0  structures 10  species 52  sequences

Family: HepC_CRE (RF00260)

Description: Hepatitis C virus (HCV) cis-acting replication element (CRE)


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 cis-acting replication element. More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.



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".

Alignment format:


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


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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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The tree shows the occurrence of this RNA across different species. More...


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

This tree was built using the fasttree method.

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

Literature references

  1. You S, Stump DD, Branch AD, Rice CM J Virol 2004;78:1352-1366. A cis-acting replication element in the sequence encoding the NS5B RNA-dependent RNA polymerase is required for hepatitis C virus RNA replication. PUBMED:14722290

  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. 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

  4. 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

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.


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 KORCID logo, Triebel SORCID logo, Marz MORCID logo
Alignment details
Alignment Number of
full 0
seed 52

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 60.0
Trusted cutoff 67.8
Noise cutoff 36.2
Covariance model Download