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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.
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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.
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...
|Number of Hits
|Fraction of Hits
|Sum of Bits
This section shows the database cross-references that we have for this Rfam family.
Pijlman GP, Funk A, Kondratieva N, Leung J, Torres S, van der Aa L, Liu WJ, Palmenberg AC, Shi PY, Hall RA, Khromykh AA Cell Host Microbe. 2008;4:579-591. A highly structured, nuclease-resistant, noncoding RNA produced by flaviviruses is required for pathogenicity. PUBMED:19064258
Moon SL, Anderson JR, Kumagai Y, Wilusz CJ, Akira S, Khromykh AA, Wilusz J RNA. 2012;18:2029-2040. A noncoding RNA produced by arthropod-borne flaviviruses inhibits the cellular exoribonuclease XRN1 and alters host mRNA stability. PUBMED:23006624
Villordo SM, Filomatori CV, Sanchez-Vargas I, Blair CD, Gamarnik AV PLoS Pathog. 2015;11:e1004604. Dengue virus RNA structure specialization facilitates host adaptation. PUBMED:25635835
Ng WC, Soto-Acosta R, Bradrick SS, Garcia-Blanco MA, Ooi EE Viruses. 2017; [Epub ahead of print] The 5' and 3' Untranslated Regions of the Flaviviral Genome. PUBMED:28587300
Iwakawa HO, Mizumoto H, Nagano H, Imoto Y, Takigawa K, Sarawaneeyaruk S, Kaido M, Mise K, Okuno T J Virol. 2008;82:10162-10174. A viral noncoding RNA generated by cis-element-mediated protection against 5'->3' RNA decay represses both cap-independent and cap-dependent translation. PUBMED:18701589
Steckelberg AL, Akiyama BM, Costantino DA, Sit TL, Nix JC, Kieft JS Proc Natl Acad Sci U S A. 2018;115:6404-6409. A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure. PUBMED:29866852
Steckelberg AL, Vicens Q, Costantino DA, Nix JC, Kieft JS RNA. 2020; [Epub ahead of print] The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold. PUBMED:32848042
External database links
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.
|Predicted; LocARNA 2.0.0RC8
cmbuild -F CM SEED
cmcalibrate --mpi CM
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 742849.287494 CM SEQDB