Ec_OxyS,

cmscan-Rfam

Family :

OxyS

Id:

RF00035

Type:

Gene; sRNA;

Taxonomy:

Bacteria;

Ontology:

Not found

Description:

OxyS is a small untranslated RNA which is induced in response to oxidative stress in Escherichia
coli. This novel RNA acts as a global regulator to activate or repress the expression
of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s)
subunit of RNA polymerase [1]. OxyS is bound by the Hfq protein, that increases the
OxyS RNA interaction with its target messages [2].

Score:

139.3

E-value:

4.2e-32

From sequence:

1

To sequence:

110

Alignments:

                                                                                                                     NC
               <<<<<<<-<<<<-<<-<<___________>>->>-->>>>>>>>>>>,,<<<<______>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<____ CS
   RF00035   1 ggaaCGGAGCgGuacCuCuUUUAACCCUUGaAguCACcGCCCGuuccGAGgGuuUCUCAaCcCGAAUAACUAAAGCCAACGUGAACUUUUGcGGacCUCcA 101
               G:AACGGAGC:G+ACCUCUUUUAACCCUUGAAGUCAC:GCCCGUU:CGAG:GUUUCUCAAC:CGAAUAACUAAAGCCAACGUGAACUUUUGCGGA:CUCCA
  Ec_OxyS,   1 GAAACGGAGCGGCACCUCUUUUAACCCUUGAAGUCACUGCCCGUUUCGAGAGUUUCUCAACUCGAAUAACUAAAGCCAACGUGAACUUUUGCGGAUCUCCA 101
               ***************************************************************************************************** PP

                         NC
               _>>>>>>>: CS
   RF00035 102 uGguCCgCU 110
               +G:UCCGCU
  Ec_OxyS, 102 GGAUCCGCU 110
               ********* PP

RNAfold
>Ec_OxyS,
aaacggagcggcaccucuuuuaacccuugaagucacugcccguuucgaga
guuucucaacucgaauaacuaaagccaacgugaacuuuugcggaucucca
ggauccgcu
...((((((((((...((((........))))....)).)))))))).(((((....)))))...........................((((((((...)))))))). (-29.40)

Length sequence

: 109

Length match:

108