Viral RNA families

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Rfam collaborates with the European Virus Bioinformatics Centre (EVBC) aiming to provide a comprehensive database for virologists interested in RNA secondary structures.
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Coronaviridae RNA families

SARS-Cov-2 Rfam model

Rfam contains 10 families representing the entire 5'- and 3'- untranslated regions (UTRs) for Alpha-, Beta-, Gamma-, and Deltacoronaviruses. A specialised set of alignments for the subgenus Sarbecovirus is also provided, including the SARS-CoV-1 and SARS-CoV-2 UTRs.

There are also 4 non-UTR families, including Coronavirus packaging signal, Coronavirus frameshifting stimulation element, Coronavirus s2m RNA, and Coronavirus 3'-UTR pseudoknot.

View Coronaviridae families

Flaviviridae RNA families

Accession Rfam ID Description
RF03546 Flavivirus-5UTR Flavivirus 5' UTR
RF00185 Flavi_CRE Flavivirus 3' UTR cis-acting replication element (CRE)
RF00525 Flavivirus_DB Flavivirus DB element
RF03547 Flavi_xrRNA General Flavivirus exoribonuclease-resistant RNA element
RF03545 Flavi_ISFV_CRE Insect-specific Flavivirus 3' UTR cis-acting replication element (CRE)
RF03544 Flavi_ISFV_repeat_Ra Insect-Specific Flavivirus 3' UTR repeats Ra
RF03543 Flavi_ISFV_repeat_Rb Insect-Specific Flavivirus 3' UTR repeats Rb
RF03542 Flavi_ISFV_repeat_Ra_Rb Insect-Specific Flavivirus 3' UTR repeats Ra and Rb elements
RF03541 Flavi_ISFV_xrRNA Insect-specific Flavivirus exoribonuclease-resistant RNA element
RF03540 Flavi_NKV_CRE No-Known-Vector Flavivirus 3' UTR cis-acting replication element (CRE)
RF03539 Flavi_NKV_xrRNA No-known vector Flavivirus exoribonuclease-resistant RNA element
RF03538 Flavi_TBFV_CRE Tick-borne Flavivirus 3' UTR cis-acting replication element (CRE)
RF03537 Flavi_TBFV_SL6 Tick-borne Flavivirus short stem-loop SL6
RF03536 Flavi_TBFV_xrRNA Tick-borne Flavivirus exoribonuclease-resistant RNA element

Work in progress

We are working on adding RNA families from other viruses, such as Hepacivirus (Hepatitis C viruses), Filoviridae (e.g. Ebolavirus) and Rhabdoviridae (e.g. Rabies viruses).

Please contact Rfam if you are interested in a specific virus family or if you have feedback about this project.