gi_545778205_gb_U000_16

cmsearch-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:

129.5

E-value:

1.5e-28

From sequence:

3055983

To sequence:

3056166

Alignments:

                                v                              v                                  v              NC
                               :<<<<<<<<<<<<<<-<<<-------------<<<<-<<<<<<----------------.<<<-<<<<<----<<<<<<<- CS
               RF00013       1 aaauccCUGcggUGUUCGucAguugcuuauaaguccCUGAgCCgAuaauuUuuuuaauu.GGGagcccuaucUuucaagug 80     
                               A :UC:CUG:G:UGUUCG: AG +G++ A    :CCCUGAGCCGAUA UU  U+  A++ G::+G:: : ++ ::C:::UG
  gi_545778205_gb_U000 3055983 AUUUCUCUGAGAUGUUCGCAAGCGGGCCAG--UCCCCUGAGCCGAUAUUUCAUACCACAaGAAUGUGGCGCUCCGCGGUUG 3056061
                               ******************************..79999******************************************** PP

                                                                           v                              v      NC
                               ----<<---<<<<<______>>>>>-->>----->>>>>>>-->>>>>->>>------------->>>>>>->>>>----- CS
               RF00013      81 GuGuGcAaGCCuggCUUGuAccaGGAAgCcuaAAacuugaaacagggcaCCCACCUggaAcagCaGGuUCAAggacuuaau 161    
                               GUG+GCA+GC::GG  +GU CC::GAAGCCU AAA:::G::AC: ::CA::CACCU+GAAC+  +GGUUCAAGG:  UA++
  gi_545778205_gb_U000 3056062 GUGAGCAUGCUCGGUCCGU-CCGAGAAGCCUUAAAACUGCGACGACACAUUCACCUUGAACCAAGGGUUCAAGGGU-UACA 3056140
                               *******************.****************************************************9997.8899 PP

                                                       v   NC
                               -------->>>>>>>>>>>>>>>>>:: CS
               RF00013     162 gacgaCaaaCGGCAccgCGGggauuuu 188    
                               G C  C  :CGGCA:C:CGG:GA: ++
  gi_545778205_gb_U000 3056141 GCCUGCG-GCGGCAUCUCGGAGAUUCC 3056166
                               9999999.******************* PP

RNAfold
>gi_545778205_gb_U000_16
AAUUUCUCUGAGAUGUUCGCAAGCGGGCCAGUCCCCUGAGCCGAUAUUUC
AUACCACAAGAAUGUGGCGCUCCGCGGUUGGUGAGCAUGCUCGGUCCGUC
CGAGAAGCCUUAAAACUGCGACGACACAUUCACCUUGAACCAAGGGUUCA
AGGGUUACAGCCUGCGGCGGCAUCUCGGAGAUUCCCU
....((((((((((((.(((..((((((....(((.((((((.....((((........(((((((.((...(((((((..((((....(((((.....)))))....)))).))))))).)).)))))))....)))).....)))))).))).....)))))).)))))))))))))))...... (-80.10)

Length sequence

: 187

Length match:

182