chr24_23

cmsearch-Rfam

Family :

U6

Id:

RF00026

Type:

Gene; snRNA; splicing;

Taxonomy:

Eukaryota; Viruses;

Ontology:

GO:0000353 formation of quadruple SL/U4/U5/U6 snRNPRF00026

Description:

U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative
secondary structure consensus base pairing is confined to a short 5' stem loop, but U6
snRNA is thought to form extensive base-pair interactions with U4 snRNA [2]. This model hits
a large number of sequences in vertebrate genomes, which appear to be U6 derived pseudogenes
or repeats. This family has a high significance threshold to minimise this problem, but many
annotated pseudogenes remain.

Score:

61.9

E-value:

2.5e-13

From sequence:

600346

To sequence:

600249

Alignments:

                  v            v                                                                                  NC
                 <<<<<______>>>>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: CS
  RF00026      1 guccccUUCGggggacaUaUggUaAAaUUGgAACgAUACAGAGAAGAUUAGCAUGGCCCCUGCaCAAGGAUGACACguauaauagAGAgauguacc 96    
                 G CCC UUCGGGGG CAU  +  AAA U G+AA    ACAGAGAAGAUUAGCA    CCCUGC+CAAGG UGA     AU +U+GAGAGAU+UA C
    chr24 600346 GCCCC-UUCGGGGGACAUCCAC-AAACUGGAAAUUCAACAGAGAAGAUUAGCACUCUCCCUGCGCAAGGCUGAUGUCAAUCUUCGAGAGAUAUAGC 600253
                 *****.****888888888776.778888999999999******************************************************9998 PP

                          NC
                 :::::::: CS
  RF00026     97 auaUUUUU 104   
                     UUUU
    chr24 600252 ----UUUU 600249
                 ....9*** PP

RNAfold
>chr24_23
GGAAAAGCUAUAUCUCUCGAAGAUUGACAUCAGCCUUGCGCAGGGAGAGU
GCUAAUCUUCUCUGUUGAAUUUCCAGUUUGUGGAUGUCCCCCGAAGGGGC
UCC
(((((..(.(((......((((((((.(((...((((....))))...))).))))))))..))).)..))))).......(((.(((((.....)))))))) (-25.60)

Length sequence

: 103

Length match:

96