gi_545778205_gb_U000_190

cmsearch-Rfam

Family :

RNAI

Id:

RF00106

Type:

Gene; antisense;

Taxonomy:

Eukaryota; Bacteria; Viruses;

Ontology:

GO:0060910 negative regulation of DNA replication initiation involved in plasmid copy number maintenance

Description:

RNAI is an antisense repressor of the replication of some E. coli plasmids, including ColE1. Plasmid
replication is usually initiated by RNAII, which acts as a primer by binding to its
template DNA. The complementary RNAI binds RNAII prohibiting it from its initiation role. The rate
of degradation of RNAI is therefore a major factor in control of plasmid replication. This
rate of degradation is aided by the pcnB (plasmid copy number B) gene product, which
polyadenylates the 3' end of RNAI targeting it for degradation by PNPase. Please note: This
family contains subsequences annotated as human (Z96734), Arabidopsis (AB003142), Xenopus (X91243) and S. pombe (L25927,
L25928), which match with highly significant scores. These eukaryotic matches are almost certainly the result
of vector contamination.

Score:

29.2

E-value:

0.0035

From sequence:

2653311

To sequence:

2653385

Alignments:

                                                   v                     v                                      NC
                               :::::::<~~~~~~>,,<<<<<<<<<<<<_____>>>>>>>>>>>>--<<<<<<<<<<<<<____>>>>>>>>>->>>>: CS
               RF00106       1 aguAUUUG*[28]*CucGGuucggggagcugccAgcuccccgaaCCuuCGaaaaaCCgCCcuccagGGcGGuuuUuuCGU 102    
                               ++ AUUU:      :  G:: :: ::A:: G   ::U:: :: ::C  ::AAAAACCGCC      GGCGGUUU UU::U
  gi_545778205_gb_U000 2653311 CAGAUUUA*[ 5]*UGAGCCAGUGAAAUAAG---UAUUUUACAGGCAAUAAAAAACCGCCGAAUUUGGCGGUUU-UUUAU 2653385
                               *******6...7..68899999999998854...888999999999***************************9.999** PP

RNAfold
>gi_545778205_gb_U000_190
UGGGGCGCGCGGGCAGAUUUACCGGUUGAGCCAGUGAAAUAAGUAUUUUA
CAGGCAAUAAAAAACCGCCGAAUUUGGCGGUUUUUUAUUGCUAGUCUGGU
UC
...(((..((.((........)).))...))).(((((((....))))))).((((((((((((((((((....)))))))))))))))))).......... (-38.20)

Length sequence

: 102

Length match:

73