Wikipedia annotation Edit Wikipedia article
The Rfam group coordinates the annotation of Rfam data in Wikipedia. This motif is described by a Wikipedia entry entitled Stem-loop but we are unable to retrieve the article content at this time. More...
The wikipedia text that you see displayed on our web site is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button above ("Edit wikipedia entry") takes you to the edit page for the article directly within wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed by our site until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
Things you should know
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia entry" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer’s IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at email@example.com and we will try to help.
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.
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 16 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||1c04||E||37 - 52|
|2||1j5e||A||243 - 273|
|2||1mms||C||37 - 52|
|2||1qa6||C||37 - 52|
|2||1s72||0||1189 - 1208|
|2||2avy||A||247 - 277|
|2||1u9s||A||102 - 120|
|2||1y69||0||2323 - 2350|
|2||2aw4||B||1086 - 1103|
|2||2j01||A||718 - 741|
|2||2a2e||A||150 - 170|
|2||2i82||E||1 - 21|
|2||1ffk||0||1698 - 1718|
|2||1giy||A||1133 - 1152|
|2||1mt4||A||2 - 23|
|2||3hhn||C||102 - 121|
There are 108 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||RF00004||U2 spliceosomal RNA||30||0.144||392.1|
|3||RF00007||U12 minor spliceosomal RNA||31||0.500||372.3|
|3||RF00009||Nuclear RNase P||30||0.259||386.0|
|3||RF00010||Bacterial RNase P class A||376||0.821||5926.2|
|3||RF00018||CsrB/RsmB RNA family||8||0.211||80.8|
|3||RF00024||Vertebrate telomerase RNA||4||0.108||47.5|
|3||RF00029||Group II catalytic intron||13||0.141||139.3|
|3||RF00043||R1162-like plasmid antisense RNA||4||0.500||47.1|
|3||RF00050||FMN riboswitch (RFN element)||14||0.097||154.6|
|3||RF00096||U8 small nucleolar RNA||11||0.200||123.8|
|3||RF00156||Small nucleolar RNA SNORA70||9||0.209||96.8|
|3||RF00166||PrrB/RsmZ RNA family||35||0.946||493.9|
|3||RF00177||Bacterial small subunit ribosomal RNA||99||1.000||2802.4|
|3||RF00209||Pestivirus internal ribosome entry site (IRES)||2||0.080||20.4|
|3||RF00224||FGF-2 internal ribosome entry site (IRES)||4||0.667||41.9|
|3||RF00263||Small nucleolar RNA SNORA68||5||0.192||59.3|
|3||RF00291||Small nucleolar RNA snoR639/H1||5||0.556||55.8|
|3||RF00357||Small nucleolar RNA R44/J54/Z268 family||2||0.069||20.0|
|3||RF00373||Archaeal RNase P||9||0.129||147.4|
|3||RF00386||Enterovirus 5' cloverleaf cis-acting replication element||68||0.425||724.3|
|3||RF00403||Small nucleolar RNA SNORA41||2||0.065||23.7|
|3||RF00495||Heat shock protein 70 (Hsp70) internal ribosome entry site (IRES)||7||0.500||74.9|
|3||RF00513||Tryptophan operon leader||3||0.136||36.0|
|3||RF00514||Histidine operon leader||9||0.273||96.5|
|3||RF00515||PyrR binding site||5||0.122||83.6|
|3||RF00548||U11 spliceosomal RNA||7||0.097||77.0|
|3||RF00558||Ribosomal protein L20 leader||11||0.256||135.9|
|3||RF00602||Small Cajal body specific RNA 21||6||0.250||99.9|
|3||RF00603||Small nucleolar RNA SNORD23||2||0.133||21.5|
|3||RF00604||Small nucleolar RNA SNORD88||2||0.057||23.1|
|3||RF00617||flavivirus capsid hairpin cHP||11||0.186||123.1|
|3||RF00629||Pseudomonas sRNA P24||7||0.500||101.1|
|3||RF00630||Pseudomonas sRNA P26||10||0.370||108.3|
|3||RF00634||S-adenosyl methionine (SAM) riboswitch,||3||0.075||34.9|
|3||RF01071||Ornate Large Extremophilic RNA||5||0.250||58.5|
