Summary
Wikipedia annotation Edit Wikipedia article
The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry Hepatitis C virus stem-loop VII. More...
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
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
Species distribution
Sunburst controls
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Colour assignments
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Selections
Click on a node to select that node and its sub-tree.
Clear selection
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...
Tree controls
HideThe 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.
Motif matches
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...
Original order | Motif Accession | Motif Description | Number of Hits | Fraction of Hits | Sum of Bits | Image |
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7 | RM00005 | CsrA/RsmA binding motif | 33 | 0.300 | 309.7 |
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References
This section shows the database cross-references that we have for this Rfam family.
Literature references
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Lee H, Shin H, Wimmer E, Paul AV J Virol 2004;78:10865-10877. Cis-acting RNA signals in the NS5B C-terminal coding sequence of the hepatitis C virus genome. PUBMED:15452207
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Pirakitikulr N, Kohlway A, Lindenbach BD, Pyle AM Mol Cell. 2016;62:111-120. The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures. PUBMED:26924328
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Romero-Lopez C, Berzal-Herranz A Int J Mol Sci. 2020; [Epub ahead of print] The Role of the RNA-RNA Interactome in the Hepatitis C Virus Life Cycle. PUBMED:32098260
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Fricke M, Dunnes N, Zayas M, Bartenschlager R, Niepmann M, Marz M RNA. 2015;21:1219-1232. Conserved RNA secondary structures and long-range interactions in hepatitis C viruses. PUBMED:25964384
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Mauger DM, Golden M, Yamane D, Williford S, Lemon SM, Martin DP, Weeks KM Proc Natl Acad Sci U S A. 2015;112:3692-3697. Functionally conserved architecture of hepatitis C virus RNA genomes. PUBMED:25775547
External database links
Sequence Ontology: | SO:0000205 (three_prime_UTR); SO:0000837 (UTR_region); |
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 | Kevin Lamkiewicz; Sandra Triebel; Manja Marz; | ||||||
Structure source | Predicted; BM VeGETA v. 0.4, LocARNA 2.0.0RC8, RNAfold | ||||||
Type | Cis-reg; | ||||||
Author |
Lamkiewicz K |
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Alignment details |
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Model information
Build commands |
cmbuild -F CM SEED
cmcalibrate --mpi CM
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Search command |
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
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Gathering cutoff | 63.0 |
Trusted cutoff | 63.2 |
Noise cutoff | 36.3 |
Covariance model | Download |