# STOCKHOLM 1.0
#=GF ID rncO
#=GF AC RF00552
#=GF DE rncO
#=GF AU Moxon SJ; 0000-0003-4644-1816
#=GF GA 43.0
#=GF NC 41.7
#=GF TC 43.0
#=GF SE PMID:8972772
#=GF SS Published; PMID:8972772
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 25.73 -Z 2958934 CM SEQDB
#=GF DR GO; 0043488; regulation of mRNA stability;
#=GF DR SO; 0000655; ncRNA;
#=GF RN [1]
#=GF RM 8972772
#=GF RT RNase III autoregulation: structure and function of rncO, the
#=GF RT posttranscriptional "operator".
#=GF RA Matsunaga J, Simons EL, Simons RW
#=GF RL RNA 1996;2:1228-1240.
#=GF CC This family represents a bacterial regulatory element (rncO) found in the
#=GF CC rnc leader sequence. The rnc operon is negatively auto-regulated by
#=GF CC transcript stability. rnc, the first gene in the operon codes for RNase
#=GF CC III which cleaves the long rncO stem II leading to transcript degradation
#=GF CC and a reduction in translation [1].
#=GF WK rncO
#=GF SQ 18

CP000720.1/1337539-1337720   GAGCGAUAAAGUUGGCUCUCUUAU-GGGAGCCACUGCAAACGAAACAGUUUUGU----CUUGGUUAUUUUUG-------------------------------UCGGUCAGAC---CUGUUCCGUAUGCUGUAGUU-UUUGACGCAUUCUUGAUC----UAUUGGUAACUCAUGAAUCCCAUCGUAAUAAACAGGCUGCA
AM286415.1/1137336-1137517   AGCGAUAAAAGUUGGCUC-UUUUAUGGGGGCCACUGCAAACGAAACAGUUUUGU-CUU--------------GGUA--------UUAU------UGGCCGAUCA---------GACCUGUUCCGUCUGCUGUAGUU-UUUGACGCAUUCUUGAUC----UAUUGGUAACUCAUGAACCCCAUCGUAAUAAAUAGGCUACA
CP000653.1/3324072-3323909   GAAGUUUAAGGUUGGCGC-AGAGC-CAGUGCCACGGCACACGAAACCGCGUUGGUUUUC----------------------------U-----------------------CAGGUCGGUUUCGUGUGCUGCA-UU-UUUGACGCAUUC---AUU----UAUUGGUAUAGCAUGAACCCCAUCGUAAUUAAUCGGCUUCA
CP000647.1/3179206-3179016   GAAGUUUUUGGUUGUCGCUCUGCC-GGGUGACACUGCACACGAAAGCGUAUUGG--UC--------------UGU-UUCAAAUUACUGUUUGAA--GCGAAUGCU------CAGGUCGGUUUCGUGUGCUGCA-UC-UUUGACGCAUUC---AUU----UAUUGGUAACGCAUGAACCCCAUCGUAAUUAAUCGGCUUCA
U48415.1/72-282              GAAGUUUUAGGUUG-CGC-CGUUU-GGUCGCCACGGCACACGAAACAGCGUUGG--UU-AUAGACAACCUUCUUUCCGCUGCAGCGAUGCGGCAGGACAGAUGACGUGUAUCAGGUCUGUUUCGUGUGCUGGA-UU-GUUGACGCAUUC---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCA
CP000243.1/2845964-2845756   GAAGUUUAAGGUUGGCAC-CUCCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCG-----CUA-AACUGCAGCGAAGCAGUUAGCAGAGCUAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCA
CP000034.1/2599063-2598849   GAAGUUUAAGGUUGGCAC-CUCCA-GGUUUCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGCUAAACUGAAACUGCAGCGAAGCAGUUAGCAGAGCCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCA
D64044.1/11691-11477         GAAGUUUAAGGUUGGCAC-CUCCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGGUAAACUGAAACUGCAGCGAACGAGUUAGCAGAACCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCA
AE014075.1/2967090-2966876   GAAGUUUAAGGUUGGCAC-CUCCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGGUAAACUGAAACUGCAGUGAAGCAGUUAGCCGAGCCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCA
CP000266.1/2697918-2697704   GAAGUUUAAGGUUGGCAC-CUCCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGCUAAACUGAAACUGCAGCGAAGCAGUUAGCAGAGCCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCA
