Wikipedia annotation Edit Wikipedia article
Before you edit for the first time
You should take a few minutes to view the following pages:
Things you should know
How your contribution will be recorded
Information we would like to see added
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 ?
If you have problems editing or experience problems with these pages please contact us.
You can choose from two different sequence viewers:
- Gapped FASTA
- Ungapped FASTA
Submit a new alignment
Normal: this plot simply colours each stem loop
The R-chie arc diagrams were calculated using R-chie:
You can view the secondary structure of the family using the here.applet. You can see more information about VARNA iself
Current Rfam structure
R-scape optimised structure
- Statistically significant basepair with covariation
- 97% conserved nucleotide
- 90% conserved nucleotide
- 75% conserved nucleotide
- 50% conserved nucleotide
- R: A or G
- Y: C or U
you can pan and zoom to see more details
or hover over nucleotides and basepairs.
Move your mouse over the image to show details and click to show full image.
- Arc colours
- 100% canonical basepair
- Nucleotide colours
- Valid basepairing
- Two-sided covariation
- One-sided covariation
Weight segments by...
Change the size of the sunburst
Click on a node to select that node and its sub-tree.
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this RNA across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
This page displays the predicted phylogenetic tree for the alignment. More...
Note: You can also download the data file for the seed tree.
This section shows the database cross-references that we have for this Rfam family.
Rau MH, Bojanovic K, Nielsen AT, Long KS BMC Genomics. 2015;16:1051. Differential expression of small RNAs under chemical stress and fed-batch fermentation in E. coli. PUBMED:26653712
External database links
|Gene Ontology:||GO:0006950 (response to stress); GO:0006113 (fermentation);|
|Sequence Ontology:||SO:0000370 (small_regulatory_ncRNA);|
Curation and family details
|Seed source||Argasinska J|
|Structure source||Predicted; RNAfold|
cmbuild -F CM SEED
cmcalibrate --mpi CM
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize 128 CM SEQDB