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 Sequence motif 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 firstname.lastname@example.org 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 115 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||12||0.105||109.2|
|3||RF00024||Vertebrate telomerase RNA||5||0.135||48.2|
|3||RF00028||Group I catalytic intron||3||0.250||28.1|
|3||RF00053||mir-7 microRNA precursor||10||0.175||98.8|
|3||RF00114||Ribosomal S15 leader||7||0.090||54.2|
|3||RF00150||Small nucleolar RNA SNORD42||3||0.429||24.1|
|3||RF00151||Small nucleolar RNA SNORD58||2||0.061||23.8|
|3||RF00225||Tobamovirus internal ribosome entry site (IRES)||4||0.571||52.0|
|3||RF00234||glmS glucosamine-6-phosphate activated ribozyme||2||0.111||21.0|
|3||RF00278||Small nucleolar RNA SNORD50||3||0.115||28.3|
|3||RF00303||Small nucleolar RNA snoR86||2||0.182||19.9|
|3||RF00623||Pseudomonas sRNA P1||3||0.214||23.4|
|3||RF01181||Small nucleolar RNA snR77||15||1.000||211.3|
|3||RF01203||Small nucleolar RNA snR47||10||0.588||150.2|
|3||RF01214||Small nucleolar RNA snR51||3||0.176||25.6|
|3||RF01241||Small nucleolar RNA SNORA81||18||0.643||189.9|
|3||RF01265||Small nucleolar RNA snR42||2||0.400||23.0|
|3||RF01272||Small nucleolar RNA snR86||2||0.400||21.4|
|3||RF01296||Small nucleolar RNA U85||10||0.476||100.4|
|3||RF01387||isrC Hfq binding RNA||3||0.188||29.6|
|3||RF01402||STnc150 Hfq binding RNA||9||1.000||207.3|
|3||RF01408||sraL Hfq binding RNA||2||0.333||18.4|
|3||RF01419||Antisense RNA which regulates isiA expression||31||0.101||318.4|
|3||RF01459||Listeria sRNA rliE||3||0.750||26.8|
|3||RF01461||Listeria sRNA rli22||6||1.000||58.5|
|3||RF01471||Listeria sRNA rliB||2||0.500||28.2|
|3||RF01473||Listeria sRNA rli41||6||1.000||65.5|
|3||RF01477||Listeria sRNA rli43||8||2.000||72.7|
|3||RF01496||A. fumigatus sRNA Afu_182||2||0.105||16.6|
|3||RF01592||small nucleolar RNA snoR17||3||0.600||32.7|
|3||RF01603||small nucleolar RNA snoR29||4||1.333||30.4|
|3||RF01606||small nucleolar RNA snoR31||3||1.000||27.9|
|3||RF01675||Pseudomonas sRNA CrcZ||19||1.000||1922.9|
|3||RF01692||Bacteroidete tryptophan peptide leader RNA||13||0.371||163.3|
|3||RF01808||MicX Vibrio cholerae sRNA||6||0.600||97.2|
|3||RF01824||RNA of unknown function 20||5||0.833||77.2|
|3||RF01825||RNA of unknown function 21||5||1.000||74.6|
|3||RF01830||Salmonella enterica Typhi npcRNA 44||4||0.118||38.8|
|3||RF01859||Phenylalanine leader peptide||38||0.535||517.0|
|3||RF01865||Manganese dependent ribozyme in Vg1 mRNA||2||0.500||19.7|
|3||RF01871||Metastasis associated lung adenocarcinoma transcript 1||5||0.294||61.1|
|3||RF01873||Polled intersex syndrome regulated transcript 1||12||0.667||99.6|
|3||RF01888||Embryonic ventral forebrain RNA 1 conserved region 2||14||0.737||144.3|
|3||RF01931||Bithoraxoid conserved region 3||4||1.000||49.8|
|3||RF01960||Eukaryotic small subunit ribosomal RNA||37||0.407||468.6|
|3||RF02032||Giant, ornate, lake- and Lactobacillales-derived (GOLLD) RNA||4||0.114||36.6|
|3||RF02036||IMES-3 RNA motif||31||0.969||266.2|
|3||RF02039||SPRY4-IT1 conserved region 2||10||0.417||100.3|
|3||RF02042||HOXA transcript at the distal tip, conserved region 3||15||0.652||140.9|
|3||RF02045||CDKN2B antisense RNA 1 convserved region 3||4||0.222||38.1|
|3||RF02057||Salmonella enterica sRNA STnc40||6||0.353||66.9|
