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Information we would like to see added
We would value contributions that are referenced directly to the primary literature. Information on structure and function will be especially valuable.
Adding references is made much easier by this tool.
For a good example of what is possible in wikipedia, look at the Hammerhead Ribozyme entry.
Does Rfam agree with the content of the Wikipedia entry ?
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.
The community annotation is a new facility of the Rfam web site. If you have problems editing or experience problems with these pages please contact us.
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 . 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 . 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 .
- 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 . 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 . 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 . 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 10 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||3BBO||A||74 - 108|
|2||1s72||0||70 - 104|
|2||2j01||A||74 - 108|
|2||2gis||A||11 - 43|
|2||1rlg||C||1 - 25|
|2||2hvy||E||16 - 42|
|2||3cc2||0||71 - 105|
|2||2wh1||A||230 - 289|
There are 89 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||RF00009||Nuclear RNase P||23||0.198||242.4|
|3||RF00010||Bacterial RNase P class A||84||0.183||1029.0|
|3||RF00017||Metazoan signal recognition particle RNA||35||0.385||367.0|
|3||RF00024||Vertebrate telomerase RNA||27||0.730||350.4|
|3||RF00045||Small nucleolar RNA SNORA73 family||27||0.409||293.2|
|3||RF00065||Small nucleolar RNA snoR9||5||1.000||74.8|
|3||RF00095||Pyrococcus C/D box small nucleolar RNA||4||0.160||39.1|
|3||RF00162||SAM riboswitch (S box leader)||256||0.591||3219.4|
|3||RF00177||Bacterial small subunit ribosomal RNA||83||0.838||1976.8|
|3||RF00222||Bag-1 internal ribosome entry site (IRES)||5||0.333||90.6|
|3||RF00224||FGF-2 internal ribosome entry site (IRES)||2||0.333||38.3|
|3||RF00261||L-myc internal ribosome entry site (IRES)||8||0.727||123.3|
|3||RF00286||Small Cajal body specific RNA 8||5||0.227||48.3|
|3||RF00373||Archaeal RNase P||16||0.229||254.8|
|3||RF00408||Small nucleolar RNA SNORA1||3||0.103||31.4|
|3||RF00449||HIF-1 alpha IRES||2||0.118||23.4|
|3||RF00461||Vascular endothelial growth factor (VEGF) IRES A||4||0.571||39.0|
|3||RF00512||Leucine operon leader||5||0.833||52.0|
|3||RF00549||c-sis internal ribosome entry site (IRES)||10||1.000||165.4|
|3||RF00564||Small Cajal body specific RNA 11||3||0.125||42.9|
|3||RF00598||Small nucleolar RNA SNORA76||5||0.227||50.7|
|3||RF00602||Small Cajal body specific RNA 21||3||0.125||33.3|
|3||RF00603||Small nucleolar RNA SNORD23||5||0.333||66.0|
|3||RF00604||Small nucleolar RNA SNORD88||12||0.343||122.6|
|3||RF00613||Small nucleolar RNA SNORD94||6||0.286||58.3|
|3||RF00625||Pseudomonas sRNA P11||3||0.200||28.2|
|3||RF00629||Pseudomonas sRNA P24||4||0.286||37.6|
|3||RF00634||S-adenosyl methionine (SAM) riboswitch,||6||0.150||68.1|
|3||RF01052||Arthropod 7SK RNA||6||0.316||77.9|
|3||RF01069||purD RNA motif||2||0.095||18.3|
|3||RF01071||Ornate Large Extremophilic RNA||4||0.200||42.5|
|3||RF01073||Gag/pol translational readthrough site||3||0.429||30.5|
|3||RF01219||Small nucleolar RNA snoR100||2||0.222||18.8|
|3||RF01246||Small nucleolar RNA snR81||2||0.667||26.5|
|3||RF01268||Small Cajal body-specific RNA 2||11||0.550||139.7|
|3||RF01292||Small nucleolar RNA snoR2/U65||6||0.545||93.1|
