rrfD

cmscan-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:

3.8e-17

From sequence:

3

To sequence:

118

Alignments:

                      v               v       v         v         v             v           vv                  vv   NC
              (((((((((,,,,<<-<<<<<---<<--<<<<<<______.>>-->>>>-->>---->>>>>-->><<<-<<----<-<<-----<<____>>----->>-> CS
  RF00001   1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCc.GaACuCcgAAguUAAGcgcgcUugggCcagggUAGUAcuagGaUGgGuGAcCuCcUGggAA 101
              :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  GGGU  CC C UG  A:
     rrfD   3 CCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCcGAACUCAGAAGUGAAACGCCGUAGCGCCGAUG--GUAGUGUG--GGGUCUCCCCAUGCGAG 100
              *************************************************************************..********..************99999 PP

                     v v          NC
              -->>->>>.))))))))): CS
  RF00001 102 gaccagGu.gccgCaggcc 119
               A::AGG   C:GC::G:C
     rrfD 101 -AGUAGGGaACUGCCAGGC 118
              .****************** PP

RNAfold

>rrfD
GCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAG
AAGUGAAACGCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGA
GUAGGGAACUGCCAGGCAU
(((((((((((((...)))).(((...))).((((((((((...((.((...(((..((...))..)))...)))).))))))))))..(((.(((....))))))..))))))))).. (-49.10)

Length sequence

: 119

Length match:

114