Subgenomic Canonical Track Settings
Canonical Subgenomic Transcripts   (All Genes and Gene Predictions tracks)

Display mode:       Reset to defaults
List subtracks: only selected/visible    all  
 TRS sites  Transcription Regulatory Sequences (TRS) of Canonical Subgenomic Transcripts   Data format 
 Known Transcripts (gRNA and mRNA)  Canonical Subgenomic Transcripts (gRNA and mRNA)   Data format 


This track shows predicted and experimental representations of the SARS-CoV-2 transcriptome based on long-read Nanopore sequencing.

Display Conventions and Configuration

SARS-CoV-2 generates sub-genomic mRNAs (sgmRNAs) for all ORFs. The virus achieves this by recombination mechanisms in which replication machinery jumps from one of many TRS-B site (transcription regulatory sequence, body) to the TRS-L (leader sequence) during negative strand synthesis. These negative strands are then used as templates for mRNA synthesis.

On these tracks we depict the predicted mRNAs with the excised sequence drawn like introns. The ORFs predicted to be translated by these mRNAs are shown in thick boxes. The thin bars function as UTRs for that particular mRNA species.

Multiple subtracks are available:

  • TRS sites: Annotated core TRS sequence (ACGAAC) in the viral genome that allows recombination. One site TRS* differs from the canonical TRS site by 1 nt, but has experimental support and is required to generate a 7b mRNA.
  • SARS-CoV-2 Transcripts: Canonical SARS-CoV-2 Transcripts (gRNA and mRNA). Generated by recombining all TRS-B sites in the above track with the leader. Note the actual recombination breakpoints can often be drawn in multiple ways (since the TRS core motif is identical), and direct RNA sequencing suggests slightly different breakpoints, depending on the mRNA. See the experimental tracks if your analysis requires a detailed understanding of the breaks. The reported breaks in this track are only meant to be approximate.


  • TRS sites: The core TRS sequence (ACGAAC) was identified using the findMotif tool. The TRS* (AaGAAC) site identified in Kim et al was manually added to create overall agreement with their Figure 1.
  • SARS CoV-2 Transcripts: Using the TRS track, we generated mRNAs which span from nt 1-75 (the end of the TRS-L core sequence) and resume at the 3' end of all TRS-B sequences. Neither the 5' and 3' terminal ends of these RNAs, nor their internal breakpoints, should be considered exact. CDS sequences match Figure 1 from Kim et al.

Data Access

The raw data can be explored interactively with the Table Browser, or combined with other datasets in the Data Integrator tool. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server.

Annotations can be converted from binary to ASCII text by our command-line tool bigBedToBed. Instructions for downloading this command can be found on our utilities page. The tool can also be used to obtain features within a given range without downloading the file, for example:

bigBedToBed -chrom=NC_045512v2 -start=0 -end=29902 stdout

Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.


Thanks to Jason Fernandes (Haussler-lab, UCSC) for preparing this track.


Kim D, Lee JY, Yang JS, Kim JW, Kim VN, Chang H. The Architecture of SARS-CoV-2 Transcriptome. Cell. 2020 Apr 18;. PMID: 32330414; PMC: PMC7179501