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For a good example of what is possible in wikipedia, look at the Hammerhead Ribozyme entry.
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Rfam has chosen to create Wikipedia entries for all of our RNA families and to open them up to community annotation. While the original Wikipedia article that we import was (in most cases) generated from Rfam annotations, the Wikipedia article you see now may bear little resemblance to that original text. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Rfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
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If you are interested in contributing to a wide range of articles relating to RNA, see the Wikiproject RNA page.
Group II introns are a large class of self-catalytic ribozymes and mobile genetic elements found within the genes of all three domains of life. Ribozyme activity (e.g., self-splicing) can occur under high-salt conditions in vitro. However, assistance from proteins is required for in vivo splicing. In contrast to group I introns, intron excision occurs in the absence of GTP and involves the formation of a lariat, with an A-residue branchpoint strongly resembling that found in lariats formed during splicing of nuclear pre-mRNA. It is hypothesized that pre-mRNA splicing (see spliceosome) may have evolved from group II introns, due to the similar catalytic mechanism as well as the structural similarity of the Domain V substructure to the U6/U2 extended snRNA. Finally, their ability to site-specifically mobilize to new DNA sites has been exploited as a tool for biotechnology.
Structure and catalysis
The secondary structure of group II introns is characterized by six typical stem-loop structures, also called domains I to VI or DI to DVI. The domains radiate from a central core that brings the 5' and 3' splice junctions into close proximity. The proximal helix structures of the six domains are connected by a few nucleotides in the central region (linker or joiner sequences). Due to its enormous size, the domain I was divided further into subdomains a, b, c, and d. Sequence differences of group II introns that led to a further division into subgroups IIA, IIB and IIC were identified, along with varying distance of the bulged adenosine in domain VI (the prospective branch point forming the lariat) from the 3' splice site, and the inclusion or omission of structural elements such as a coordination loop in domain I, which is present in IIB and IIC introns but not IIA. Group II introns also form very complicated RNA Tertiary Structure.
Group II introns possess only a very few conserved nucleotides, and the nucleotides important for the catalytic function are spread over the complete intron structure. The few strictly conserved primary sequences are the consensus at the 5' and 3' splicing site (...↓GUGYG&... and ...AY↓..., with the Y representing a pyrimidine), some of the nucleotides of the central core (joiner sequences), a relatively high number of nucleotides of DV and some short-sequence stretches of DI. The unpaired adenosine in DVI (marked by an asterisk in the figure and located 7 or 8 nt away from the 3' splicing site) is also conserved and plays a central role in the splicing process. The 2' hydroxyl of the bulged adenosine attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. This results in a branched intron lariat connected by a 2' phosphodiester linkage at the DVI adenosine.
Protein machinery is required for splicing in vivo, and long-range intron-intron and intron-exon interactions are important for splice site positioning, as well as a number of tertiary contacts between motifs, including kissing-loop and tetraloop-receptor interactions. In 2005, A. De Lencastre et al. found that during splicing of Group II introns, all reactants are preorganized before the initiation of splicing. The branch site, both exons, the catalytically essential regions of DV and J2/3, and ε−ε' are in close proximity before the first step of splicing occurs. In addition to the bulge and AGC triad regions of DV, the J2/3 linker region, the ε−ε' nucleotides and the coordination loop in DI are crucial for the architecture and function of the active-site.
The first crystal structure of a group II intron was resolved in 2008 for the Oceanobacillus iheyensis group IIC catalytic intron, and was joined by the Pylaiella littoralis (P.li.LSUI2) group IIB intron in 2014. Attempts have been made to model the tertiary structure of other group II introns, such as the ai5γ group IIB intron, using a combination of programs for homology mapping onto known structures and de novo modeling of previously unresolved regions. Group IIC are characterized by a catalytic triad made up by CGC, while Group IIA and Group IIB are made up by AGC catalytic triad, which is more similar to the catalytic triad of the spliceosome. It is believed that the Group IIC are also smaller, more reactive and more ancient. The first step of splicing in Group IIC intron is done by water and it form a linear structure instead of lariat.
Distribution and phylogeny
Group II introns are found in rRNA, tRNA, and mRNA of organelles (chloroplasts and mitochondria) in fungi, plants, and protists, and also in mRNA in bacteria. The first intron to be identified as distinct from group I was the ai5γ group IIB intron, which was isolated in 1986 from a pre-mRNA transcript of the oxi 3 mitochondrial gene of Saccharomyces cerevisiae.
A subset of group II introns encode essential splicing proteins, known as intron-encoded proteins or IEPs, in intronic ORFs. The length of these introns can, as a result, be up to 3 kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps, with both also using magnesium ions to stabilize the leaving group in each step, which has led some to theorize a phylogenetic link between group II introns and the nuclear spliceosome. Further evidence for this link includes structural similarity between the U2/U6 junction of spliceosomal RNA and domain V of group II introns, which contains the catalytic AGC triad and much of the heart of the active site, as well as parity between conserved 5' and 3' end sequences.
- Lambowitz AM, Zimmerly S (August 2011). "Group II introns: mobile ribozymes that invade DNA". Cold Spring Harbor Perspectives in Biology. 3 (8): a003616. doi:10.1101/cshperspect.a003616. PMC 3140690. PMID 20463000.
- Seetharaman M, Eldho NV, Padgett RA, Dayie KT (February 2006). "Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA". RNA. 12 (2): 235–47. doi:10.1261/rna.2237806. PMC 1370903. PMID 16428604.