|3||RF02075||Enterobacterial sRNA STnc230||6||0.545||73.4|
|3||RF02076||Gammaproteobacterial sRNA STnc100||3||0.125||27.9|
|3||RF02080||Salmonella enterica sRNA STnc170||5||1.667||54.7|
|3||RF02081||Enterobacterial sRNA STnc550||6||0.545||57.9|
|3||RF02101||Highly up-regulated in liver cancer conserved region||7||0.368||82.3|
|3||RF02103||Deleted in lymphocytic leukemia 1 conserved region 1||3||0.115||29.2|
|3||RF02112||DLG2 antisense RNA 1 conserved region 1||5||0.238||47.8|
|3||RF02132||HOXB13 antisense RNA 1 conserved region 1||7||0.583||73.2|
|3||RF02142||HOXA11 antisense RNA 1 conserved region 6||21||1.000||312.5|
|3||RF02154||Non-protein coding RNA, upstream of F2R/PAR1 conserved region 1||5||0.556||42.2|
|3||RF02157||NPPA antisense RNA 1 conserved region 2||12||0.750||123.6|
|3||RF02158||NPPA antisense RNA 1 conserved region 3||4||0.167||36.5|
|3||RF02159||Prostate androgen-regulated transcript 1 conserved region 1||6||0.273||62.7|
|3||RF02160||Prostate androgen-regulated transcript 1 conserved region 2||8||0.276||88.6|
|3||RF02170||Pvt1 oncogene conserved region 7||3||0.375||23.3|
|3||RF02179||ST7 antisense RNA 1 conserved region 1||2||0.080||24.1|
|3||RF02183||ST7 overlapping transcript 3 conserved region 1||3||0.107||25.7|
|3||RF02187||ST7 overlapping transcript 4 conserved region 1||2||0.083||21.0|
|3||RF02192||T-cell leukemia/lymphoma 6 conserved region 2||7||0.583||96.7|
|3||RF02194||Bacterial antisense RNA HPnc0260||8||0.258||71.8|
|3||RF02199||TTC28 antisense RNA 1 conserved region 2||3||0.375||25.0|
|3||RF02212||ZFAT antisense RNA 1 conserved region 2||6||0.545||79.4|
|3||RF02415||Listeria sRNA rliG||3||0.600||38.6|
|3||RF02422||Burkholderia sRNA Bp1_Cand738_SIPHT||9||0.429||75.6|
|3||RF02446||Streptococcus sRNA SpR18||18||0.783||149.2|
|3||RF02447||Streptococcus sRNA SpR19||2||0.087||21.0|
|3||RF02449||Bacillus sRNA ncr1015||3||0.188||28.5|
|3||RF02530||Ure2 internal ribosome entry site (IRES)||5||1.000||91.6|
|3||RF02540||Archaeal large subunit ribosomal RNA||61||0.670||525.0|
|3||RF02541||Bacterial large subunit ribosomal RNA||31||0.304||385.9|
|3||RF02542||Microsporidia small subunit ribosomal RNA||8||0.174||86.0|
|3||RF02543||Eukaryotic large subunit ribosomal RNA||25||0.284||401.9|
|3||RF02545||Trypanosomatid mitochondrial small subunit ribosomal RNA||4||1.000||79.9|
|3||RF02575||Drosophila melanogaster stable intronic sequence RNA 1||3||1.000||28.8|
|3||RF02737||Soft rot Enterobacteriaceae Rev 13 asRNA||3||1.000||53.5|
|3||RF02738||Soft rot Enterobacteriaceae Rev 24 asRNA||2||0.500||22.7|
|3||RF02742||Soft rot Enterobacteriaceae Rev 72 asRNA||3||1.000||34.7|
|3||RF02745||Soft rot Enterobacteriaceae Rev 42 5'UTR||3||1.000||37.5|
This section shows the database cross-references that we have for this Rfam motif.
Sonnleitner E, Abdou L, Haas D Proc Natl Acad Sci U S A. 2009;106:21866-21871. Small RNA as global regulator of carbon catabolite repression in Pseudomonas aeruginosa. PUBMED:20080802
External database links
|Gene Ontology:||GO:0006401 (RNA catabolic process); GO:0006109 (regulation of carbohydrate metabolic process);|
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||Gardner PP|
|Type||Specific Recognition Motif|
cmbuild -F CM SEED
cmcalibrate --mpi --seed 1 CM
|Covariance model||Download the Infernal CM for the motif here|