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Clan: Coronavirus-3UTR (CL00117)


Coronavirus 3' UTR

The Coronavirus clan groups structured RNA elements found in Coronavirus genomes.

This clan contains 7 families and the total number of sequence regions in the clan is 159.

Literature references

  1. Madhugiri R, Fricke M, Marz M, Ziebuhr J, Adv Virus Res. 2016;96:127-163.: Coronavirus cis-Acting RNA Elements. 27712622


This clan contains the following 7 member families:

s2m Corona_pk3 aCoV-3UTR bCoV-3UTR gCoV-3UTR dCoV-3UTR Sarbecovirus-3UTR


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 mapping between the Rfam families in this clan, the corresponding EMBL entries, and the region of the three-dimensional structures that are available for that sequence.

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Secondary structures

This tool allows you to view the secondary structure images of two clan members side-by-side. Choose the family structures using the two drop-down menus below.


The table below shows the number of occurrences of each family throughout the sequence database. In brackets beside each number is the percentage of the total number of sequence hits for the clan that are represented by this family. The rightmost column provides a link to the alignments tab for each family.

Rfam family Num. regions Alignment
Sarbecovirus-3UTR (RF03125) 86 (54.1%) View
dCoV-3UTR (RF03124) 7 (4.4%) View
gCoV-3UTR (RF03123) 7 (4.4%) View
bCoV-3UTR (RF03122) 22 (13.8%) View
aCoV-3UTR (RF03121) 28 (17.6%) View
Corona_pk3 (RF00165) 3 (1.9%) View
s2m (RF00164) 6 (3.8%) View