chr23_8

cmsearch-Rfam

Family :

Plant_U3

Id:

RF01847

Type:

Gene; snRNA; snoRNA; CD-box;

Taxonomy:

Eukaryota;

Ontology:

GO:0006396 RNA processingRF01847

Description:

Small nucleolar RNAs (snoRNAs) are involved in the processing and modification of rRNA in the nucleolus.
There are two main classes of snoRNAs: the box C/D class, and the box H/ACA
class. U3 snoRNA is a member of the box C/D class. Indeed, the box C/D
element is a subset of the six short sequence elements found in all U3 snoRNAs,
namely boxes A, A', B, C, C', and D. The U3 snoRNA secondary structure is
characterised by a small 5' domain (with boxes A and A'), and a larger 3'
domain (with boxes B, C, C', and D), the two domains being linked by a
single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive
to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is
functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the
hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both
the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA.
The box C'/D motif is also necessary for nucleolar localisation, stability and hyper-methylation of U3
snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are
necessary for the rRNA processing functions of U3 snoRNA.

Score:

23.4

E-value:

0.0038

From sequence:

216635

To sequence:

216496

Alignments:

                                  v     v                    vvv v    v     v    v vvv                            NC
                 <<<-<<<----.-<<<<<<___>>>>>>--->>>->->>,,,,<<<<-<<<<<<_____>>>>>>->>>>--------(((((------------- CS
  RF01847      1 aCGACCuUACU.UGAACAGGAUCUGUUCUAUaGGcUCGuACcucuGuauccuuuauuucaaaggaGaCagGaucuUaAgcCcGGuuGAuGAaucaU 95    
                 AC     UACU U AACAG AUC GUU UAU      GUAC +C     :CUU AUU + AAG:  AC G  U+U A ::CC G+UGAUGA    U
    chr23 216635 ACCG---UACUcUGAACAGAAUC-GUUUUAU----GAGUACAAC----CUCUUAAUUGAAAAGAA-ACCGAGUUUCACAUCCUGAUGAUGACGGUU 216553
                 **98...9**989*****98876.*******....99*****98....77777788887777777.566777777799****************** PP

                          vv                   vv                      NC
                 -((((((((((((,~~~~~~~~~~~~,,))))))))))))-------))))): CS
  RF01847     96 GgCcgugcggcCaG*[59]**[26]*GauGgccgcacgGcugUCUGACgGgcu 221   
                 G:: :::C:  C:G              :G  :G::: ::U+ C GA GG:: 
    chr23 216552 GCUUUCUCCGCCCG*[ 6]**[12]*--GGCAGGAGAGAGUUCCAGAAGGAUC 216496
                 ********987765...*.....9....56679******************** PP

RNAfold
>chr23_8
CCACCUCCACGGCGGGAAGGUGGAACGGCGAAACGAAAAGGAUCCUUCUG
GAACUCUCUCCUGCCGUUCAUCGAAACGCUCUCCGGGCGGAGAAAGCAAC
CGUCAUCAUCAGGAUGUGAAACUCGGUUUCUUUUCAAUUAAGAGGUUGUA
CUCAUAAAACGAUUCUGUUCAGAGUACGGUCUUGCUUUGAGAAGGACGGA
UCCACGCGAAGAAAUGCAUUU
((((((((......)).))))))..((......))....((((((.((.....((.(((((..(((.....((...)).....)))..))))).)).(((((...((((......))))....))))).((((((((....((((((((((((....((((....))))..))))))))))))...)))))))))).))))))..((........)).... (-64.10)

Length sequence

: 221

Length match:

138