Schema for Subgenomic Observed - Subgenomic Transcripts found in long-read sequences by Kim et al. 2020
  Database: wuhCor1    Primary Table: Kim_non-TRS_sgmRNAs Data last updated: 2020-04-27
Big Bed File Download: /gbdb/wuhCor1/bbi/kim2020/Kim_notTRS.bb
Item Count: 99
The data is stored in the binary BigBed format.

Format description: Browser Extensible Data
fieldexampledescription
chromNC_045512v2Reference sequence chromosome or scaffold
chromStart0Start position in chromosome
chromEnd29903End position in chromosome
namensp2Name of item.
score1000Score (0-1000)
strand++ or - for strand
thickStart265Start of where display should be thick (start codon)
thickEnd2155End of where display should be thick (stop codon)
reserved0,0,0Used as itemRgb as of 2004-11-22
blockCount2Number of blocks
blockSizes1853,428Comma separated list of block sizes
chromStarts0,29475Start positions relative to chromStart

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
NC_045512v2029903nsp21000+26521550,0,021853,4280,29475
NC_045512v2029903nsp2648+26521550,0,021988,4270,29476
NC_045512v2029903nsp2395+26521550,0,021988,4240,29479
NC_045512v2029903nsp2342+26521550,0,021853,4250,29478
NC_045512v2029903nsp2337+26521550,0,021523,5880,29315
NC_045512v2029903nsp3305+26521550,0,026807,5790,29324
NC_045512v2029903nsp2293+26521550,0,021988,5770,29326
NC_045512v2029903nsp2281+26521550,0,021859,8160,29087
NC_045512v2029903nsp2272+26521550,0,021853,5780,29325
NC_045512v2029903nsp2256+26521550,0,021620,12130,28690

Subgenomic Observed (kimTranscripts) Track Description
 

Description

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.

Methods

  • 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 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.

Credits

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

References

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