chr15_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:

38.0

E-value:

5.1e-05

From sequence:

325164

To sequence:

325275

Alignments:

                               v v  v    vv   v                v   vv     v  v  v   v  v                          NC
                 (((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>>-->>---->>>>>-->><<<-<<----<-<<-----<<____>>---- CS
  RF00001      1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCcgAAguUAAGcgcgcUugggCcagggUAGUAcuagGaUGgGuGAcCuCcU 96    
                 G::::CG:CCAU C A  G GAAA+CACC :AUCCC+ CCGA  U: GAA   AAGC C     GGC  :    GU CU+  +U: GUG  : C  
    chr15 325164 GAGCACGACCAUGCCAAGGAGAAAACACCACAUCCCGCCCGAUUUGCGAA---AAGCACUCACAGGCUUA----GUGCUGAUGUCGGUGUUGGCUC 325252
                 ************************99***********************9...99************998....688******************* PP

                        v  v             NC
                 ->>->-->>->>>))))))))): CS
  RF00001     97 GggAAgaccagGugccgCaggcc 119   
                 GGGAA  +:A GUG:CG::::C+
    chr15 325253 GGGAACCUUACGUGUCGUGCUCU 325275
                 ****9898999************ PP

RNAfold
>chr15_1
UGUGAGCACGACCAUGCCAAGGAGAAAACACCACAUCCCGCCCGAUUUGC
GAAAAGCACUCACAGGCUUAGUGCUGAUGUCGGUGUUGGCUCGGGAACCU
UACGUGUCGUGCUCUUUUU
...(((((((((.(((((...(((..(((((((((((.(((.......)))...((((((.........))))))))))).))))))..))).)).......))))))))))))..... (-40.80)

Length sequence

: 119

Length match:

110