gi_545778205_gb_U000_47

cmsearch-Rfam

Family :

CsrC

Id:

RF00084

Type:

Gene; sRNA;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

Description:

The 245 nucleotide sRNA of Escherichia coli, CsrC, was discovered using a genetic screen for factors
that regulate glycogen biosynthesis. CsrC RNA binds multiple copies of CsrA Pfam:PF02599, a protein that
post-transcriptionally regulates central carbon flux, biofilm formation and motility in E. coli. CsrC antagonises the
regulatory effects of CsrA, presumably by sequestering this protein. The discovery of CsrC is intriguing,
in that a similar sRNA, CsrB, performs essentially the same function. Both sRNAs possess similar
imperfect repeat sequences (18 in CsrB, nine in CsrC), primarily localised in the loops of
predicted hairpins, which may serve as CsrA binding elements. Transcription of csrC increases as the
culture approaches the stationary phase of growth and is indirectly activated by CsrA via the
response regulator UvrY [1]. This RNA was also discovered in E. coli during a large
scale screen [2]. The gene called SraK, was highly abundant in stationary phase, but low
levels could be detected in exponentially growing cells as well [2].

Score:

42.8

E-value:

3e-11

From sequence:

4051287

To sequence:

4051243

Alignments:

                                                                             NC
                               ,,,,,,,,,<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>> CS
               RF00084     200 GUgAGUcAaGaaaaaaGGCGaCaGauUacuCuGuCGCCuuuuuuC 244    
                               G  AG  AAGAAAAAAGGCGACAGAUUACUCUGUCGCCUUUUUUC
  gi_545778205_gb_U000 4051287 GCAAGCAAAGAAAAAAGGCGACAGAUUACUCUGUCGCCUUUUUUC 4051243
                               ********************************************* PP

>>

RNAfold
>gi_545778205_gb_U000_47
AUUAAACGGAAAUGGAAUCAACACGGAUUGUUCCGGCUAAAGGAAAAACA
GGGUGUGUUGGCGGCCUGCAAGGAUUGUAAGACCCGUUAAGGGUUAUGAG
UCAGGAAAAAAGGCGACAGAGUAAUCUGUCGCCUUUUUUCUUUGCUUGCU
UUCUGUUAGAUUCCGCCGCAAAUCUAUACUGAAUAAAACGGCUAAAAGAC
GAACCAUUAUGAAACCAUCAUCUUCAAACUCACGCAGCAAAGGUCAUGCA
AAAG
......(((...(((((((...(((((..(((((.......))))...((((.(((....))).))))............(((((.....)))))..((((.((((((((((((((((((....)))))))))))))))))).)))).)..)))))..))))))))))...((((...(((.......((.........)).......((((.....)))).............)))...)))).......... (-70.20)

Length sequence

: 254

Length match:

43