gi_545778205_gb_U000_51

cmsearch-Rfam

Family :

ctRNA_p42d

Id:

RF00489

Type:

Gene; antisense;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

Description:

This family represents a group of ctRNAs (or counter-transcribed RNAs) from p42d and related plasmids. ctRNAs
are small, highly structured, antisense sequences which are involved in negative regulation. Members of this
family are known to bind to the mRNA of repC causing translational repression [1]. This
model contains the predicted stem-loop structure followed by a U-rich tract which is proposed to
act as a Rho-independent transcriptional terminator.

Score:

26.9

E-value:

0.0021

From sequence:

848370

To sequence:

848335

Alignments:

                                                                    NC
                              ::::<<<<<<<<~~~~~~>>>>>>>>::::::::::: CS
               RF00489      1 AGAAaGGCUUCC*[15]*GGGGGCCuUUUUCUUUUGC 46    
                              A A  GGCU:CC      GG:GGCC UUUU UUUUGC
  gi_545778205_gb_U000 848370 AAAGCGGCUUCC*[ 5]*GGAGGCCGUUUUGUUUUGC 848335
                              ************...8..******************* PP

>>

RNAfold
>gi_545778205_gb_U000_51
GGCUGCAAAACAAAACGGCCUCCUGUCAGGAAGCCGCUUUUAUCG
...............((((.((((...)))).))))......... (-11.30)

Length sequence

: 45

Length match:

34