# STOCKHOLM 1.0
#=GF ID MPMV_package
#=GF AC RF00459
#=GF DE Mason-Pfizer monkey virus packaging signal
#=GF AU Moxon SJ; 0000-0003-4644-1816
#=GF GA 54.0
#=GF NC 53.9
#=GF TC 54.0
#=GF SE PMID:14687944, INFERNAL
#=GF SS Predicted; PFOLD; Moxon SJ
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 24.34 -Z 2958934 CM SEQDB
#=GF DR GO; 0019072; viral genome packaging;
#=GF DR SO; 0000655; ncRNA;
#=GF RN [1]
#=GF RM 14687944
#=GF RT Mutational analysis of the predicted secondary RNA structure of the
#=GF RT Mason-Pfizer monkey virus packaging signal.
#=GF RA Mustafa F, Lew KA, Schmidt RD, Browning MT, Rizvi TA
#=GF RL Virus Res 2004;99:35-46.
#=GF RN [2]
#=GF RM 7884866
#=GF RT Secondary structure model of the Mason-Pfizer monkey virus 5' leader
#=GF RT sequence: identification of a structural motif common to a variety of
#=GF RT retroviruses.
#=GF RA Harrison GP, Hunter E, Lever AM
#=GF RL J Virol 1995;69:2175-2186.
#=GF CC This family represents a group of sequences that are related to the
#=GF CC Mason-Pfizer monkey virus (MPMV) packaging signal. The packaging signal is
#=GF CC located in the 5' UTR and is required for specific RNA encapsidation [1].
#=GF WK Mason-Pfizer_monkey_virus_packaging_signal
#=GF ** seedtax: Eukaryota; Viruses
#=GF SQ 9

AF126467.1/349-623       UGGCGCC-C-AACGUG---GGGC-U-GGAUACGA--GGGAAUC-CUGUGAGGAA---GAG----AGCGCG-UAACACGGCCGGCAGUCA-AAGUGAAAG------AAAAACC---UUCCA--GCUGCCGCGGGAACCUGCCGCGUC--GG-CAAUAAAGGUAAGCGUUGCG-UUCGAAUAUGGGACAAGAAUUAAGCCAA
M11841.1/351-632         UGGCGCC-C-AACGUG---GCGU-U-GGAUACGA--GGGAAUU-UCGUGAGGAA---GAC----GACGCGGUUUGCCGGCCCG--GAUUAAAAGAGAAACGAAA-GUAAACU---UUCUUCGGCCGCCGCGGGAGCCUGCCGCGUA--GGACCUGAA-AGUAAGUGGUGCG-CUCGGAUAUGGGGCAGGAAUUAAGCCAG
M16605.1/349-623         UGGCGCC-C-AACGUG---GGGC-U-GGAUACGA--GGGAAUC-CUGUGAGGAA---GAG----AGCGCG-UAACACGGCCGGCAGUCA-AAGUGAAAG------AAAAACC---UUCCA--GCUGCCGCGGGAGCCUGCCGCGUC--GG-CAAUAAAGGUAAGCGUUGCG-CUCAAAUAUGGGACAAGAAUUAAGCCAA
AF033815.1/123-398       UGGCGCC-C-AACGUG---GGGC-U-GGAUACGA--GGGAAUU-UCGUGAGGAA---GAC----GACGCG-UUCGCCGGCCGGC-GAUUAAAAGUGAAAG------UAAACUC--UCUU--GGCCGCCGCGGGAACCUGCCGCGUU--GGACCU-GAAAGUAAGUGUUGCG-CUCGGAUAUGGGGCAAGAAUUAAGCCAG
AANU01253468.1/8032-8307 UGGCGCCUC-AACGUG---GAGCCU-GGAAACGA--GGGAUUC--CGUGAGGAA---GAG----GACGCG-AAAGAACGGUCGACCUUCAAGGUGAAACU-----AAACUCC---UCCGA--UC-ACCGCGGGAACCUGCCGCGUC--AG-AAUUGAAGGUAAGUGACGUG-UCCG-AAAUGGGACAAGAAUUAAGUCAA
AC113268.8/165062-164780 UGGCGCC-UGAACAGG---GACC-U-GGA---AACGAGGGACU-CCGUGAGGAA---GAG----GACGCCAAAGGACGGUCGACCGCUAACCCAGACAAAAGGAGUAAAACUC--UUCCG-AUCA-CCGCGGGAACCUGCUGCGUC--UGAAUCGAA-GGUAAGUGGCGCG-UCCG-AAAUGGGACAAGAAUUAAGUCAG
