# STOCKHOLM 1.0
#=GF ID CopA
#=GF AC RF00042
#=GF DE CopA-like RNA
#=GF AU Bateman A; 0000-0002-6982-4660
#=GF GA 60.0
#=GF NC 59.8
#=GF TC 62.2
#=GF SE Bateman A
#=GF SS Predicted; PFOLD; Moxon SJ
#=GF TP Gene; antisense;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 27.46 -Z 2958934 CM SEQDB
#=GF DR SO; 0000644; antisense_RNA;
#=GF DR GO; 0003729; mRNA binding;
#=GF RN [1]
#=GF RM 2421250
#=GF RT Structural analysis of an RNA molecule involved in replication control of
#=GF RT plasmid R1.
#=GF RA Gerhart E, Wagner H, Nordstrom K
#=GF RL Nucleic Acids Res 1986;14:2523-2538.
#=GF RN [2]
#=GF RM 11894917
#=GF RT Post-transcriptional control of expression of the repA gene of plasmid R1
#=GF RT mediated by a small RNA molecule.
#=GF RA Light J, Molin S
#=GF RL EMBO J 1983;2:93-98.
#=GF RN [3]
#=GF RM 11502000
#=GF RT Real time kinetic studies of the interaction between folded antisense and
#=GF RT target RNAs using surface plasmon resonance.
#=GF RA Nordgren S, Slagter-Jager JG, Wagner GH
#=GF RL J Mol Biol 2001;310:1125-1134.
#=GF RN [4]
#=GF RM 28854680
#=GF RT The CTX-M-14 plasmid pHK01 encodes novel small RNAs and influences host
#=GF RT growth and motility.
#=GF RA Jiang X, Liu X, Law COK, Wang Y, Lo WU, Weng X, Chan TF, Ho PL, Lau TCK
#=GF RL FEMS Microbiol Ecol. 2017; [Epub ahead of print]
#=GF CC In several groups of bacterial plasmids, antisense RNAs regulate copy
#=GF CC number through inhibition of replication initiator protein synthesis.
#=GF CC These RNAs are characterised by a long hairpin structure interrupted by
#=GF CC several unpaired residues or bulged loops. In plasmid R1, the inhibitory
#=GF CC complex between the antisense RNA (CopA) and its target mRNA (CopT) is
#=GF CC characterised by a four-way junction structure and a side-by-side helical
#=GF CC alignment [3].
#=GF WK CopA-like_RNA
#=GF SQ 37

AB011549.2/72471-72383       AUAGCUGAAUUGUUGGCUAUACGGUUU--AAGUGGGCCCCGGUAAUCUU-CUC--AGUCGCCAAAC-UUUCUGAAGAUUAUCGGGGUUUUUGCUU
AB024946.1/39191-39282       AUAGCUGAAUUGUUGGCUAUACGGUUUUUA-GAUGGCCCCGGUAAUCUU-UCUGUACUCGCCAAAG-UUAAAGAAGAUUAUCGGGGUUUUUGCUU
AB040415.1/24427-24516       AUAGCCUGAUUGGUGGCUAUACAGUUU--AAGUAGGCCCCGUUAAUCUU-U-CGUUCCCGCCAAGA-AAUGAGAAGAUUAUCGGGGUUUUUGCUU
