Rfam: Family: CRISPR-DR6 (RF01319)
Sequences
Alignment
There are various ways to view or download the seed alignments that we store. You can use a sequence viewer to look at them, or you can look at a plain text version of the sequence in a variety of different formats. More...
View options
You can view Rfam seed alignments in your browser in various ways. Choose the viewer that you want to use and click the "View" button to show the alignment in a pop-up window.
Formatting options
You can view or download Rfam seed 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".
Download
Download a gzip-compressed, Stockholm-format file containing the seed alignment for this family. You may find RALEE useful when viewing sequence alignments.
Submit a new alignment
We're happy receive updated seed alignments for new or existing families. Submit your new alignment and we'll take a look.
Secondary structure
This section shows a variety of different secondary structure representations for this family. More...
You can view the secondary structure of the family using the VARNA applet. You can see more information about VARNA iself here.
Current Rfam structure
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R-scape optimised structure
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- Colours
- Statistically significant basepair with covariation
- 97% conserved nucleotide
- 90% conserved nucleotide
- 75% conserved nucleotide
- 50% conserved nucleotide
- Nucleotides
- R: A or G
- Y: C or U
Tip: The diagrams are interactive:
you can pan and zoom to see more details
or hover over nucleotides and basepairs.
R-scape is a method for testing whether covariation analysis supports the presence of a conserved RNA secondary structure. This page shows R-scape analysis of the secondary structure from the Rfam seed alignment and a new structure with covariation support that is compatible with the same alignment.
To find out more about the method, see the R-scape paper by Rivas et al., 2016. The structures are visualised using R2R.
Species distribution
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Selections
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
The tree shows the occurrence of this RNA across different species. More...
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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
Trees
This page displays the predicted phylogenetic tree for the alignment. More...
Note: You can also download the data file for the seed tree.
References
This section shows the database cross-references that we have for this Rfam family.
Literature references
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Grissa I, Vergnaud G, Pourcel C; BMC Bioinformatics. 2007;8:172. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. PUBMED:17521438
External database links
| Gene Ontology: | GO:0006952 (defense response); |
| Sequence Ontology: | SO:0001459 (CRISPR); |
| External sites: | 1: http://crispr.u-psud.fr/crispr/CRISPRHomePage.php |
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.
Curation
| Seed source | Predicted; WAR; Wilkinson A | ||||||
| Structure source | Predicted; WAR; Wilkinson A | ||||||
| Type | Gene; CRISPR; | ||||||
| Author |
Wilkinson A
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| Alignment details |
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Model information
| Build commands |
cmbuild -F CM SEED cmcalibrate --mpi CM |
| Search command |
cmsearch --cpu 4 --verbose --nohmmonly -T 27.19 -Z 2958934 CM SEQDB |
| Gathering cutoff | 39.0 |
| Trusted cutoff | 39.4 |
| Noise cutoff | 38.9 |
| Covariance model | Download |