|3||RF01089||Pseudoknot of the regulatory region of the repBA gene||2||0.286||20.2|
|3||RF01268||Small Cajal body-specific RNA 2||3||0.150||31.2|
|3||RF01330||CRISPR RNA direct repeat element||6||1.000||78.3|
|3||RF01390||isrG Hfq binding RNA||5||1.000||51.7|
|3||RF01401||rseX Hfq binding RNA||7||0.583||79.8|
|3||RF01529||Cauldobacter sRNA CC3552||2||1.000||24.7|
|3||RF01675||Pseudomonas sRNA CrcZ||17||0.895||191.9|
|3||RF01708||L17 ribosomal protein downstream element||6||0.115||71.2|
|3||RF01796||Fumarate/nitrate reductase regulator sRNA||3||0.188||34.0|
|3||RF01808||MicX Vibrio cholerae sRNA||5||0.500||61.9|
|3||RF01849||Alphaproteobacteria transfer-messenger RNA||11||0.099||140.2|
|3||RF01850||Betaproteobacteria transfer-messenger RNA||2||0.286||22.8|
|3||RF01852||Selenocysteine transfer RNA||9||0.083||106.3|
|3||RF01959||Archaeal small subunit ribosomal RNA||86||1.000||4568.1|
|3||RF01960||Eukaryotic small subunit ribosomal RNA||36||0.396||526.2|
|3||RF02033||HNH endonuclease-associated RNA and ORF (HEARO) RNA||12||0.109||145.4|
|3||RF02053||Enterobacterial sRNA STnc430||5||0.714||55.8|
|3||RF02055||Enterobacterial sRNA STnc380||4||0.800||50.8|
|3||RF02057||Salmonella enterica sRNA STnc40||2||0.118||23.8|
|3||RF02065||Enterobacterial sRNA STnc340||3||0.750||34.8|
|3||RF02074||Enterobacterial sRNA STnc240||8||0.533||89.3|
|3||RF02103||Deleted in lymphocytic leukemia 1 conserved region 1||3||0.115||35.4|
|3||RF02118||FMR1 antisense RNA 1 conserved region 2||9||0.360||112.2|
|3||RF02189||ST7 overlapping transcript 4 conserved region 3||2||0.100||22.8|
|3||RF02219||ZNRD1 antisense RNA 1 conserved region 2||2||0.059||22.0|
|3||RF02230||Proteobacterial sRNA sX11||2||0.200||20.2|
|3||RF02249||Six3os1 conserved region 4||2||0.286||20.4|
|3||RF02276||Hammerhead ribozyme (type II)||3||0.125||34.3|
|3||RF02278||Betaproteobacteria toxic small RNA||7||0.137||87.0|
|3||RF02342||Alphaproteobacterial sRNA ar7||6||0.207||68.7|
|3||RF02343||Alphaproteobacterial sRNA ar9||16||0.571||166.8|
|3||RF02351||Proteobacteria sRNA psRNA14||2||0.667||23.7|
|3||RF02354||Bradyrhizobiaceae sRNA BjrC80||7||0.467||83.6|
|3||RF02356||Alphaproteobacterial sRNA BjrC1505||3||0.120||35.7|
|3||RF02357||RNaseP truncated form||7||0.778||92.6|
|3||RF02379||Cia-dependent small RNA csRNA1||8||0.167||97.7|
|3||RF02423||Burkholderia sRNA Bp1_Cand871_SIPHT||14||0.933||170.8|
|3||RF02471||Actinobacteria sRNA Ms_IGR-5||6||0.286||66.5|
|3||RF02502||Rhizobiales sRNA Atu_C8||3||0.111||31.2|
|3||RF02524||Streptococcus sRNA sagA||3||0.500||37.0|
|3||RF02540||Archaeal large subunit ribosomal RNA||83||0.912||3404.2|
|3||RF02541||Bacterial large subunit ribosomal RNA||102||1.000||3700.8|
|3||RF02542||Microsporidia small subunit ribosomal RNA||43||0.935||832.7|
|3||RF02543||Eukaryotic large subunit ribosomal RNA||80||0.909||2165.6|
|3||RF02630||Hfq-regulated sRNA 12||2||1.000||28.6|
|3||RF02684||Type-P5 twister ribozyme||4||0.267||47.2|
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
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
Gutell RR, Cannone JJ, Konings D, Gautheret D J Mol Biol. 2000;300:791-803. Predicting U-turns in ribosomal RNA with comparative sequence analysis. PUBMED:10891269
Quigley GJ, Rich A Science. 1976;194:796-806. Structural domains of transfer RNA molecules. PUBMED:790568
External database links
|External sites:|| 1: http://rna.bgsu.edu/FR3D/MotifLibrary/Hairpins/LIB70006_HL_cWW_tSH_U_turn.html
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 U-CM U-SEED
cmcalibrate --mpi --seed 1 U-CM
|Covariance model||Download the Infernal CM for the motif here|