CP000036.1/2601301-2601087   GAAGUUUAAGGUUGGCAC-CUUCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGGUAAACUGAAACUGCAGCGAAGCAGUUAGCAGAGCCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCA
BX571870.1/149010-148833     UCAAACUUAAACUGGCUC-CUAUA-AGGGGCCAGUGCAAACGCAACAGUUUUG---UCG-------------GGG----------GUU--------CCUGUAA--------CAGGUCUGUUGCGUGUGCGUUU-UUAUUUGACGAAUUC---UGACCGAUAUUGGUAGCACAUGAAUCCCAUCGUAAUUAACAGAUUGCA
ABEH02000006.1/190140-190351 GAAGUUUUAGGUUGGCGU-CGUUU-GGUCGCCACGGCACACGAAACAGCGUUGG--UU-AUAGACAACCUUCUUUCCGCUGCAGCGAUGCGGCAGGACAGAUGACGUGUAUCAGGUCUGUUUCGUGUGCUGGA-UU-GUUGACGCAUUC---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCA
CP001127.1/2726770-2726559   GAAGUUUUAGGUUGGCGC-CGUUU-GGUCGCCACGGCACACGAAACAGCGUUGG--UU-AUAGACAACCUUCUUUCCACUGCAGCGAUGCGGCAGGACAGAUGACGUGUAUCAGGUCUGUUUCGUGUGCUGGA-UU-GUUGACGCAUUC---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCA
CU928164.2/2878743-2878529   GAAGUUUAAGGUUGGCAC-CUCCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGGUAAACUGAAACUGCAGCGAAGCAGUUAGCAGAGCCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCA
CP000946.1/1208700-1208914   GAAGUUUAAGGUUGGCAC-CUCCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGGUAAACUGAAACUGCAGCGAAGCAGUUAGCAGAACCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCA
AAMK02000008.1/26052-26266   GAAGUUUAAGGUUGGCAC-CUCCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGCUAAACUGAAACUGCAGCGAAGCAGUUAGCAGAGCCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCA
CP001383.1/2739127-2738913   GAAGUUUAAGGUUGGCAC-CUUCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGCUAAACUGAAACUGCAGCGAAGCAGUUAGCAGAGCCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCA
#=GC SS_cons                 ::::::::::::<<<<<<.<____.>>->>>>><<<<<<<<<<<<<<<------.-<<-<<<<<<-------<<<-<<<<<<______>>>>>>-->>>------>>>>>>-->>->>>>>>>>>>>>>>>::.::.::::::::::::...:::....::::::::::::::::::::::::::::::::<<<<<<<<_
#=GC RF                      GAAguUUaAgGUUGGCgC.cuuua.gGucGCCAcgGCAcACGaAACaGcgUUGg.ccccauauacaguuaaacggacgCugcAgcgaagcaGcgaGccgaaucauguauauCAggUCuGUUuCGUgUGCcgaA.UU.gUUGACGCAUUc...AUu....UAUUGGUAuCgCAUGAAcCCCAUCGUAAUUAAucgGCUucA

CP000720.1/1337539-1337720   GCGGAAGCUGGGCUACACUUUCCAAC
AM286415.1/1137336-1137517   GCGGAAGCUGGGCUACACUUUUCAAC
CP000653.1/3324072-3323909   ACGGAAGCUGGGCUACACUUUUCAGC
CP000647.1/3179206-3179016   ACGAAAGCUGGGCUACACUUUUCAUC
U48415.1/72-282              ACGGAAGCUGGGCUACACUUUUAAUC
CP000243.1/2845964-2845756   ACGGAAGCUGGGCUACACUUUUAAUC
CP000034.1/2599063-2598849   ACGGAAGCUGGGCUACACUUUUAAUC
D64044.1/11691-11477         ACGGAAGCUGGGCUACACUUUUAAUC
AE014075.1/2967090-2966876   ACGGAAGCUGGGCUACACUUUUAAUC
CP000266.1/2697918-2697704   ACGGAAGCUGGGCUACACUUUUAAUC
CP000036.1/2601301-2601087   ACGGAAGCUGGGCUACACUUUUAAUC
BX571870.1/149010-148833     GCGUAAGCUGGGGUACACUUUUGAUC
ABEH02000006.1/190140-190351 ACGGAAGCUGGGCUACACUUUUAAUC
CP001127.1/2726770-2726559   ACGGAAGCUGGGCUACACUUUUAAUC
CU928164.2/2878743-2878529   ACGGAAGCUGGGCUACACUUUUAAUC
CP000946.1/1208700-1208914   ACGGAAGCUGGGCUACACUUUUAAUC
AAMK02000008.1/26052-26266   ACGGAAGCUGGGAUACACUUUUAAUC
CP001383.1/2739127-2738913   ACGGAAGCUGGGCUACACUUUUAAUC
#=GC SS_cons                 ___>>>>>>>>:::::::::::::::
#=GC RF                      ACGgaAGCuggGcUACACUUUUaAuC
//
