gi_545778205_gb_U000_8

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:

77.2

E-value:

6e-16

From sequence:

228758

To sequence:

228873

Alignments:

                                      v               v       v         v         v             v           vv    NC
                              (((((((((,,,,<<-<<<<<---<<--<<<<<<______.>>-->>>>-->>---->>>>>-->><<<-<<----<-<<--- CS
               RF00001      1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCc.GaACuCcgAAguUAAGcgcgcUugggCcagggUAGUAcuagG 82    
                              :C::GC:G C UA:C+::G:G+   CACC:GA CCCAU C G ACUC:GAAG  AA C:C::U+G: CC+::G  G:A  + G
  gi_545778205_gb_U000 228758 CCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCcGAACUCAGAAGUGAAACGCCGUAGCGCCGAUG--GUAGUGUG 228838
                              *************************************************************************..******** PP

                                             vv         v v          NC
                              --<<____>>----->>->-->>->>>.))))))))): CS
               RF00001     83 aUGgGuGAcCuCcUGggAAgaccagGu.gccgCaggcc 119   
                                GGGU  CC C UG  A: A::AGG   C:GC::G:C
  gi_545778205_gb_U000 228839 --GGGUCUCCCCAUGCGAG-AGUAGGGaACUGCCAGGC 228873
                              ..************99999.****************** PP

>>

RNAfold
>gi_545778205_gb_U000_8
GCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAG
AAGUGAAACGCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGA
GUAGGGAACUGCCAGGCAU
(((((((((((((...)))).(((...))).((((((((((...((.((...(((..((...))..)))...)))).))))))))))..(((.(((....))))))..))))))))).. (-49.10)

Length sequence

: 119

Length match:

114