gi_545778205_gb_U000_50

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:

24.6

E-value:

0.0099

From sequence:

2887562

To sequence:

2887520

Alignments:

                                                                              NC
                               ::::<<<<<<<<--<<<<____>>>>->>>>>>>>::::::::::: CS
               RF00489       1 AGAAaGGCUUCCACGACGGCaACGUUuGGGGGCCuUUUUCUUUUGC 46     
                                 AAA GC:UC   G C:G AA:G U  GG:GC UUUUU UUUUGC
  gi_545778205_gb_U000 2887562 UUAAACGCCUCU--GUCAGAAAUGAU-GGGGGCGUUUUUAUUUUGC 2887520
                               ***********8..99**********.7****************** PP

RNAfold
>gi_545778205_gb_U000_50
CGCAAAAUAAAAACGCCCCCAUCAUUUCUGACAGAGGCGUUUAAUU
..........(((((((.(..(((....)))..).))))))).... (-10.60)

Length sequence

: 46

Length match:

41