The $Organism mRNA track shows alignments between viral proteins in SwissProt and the $Organism draft sequence. Aligning regions (usually exons) are shown as black boxes connected by lines for gaps (spliced out introns usually). In full display, arrows on the introns indicate the direction of transcription.
Swissprot coronavirus proteins are aligned against the $Organism draft sequence using the BLAT program (translated alignments). These alignments are filtered for alignments greater than 67% (as they usually would be for vertebrate genomes) because viruses evolve so quickly and there is much greater variance.
The $Organism viral protein track is produced at UCSC from protein sequence data submitted to the international public sequence databases by scientists worldwide.