gi_545778205_gb_U000_49

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:

33.5

E-value:

2.5e-05

From sequence:

1295355

To sequence:

1295319

Alignments:

                                                                       NC
                               ::::<<<<<<<<--~~~~~~>>>>>>>>::::::::::: CS
               RF00489       1 AGAAaGGCUUCCAC*[13]*GGGGGCCuUUUUCUUUUGC 46     
                               A AA GGC:UCCAC      GGG:GCC UUUUCUU UGC
  gi_545778205_gb_U000 1295355 AUAACGGCUUCCAC*[ 4]*GGGAGCCGUUUUCUUAUGC 1295319
                               ************98...7..******************* PP

>>

RNAfold
>gi_545778205_gb_U000_49
AGUGGCAUAAGAAAACGGCUCCCUGUUGUGGAAGCCGUUAUAGUGC
....((((.....(((((((.((......)).)))))))...)))) (-15.30)

Length sequence

: 46

Length match:

35