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
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.
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.
be converted from binary to ASCII text by our command-line tool bigBedToBed.
Instructions for downloading this command can be found on our
The tool can also be used to obtain features within a given range without downloading the file,
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/bbi/kim2020/Kim_TRS.bb -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