chr11_1

cmsearch-Rfam

Family :

5S_rRNA

Id:

RF00001

Type:

Gene; rRNA;

Taxonomy:

Eukaryota; Bacteria; Viruses; Archaea;

Ontology:

GO:0003735 structural constituent of ribosomeRF00001

Description:

5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes
and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs
are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it
has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind
to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA
transcription, TFIIIA also stabilises 5S rRNA until it is required for transcription.

Score:

40.6

E-value:

1e-05

From sequence:

341205

To sequence:

341323

Alignments:

                 vv     v        v v                                       v v     v                              NC
                 (((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>>-->>---->>>>>-->><<<-<<----<-<<-----<<____>>---- CS
  RF00001      1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCcgAAguUAAGcgcgcUugggCcagggUAGUAcuagGaUGgGuGAcCuCcU 96    
                   : :CG CCAU  :  : :GAAA:CACC    CCC+UC G      GAAG:UA GC: :   : G   :G  AGU CU+ GAU::G GA:: C  
    chr11 341205 CAGUACGACCAUGUUUUGAUGAAAACACCGUGUCCCGUCUGGCUUGUGAAGUUAGGCGCCCACAGGGUUAGUCAGUCCUGAGAUCAGCGAUGGCUC 341300
                 ************************************************************************************************ PP

                            v  v     vv  NC
                 ->>->-->>->>>))))))))): CS
  RF00001     97 GggAAgaccagGugccgCaggcc 119   
                  GGAA AC:   UG CG: :  C
    chr11 341301 AGGAACACUGGGUGCCGUGCCCC 341323
                 *********************** PP

>>

RNAfold
>chr11_1
AGUACGACCAUGUUUUGAUGAAAACACCGUGUCCCGUCUGGCUUGUGAAG
UUAGGCGCCCACAGGGUUAGUCAGUCCUGAGAUCAGCGAUGGCUCAGGAA
CACUGGGUGCCGUGCCCC
.((((((((.((((((....))))))((.(((..((((((((((...))))))))))...))).)).....((((((((((.(((....))))))))))...))))))..)))))... (-41.50)

Length sequence

: 118

Length match:

117