gi_545778205_gb_U000_229

cmsearch-Rfam

Family :

S15

Id:

RF00114

Type:

Cis-reg; leader;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

Description:

The E. coli Ribosomal S15 gene 5' UTR can form two alternative structures. One that is
a series of three hairpins, The other includes a pseudoknot. This structure causes translational regulation
of the S15 protein. The alignment of this family contains only the final two hairpins
which are conserved in other species, and also includes the complete region that forms the
alternate structures.

Score:

22.8

E-value:

0.0078

From sequence:

4179932

To sequence:

4180052

Alignments:

                                          v          v                          vvv                    vvv       NC
                               ::::::<<<<<<___.._____>>>>>>----------.----------<<<<<<<____._______>>>>>>>:::::: CS
               RF00114       1 ugugaUcgCuGaAUU..AGaGAuCgGcgaccauuuuuu.uuuuuauuuuuuuGGaGUuau.AaaAUGUCuCUaagUGcUGA 77     
                               U  G+U:G :: A U  AG+GA :: C: + AUUUU U U  ++A+ +U   G AG +A+  +AAUG CU U   U +U A
  gi_545778205_gb_U000 4179932 UCCGUUUGGAGGAGUgaAGUGAGUUCCAGAGAUUUUCUcUGGCAAACAUCCAGGAGCAAAgCUAAUGGCUUUAAAUCUUCA 4180012
                               *************************************877777777777778***************************** PP

                                                                        NC
                               :::::::::::::::::::::::::::::::::::::::: CS
               RF00114      78 AGaaAAAGCaaAAAUCGUUgCuGAaUUCGguCGuGauGaA 117    
                               AGA AAA  A++ AU GUUGCUGAA UC G  ++G  G+ 
  gi_545778205_gb_U000 4180013 AGACAAACAAGCGAUUGUUGCUGAAGUCAGCGAAGUAGCC 4180052
                               **************************************** PP

RNAfold
>gi_545778205_gb_U000_229
CCGUUUGGAGGAGUGAAGUGAGUUCCAGAGAUUUUCUCUGGCAAACAUCC
AGGAGCAAAGCUAAUGGCUUUAAAUCUUCAAGACAAACAAGCGAUUGUUG
CUGAAGUCAGCGAAGUAGCC
..((((.(((((.(((((......(((((((...))))))).......(((..(((...)))..))))))))..))))).))))......((.....((((((....))))))....)). (-34.50)

Length sequence

: 120

Length match:

119