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We would value contributions that are referenced directly to the primary literature. Information on structure and function will be especially valuable.
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For a good example of what is possible in wikipedia, look at the Hammerhead Ribozyme entry.
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If you are interested in contributing to a wide range of articles relating to RNA, see the Wikiproject RNA page.
Internal-loops (also termed interior loops) in RNA are found where the double stranded RNA separates due to no Watson-Crick base pairing between the nucleotides. Internal-loops differ from Stem-loops as they occur in middle of a stretch of double stranded RNA. The non-canonicoal residues result in the double helix becoming distorted due to unwinding, unstacking and kinking.
Internal-loops can be classified as either symmetrical or asymmetrical, with some asymmetrical internal-loops, also known as bulges. Many important structural motifs are composed of internal loops such as the C-loop, the docking-elbow, kink-turns (k-turn), the right-angle, the sarcin/ricin loops (also called bulged-G motifs), the twist-up motif and the UAA/GAN internal loop motif.
- Lescoute, A; Leontis, NB; Massire, C; Westhof, E (2005). "Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments". Nucleic Acids Research. 33 (8): 2395–409. doi:10.1093/nar/gki535. PMC 1087784. PMID 15860776.
- Lehmann, J; Jossinet, F; Gautheret, D (May 1, 2013). "A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders". Nucleic Acids Research. 41 (10): 5494–502. doi:10.1093/nar/gkt219. PMC 3664808. PMID 23580544.
- Klein, D.J. (2001). "The kink-turn: a new RNA secondary structure motif". The EMBO Journal. 20 (15): 4214–4221. doi:10.1093/emboj/20.15.4214. ISSN 1460-2075. PMC 149158.
- Schroeder, KT; McPhee, SA; Ouellet, J; Lilley, DM (Aug 2010). "A structural database for k-turn motifs in RNA". RNA. 16 (8): 1463–8. doi:10.1261/rna.2207910. PMC 2905746. PMID 20562215.
- Grabow, WW; Zhuang, Z; Swank, ZN; Shea, JE; Jaeger, L (Nov 23, 2012). "The right angle (RA) motif: a prevalent ribosomal RNA structural pattern found in group I introns". Journal of Molecular Biology. 424 (1–2): 54–67. doi:10.1016/j.jmb.2012.09.012. PMC 3488136. PMID 22999957.
- Szewczak, AA; Moore, PB (Mar 17, 1995). "The sarcin/ricin loop, a modular RNA". Journal of Molecular Biology. 247 (1): 81–98. doi:10.1006/jmbi.1994.0124. PMID 7897662.
- Leontis, NB; Westhof, E (Oct 30, 1998). "A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs". Journal of Molecular Biology. 283 (3): 571–83. doi:10.1006/jmbi.1998.2106. PMID 9784367.
- Moore PB (1999). "Structural motifs in RNA". Annu. Rev. Biochem. 68: 287–300. doi:10.1146/annurev.biochem.68.1.287. PMID 10872451.
- Zhong, C; Zhang, S (Feb 2012). "Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment". Nucleic Acids Research. 40 (3): 1307–17. doi:10.1093/nar/gkr804. PMC 3273805. PMID 21976732.
- Lee, JC; Gutell, RR; Russell, R (Jul 28, 2006). "The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions". Journal of Molecular Biology. 360 (5): 978–88. doi:10.1016/j.jmb.2006.05.066. PMID 16828489.
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 12 PDB entires which have been used to build the motif model.
The table of results below may be sorted by clicking on the column titles, or restored to the original order .
|Original order||PDB ID||PDB chain ID||PDB Residues|
|2||2gya||0||2535 - 2588|
|2||1yhq||0||544 - 612|
|2||1j5a||A||873 - 928|
|2||1c2w||B||2676 - 2731|
|2||1giy||A||908 - 963|
|2||3cpw||0||543 - 611|
|2||1FFK||0||953 - 1011|
|2||1NKW||0||874 - 927|
|2||1J5E||362 - 389|
|2||1S1I||3||1418 - 1443|
|2||1S72||954 - 1010|
|2||2AW4||B||847 - 930|
There are 31 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||RF00010||Bacterial RNase P class A||49||0.107||668.9|
|3||RF00024||Vertebrate telomerase RNA||8||0.216||92.5|
|3||RF00073||mir-156 microRNA precursor||4||0.400||41.6|
|3||RF00090||Small nucleolar RNA SNORA74||5||0.208||65.1|
|3||RF00177||Bacterial small subunit ribosomal RNA||32||0.323||422.7|
|3||RF00222||Bag-1 internal ribosome entry site (IRES)||2||0.133||32.2|
|3||RF00334||Small nucleolar RNA SNORA3/SNORA45 family||3||0.500||43.5|
|3||RF00604||Small nucleolar RNA SNORD88||7||0.200||78.4|
|3||RF01268||Small Cajal body-specific RNA 2||2||0.100||21.5|
|3||RF01675||Pseudomonas sRNA CrcZ||2||0.105||21.4|
|3||RF01855||Plant signal recognition particle RNA||8||0.127||121.4|
|3||RF01857||Archaeal signal recognition particle RNA||7||0.132||92.5|
|3||RF01959||Archaeal small subunit ribosomal RNA||22||0.256||285.3|
|3||RF01960||Eukaryotic small subunit ribosomal RNA||15||0.165||194.2|
|3||RF01989||Selenocysteine insertion sequence 3||3||0.125||34.0|
|3||RF02041||HOXA transcript at the distal tip, conserved region 2||3||0.120||31.4|
|3||RF02353||Bradyrhizobiaceae sRNA BjrC68||4||0.333||47.2|
|3||RF02502||Rhizobiales sRNA Atu_C8||3||0.111||33.7|
|3||RF02514||5' ureB small RNA||2||0.154||20.5|
|3||RF02531||Nrf2 internal ribosome entry site (IRES)||2||0.100||22.3|
|3||RF02540||Archaeal large subunit ribosomal RNA||90||0.989||3182.1|
|3||RF02541||Bacterial large subunit ribosomal RNA||99||0.971||3303.8|
|3||RF02542||Microsporidia small subunit ribosomal RNA||6||0.130||71.9|
|3||RF02543||Eukaryotic large subunit ribosomal RNA||26||0.295||335.2|
|3||RF02746||antisense RNA of rseC mRNA||2||0.286||21.2|
|3||RF02830||Streptomyces RNA 1601||2||0.333||23.8|
This section shows the database cross-references that we have for this Rfam motif.
Zhong C, Zhang S Nucleic Acids Res. 2012;40:1307-17. Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment. PUBMED:21976732
Lescoute A, Leontis NB, Massire C, Westhof E Nucleic Acids Res. 2005;33:2395-409. Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments. PUBMED:15860776
Zhong C, Tang H, Zhang S Nucleic Acids Res. 2010;38:e176. RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment. PUBMED:20696653
Cruz JA, Westhof E Nat Methods. 2011;8:513-21. Sequence-based identification of 3D structural modules in RNA with RMDetect. PUBMED:21552257
External database links
|External sites:|| 1: http://rnafrabase.cs.put.poznan.pl/?act=pdbdetails&id=1S72
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.
|Seed source||Published; PMID:21976732|
cmbuild -F CM SEED
cmcalibrate --seed 1 CM
|Covariance model||Download the Infernal CM for the motif here|