TABLE 2.
Properties of predicted coronavirus intra-5′ UTR stem-loop III, stem-loop III-associated ORF, and ORF-encoded oligonucleotide
| Coronavirus | Free energy of stem-loop III in positive strand (kcal/mol)a | Free energy of stem-loop III in negative strand (kcal/mol)a | Kozak context of short ORF start codon | Predicted no. of amino acids encoded by short ORF | Amino acid sequence of short ORF product |
|---|---|---|---|---|---|
| BCoV-Mebus | −9.1 | −3.0 | UCUaugC | 8 | MLVGVDFS |
| HCoV-OC43 | −9.1 | −3.0 | UCUaugC | 8 | MLVGVDFS |
| HECoV-4408 | −11.5 | −6.1 | UCUaugC | 8 | MPVGVDFS |
| HEV-67N | −9.1 | −3.0 | UCUaugC | 8 | MLVGVDFS |
| ECoV-NC99 | −5.1 | −4.2 | UCUaugC | 8 | MLASLDFS |
| MHV-A59 | −9.0 | −9.3 | UCCaugC | 8 | MPAGLVLS |
| MHV-JHM | −9.0 | −9.3 | UCCaugC | 8 | MPVGLVLS |
| MHV-2 | −9.0 | −8.6 | UCCaugC | 8 | MPVGLVLS |
| TGEV-Purdue | −12.9b | −9.0b | UCUaugA | 3 | MKS |
| HCoV-229E | −17.4b | −6.7b | GCUaugG | 11c | MAGIFDAGVVVc |
| IBV-Beau M42 | −19.9b | −18.4b | UGGaugG | 11 | MAPGHLSGFCY |
a
As determined by the Zuker algorithm.
b
For TGEV, HCoV-229E, and IBV, the Zuker algorithm predicts a larger stem-loop than for the group 2 coronaviruses.
c
A second ORF beginning 16 nt downstream from the first encodes the amino acid sequence MLES.