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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...
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.
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".
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.
Weight segments by...
Change the size of the sunburst
Click on a node to select that node and its sub-tree.
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
The tree shows the occurrence of this RNA across different species. More...
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.
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.
Baranov PV, Henderson CM, Anderson CB, Gesteland RF, Atkins JF, Howard MT Virology 2005;332:498-510. Programmed ribosomal frameshifting in decoding the SARS-CoV genome. PUBMED:15680415
Zhang K, Zheludev IN, Hagey RJ, Wu MT, Haslecker R, Hou YJ, Kretsch R, Pintilie GD, Rangan R, Kladwang W, Li S, Pham EA, Bernardin-Souibgui C, Baric RS, Sheahan TP, D Souza V, Glenn JS, Chiu W, Das R bioRxiv. 2020; [Epub ahead of print] Cryo-electron Microscopy and Exploratory Antisense Targeting of the 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome. PUBMED:32743589
External database links
|GO:0075523 (viral translational frameshifting);
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.
|Moxon SJ, Nawrocki E, Ontiveros-Palacios N
cmbuild -F CM SEED
cmcalibrate --mpi CM
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 742849.287494 CM SEQDB