ssrS

cmscan-Rfam

Family :

6S

Id:

RF00013

Type:

Gene;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

Description:

E. coli 6S RNA was the first non coding RNA to be sequenced, but its function
was unknown until recently. It consists of 184 nucleotides that fold into an extended hairpin
structure with a large single-stranded internal bulge. The 6S RNA specifically associates with RNA polymerase
holoenzyme containing the sigma70 specificity factor. This interaction represses expression from a sigma70-dependent promoter during
stationary phase [1]. 6S RNA homologs have recently been identified in most bacterial genomes [2,3].
Many Gram-positive species have two copies of 6S RNA. In Bacillus subtilis, both copies appear
to interact with RNA polymerase holoenzyme containing the housekeeping sigma factor and be expressed during
different stages of growth. In many proteobacteria, 6S RNA may be processed from a transcript
encoding homologs of the E. coli YgfA protein which is a putative methenyltetrahydrofolate synthetase.

Score:

125.0

E-value:

2e-28

From sequence:

1

To sequence:

183

Alignments:

               v v                            v                                  v                                   NC
              :<<<<<<<<<<<<<<-<<<-------------<<<<-<<<<<<----------------.<<<-<<<<<----<<<<<<<-----<<---<<<<<______> CS
  RF00013   1 aaauccCUGcggUGUUCGucAguugcuuauaaguccCUGAgCCgAuaauuUuuuuaauu.GGGagcccuaucUuucaagugGuGuGcAaGCCuggCUUGuAc 101
              A :UC:CUG:G:UGUUCG: AG +G++ A    :CCCUGAGCCGAUA UU  U+  A++ G::+G:: : ++ ::C:::UGGUG+GCA+GC::GG  +GU C
     ssrS   1 AUUUCUCUGAGAUGUUCGCAAGCGGGCCAG--UCCCCUGAGCCGAUAUUUCAUACCACAaGAAUGUGGCGCUCCGCGGUUGGUGAGCAUGCUCGGUCCGU-C 99 
              ******************************..79999***************************************************************.* PP

                                     v                              v                           v v   NC
              >>>>-->>----->>>>>>>-->>>>>->>>------------->>>>>>->>>>------------->>>>>>>>>>>>>>>>>:: CS
  RF00013 102 caGGAAgCcuaAAacuugaaacagggcaCCCACCUggaAcagCaGGuUCAAggacuuaaugacgaCaaaCGGCAccgCGGggauuuu 188
              C::GAAGCCU AAA:::G::AC: ::CA::CACCU+GAAC+  +GGUUCAAGG:  UA++G C  C  :CGGCA:C:CGG:G : U+
     ssrS 100 CGAGAAGCCUUAAAACUGCGACGACACAUUCACCUUGAACCAAGGGUUCAAGGGU-UACAGCCUGCG-GCGGCAUCUCGGAG-AUUC 183
              ***************************************************9997.88999999999.**************.9*** PP

RNAfold
>ssrS
UUUCUCUGAGAUGUUCGCAAGCGGGCCAGUCCCCUGAGCCGAUAUUUCAU
ACCACAAGAAUGUGGCGCUCCGCGGUUGGUGAGCAUGCUCGGUCCGUCCG
AGAAGCCUUAAAACUGCGACGACACAUUCACCUUGAACCAAGGGUUCAAG
GGUUACAGCCUGCGGCGGCAUCUCGGAGAUUC
..((((((((((((.(((..((((((....(((.((((((.....((((........(((((((.((...(((((((..((((....(((((.....)))))....)))).))))))).)).)))))))....)))).....)))))).))).....)))))).)))))))))))))))... (-80.10)

Length sequence

: 182

Length match:

182