This track shows predicted and experimental representations of the SARS-CoV-2 transcriptome based on long-read Nanopore sequencing.
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:
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 http://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/bbi/kim2020/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