Summary
Clan
This family is a member of clan (CL00104), which contains the following 2 members:
AHBV_epsilon HBV_epsilonWikipedia 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.
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
HideWeight segments by...
Change the size of the sunburst
Colour assignments
Archea | Eukaryota |
Bacteria | Other sequences |
Viruses | Unclassified |
Viroids | Unclassified sequence |
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...
Loading...
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.
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 HBV_epsilon family has been found.
Loading structure mapping...
References
This section shows the database cross-references that we have for this Rfam family.
Literature references
-
Beck J, Nassal M World J Gastroenterol. 2007;13:48-64 Hepatitis B virus replication. PUBMED:17206754
-
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
-
Kramvis A, Kew MC J Viral Hepat. 1998;5:357-367 Structure and function of the encapsidation signal of hepadnaviridae. PUBMED:9857345
-
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
Gene Ontology: | GO:0019079 (viral genome replication); |
Sequence Ontology: | SO:0005836 (regulatory_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 | Chen A, Brown C | ||||||
Structure source | Published; PMID:12409471 | ||||||
Type | Cis-reg; | ||||||
Author | Chen A, Brown C | ||||||
Alignment details |
|
Model information
Build commands |
cmbuild -F CM SEED
cmcalibrate --mpi CM
|
Search command |
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
|
Gathering cutoff | 45.0 |
Trusted cutoff | 61.0 |
Noise cutoff | 40.1 |
Covariance model | Download |