gi_545778205_gb_U000_71

cmsearch-Rfam

Family :

group-II-D1D4-4

Id:

RF02003

Type:

Intron;

Taxonomy:

Eukaryota; Bacteria; Archaea;

Ontology:

GO:0000373 Group II intron splicing

Description:

Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and
protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6
structural domains (usually designated dI to dVI. This model and alignment represents only domains V
and VI. A subset of group II introns also encode essential splicing proteins in intronic
ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in
almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of
a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack
on the 3' splice site by the 3' OH of the upstream exon. Protein machinery
is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important
for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB
which differ in splice site consensus, distance of bulged A from 3' splice site, some
tertiary interactions, and intronic ORF phylogeny [1].

Score:

67.8

E-value:

9e-14

From sequence:

4501332

To sequence:

4501193

Alignments:

                                                      v              v           v v           v      v          NC
                               :::::::::::::::::::<<<<<___________.__>>>>>,,,,,,,<<<<<<<<<<<---<<____>>--->>>>>> CS
               RF02003       1 cAGCgGGUGaAAGUCCcGuccgGgaAauaGcCagu.aGcCcggUAGCuAgggcggCggcgugggggGuAAccaaaacgccG 80     
                               C G+ GGUGAAAGUCC  +CC G +AA + +C  U +G C GG AG +   G :GC:G::: GG GGUAAC AAA:::C:G
  gi_545778205_gb_U000 4501332 CCGUCGGUGAAAGUCCGCCCCGGCUAACUCUCGCUcCGACUGGAAGGACAAGAAGCGGUCCAGGAGGUAACAAAAGGGCUG 4501252
                               ************************99999999999899******************************************* PP

                                      v v                                                   NC
                               ----.>>>>>,,,,,,<<<<<<_____>>>>>>,,<<<_.__________>>>::::::: CS
               RF02003      81 AAGC.ccgccGACAAAggccgcuauaGgcggccgagCgA.aucugCAGGCcGuAACGuaA 138    
                               AA C C: C    AA G:C::CU+ AGG::G:C+ :CG  +U+UGC+GGCCG:AACGU+A
  gi_545778205_gb_U000 4501251 AAUCuCUCCCUGAAACGACUUCUUCAGGAAGUCA-ACGGgUUAUGCGGGCCGUAACGUGA 4501193
                               ****888888788888*****************9.88751567889************** PP

RNAfold
>gi_545778205_gb_U000_71
CACGUUACGGCCCGCAUAACCCGUUGACUUCCUGAAGAAGUCGUUUCAGG
GAGAGAUUCAGCCCUUUUGUUACCUCCUGGACCGCUUCUUGUCCUUCCAG
UCGGAGCGAGAGUUAGCCGGGGCGGACUUUCACCGACGG
..(((..(((.((((....((((....((((((((((......)))))))))).......((.((((((((.((..(((((..((.....))...)))))..))))))))))...)))))))))).......)))))). (-42.40)

Length sequence

: 139

Length match:

138