AAIY01568405.1/1114-839  UGGCACC-C-AAUGCG---GGGC-CCGGAUACGA--GGG-AUA-CCGUGAGGAA---GAA----GGCGC--AAAGGAGGCCGGC-GAGUAAAAGUGAGAG-----AAAAUUC---CUUC--GGCCACCGCAGGAGCCUGCUGCGCUGAGGCUGAAGGUGAGUAAAA--GAG-CCUGAAAAUGGGACAAGAAUUAAGCCAC
AAHX01057948.1/6286-6014 UGGUGCC-C-ACUGUGUGGGGCC-U-GUAUACAG--GGGCUUUAUCUUGAGGAA---GAA----GAC----UCAGGUGGCUGGCUUUGUAUACAGAAAU----------UCC---UUUGA-AU--GUCGAGGGAGCCUGCCGUGGC--UGAAACGAAGGGGAGUGAUAGAA-UCUGAAUAUGGGACAAGCAUUAAGCUAA
ABDC01313292.1/5294-5577 UGGCGCC-C-AACGUG---GGGC-UCGGAUACGA--GGGAUGC-A-GUGAGGACAUGGACGUGUGUCGCC-AAAGCUCGUAGGGACCGAGCAGCUUAAAG-----UGAAAGUGCCUUCGA--CCA-UUGCGGGAGCCUGCCUCGCU--UGAGUA-AAAGUUGA---AUGCGUCUGCAAAAAUGGGCAGGAACUUAGCCAA
#=GC SS_cons             :::::<<.<.---<<<...____._.___>>>--..>>>::::.<<<<______..._>>....>>::::.:::::::::::::::::::::::::::::.....::::<<<...<<---.-<<<--<<<<<_______>>>>>--..>>->--->>->>>:::::<<<<-.<<<<____>>>>>>>>::::<<<<<<__
#=GC RF                  UGGCGCC.C.AAcGug...GggC.U.GGAuaCGA..GGGaauu.ccgUGAGGAA...GAc....ggCGCg.uaaGaugGccGGcaguuuAaAaugaAAag.....aaAAacc...uucua.agCcgcCGcGGGAgCCUGCCgCGuu..gGAcaauaaagguaAguguuGcG.cccgAAuAuggggCaaGAAUUaaGCcAa

AF126467.1/349-623       CAUGAACUUUAUGUAGAACAGUUAAAAAAGGCUCUAAAGACACGGGGAGUAAAGGUUAAGGGUAAUGAUUUACUCAAAUUCUUUGAUUUUGUAAAGGAUACCUGCCCUU
M11841.1/351-632         CACGAACGUUAUGUGGAACAAUUAAAACAGGCUUUAAAGACACGGGGAGUAAAGGUUAAAUAUGCUGAUCUCUUAAAGUUUUUUGAUUUUGUAAAGGAUACUUGUCCUU
M16605.1/349-623         CAUGAACUCUAUGUAGAACAAUUAAAAAAGGCUCUAAAGACACGGGGAGUAAAGGUUAAGGGUAAUGAUUUGCUCAAAUUCUUUGAUUUUGUAAAGGAUACCUGCCCUU
AF033815.1/123-398       CAUGAACGUUAUGUAGAACAAUUGAAGCAGGCUUUAAAGACACGGGGAGUAAAGGUUAAAUAUGCUGAUCUUUUGAAAUUUUUUGAUUUUGUGAAGGAUACUUGUCCUU
AANU01253468.1/8032-8307 CAUCAAAUCUAUGUAGGACAAUUAAAAGAGGCUUUAAAGAUACGAGGAGUAAAGGUUAAAUGUAAUGAUUUGUUUAAAUUUUUUGAUUUUGUAAAAGACACUUGCCCUU
AC113268.8/165062-164780 CAUCAGAUCUAUGUAGGACAAUUAAAAGAGGCUUUAAAGAUACGAGGAGUAAAGGUUAAAGGUAAUGAUUUGUUUAAGUUUUUUGAUUUUGUAAAAGAUACUUGCCCUU
AAIY01568405.1/1114-839  CAUCAGAUUUAUGUGAGACAAUUGAAAGAGGCUUUAAAGGCACGAGGAGUAAAGGUGAAUAGUGAGGAUUUAUUCAAAUUUUUUGGCUUUAUAAAAGAUAUGUGUCGUU
AAHX01057948.1/6286-6014 CAUGAGGUCUUUGUGAAACAAUUAAAAGAGGCAUUAAAGGUUCGAGGAGUAAAGGUAAAAACCAACGAUCUGUUUACAUUUUUUGAUUUUGUUAAGGAUCUUUGUCCUU
ABDC01313292.1/5294-5577 CAUCAAUUGUAUGUAACACAAUUGAGGGAAGUGUUAAAUACACGAAGAGUAAAGGUUGCAAAAGCAGAUUUGUUUAGAUUCUUUGAUUUUAUAAAGGAUGUGUGCCCCU
#=GC SS_cons             _____________________________>>>->>>::::::<<<<<<<<--<<<<<<_______>>>>>>------>>>>>>>>::::::::<<<<<<____>>>>>>
#=GC RF                  CAUgAaaUuUAUGUagaACAAUUaAAAgAgGCuuuAAAGAcACGaggAGuAAAgGUcaAaaguaaugAUcUgUUuAaaUUcuuUGAUUUUGUAAagGauacuUguCcuU
//
