gi_545778205_gb_U000_12

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:

3946702

To sequence:

3946817

Alignments:

                                       v               v       v         v         v             v           vv  NC
                               (((((((((,,,,<<-<<<<<---<<--<<<<<<______.>>-->>>>-->>---->>>>>-->><<<-<<----<-<<- CS
               RF00001       1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCc.GaACuCcgAAguUAAGcgcgcUugggCcagggUAGUAcua 80     
                               :C::GC:G C UA:C+::G:G+   CACC:GA CCCAU C G ACUC:GAAG  AA C:C::U+G: CC+::G  G:A  +
  gi_545778205_gb_U000 3946702 CCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCcGAACUCAGAAGUGAAACGCCGUAGCGCCGAUG--GUAGUG 3946780
                               *************************************************************************..****** PP

                                                vv         v v          NC
                               ----<<____>>----->>->-->>->>>.))))))))): CS
               RF00001      81 gGaUGgGuGAcCuCcUGggAAgaccagGu.gccgCaggcc 119    
                                G  GGGU  CC C UG  A: A::AGG   C:GC::G:C
  gi_545778205_gb_U000 3946781 UG--GGGUCUCCCCAUGCGAG-AGUAGGGaACUGCCAGGC 3946817
                               **..************99999.****************** PP

>>

RNAfold
>gi_545778205_gb_U000_12
GCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAG
AAGUGAAACGCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGA
GUAGGGAACUGCCAGGCAU
(((((((((((((...)))).(((...))).((((((((((...((.((...(((..((...))..)))...)))).))))))))))..(((.(((....))))))..))))))))).. (-49.10)

Length sequence

: 119

Length match:

114