# STOCKHOLM 1.0
#=GF ID MicC
#=GF AC RF00121
#=GF DE MicC RNA
#=GF AU Moxon SJ; 0000-0003-4644-1816
#=GF GA 90.0
#=GF NC 71.8
#=GF TC 96.4
#=GF PI IS063
#=GF SE Hershberg R
#=GF SS Predicted; PFOLD
#=GF TP Gene; sRNA;
#=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; 0040033; sRNA-mediated gene silencing;
#=GF DR GO; 0003729; mRNA binding;
#=GF DR SO; 0000370; small_regulatory_ncRNA;
#=GF RN [1]
#=GF RM 12069726
#=GF RT A bioinformatics based approach to discover small RNA genes in the
#=GF RT Escherichia coli genome.
#=GF RA Chen S, Lesnik EA, Hall TA, Sampath R, Griffey RH, Ecker DJ, Blyn LB
#=GF RL Biosystems 2002;65:157-177.
#=GF RN [2]
#=GF RM 15466019
#=GF RT MicC, a second small-RNA regulator of Omp protein expression in
#=GF RT Escherichia coli.
#=GF RA Chen S, Zhang A, Blyn LB, Storz G
#=GF RL J Bacteriol 2004;186:6689-6697.
#=GF RN [3]
#=GF RM 29211019
#=GF RT Dual Regulation of the Small RNA MicC and the Quiescent Porin OmpN in
#=GF RT Response to Antibiotic Stress in Escherichia coli.
#=GF RA Dam S, Pages JM, Masi M
#=GF RL Antibiotics (Basel). 2017; [Epub ahead of print]
#=GF CC MicC (previously known as IS063 [1]) is located between the ompN and ydbK
#=GF CC genes in E. coli. This family of Hfq-associated sRNA is thought to be a
#=GF CC regulator of OmpC expression. MicC inhibits the 30S ribosome binding
#=GF CC through a conserved 22 bp RNA duplex near the start codon of the ompC
#=GF CC mRNA. Along with Rfam:RF00033 it may act in conjunction with EnvZ-OmpR
#=GF CC two-component system to control the OmpF/OmpC protein ratio in response to
#=GF CC a variety of environmental stimuli [2]. The expression of micC was shown
#=GF CC to be increased in the presence of beta-lactam antibiotics. The metabolic
#=GF CC activity of E.coli expressing either OmpC or OmpF was strongly inhibited
#=GF CC upon exposure to beta-lactams [3].
#=GF WK MicC_RNA
#=GF SQ 8

AL627270.1/60166-60286     CCUGUUAUAUGCCUUUAUUGUCAC---AUAUUCAUUUUGUCGUUGGGCCAUUGC---GUUAACCU-UUGCUUUCCAGCGUAUAAAUUGACAAGCCCGAAC-GGAU----GUUCGGGCUUUUUUUGUCUA-UGGA
AJ277528.1/288-168         CGUGUUAUAUGCCUUUAUUGUCAC----GUUUAUUUUUC--GUUGACGUAUUGAUA-GCUAUUAU-UAAUUAGCCAGCGAAUAAAUUGACAAGCCCGAACAACCC----GUUCGGGCUUUUUUUUGGGU-UCCA
CP000034.1/1341223-1341344 CGGGUUAUAUGCCUUUAUUGUCAC---AGAUUUUAUUUUCUGUUGGGCCAUUGC---AUUGCUAC-UGAUUUUCCAACAUAUAAAAAGACAAGCCCGAAC-AGUC----GUCCGGGCUUUUUUUUAGAAUUGGA
AACY022965012.1/342-461    CGUGUUAUAUGCCUUUAUUGUCAC---GUUUUAUUUUUC--GUUGGUAUAUUGAUG-GUAAUUAU-UAAUUAGCCAGCGAAUAAAUUGACAAGCCCGAAC-AACU----GUUCGGGCUUUUUUUUGG--UUCCA
EF682131.1/218-344         UGGGUUAUAUGCCUUUAUUGUCAUUUAAAAUUUAUAUUGUUGCCGUCUCAUUCAUAUCGAAUGAU-UAAUUCGUCGGAAAAU-----GACAAGCCCGAAUAGUUUUACUAUUCGGGCUUUUUUUAUUGC-GCCA
CP000647.1/1603837-1603960 CGCGUUAUAUGCCUUUAUUGUCAUGCCAAUAAUUUAUUGUUGCCGUCUCAUUCUGC-GGAAUGAUGUUGUUUAUCGGUAAAA----CGACAAGCCCGAACGUUGU----GUUCGGGCUUUUUUUAUGGA-CAAA
AE006468.1/1745789-1745671 CCUGUUAUAUGCCUUUAUUGUCAC---AUAUUCAUUUUGUCGCUGGGCCAUUGC---GUUAACCU-UUGCUUUCCAGCGUAUAAAUUGACAAGCCCGAAC-GGAU----GUUCGGGCUUUUUUUGU---UUCCA
CP001509.3/1412677-1412798 CGGGUUAUAUGCCUUUAUUGUCAC---AGAUUUUAUUUUCUGUUGGGCCAUUGC---AUUGCCAC-UGAUUUUCCAACAUAUAAAAAGACAAGCCCGAAC-AGUC----GUCCGGGCUUUUUUUUUAGAAUUGG
#=GC SS_cons               ::::::<<<<<____>>->>>:::...::::::::::::::<<<<<<_________.________.______>>>>>>:::::::::<<-<<<<<<<<<<.____....>>>>>>>>>>>>::::::::.::::
#=GC RF                    CguGUUAuAUGCCUUUAUUgUCAc...AuaUUuuUuUUguugcuGgcucAUUgaua.guuAuuAU.UaaUUugcCagcaaAUAAAuuGACAAGCCCGaAC.auuu....GUuCGGGCUUUUUUUuugga.uccA
//
