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For a good example of what is possible in wikipedia, look at the Hammerhead Ribozyme entry.
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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...
These trees were generated using either a maximum likelihood approach or neighbour-joining. If the number of sequences in the alignment was less than or equal to 64 then the maximum likelihood approach of Rivas and Eddy was used . For families with more than 64 sequences in the alignment the neighbour-joining approach with F84 distances as implemented in phylip was used .
Note: You can also download the data file for the seed tree.
We do not have tree information for this family. This is most likely due to the size of the family and the number of species covered. For very large families it is too computationally expensive to calculate trees and the resulting tree images would be too large to display in a browser.
There are 1 motifs which match this family.
This section shows the Rfam motifs that match sequences within the seed alignment of this family. 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...
Motifs in this context are defined as recurring RNA sequences and/or secondary structures found within larger structures that can be modeled by either a covariance model (CM) or a profile HMM. The motifs models come from release 0.3 of the RMfam database available at github.
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||Motif Accession||Motif Description||Number of Hits||Fraction of Hits||Sum of Bits||Image|
This section shows the database cross-references that we have for this Rfam family.
Chen X, Taylor DW, Fowler CC, Galan JE, Wang HW, Wolin SL Cell. 2013;153:166-177. An RNA degradation machine sculpted by Ro autoantigen and noncoding RNA. PUBMED:23540697
Chen X, Sim S, Wurtmann EJ, Feke A, Wolin SL RNA. 2014;20:1715-1724. Bacterial noncoding Y RNAs are widespread and mimic tRNAs. PUBMED:25232022
External database links
|Sequence Ontology:||SO:0000405 (Y_RNA);|
Curation and family details
This section shows the detailed information about the Rfam family. 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||Argasinska J|
|Structure source||Published; PMID:23540697|
cmbuild -F CM SEED
cmcalibrate --mpi CM
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize 128 CM SEQDB