gi_545778205_gb_U000_228

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:

115.6

E-value:

1.5e-28

From sequence:

3311742

To sequence:

3311628

Alignments:

                                                                                                                 NC
                               ::::::<<<<<<________>>>>>>--------------------<<<<<<<___________>>>>>>>:::::::::: CS
               RF00114       1 ugugaUcgCuGaAUUAGaGAuCgGcgaccauuuuuuuuuuuauuuuuuuGGaGUuauAaaAUGUCuCUaagUGcUGAAGaa 81     
                               UG+GAUCGCUGAAUUAGAGAUCGGCG+CC+UU +U  U+U+++U+ UUUGGAGUU+UAAAAUGUCUCUAAGU+CUGAAG+A
  gi_545778205_gb_U000 3311742 UGGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAU--UCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCA 3311664
                               ***********************************..******************************************** PP

                                                                    NC
                               :::::::::::::::::::::::::::::::::::: CS
               RF00114      82 AAAGCaaAAAUCGUUgCuGAaUUCGguCGuGauGaA 117    
                               A AGC+AAAAUCGUU CUGA UU+GGUCGUGA+G+A
  gi_545778205_gb_U000 3311663 ACAGCUAAAAUCGUUUCUGAGUUUGGUCGUGACGCA 3311628
                               ************************************ PP

>>

RNAfold
>gi_545778205_gb_U000_228
UGCGUCACGACCAAACUCAGAAACGAUUUUAGCUGUUGCUUCAGUACUUA
GAGACAUUUUAAAACUCCAAAGUAUAUAGAAUGAAAGGACGCCGAUCUCU
AAUUCAGCGAUCCCAG
.(((((.........(((.......(((..(((....)))..))).....))).(((((((..(((....)))...)))))))....))))).((((.((.....)).)))).... (-17.70)

Length sequence

: 116

Length match:

113