1  structure 6  species 36  sequences

Family: HBV_epsilon (RF01047)

Description: HBV RNA encapsidation signal epsilon



This family is a member of clan (CL00104), which contains the following 2 members:

AHBV_epsilon HBV_epsilon

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry HBV RNA encapsidation signal epsilon. 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...

Tree controls


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...

This tree was built using the fasttree method.

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


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 HBV_epsilon family has been found.

Loading structure mapping...


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

Literature references

  1. Beck J, Nassal M World J Gastroenterol. 2007;13:48-64 Hepatitis B virus replication. PUBMED:17206754

  2. Flodell S, Schleucher J, Cromsigt J, Ippel H, Kidd-Ljunggren K, Wijmenga S Nucleic Acids Res. 2002;30:4803-4811 The apical stem-loop of the hepatitis B virus encapsidation signal folds into a stable tri-loop with two underlying pyrimidine bulges. PUBMED:12409471

  3. Kramvis A, Kew MC J Viral Hepat. 1998;5:357-367 Structure and function of the encapsidation signal of hepadnaviridae. PUBMED:9857345

  4. LeBlanc RM, Kasprzak WK, Longhini AP, Olenginski LT, Abulwerdi F, Ginocchio S, Shields B, Nyman J, Svirydava M, Del Vecchio C, Ivanic J, Schneekloth JS Jr, Shapiro BA, Dayie TK, Le Grice SFJ J Biomol Struct Dyn. 2021; [Epub ahead of print] Structural insights of the conserved "priming loop" of hepatitis B virus pre-genomic RNA. PUBMED:34155954

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 Chen A, Brown C
Structure source Published; PMID:12409471
Type Cis-reg;
Author Chen A, Brown C
Alignment details
Alignment Number of
full 3
seed 33

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 45.0
Trusted cutoff 83.7
Noise cutoff 38.5
Covariance model Download