RyeE,

cmscan-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:

8.2e-22

From sequence:

1

To sequence:

86

Alignments:

                                                                                                    NC
             ::::::::::::::::::::::.:::::::::::::::<<<<______>>>>-<<<<<<<<<<<______>>>>>>>>>>>::::: CS
  RF00112  1 ucGauuAAAAacAuaAaCuAaA.AAUguUAGcaauACuAGGAACCACCUCCUUgGCCcGcgcAAUCUCCCUUgcgCgGGCcUuUUu 85
             UCG+U+AAAAACAUAA+C+A+A AAUG+UAGC++UAC+AGGAACCACCUCCUU:GCC:G:G:AAUCUCCCUU:C:C:GGC:U+UUU
    RyeE,  1 UCGCUGAAAAACAUAACCCAUAaAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU 86
             *********************9899999********************************************************** PP

RNAfold
>RyeE,
cgcugaaaaacauaacccauaaaaugcuagcuguaccaggaaccaccucc
uuagccuguguaaucucccuuacacgggcuuauuu
.((((......................))))......((((......)))).(((((((((((......)))))))))))..... (-19.50)

Length sequence

: 85

Length match:

84