gi_545778205_gb_U000_72

cmsearch-Rfam

Family :

group-II-D1D4-6

Id:

RF02005

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:

19.9

E-value:

0.0017

From sequence:

4501323

To sequence:

4501067

Alignments:

                                          v       v v       v v     v vv     v     v     vvvv      vvvv        v NC
                               :::::::::::<<<<<.--<<<_______>>>->>>>>,<<<<--<<.<<<<<<<<-<<<<<<____>>>>>>->>>---> CS
               RF02005       1 AaAGUCCccuaccggg.AAgGuuUAGCcAaCcAcccggacccCGAGu.cuuGCgccgcccccgGuaAcggggguggcGAAG 79     
                               AAAGUCC C++ C G   A+: +U GC   : A C GGA  :: A   :::G ::  C    GGUAAC    G  ::GAA 
  gi_545778205_gb_U000 4501323 AAAGUCCGCCC-CGG-cUAACUCUCGCUCCG-A-CUGGAAGGACA--aGAAGCGGUCCAGGAGGUAACAAAAGGGCUGAAU 4501249
                               ******44444.433.355555565555555.5.33444444444..5677777778999999999999999999999999 PP

                                      v               vv                                                         NC
                               >>->>..>>.-..........>>>>-------------------....................-----(--(((.(((-- CS
               RF02005      80 CgUag..aC.A..........GggggAaGugcaaaGGCcguGcu....................gauAUuGAGCc.cCGAA 126    
                               C: ::     A          ::  GAAGU  A +GG ++UGC                      ++A : AGCC :CGAA
  gi_545778205_gb_U000 4501248 CUCUCccU-gAaacgacuucuUCAGGAAGUCAACGGGUUAUGCGggccguaacgugagugaacaCUGAGC-AGCCaUCGAA 4501170
                               99987542.236777777666556667777777778888877779**9999**99998887775555555.9**988**** PP

                                           v          v             v                                      v     NC
                               -----------(((((,<<<--<<<<_________>>>>--->>>,.,,,<<<<<<<<~~~~~~>>>>>>>>,)))))))) CS
               RF02005     127 AuaaucuaaUuccGGggGcCGAcgcugUcgucauaagcgGAAGgCA.ACAccgaccgg*[16]*ccggucggccCCggCGg 216    
                               AU       U+: GGG+GC GAC C:    +  +A:G GGAA GC  AC ::GACCG        CGGUC:: CCC :CG:
  gi_545778205_gb_U000 4501169 AUGCC---GUCGAGGGUGCUGACACGCCACAAUAACGGGGAAGGCCgACGAUGACCGG*[19]*UCGGUCAUACCCACCGG 4501079
                               *9998...899***************777777777*********85489999999984...4..79999999********* PP

                                            NC
                               )))---)::::: CS
               RF02005     217 gGUCugaGAgCc 228    
                               GGU  +:G G C
  gi_545778205_gb_U000 4501078 GGUUGUGGUGUC 4501067
                               ************ PP

RNAfold
>gi_545778205_gb_U000_72
ACACCACAACCCCGGUGGGUAUGACCGAUGCCUUUCUCACUCUCUUCCCG
GUCAUCGUCGGCCUUCCCCGUUAUUGUGGCGUGUCAGCACCCUCGACGGC
AUUUCGAUGGCUGCUCAGUGUUCACUCACGUUACGGCCCGCAUAACCCGU
UGACUUCCUGAAGAAGUCGUUUCAGGGAGAGAUUCAGCCCUUUUGUUACC
UCCUGGACCGCUUCUUGUCCUUCCAGUCGGAGCGAGAGUUAGCCGGGGCG
GACUUU
((.((((((...(((.((((.((((.((((((.................)).))))))))))))...)))...)))))).))(((.((.((((((((((.....((..(((((....(((......)))....)))))))......)))))))((((((((((......)))))))))).......((.((((((((.((..(((((..((.....))...)))))..))))))))))...)).))))).)))... (-84.10)

Length sequence

: 256

Length match:

255