Skip to main content
[Preprint]. 2020 Sep 2:2020.06.02.130955. Originally published 2020 Jun 3. [Version 2] doi: 10.1101/2020.06.02.130955

Extended Data Figure 1. PhyloCSF signal for polyprotein ORF1.

Extended Data Figure 1.

UCSC Genome Browser view SARS-CoV-2 genome for polyprotein ORF1ab showing UniProt gene annotations for individual non-structural proteins (nsp), PhyloCSF tracks (green) in each of 3 reading frames, and Synonymous Constraint Elements (SCEs, red), along with phastCons/phyloP nucleotide-level constraint (green/blue). Polyprotein 1ab is processed into 16 mature peptides nsp1-nsp16. PhyloCSF signal shows clear protein-coding signal for all proteins, indicating clearly that all are functional proteins (except nsp11, red circle, discussed in the main text). PhyloCSF signal captures the correct frame throughout the entire length of each protein (except nsp3, where some small regions show reduced frame-2 signal and/or increased frame-3 signal, but upon inspection these are only stop-codon-free in frame-2 and do not represent dual-coding candidates).