Schema for Rfam - Rfam families
  Database: wuhCor1    Primary Table: rfam    Row Count: 5   Data last updated: 2020-04-27
Format description: Browser extensible data
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom NC_045512v2varchar(255) values Reference sequence chromosome or scaffold
chromStart 1int(10) unsigned range Start position in chromosome
chromEnd 299int(10) unsigned range End position in chromosome
name Sarbecovirus-5UTRvarchar(255) values Name of item
score 1int(10) unsigned range Optional score, nominal range 0-1000

Sample Rows
 
binchromchromStartchromEndnamescore
585NC_045512v21299Sarbecovirus-5UTR1
585NC_045512v21346913550Corona_FSE1
585NC_045512v22953629870Sarbecovirus-3UTR1
585NC_045512v22960329662Corona_pk31
585NC_045512v22972729769s2m1

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Rfam (rfam) Track Description
 

Rfam families

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

Methods

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.

Credits

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.

References