gi_545778205_gb_U000_194

cmsearch-Rfam

Family :

rncO

Id:

RF00552

Type:

Cis-reg;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

Description:

This family represents a bacterial regulatory element (rncO) found in the rnc leader sequence. The rnc
operon is negatively auto-regulated by transcript stability. rnc, the first gene in the operon codes
for RNase III which cleaves the long rncO stem II leading to transcript degradation and
a reduction in translation [1].

Score:

256.9

E-value:

3.3e-62

From sequence:

2704223

To sequence:

2704009

Alignments:

                                                                                                                 NC
                               ::::::::::::<<<<<<<____>>->>>>><<<<<<<<<<<<<<<------.-<<-<<<<<<-------<<<-<<<<<<_ CS
               RF00552       1 gAAguUUaAgGUUGGCgCcUuuagGucGCCAcgGCAcACGaAACaGcgUUGg.ccccauauacaguuaaacggacgCugcA 80     
                               GAAGUUUAAGGUUGGC:CCU +AGGU:GCCAC:GCACACGAAACAGCGUUGG CCCCAUAUAC+G UAAAC:GA::CUGCA
  gi_545778205_gb_U000 2704223 GAAGUUUAAGGUUGGCACCUCCAGGUUGCCACGGCACACGAAACAGCGUUGGuCCCCAUAUACCGGUAAACUGAAACUGCA 2704143
                               *****************************************************9*************************** PP

                                                                                                                 NC
                               _____>>>>>>-->>>------>>>>>>-->>->>>>>>>>>>>>>>>--------------------------------- CS
               RF00552      81 gcgaugcaGcgaGccgaaucauguauauCAggUCuGUUuCGUgUGCcgaAUUuUUGACGCAUUcAUuUAUUGGUAuCgCAU 161    
                               GCGA+GCAG::AGC:GAA+CAUGUAUAUCAGGUCUGUUUCGUGUGC:GAAUU+UUGACGCAUU+AUUUAUUGGUAUCGCAU
  gi_545778205_gb_U000 2704142 GCGAAGCAGUUAGCAGAACCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAAUUGUUGACGCAUUUAUUUAUUGGUAUCGCAU 2704062
                               ********************************************************************************* PP

                                                                                     NC
                               ------------------<<<<<<<<____>>>>>>>>::::::::::::::: CS
               RF00552     162 GAAcCCCAUCGUAAUUAAccgGCUucAaCGgaAGCuggGcUACACUUUUaAuC 214    
                               GAACCCCAUCGUAAUUAA:CGGCUUCAACGGAAGCUG:GCUACACUUUUAAUC
  gi_545778205_gb_U000 2704061 GAACCCCAUCGUAAUUAAUCGGCUUCAACGGAAGCUGGGCUACACUUUUAAUC 2704009
                               ***************************************************** PP

>>

RNAfold
>gi_545778205_gb_U000_194
AUUAAAAGUGUAGCCCAGCUUCCGUUGAAGCCGAUUAAUUACGAUGGGGU
UCAUGCGAUACCAAUAAAUAAAUGCGUCAACAAUUCAGCACACGAAACAG
ACCUGAUAUACAUGGUUCUGCUAACUGCUUCGCUGCAGUUUCAGUUUACC
GGUAUAUGGGGACCAACGCUGUUUCGUGUGCCGUGGCAACCUGGAGGUGC
CAACCUUAAACUUC
.....((((..(((((((((((....)))))((........)).))))(((.((((.................)))).)))......(((((((((((((.(((.((((((.((((.(((..((((((......)))))).)))...)))))))))).))).......)))))))))))))..(((((.((....)))))))..))...)))). (-68.20)

Length sequence

: 214

Length match:

213