V00351.1/909-819             AUAGCUGAAUUGUUGGCUAUACGGUUU--AAGUGGGCCCCGGUAAUCUU-UUCGUAUUCGCCAAAG-UUGAAGAAGAUUAUCGGGGUUUUUGCUU
X02302.1/564-474             AUAGCUGAAUUGUUGGCUAUACGGUUU--AAGUGGGCCCCGGUAAUCUU-UUCGUACUCGCCAAAG-UUGAAGAAGAUUAUCGGGGUUUUUGCUU
X55895.1/565-474             AUAGCUGAAUUGUUGGCUAUACGGUUUUUA-GAUGGCCCCGGUAAUCUU-UCUGCACUCGCCAAAG-UUAGAGAAGAUUAUCGGGGUUUUCGCUU
Y13308.1/1294-1207           AUAGAGCAACAGC-UUCUAUACAGUUUU-AAGUAGGCCCCGGUAAUCUU-CGA--CUCCGCCAAGAAUUGA--AAGAUUUCCGGGGUUUUUGCUU
AF053946.1/59545-59456       AUAGAGCAACAGC-UUCUAUACAGUUUU-AAGUGGGCCCCGGUAACCUU-CUCG-CCUCGCCAAAG-AUGAGGAAGUUUAUCGGGGUUUUUGCUU
AF177050.1/3124-3034         AUAGCUUGAUUGUUGGCUAUACGGUUU--AAGUGGGCCCCGGUAAUCUU-UUCUGACUCGCCAAAG-UUGAAGAAGAUUAUCGGGGUUUUUGCUU
AF348706.1/209069-208980     AUAGCUUGAUUGUUGGCUAUACGGUUU--AAGUGGGCCCCGGUAAUCUU-U-CUGACUCGCCAAAG-UUAAAGAAGAUUAUCGGGGUUUUUGCUU
AJ009980.1/414-326           AUAGAGCAACAGC-UUCUAUGCAGUUU--AUGAAGGCCCCGUUAAUCUU-UUCCU-UCCGCCAAGA-UUGAAGAAGAUUAUCGGGGUUUUUGCUU
AJ009981.1/403-317           AUAGAGCAACAGC-UUCUAUACAGUUU--AGGUAAGCCCCGGUAAUCUU-C--UACGUCGCCAAACAUUGA--AAGAUUAUCGGGGUUUUGUCUU
AY091607.1/5757-5846         AUAGCUGAAUUGUUGGCUAUACGGUUUUUAGAUGG-CCCCGGUAAUCUU-U-CUA-GUCGCCAAAC-UUGAAGAAGAUUAUCGGGGUUUUCACUU
J01762.1/1156-1066           AUAGCUGAAUUGUUGGCUAUACGGUUU--AAGUGGGCCCCGGUAAUCUU-UUCGUACUCGCAAAAG-UUGAAGAAGAUUAUCGGGGUUUUUGCUU
M16167.1/665-575             AUAGCUGAAUUGUUGGCUAUACGGUUU--AAGUGGACCCCGGUAAUCUU-CUCCUCGUCGCCAAAC-UAGAUGAAGAUUAUCGGGUUUUUUGCUU
M16168.1/1216-1126           AUAGCUGAAUUGUUGGCUAUACGGUUU--AAGUGGAUCCCGGUAAUCUU-CUCCUCGUCGCCAAAC-UAGAUGAAGAUUAUCGGGGUUUUUGCUU
AF401292.1/3686-3599         AUAGAGCAACAGC-UUCUAUGCGGUUUU-UAGAUGGCCCCGGUAAUCUU-CUU--CGUCGCCAAACAUAGA--AAGAUUAUCGGGGUUUUCGCUU
CP000244.1/1306-1218         AUAGCUGAAUUGUUGGCUAUACGGUUUC-UUGUUAGCCCCGGUAAUCUU-CUU--CGUCGCCAAACAUAGA--AAGAUUAUCGGGGUUUUUGCUU
M13472.1/235-144             AUAGCUGAAUUGUUGGCUAUACGGUUU--AAGUGGGCCCCGGUAAUCUUCUUCGCAGUCGCCAAAC-UUGACGAAGAUUAUCGGGGUUUUUGCUU
AF135182.4/22566-22477       AUAGAGCAACAGC-UUCUAUACAGCUUU-GAGUGAGCCCCGUUAAUCUU-U-CGUCUCCGCCAAGA-AAUGAGAAGAUUAUCGGGGUUUUUGCUU
DQ381420.1/54109-54021       AUAGCUGAAUUGUUGGCUAUGCGGUUUU-AUG-GGGCCCCGGUAAUCUU-U--CUAGUCGCCAAAC-UUGAAGAAGAUUAUCGGGGUUUUCGCUU
