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Rfam families   (All mRNA and EST tracks)

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Assembly: SARS-CoV-2 Jan. 2020 (NC_045512.2)
Data last updated at UCSC: 2020-04-28

Rfam families

The SARS-CoV-2 genome was annotated using the structured RNA families from the Rfam database including the following Coronavirus-specific families:


The annotations were generated using the Infernal cmsearch program and the Rfam covariance models (release 14.2). The cmsearch output was manually edited to remove the lower-scoring Betacoronavirus-5UTR and Betacoronavirus-3UTR families that belong to the same Rfam clans as the Sarbecovirus-5UTR and Sarbecovirus-3UTR families (CL00116 and CL00117).

The alignments and the secondary structure were produced using LocARNA and refined based on the latest literature.


The curated Sarbecovirus alignments were provided by Kevin Lamkiewicz and Manja Marz (Friedrich Schiller University Jena). Eric Nawrocki (NCBI) revised the existing Rfam entries (RF00164, RF00165, and RF00507). We also thank Ramakanth Madhugiri (Justus Liebig University Giessen) for reviewing the Coronavirus UTR alignments. The track was prepared by the Rfam team.

This work is part of the BBSRC funded project to expand the coverage of viral RNAs in Rfam.