chr11_3

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:

99.4

E-value:

6.7e-21

From sequence:

68610

To sequence:

68492

Alignments:

                       v                                                                                           NC
                (((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>>-->>---->>>>>-->><<<-<<----<-<<-----<<____>>-----> CS
  RF00001     1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCcgAAguUAAGcgcgcUugggCcagggUAGUAcuagGaUGgGuGAcCuCcUGg 98   
                G::U:CG CCAUAC: G:G:GAAA:CACC: AUCCC+UCCGA  U :GAAG:UAAGC:C:C  :GGC: :G UAGUACU+ G+U::GUGA::+C  GG
    chr11 68610 GAGUACGACCAUACUUGAGUGAAAACACCAUAUCCCGUCCGAUUUGUGAAGUUAAGCACUCACAGGCUCAGUUAGUACUGAGGUCAGUGAUGACUCGG 68513
                ************************************************************************************************** PP

                            v         NC
                >->-->>->>>))))))))): CS
  RF00001    99 gAAgaccagGugccgCaggcc 119  
                GAA  C: :GUG CG:A::CC
    chr11 68512 GAACCCUGAGUGCCGUACUCC 68492
                ********************* PP

>>

RNAfold
>chr11_3
GAGUACGGCACUCAGGGUUCCCGAGUCAUCACUGACCUCAGUACUAACUG
AGCCUGUGAGUGCUUAACUUCACAAAUCGGACGGGAUAUGGUGUUUUCAC
UCAAGUAUGGUCGUACUC
(((((((((.........(((((.((((....))))((((((....))))))(((((((((.....)).)))))....)).)))))...((((....))))........))))))))) (-37.00)

Length sequence

: 118

Length match:

117