gi_545778205_gb_U000_53

cmsearch-Rfam

Family :

CyaR_RyeE

Id:

RF00112

Type:

Gene; sRNA;

Taxonomy:

Eukaryota; Bacteria; Viruses;

Ontology:

Not found

Description:

This sRNA was originally identified in a large scale screen of E. coli. It was shown
to bind Hfq and called RyeE [1]. This sRNA has since been characterised as a
post-transcriptional regulator of the 18 kDa OmpX porin in Salmonella [2]. Phylogenetic and mutational analyses
suggest that a conserved RNA hairpin of this sRNA which features a C-rich apical loop,
acts to sequester the Shine-Dalgarno sequence of ompX mRNA and inhibits translational initiation [2]. The
expression of this sRNA has been shown to be tightly controlled by the cyclic AMP
receptor protein, CRP and has been renamed CyaR (cyclic AMP-activated RNA)[2]. CyaR appears to be
highly conserved amongst enterobacteria and the cyaR gene is frequently located downstream of the yegQ
gene.

Score:

99.7

E-value:

1.8e-20

From sequence:

2167112

To sequence:

2167197

Alignments:

                                                                                                                 NC
                               ::::::::::::::::::::::.:::::::::::::::<<<<______>>>>-<<<<<<<<<<<______>>>>>>>>>>> CS
               RF00112       1 ucGauuAAAAacAuaAaCuAaA.AAUguUAGcaauACuAGGAACCACCUCCUUgGCCcGcgcAAUCUCCCUUgcgCgGGCc 80     
                               UCG+U+AAAAACAUAA+C+A+A AAUG+UAGC++UAC+AGGAACCACCUCCUU:GCC:G:G:AAUCUCCCUU:C:C:GGC:
  gi_545778205_gb_U000 2167112 UCGCUGAAAAACAUAACCCAUAaAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCU 2167192
                               *********************9899999***************************************************** PP

                                     NC
                               ::::: CS
               RF00112      81 UuUUu 85     
                               U+UUU
  gi_545778205_gb_U000 2167193 UAUUU 2167197
                               ***** PP

RNAfold
>gi_545778205_gb_U000_53
CGCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCC
UUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU
.((((......................))))......((((......)))).(((((((((((......)))))))))))..... (-19.50)

Length sequence

: 85

Length match:

84