0  structures 1  species 6  sequences

Family: EBER2 (RF02712)

Description: Epstein-Barr virus EBER2


Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry Epstein–Barr virus-encoded small RNAs. 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...

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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.

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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. Shen ZC, Luo B, Chen JN, Chao Y, Shao CK, Liu QQ, Wang Y PLoS One. 2015;10:e0121420. High prevalence of the EBER variant EB-8m in endemic nasopharyngeal carcinomas. PUBMED:25807550

  2. Lei H, Li T, Hung GC, Li B, Tsai S, Lo SC BMC Genomics. 2013;14:804. Identification and characterization of EBV genomes in spontaneously immortalized human peripheral blood B lymphocytes by NGS technology. PUBMED:24252203

  3. Lin Z, Wang X, Strong MJ, Concha M, Baddoo M, Xu G, Baribault C, Fewell C, Hulme W, Hedges D, Taylor CM, Flemington EK J Virol. 2013;87:1172-1182. Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains. PUBMED:23152513

  4. Lee WK, Kim SM, Sim YS, Cho SG, Park SH, Kim CW, Park JG In Vitro Cell Dev Biol Anim. 1998;34:97-100. B-lymphoblastoid cell lines from cancer patients. PUBMED:9542645

  5. Lee N, Moss WN, Yario TA, Steitz JA Cell. 2015;160:607-618. EBV noncoding RNA binds nascent RNA to drive host PAX5 to viral DNA. PUBMED:25662012

  6. Lerner MR, Andrews NC, Miller G, Steitz JA Proc Natl Acad Sci U S A. 1981;78:805-809. Two small RNAs encoded by Epstein-Barr virus and complexed with protein are precipitated by antibodies from patients with systemic lupus erythematosus. PUBMED:6262773

  7. Moss WN, Lee N, Pimienta G, Steitz JA RNA Biol. 2014;11:10-17. RNA families in Epstein-Barr virus. PUBMED:24441309

  8. Samanta M, Takada K Cancer Sci. 2010;101:29-35. Modulation of innate immunity system by Epstein-Barr virus-encoded non-coding RNA and oncogenesis. PUBMED:19886912

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 Quinones-Olvera N
Structure source Published; PMID:25662012
Type Gene; sRNA;
Author Quinones-Olvera NORCID logo
Alignment details
Alignment Number of
full 3
seed 3

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize 128 CM SEQDB
Gathering cutoff 125.0
Trusted cutoff 125.7
Noise cutoff 75.5
Covariance model Download