chr31_18

cmsearch-Rfam

Family :

U2

Id:

RF00004

Type:

Gene; snRNA; splicing;

Taxonomy:

Eukaryota;

Ontology:

GO:0045131 pre-mRNA branch point bindingRF00004

Description:

U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary
binding between U2 snRNA (in an area lying towards the 5' end but 3' to
hairpin I) and the branchpoint sequence (BPS) of the intron results the bulging out of
an unpaired adenosine, on the BPS, which initiates a nucleophilic attack at the intronic 5'
splice site, thus starting the first of two transesterification reactions that mediate splicing.

Score:

79.1

E-value:

7e-15

From sequence:

251703

To sequence:

251558

Alignments:

                                                                                                                  NC
                 ::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,<<<<<<<___>>>>>>>,,,,,,,,,,,, CS
  RF00004      1 AUacCUUCucgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCUUauCAGUuUAAuAuCUGauAuggcccccAuugggggccaauuauaUUAaa 96    
                 AUA CUUCUCGGC: UUU:GCUAAGAUCA GU UA  A CUGUUCUUAUCAG +UAA+  CUGAUA+:GCC:   U+  :GGC:AA       AA+
    chr31 251703 AUAUCUUCUCGGCUAUUUAGCUAAGAUCAUGUUUAUAAACUGUUCUUAUCAGAGUAACUCCUGAUACUGCCU---UC--GGGCAAA-----GGAAU 251618
                 ******************************************************************999988...88..8899999.....34455 PP

                                                                                       NC
                 ,,,,,,,,,,,,,,,,~~~~~~,,<<<<<<-<<<<<<___________>>>>>>-->>>>>>::::::: CS
  RF00004     97 uuaAUUUUUggaacua*[34]*acggguugaccuggcaUUGCAcUaccgccagguucagcccAcccuuu 193   
                   AA UU U + +C+A       +:G:::: CCUGG:  U CAC ++ :CCAGG  ::::C:AC+++UU
    chr31 251617 AGAAAUUAUAAGUCGA*[ 1]*GUUGUUUC-CCUGGAGCUCCACCUU-UCCAGG--GGAGCAACUUCUU 251558
                 5555555555555555...5..99******.***************9.******..************* PP

RNAfold
>chr31_18
AGAUGCUGUGCCCCGGGAAAAAAAAGAAGUUGCUCCCCUGGAAAGGUGGA
GCUCCAGGGAAACAACCUCGACUUAUAAUUUCUAUUCCUUUGCCCGAAGG
CAGUAUCAGGAGUUACUCUGAUAAGAACAGUUUAUAAACAUGAUCUUAGC
UAAAUAGCCGAGAAGAUAUGCUACACGAGGCGUUCACAAAAGC
......(((..(((.(((.............((((((((....))).)))))))).)))..))).(((((.(((((.......(((((((((((....)))))....)))))).......))))).............((((.((((.(((....))).))))...)))).....)))))............. (-49.20)

Length sequence

: 193

Length match:

144