dsrA

cmscan-Rfam

Family :

DsrA

Id:

RF00014

Type:

Gene; sRNA;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

Description:

DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation,
by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA
can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA
is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is
essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as
a transcription terminator, can be substituted by the trp transcription terminator without loss of either
DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream
leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message
might be important for translational regulation.

Score:

90.2

E-value:

1.3e-18

From sequence:

1

To sequence:

85

Alignments:

                                                                                                     NC
             :::<<<<<<<_____>>>>>>>,,,<<<<<.<<<<<<<<_____>>>>>>>>->>->>>-<<<<<<<.-<<____>>->>>>>>>:: CS
  RF00014  1 aaCaCauCaGAUUUCCuGguGuAACgaauu.uuuaaGugCUUCUugCuuaagCaaGuucaauCCcGa.cccCuucggGuCgGGauUU 85
             A  ACAUCAGAUUUCCUGGUGUAAC:AAUU UUUAAGUGCUUCUUGCUUAAGCAAGUU: AUCCCGA CCCCU++GGGUCGGGAUU 
     dsrA  1 AC-ACAUCAGAUUUCCUGGUGUAACGAAUUuUUUAAGUGCUUCUUGCUUAAGCAAGUUUCAUCCCGAcCCCCUCAGGGUCGGGAUU- 85
             *8.**************************99************************************44555555**********8. PP

RNAfold
>dsrA
CACAUCAGAUUUCCUGGUGUAACGAAUUUUUUAAGUGCUUCUUGCUUAAG
CAAGUUUCAUCCCGACCCCCUCAGGGUCGGGAUU
.(((((((.....)))))))...(((((((((((((.......))))))).)))))).((((((((((.....)))))))))). (-31.90)

Length sequence

: 84

Length match:

83