gi_545778205_gb_U000_202

cmsearch-Rfam

Family :

RprA

Id:

RF00034

Type:

Gene; sRNA;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

GO:0003729 mRNA binding

Description:

Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a
double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the
translation initiation site. Clones carrying rprA (RpoS regulator RNA A) increased the translation of RpoS.
The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is
predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate
in the positive regulation of RpoS translation. RprA also appears to bind to the RpoS
leader [2]. RprA is non-essential [1]. The Y. pestis homologue was detected by similarity to
the E. coli gene (pers obs. Bateman A).

Score:

117.6

E-value:

2.6e-18

From sequence:

1770372

To sequence:

1770479

Alignments:

                                                                                                                 NC
                               :<<<<_____________>>>>,,,,,,,,,<<-<<_____>>->>,,,,,,,,,,,,,,,<<<___>>>,,,,,,,,<<< CS
               RF00034       1 AcguuucUAaAuuAAcuuaaugauuuuuAaucaUggaaaUccccugauuGAAauaacGaAUUGCUGUGUGUAGUCUUUGCC 81     
                               ACG:UU+UAAAU+AAC+UA:UGAUUU+UAA CAUGGAAAUCCCCUGA+UGAAA+AACGAAUUGCUGUGUGUAGUCUUUGCC
  gi_545778205_gb_U000 1770372 ACGGUUAUAAAUCAACAUAUUGAUUUAUAAGCAUGGAAAUCCCCUGAGUGAAACAACGAAUUGCUGUGUGUAGUCUUUGCC 1770452
                               ********************************************************************************* PP

                                                           NC
                               <<<<______>>>>>>>:::::::::: CS
               RF00034      82 cgUCaCCUAaGAcgGGCUUUUUUUUuu 108    
                               C:UC+CC A GA:GGGCUUUUUUUU++
  gi_545778205_gb_U000 1770453 CAUCUCCCACGAUGGGCUUUUUUUUAA 1770479
                               *************************** PP

RNAfold
>gi_545778205_gb_U000_202
CGGUUAUAAAUCAACAUAUUGAUUUAUAAGCAUGGAAAUCCCCUGAGUGA
AACAACGAAUUGCUGUGUGUAGUCUUUGCCCAUCUCCCACGAUGGGCUUU
UUUUUAA
.(.(((((((((((....))))))))))).)..((....)).................(((((.....)))))....(((((((......))))))).......... (-24.80)

Length sequence

: 107

Length match:

106