Viral RNA families

EVBC logo

Rfam is collaborating with the European Virus Bioinformatics Centre (EVBC), with an aim to provide a comprehensive database for virologists interested in RNA secondary structures.
Learn more about EVBC →

Coronaviridae RNA families

In Rfam release 14.2 we created 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

SARS-Cov-2 Rfam model
Accession Rfam ID Description
RF00507 Corona_FSE Coronavirus frameshifting stimulation element
RF00164 s2m Coronavirus 3' stem-loop II-like motif (s2m)
RF00165 Corona_pk3 Coronavirus 3' UTR pseudoknot
RF03116 aCoV-5UTR Alphacoronavirus 5'UTR
RF03117 bCoV-5UTR Betacoronavirus 5'UTR
RF03118 gCoV-5UTR Gammacoronavirus 5'UTR
RF03119 dCoV-5UTR Deltacoronavirus 5'UTR
RF03120 Sarbecovirus-5UTR Sarbecovirus 5'UTR
RF03121 aCoV-3UTR Alphacoronavirus 3'UTR
RF03122 bCoV-3UTR Betacoronavirus 3'UTR
RF03123 gCoV-3UTR Gammacoronavirus 3'UTR
RF03124 dCoV-3UTR Deltacoronavirus 3'UTR
RF03125 Sarbecovirus-3UTR Sarbecovirus 3'UTR

Hepacivirus RNA families

In release 14.10, we have updated 9 HCV families to better reflect their secondary structures.

In release 14.8, we have added 4 new Hepatitis C RNA families, and have updated 5 existing families. We have also removed 4 families: RF02585, RF02586, RF02587, RF02588.

HCV families
Accession Rfam ID Description
RF00061 IRES_HCV Hepatitis C virus internal ribosome entry site
RF00260 HepC_CRE Hepatitis C virus (HCV) cis-acting replication element (CRE)
RF00620 HCV_ARF_SL Hepatitis C alternative reading frame stem-loop
RF00468 HCV_SLVII Hepatitis C virus stem-loop VII
RF00481 HCV_X3 Hepatitis C virus 3'X element
RF04218 HCV_5BSL1 Hepatitis C virus stem-loop I
RF04219 HCV_J750 J750 non-coding RNA (containing SLSL761 and SL783)
RF04220 HCV_SL588 SL588 non-coding RNA
RF04221 HCV_SL669 SL669 non-coding RNA

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 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.