AJ698720.1/112849-112760     AUAGAGCAACAGC-UUCUAUACAGUUU--AAGUAGGCCCCGUUAAUCUU-CUCUUAGUCGCCAAAC-CUGGUGAAGAUUAUCGGGGUUUUUGCUU
CP000035.1/176755-176665     AUAGCUUGAUUGUUGGCUAUACGGUUUU-UAGAUGGCCCCGGUAAUCUU-U-CUCACUCGCCAAAG-UUAAAGAAGAUUAUCGGGGUUUUUGCUU
AY517905.1/24841-24927       AUAGCCUGAUUGGUGGCUAUACAGUUU--AAGUAGGCCCCGUUAAUCUU-CGU---CCCGCCAAGAAAUGA--AAGAUUAUCGGGGUUUUUGCUU
AJ851089.1/21862-21772       AUAGAGCAACAGC-UUCUAUGCAGUUUC-UUGUUAGCCCCGGUAAUCUU-CUCUUAGUCGCCAAAC-CUGGUGAAGAUUAUCGGGGUUUUUGCUU
M26937.1/556-467             AUAGAGCAACCGC-UUCUAUGCAGUUUC-UUGUUAGCCCCGAUAAUCUU-U-CUCACUCGCCAAAG-UUAAAGAAGAUUAUCGGGGUUUUCACUU
AY214164.3/3313-3404         AUAGAGCAACAGC-UUCUAUGCGGUUUC-UUGUUAGCCCCGUUAAUCUUCUUCUCAGUCGCCAAAC-UUGCUGAAGAUUAUCGGGGUUUUCACUU
M27528.1/169-82              AUAGCUGAAUUGUUGGCUAUGUGGUUUU-AUGGGG--CCCGAUAAUCUU-U--CUAAUCGCCAAAC-UUGAAGAAGAUUAUCGGGGUUUUCACUU
ABAN01000047.1/12752-12665   AUAGCCUGAUUGGUGGCUAUACAGUUU--AGGUAAGCCCCGGUAAUCUU-CUU--CGUCGCCAAACAUUGA--AAGAUUAUCGGGGUUUUGUCUU
AB255435.1/103133-103043     AUAGCUGAAUUGUUGGCUAUACGGUUUU-UAGAUGGCCCCGGUAAUCUU-U-CUGACUCGCCAAAG-UUAAAGAAGAUUAUCGGGGUUUUCACUU
AAJT02000104.1/9003-9093     AUAGCUGAAUUGUUGGCUAUACGGUUUC-UUGUUAGCCCCGGUAAUCUU-U-CUCACUCGCCAAAG-UUAAAGAAGAUUAUCGGGGUUUUCACUU
AAJX02000085.1/4103-4193     AUAGCUGAAUUGUUGGCUAUACGGUUUU-AUG-GGGCCCCGGUAAUCUU-CUCUUAGUCGCCAAAC-UUCUCGAAGAUUAUCGGGGUUUUUGCUU
AAJW02000029.1/47300-47209   AUAGCUGAAUUGUUGGCUAUACGGUUUU-UAGAUGGCCCCGUUAAUCUU-CUCUUAGUCGCCAAAC-UUGCUGAAGAUUAUCGGGGUUUUCACUU
AAJT02000054.1/33351-33263   AUAGCUGAAUUGUUGGCUAUACGGUUUU-UAGAUGGCCCCGGUAAUCUU-CUU--CGUCGCCAAACAUAGA--AAGAUUAUCGGGGUUUUCGCUU
CP001123.1/1907-1997         AUAGAGCAACAGU-UUCUAUGUUGUCU--AAAUUGCCCCCGAUAAUCUU-UUUACUGGUCCAAAAAGUGAAACAAGAUUAUCGGGGGUUGUUUUU
AAMK02000010.1/115535-115445 AUAGAGCAACAGC-UUCUAUGCAGUUUC-UUGUUAGCCCCGUUAAUCUU-UCUGGACUCGCCAAAG-UUAGAGAAGAUUAUCGGGGUUUUCACUU
CP001143.1/36115-36202       AUAGCCUGAUUGGUGGCUAUACAGUUU--AAGUAGGCCCCGUUAAUCUU-CUG--UCCCGCCAAGAAUAGA--AAGAUUAUCGGGGUUUUUGCUU
#=GC SS_cons                 <<<<<__________>>>>>::::::::.<<<<<<<<<<<<<<<<<<<<.________________.______>>>>>>>>>>>>>>>>-->>>>
#=GC RF                      AUAGcuuAAuuGuUggCUAUACgGUUUu.aaGcgggCCCCGgUAAUCUU.uucuuaguCGCCAAAa.UugaaGAAGAUUAcCGGGGuucUugCuu
//