- Valadkhan S (May–Jun 2010). "Role of the snRNAs in spliceosomal active site". RNA Biology. 7 (3): 345–53. doi:10.4161/rna.7.3.12089. PMID 20458185.
- de Lencastre A, Hamill S, Pyle AM (July 2005). "A single active-site region for a group II intron". Nature Structural & Molecular Biology. 12 (7): 626–7. doi:10.1038/nsmb957. PMID 15980867.
- Somarowthu S, Legiewicz M, Keating KS, Pyle AM (February 2014). "Visualizing the ai5γ group IIB intron". Nucleic Acids Research. 42 (3): 1947–58. doi:10.1093/nar/gkt1051. PMID 24203709.
- Keating KS, Toor N, Perlman PS, Pyle AM (January 2010). "A structural analysis of the group II intron active site and implications for the spliceosome". RNA. 16 (1): 1–9. doi:10.1261/rna.1791310. PMC 2802019. PMID 19948765.
- Peebles CL, Perlman PS, Mecklenburg KL, Petrillo ML, Tabor JH, Jarrell KA, Cheng HL (January 1986). "A self-splicing RNA excises an intron lariat". Cell. 44 (2): 213–23. doi:10.1016/0092-8674(86)90755-5. PMID 3510741.
- Gordon PM, Sontheimer EJ, Piccirilli JA (February 2000). "Metal ion catalysis during the exon-ligation step of nuclear pre-mRNA splicing: extending the parallels between the spliceosome and group II introns". RNA. 6 (2): 199–205. PMID 10688359.
- Bonen L, Vogel J (June 2001). "The ins and outs of group II introns". Trends in Genetics. 17 (6): 322–31. doi:10.1016/S0168-9525(01)02324-1. PMID 11377794.
- Chu VT, Adamidi C, Liu Q, Perlman PS, Pyle AM (December 2001). "Control of branch-site choice by a group II intron". The EMBO Journal. 20 (23): 6866–76. doi:10.1093/emboj/20.23.6866. PMC 125754. PMID 11726522.
- Lehmann K, Schmidt U (2003). "Group II introns: structure and catalytic versatility of large natural ribozymes". Critical Reviews in Biochemistry and Molecular Biology. 38 (3): 249–303. doi:10.1080/713609236. PMID 12870716.
- Michel F, Umesono K, Ozeki H (October 1989). "Comparative and functional anatomy of group II catalytic introns--a review". Gene. 82 (1): 5–30. doi:10.1016/0378-1119(89)90026-7. PMID 2684776.
You can either download the motif alignment or view it directly in your browser window. More...
You can download (or view in your browser) a text representation of a Rfam alignment in various formats:
- Gapped FASTA
- Ungapped FASTA
You can view or download motif alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".
There are 18 Rfam families which match this motif.
This section shows the families which have been annotated with this motif. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...
To annotate the family with a motif model, the seed sequence was first filtered using a 0.9 fraction identity cut-off. The filtered seed was then scanned using Infernal cmscan (v1.1) with a concatenated CM file containing each of the motifs. Significance of hits between a seed sequence and the CM was based on a gathering threshold that was individually set for each motif. Only motifs where more than two and at least 10% of seed sequences scored higher than the gathering threshold were included for the next stage of processing. These subsets of motifs were then rescanned against the entire (non-filtered) seed to generate matches.
Number of Hits: the number of sequences in the family seed that score above the gathering threshold from motif.
Fraction of Hits: the fraction of sequences in the family seed that score above the gathering threshold from motif.
Sum of Bits: the sum of the bit scores of matches between the motif and the family seed sequence.
Image: plot illustrating where on the consensus secondary structure matches occur between seed sequences and the motif model.
|Original order||Family Accession||Family Description||Number of Hits||Fraction of Hits||Sum of Bits||Image|
|3||RF00011||Bacterial RNase P class B||16||0.140||174.9|
|3||RF00018||CsrB/RsmB RNA family||19||0.500||202.5|
|3||RF00026||U6 spliceosomal RNA||172||0.915||3759.8|
|3||RF00029||Group II catalytic intron||92||1.000||3204.8|
|3||RF00300||Small nucleolar RNA Z221/R21b||2||0.167||22.1|
|3||RF00413||Small nucleolar RNA SNORA19||2||0.059||27.6|
|3||RF00449||HIF-1 alpha IRES||6||0.353||73.6|
|3||RF00553||Small Cajal body specific RNA 1||4||0.138||44.2|
|3||RF01071||Ornate Large Extremophilic RNA||2||0.100||27.8|
|3||RF02356||Alphaproteobacterial sRNA BjrC1505||2||0.080||22.3|
|3||RF02384||FasX small RNA||2||0.250||20.4|
|3||RF02540||Archaeal large subunit ribosomal RNA||16||0.176||236.7|
|3||RF02541||Bacterial large subunit ribosomal RNA||21||0.206||258.2|
|3||RF02542||Microsporidia small subunit ribosomal RNA||6||0.130||64.8|
|3||RF02543||Eukaryotic large subunit ribosomal RNA||23||0.261||295.7|
This section shows the database cross-references that we have for this Rfam motif.
Seetharaman M, Eldho NV, Padgett RA, Dayie KT RNA. 2006;12:235-47. Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA. PUBMED:16428604
Valadkhan S RNA Biol. ;7:345-53. Role of the snRNAs in spliceosomal active site. PUBMED:20458185
External database links
Curation and motif details
This section shows the detailed information about the Rfam motif. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.
cmbuild -F CM SEED
|Covariance model||Download the Infernal CM for the motif here|