gi_545778205_gb_U000_195

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:

23.9

E-value:

0.0073

From sequence:

2704095

To sequence:

2704192

Alignments:

                                v                                                                                NC
                               <<<<<<<<<<<<<<<-------<<-<<<<<<--.-----<<<-<<<<<<______>>>>>>-->>>------>>>>>>--> CS
               RF00552      32 cgGCAcACGaAACaGcgUUGgccccauauacag.uuaaacggacgCugcAgcgaugcaGcgaGccgaaucauguauauCAg 111    
                               C GCACACGAAACAG      CC: AUAUACA   U+   :: ::CUGC  CG UGCAG::  ::    C  GUAUAU  :
  gi_545778205_gb_U000 2704095 CAGCACACGAAACAG-----ACCUGAUAUACAUgGUUCUGCU-AACUGCUUCGCUGCAGUUUCAGUUUACCGGUAUAUGGG 2704169
                               ***************.....57*********86157778888.*******************9****************** PP

                                                    v  NC
                               >-......>>>>>>>>>>>>>>> CS
               RF00552     112 gU......CuGUUuCGUgUGCcg 128    
                               G       CUGUUUCGUGUGC G
  gi_545778205_gb_U000 2704170 GAccaacgCUGUUUCGUGUGCCG 2704192
                               *********************** PP

RNAfold
>gi_545778205_gb_U000_195
AGCCGAUUAAUUACGAUGGGGUUCAUGCGAUACCAAUAAAUAAAUGCGUC
AACAAUUCAGCACACGAAACAGACCUGAUAUACAUGGUUCUGCUAACUGC
UUCGCUGCAGUUUCAGUUUACCGGUAUAUGGGGACCAACGCUGUUUCGUG
UGCCGUGGCAACCUGGAGGUGCCAACCUUAAACUUCGGGGGAAUAUUCUA
UACACAACGACGG
..................((..((....))..))............((((.........(((((((((((((.(((.((((((.((((.(((..((((((......)))))).)))...)))))))))).))).......)))))))))))))..(((((.((....))))))).((((........)))).................)))). (-65.20)

Length sequence

: 213

Length match:

96