|3||RF01502||Fungal signal recognition particle RNA||9||0.180||98.9|
|3||RF01643||Caenorhabditis sRNA ceN56||3||0.750||31.3|
|3||RF01848||ACEA small nucleolar RNA U3||6||0.214||56.6|
|3||RF01849||Alphaproteobacteria transfer-messenger RNA||10||0.090||105.6|
|3||RF01855||Plant signal recognition particle RNA||12||0.190||126.3|
|3||RF01857||Archaeal signal recognition particle RNA||14||0.264||185.6|
|3||RF01867||caulobacter sRNA CC2171||5||0.385||53.0|
|3||RF01946||KCNQ1 overlapping transcript 1 conserved region 1||3||0.375||29.2|
|3||RF01959||Archaeal small subunit ribosomal RNA||66||0.767||1634.1|
|3||RF01960||Eukaryotic small subunit ribosomal RNA||37||0.407||698.8|
|3||RF02005||Group II catalytic intron D1-D4-6||30||0.172||321.6|
|3||RF02042||HOXA transcript at the distal tip, conserved region 3||2||0.087||25.9|
|3||RF02122||FTX transcript, XIST regulator conserved region 5||2||0.143||22.2|
|3||RF02132||HOXB13 antisense RNA 1 conserved region 1||3||0.250||31.7|
|3||RF02141||HOXA11 antisense RNA 1 conserved region 5||2||0.071||21.5|
|3||RF02143||Hydatidiform mole associated and imprinted conserved region 1||2||0.125||21.0|
|3||RF02164||Pvt1 oncogene conserved region 1||5||0.294||54.2|
|3||RF02165||Pvt1 oncogene conserved region 2||2||0.118||21.2|
|3||RF02196||TP53 target 1 conserved region 2||2||0.167||20.0|
|3||RF02198||TTC28 antisense RNA 1 conserved region 1||2||0.143||20.3|
|3||RF02205||WT1 antisense RNA conserved region 3||3||0.158||40.6|
|3||RF02336||Giardia snoRNA GlsR1/miRNA miR6||2||1.000||28.6|
|3||RF02347||Alphaproteobacterial sRNA ar45||11||0.306||102.5|
|3||RF02355||Bradyrhizobiaceae sRNA BjrC174||2||0.133||20.0|
|3||RF02357||RNaseP truncated form||7||0.778||73.2|
|3||RF02462||Ascomycota telomerase RNA||3||0.750||31.8|
|3||RF02471||Actinobacteria sRNA Ms_IGR-5||2||0.095||21.0|
|3||RF02540||Archaeal large subunit ribosomal RNA||91||1.000||6958.4|
|3||RF02541||Bacterial large subunit ribosomal RNA||99||0.971||3865.1|
|3||RF02542||Microsporidia small subunit ribosomal RNA||25||0.543||420.7|
|3||RF02543||Eukaryotic large subunit ribosomal RNA||46||0.523||914.8|
|3||RF02605||Streptomyces sRNA scr5239||2||0.333||23.1|
|3||RF02735||Saccharopolyspora sRNA 350||2||1.000||21.0|
|3||RF02743||Saccharopolyspora sRNA 389||2||1.000||23.4|
This section shows the database cross-references that we have for this Rfam motif.
Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB J Math Biol. 2008;56:215-52. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. PUBMED:17694311
Klosterman PS, Hendrix DK, Tamura M, Holbrook SR, Brenner SE Nucleic Acids Res. 2004;32:2342-52. Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. PUBMED:15121895
Zirbel CL, Sponer JE, Sponer J, Stombaugh J, Leontis NB Nucleic Acids Res. 2009;37:4898-918. Classification and energetics of the base-phosphate interactions in RNA. PUBMED:19528080
Schroeder KT, McPhee SA, Ouellet J, Lilley DM RNA. 2010;16:1463-8. A structural database for k-turn motifs in RNA. PUBMED:20562215
Blouin S, Chinnappan R, Lafontaine DA Nucleic Acids Res. 2010 Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation. PUBMED:21169337
Meyer M, Westhof E, Masquida B RNA Biol. 2012;9:[Epub ahead of print]. A structural module in RNase P expands the variety of RNA kinks. PUBMED:22336704
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
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.
|Seed source||Published; PMID:19528080|
cmbuild -F k-turn-CM k-turn-SEED
cmcalibrate --mpi --seed 1 k-turn-CM
|Covariance model||Download the Infernal CM for the motif here|