUUAUA-UAUGUGCUAGCGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
L00163.1/3459-3644   GGAGCUAUAAUCAUAAUUUCUGAAUUAGUCAUUGGUAAUUCAA--UGCCAACCUCCACUGGGUGGGUUAAGGUUGAGGUAUAGAAUCCUAUUCGCUCCUGAUAGGAGAAAUUCUAUAUUGCUUAUA-UACGUGCUUAUGCACGUAUAUAAAUGCUCAUGCUAAAUU-GCAUGAAUGCCCCUAAGGGAUGC
AF332998.3/2078-2257 UGAUUUACCCCAUUAAUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAUCGACUUCAUAUUGCUUAUACUAUG---UAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
V00051.1/50-230      UGAUGUACCCCAUUAAUUUGGGA--UGCCAAAG--UCAUUUGA--UGCUCACCUCCACUGGGUGGAUCAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAUCGACUUCAUAUUGCUUAUA-UAUGUGCUAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAGC-
X00819.1/1874-2055   UGAUGUACCCCAAUAAUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAACGACUUCAUAUUGCUUAUA-UAUGUGCUGGUGCACACAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
U12509.1/700-876     UGAUGUACCCCAUUAAUCUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAACGACUUCAUAUUGCUUAUA-UAUGUGCUAACGAACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGG-----
AF294432.1/721-902   UGAUGUACCCCAUUAAUUUGGGA--UGCCAAAG--UCAUUUGA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAUCGACUUCAUAUUGCUUAUA-UAUGUGCUAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
K02703.1/1856-2037   UGAUGUACCCCAUUAAUUUGGGA--UGCCAAAG--UCAUUUGA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAUCGACUUCAUAUUGCUUAUA-UAUGUGCUAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
AF294433.1/721-902   UGAUGUACCCCAUUAAUUUGGGA--UGCCAAAG--UCAUUUGA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGCCCUAUUCGCUCCUGAUAGGAUCGACUUCAUAUUGCUUAUA-UAUGUGCUAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
#=GC SS_cons         ::::::::<<<<______>>>>:..:::<<<<_..___>>>>:..:::<<<<<<<<<<___>>>>---->>>>>>:<<<<<<<<<<<<<<<<_______>>>>>>---->>>>>>>>>>::<<<<<.<<<<<<<____>>>>>>>>>>>>::::<<<<<<<____>.>>>>>>::::<<<___>>>::::
#=GC RF              uGAuguAccccauuAaUUugggA..Ugcugaag..UcAuucaA..UGCcgaCCuCCaCUGGGuGGAUUAaGGucgAgguauggaguCCuauuCGCUCCUgauaGGAucgacuccauauuGCuuaua.uauGuGCUaAuGCaCauauauaaAUGCuCauGCaAAAcu.GCauGaAUGCCCCUAAGGGAuGC
//
