Subgenomic Observed Track Settings
Subgenomic Transcripts found in long-read sequences by Kim et al. 2020   (All Genes and Gene Predictions tracks)

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 Kim recomb. trans.  Subgenomic Trans.: All recombined transcripts from Kim et al. 2020   Data format 
 Kim recomb. TRS trans.  Subgenomic Trans.: Recombined transcripts from Kim et al. 2020 with a TRS   Data format 
 Kim Recomb. Novel transcripts  Recombined Subgenomic Trans.: Transcripts from Kim et al. 2020 without a TRS   Data format 
Assembly: SARS-CoV-2 Jan. 2020 (NC_045512.2)


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:

  • Kim Recombined transcripts: All RNA recombination products reported by Nanopore direct RNA sequencing in Kim et al, 2020, Cell.
  • Kim Recomb. TRS transcripts: RNA recombination products that involve the leader on the 5' end; validated by nanopore sequencing. The score is the number of reads divided by 100. RNAs with read support >100,000 are rounded to a score of 1000.
  • Kim Recomb. Novel transcripts: RNA recombination products that do not involve the leader, discovered by nanopore sequencing. RNAs with less than 100 reads were discarded. The score is the number of reads. RNAs with read support >1000 are listed as 1000.


  • Kim Recombined transcripts: was generated from Table S2 of Kim et al, 2020. This represents all RNA species identified by direct RNA sequencing. Scores are the number of reads divided by 100 (RNAs with >1000 reads are rounded to 1000).
  • Kim Recomb. TRS transcripts: generated from Table S3 of Kim et al, 2020. These viral transcripts all contain the TRS-L recombined with 3' viral sequence.
  • Kim Recomb. Novel transcripts: this track was generated from Table S4. These viral transcripts contain novel recombination events that do not involve the leader.

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