chr23_2

cmsearch-Rfam

Family :

ACEA_U3

Id:

RF01848

Type:

Gene; snRNA; snoRNA; CD-box;

Taxonomy:

Eukaryota;

Ontology:

GO:0006396 RNA processingRF01848

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:

68.5

E-value:

2.1e-12

From sequence:

216638

To sequence:

216496

Alignments:

                                                                      vv            vv                            NC
                 <<<-<<-<<<<---.--<<<<____>>>>--.>>>>.>-->.>>>,,,<<<<<<<<<_______.>>>>>>>>>------(((((----------- CS
  RF01848      1 ucGAcuGuACUCga.ACAggAUCAUUucUAU.AGUa.aAUc.CgaucuuuuuuuguuAuAaauA.aacaaaaaaccuUaAaccguGAUGAUGAauu 91    
                 ::GAC:GUACUC++ ACA::AUC  U::UAU AGUA :A C C::++UU::::    A AAA++    +::::AC     A:C:UGAUGAUGA   
    chr23 216638 AAGACCGUACUCUGaACAGAAUCG-UUUUAUgAGUAcAACCuCUUAAUUGAAA----AGAAACCg--AGUUUCAC-----AUCCUGAUGAUGAC-G 216556
                 ************999*********.***********99998899965544444....33333333..23444454.....**************.8 PP

                             v                                                   v                      NC
                 ---.(((((.((((((,,<<<<----~~~~~~>>>><<<<-<_________>->>>>,,,,))))))-)))))-------))))): CS
  RF01848     92 Gua.caccC.cgccccAAcggggAau*[51]*cccgcuucUgucaUaaauucagaagaugAggggcgUGggugaUuCUGAacgguc 220   
                 GU+ C:::C C: :CC  CG::GA+       ::CG        AU+AA            GG:+:G+G:::G+U C GAA:G:UC
    chr23 216555 GUUgCUUUCuCC-GCC--CGGAGAGC*[ 2]*UUCG--------AUGAAC-----------GGCAGGAGAGAGUUCCAGAAGGAUC 216496
                 8888*****888.***..99999976...6..9999........999876...........************************* PP

RNAfold
>chr23_2
ACCUCCACGGCGGGAAGGUGGAACGGCGAAACGAAAAGGAUCCUUCUGGA
ACUCUCUCCUGCCGUUCAUCGAAACGCUCUCCGGGCGGAGAAAGCAACCG
UCAUCAUCAGGAUGUGAAACUCGGUUUCUUUUCAAUUAAGAGGUUGUACU
CAUAAAACGAUUCUGUUCAGAGUACGGUCUUGCUUUGAGAAGGACGGAUC
CACGCGAAGAAAUGCAUUUU
.......((((((((.((.(...(((.((..(.....)..))...)))...).)).))))))))(((.(((....(((((((....)))))..)).((((...((((......))))....))))((((((((((....((((((((((((....((((....))))..))))))))))))...))))))))))((......))))).)))......... (-60.60)

Length sequence

: 220

Length match:

141