25  structures 22  species 55  sequences

Family: IRES_HCV (RF00061)

Description: Hepatitis C virus internal ribosome entry site

Summary

Clan

This family is a member of clan (CL00017), which contains the following 2 members:

IRES_HCV IRES_Pesti

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 internal ribosome entry site. 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.

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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".

Alignment format:
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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.

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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...

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Trees

This page displays the predicted phylogenetic tree for the alignment. More...

This tree was built using the fasttree method.

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Note: You can also download the data file for the seed tree.

Structures

For those sequences which have a structure in the Protein DataBank, we generate a mapping between EMBL, PDB and Rfam coordinate systems. The table below shows the structures on which the IRES_HCV family has been found.

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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
7 RM00029 UNCG tetraloop 25 0.316 281.2 Match Image

References

This section shows the database cross-references that we have for this Rfam family.

Literature references

  1. Gallego J, Varani G Biochem Soc Trans 2002;30:140-145. The hepatitis C virus internal ribosome-entry site: a new target for antiviral research. PUBMED:12023841

  2. 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

  3. Lytle JR, Wu L, Robertson HD RNA 2002;8:1045-1055. Domains on the hepatitis C virus internal ribosome entry site for 40s subunit binding. PUBMED:12212848

  4. 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

  5. Beales LP, Rowlands DJ, Holzenburg A RNA 2001;7:661-670. The internal ribosome entry site (IRES) of hepatitis C virus visualized by electron microscopy. PUBMED:11350030

  6. 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

  7. 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

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 ViennaRNA v.2.4.18
Type Cis-reg; IRES;
Author Lamkiewicz KORCID logo, Triebel SORCID logo, Marz MORCID logo
Alignment details
Alignment Number of
sequences
full 4
seed 51

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 742849.287494 CM SEQDB
Gathering cutoff 290.0
Trusted cutoff 298.2
Noise cutoff 78.3
Covariance model Download