gi_545778205_gb_U000_99

cmsearch-Rfam

Family :

L20_leader

Id:

RF00558

Type:

Cis-reg; leader;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

Description:

This family is a putative r-protein leader autoregulatory structure [1] found in B. subtilis and other
low-GC Gram-positive bacteria. It is located in the 5' untranslated regions of mRNAs encoding initiation
factor 3 followed by ribosomal proteins L35 and L20 (infC-rpmI-rplT). A Rho-independent transcription terminator structure
that is probably involved in regulation is included at the 3' end.

Score:

31.8

E-value:

0.00054

From sequence:

3639270

To sequence:

3639368

Alignments:

                                                         v          v                                            NC
                               ::::::::::~~~~~~,<<<---.<<<<<_____>>->>>-->>>------------------------------------ CS
               RF00558       1 uaaaaaAAGa*[16]*CgCCUua.gacgCaUaaAGcaguuCAGGcuaaauuauauuuuuuuuuuuuauguuauuuuuaaaG 90     
                                A A  A G+       GCCU+A  A GC UA+ GC  U CAGGC           ++UUUU   U+UGU+AU + U   G
  gi_545778205_gb_U000 3639270 GAGAUUAUGU*[ 1]*GGCCUGAu-AAGCGUAGCGC-AU-CAGGC-----------AAUUUUGCGUUUGUAAUCAGUCUCG 3639331
                               **********...6..9*****98.89**9999999.77.*****...........8888899999999999999****** PP

                                                                     NC
                               <<<<<<<<<<____>>>>>>>>>>::::::::::::: CS
               RF00558      91 gGCGGgcgugUuuacacgcCCGCcuUUUUUUUuuuuu 127    
                               :GCGGG:::GUUUAC:::CCCGC:UUUUUU U + UU
  gi_545778205_gb_U000 3639332 AGCGGGUCAGUUUACUGGCCCGCUUUUUUUAUGCGUU 3639368
                               ************************************* PP

RNAfold
>gi_545778205_gb_U000_99
UCAAUAGAUUGCAGAGAUUAUGUAGGCCUGAUAAGCGUAGCGCAUCAGGC
AAUUUUGCGUUUGUAAUCAGUCUCGAGCGGGUCAGUUUACUGGCCCGCUU
UUUUUAUGCGUUAUUAUUGCUGAAGU
......(((((((((..........(((((((..(((...)))))))))).........)))))))))......(((((((((((....))))))))))).(((((.(((.......)))))))). (-43.40)

Length sequence

: 126

Length match:

97