# STOCKHOLM 1.0
#=GF ID RNAI
#=GF AC RF00106
#=GF DE RNAI
#=GF AU Griffiths-Jones SR; 0000-0001-6043-807X
#=GF GA 47.0
#=GF NC 46.9
#=GF TC 47.2
#=GF SE Griffiths-Jones SR
#=GF SS Published; PMID:7535193
#=GF TP Gene; antisense;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 29.53 -Z 2958934 CM SEQDB
#=GF DR SO; 0000644; antisense_RNA;
#=GF DR GO; 0060910; negative regulation of DNA replication initiation involved in plasmid copy number maintenance;
#=GF RN [1]
#=GF RM 7523833
#=GF RT PcnB is required for the rapid degradation of RNAI, the antisense RNA that
#=GF RT controls the copy number of ColE1-related plasmids.
#=GF RA He L, Soderbom F, Wagner EG, Binnie U, Binns N, Masters M
#=GF RL Mol Microbiol 1993;9:1131-1142.
#=GF RN [2]
#=GF RM 7688127
#=GF RT The Escherichia coli pcnB gene promotes adenylylation of antisense RNAI of
#=GF RT ColE1-type plasmids in vivo and degradation of RNAI decay intermediates.
#=GF RA Xu F, Lin-Chao S, Cohen SN
#=GF RL Proc Natl Acad Sci U S A 1993;90:6756-6760.
#=GF RN [3]
#=GF RM 7535193
#=GF RT Surprises at the 3' end of prokaryotic RNA.
#=GF RA Cohen SN
#=GF RL Cell 1995;80:829-832.
#=GF CC RNAI is an antisense repressor of the replication of some E. coli
#=GF CC plasmids, including ColE1. Plasmid replication is usually initiated by
#=GF CC RNAII, which acts as a primer by binding to its template DNA. The
#=GF CC complementary RNAI binds RNAII prohibiting it from its initiation role.
#=GF CC The rate of degradation of RNAI is therefore a major factor in control of
#=GF CC plasmid replication. This rate of degradation is aided by the pcnB
#=GF CC (plasmid copy number B) gene product, which polyadenylates the 3' end of
#=GF CC RNAI targeting it for degradation by PNPase. Please note: This family
#=GF CC contains subsequences annotated as human (Z96734), Arabidopsis (AB003142),
#=GF CC Xenopus (X91243) and S. pombe (L25927, L25928), which match with highly
#=GF CC significant scores. These eukaryotic matches are almost certainly the
#=GF CC result of vector contamination.
#=GF WK RNAI
#=GF SQ 10

AF156893.2/4598-4498 CGAAUUUGGUUACUGCGCUCCUCCA-AGCCAG-UUACCUCGGUUCAAAGAGC-GCCAAC-UCCUCGAACCUUCGAAAAAACCGCCC---GCCAAGGCGGUUUUUUCGU
AJ132618.1/824-723   CGAAUUUGGUGGCAGCGGUCUUGUACACCCUG-UUACCACGGUUCAGAAGUUCCCCAAC-UUACUGAACCUUCGAAAAA-CCACCU---CCCCAGGUGGUUUUUUCGU
D21263.1/151-50      CGAAUUUGGUGGCAGCGGUCUUGUACACCCUG-UUACCACGGUUCAUAAACUUGCCGGU-UUAAUGAACCUUCGAAAAA-CCACCU---UGCCGGGUGGUUUUUUCGU
S42973.1/3-107       AGUAUUUGGUAUCUGCGCUCUGCUGAAGCCAG-UUACCUUCGGAAAAAGAGUUGGUAGC--UCUUGAUCCGGCAAACAAACCACCGCUGGUAGCGGUGGUUUUUUUGU
U65460.1/39-143      AGUAUUUGGUAUCUGUGCUCUGCUGAAGCCAGAUUACCUCGGUUAGAUAAUCUGCCAGGAUUAGCUAACCUUCGAAAAAACCACCU---GCCAGGGUGGUUUUUUCGU
U80803.1/804-704     CAGAUUUGGUUACUGCGUUCCUCCA-AGCCAG-UUACCGCGGUUCAAAGAGUUGGUAGC-UCUGAGAACCUUCGAAAAA-CCGCCU---UGCAGGGCGGUUUUUUCGU
X63534.1/2865-2765   UAGAUUUGGUUACUGCGCUCCUCCA-AGCCAG-UUACCGCGGUUCAAAGAGUUGGUAGC-UCAGAGAACCUUCGAAAAA-CCGCCU---UGCAGGGCGGUUUUUUCGU
X80302.1/245-141     AGUAUUUGGUAUCUGUGCUCUGCUGAAGCCAGAUUACCUCGGUUAGAUAAUCUGCCAGGAUUAGCUAACCUUCGAAAAAACCACCU---GCCAGGGUGGUUUUUUCGU
Y17716.1/6521-6420   CGUAUUUGGUGGCAGCGGUCUUGUACACCCUG-UUACCACGGUUCAGAAGUUCCCCAAC-UUACUGAACCUUCGAAAAA-CCACCU---CCCCAGGUGGUUUUUUCGU
Y17846.1/1185-1085   -AGAUUUGGUGGCAGCGGUCUUGUACACCCUG-UUACCACGGUUCAGAAGUUCCCCAAC-UUACUGAUCCUUCGAAAAA-CCACCU---CCCCAGGUGGUUUUUUCGU
#=GC SS_cons         :::::::<<<<<<<<-<<<_______>>>>>>.>>>>>::<<<<<<<<<<<<_____>>.>>>>>>>>>>::<<<<<<<.<<<<<<...____>>>>>>>>>->>>>:
#=GC RF              aguAUUUGGuggCuGcGcuCuucuaaagCCaG.ccaCCucGGuucggggagcugccAgc.uccccgaaCCuuCGaaaaa.CCgCCc...uccagGGcGGuuuUuuCGU
//
