Table 2.
SARS-CoV-2 binding sites for unphosphorylated ISGF3–induced TF
| Gene | Start | TF name | TF ID | Start position | End position | Core match score | Matrix match score | Sequence |
|---|---|---|---|---|---|---|---|---|
| S | 21563 | HOXD9 | MA0913.2 | 21578 | 21587 | 1 | 1 | GCAATAAAAC |
| S | 21563 | HOXD13 | MA0909.2 | 21578 | 21588 | 1 | 0.993 | GGCAATAAAAC |
| S | 21563 | CDX4 | MA1473.1 | 21578 | 21588 | 1 | 1 | GGCAATAAAAC |
| ORF3a | 25393 | Alx1 | MA0854.1 | 24591 | 24607 | 1 | 0.98 | AGCTCTAATTAATTGTT |
| ORF3a | 25393 | SOX21 | MA0866.1 | 26089 | 26103 | 1 | 0.91 | AACAATTTTATTGTA |
| ORF3a | 25393 | TGIF2LY | MA1572.1 | 24799 | 24810 | 1 | 0.896 | TGACAAATGGCA |
| E | 26245 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| E | 26245 | SOX21 | MA0866.1 | 26089 | 26103 | 1 | 0.91 | AACAATTTTATTGTA |
| M | 26523 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| M | 26523 | SOX21 | MA0866.1 | 26089 | 26103 | 1 | 0.91 | AACAATTTTATTGTA |
| ORF6 | 27202 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| ORF7a | 27394 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| ORF7b | 27756 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| ORF8 | 27894 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| N | 28274 | SHOX | MA0630.1 | 28490 | 28497 | 1 | 1 | TTAATTGG |
| N | 28274 | JUN | MA0488.1 | 27290 | 27302 | 1 | 0.965 | TTTATGATGTAAT |
| ORF10 | 29558 | Bach1::Mafk | MA0591.1 | 29511 | 29525 | 1 | 0.923 | GAGTTGAGTCAGCAC |
| ORF10 | 29558 | MAFA | MA1521.1 | 29327 | 29341 | 1 | 0.923 | ATGCTTATTCAGCAA |
| S | 21563 | HOXD9 | MA0913.2 | 21578 | 21587 | 1 | 1 | GCAATAAAAC |
| S | 21563 | HOXD13 | MA0909.2 | 21578 | 21588 | 1 | 0.993 | GGCAATAAAAC |
| S | 21563 | CDX4 | MA1473.1 | 21578 | 21588 | 1 | 1 | GGCAATAAAAC |
| ORF3a | 25393 | Alx1 | MA0854.1 | 24591 | 24607 | 1 | 0.98 | AGCTCTAATTAATTGTT |
| ORF3a | 25393 | SOX21 | MA0866.1 | 26089 | 26103 | 1 | 0.91 | AACAATTTTATTGTA |
| ORF3a | 25393 | TGIF2LY | MA1572.1 | 24799 | 24810 | 1 | 0.896 | TGACAAATGGCA |
| E | 26245 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| E | 26245 | SOX21 | MA0866.1 | 26089 | 26103 | 1 | 0.91 | AACAATTTTATTGTA |
| M | 26523 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| M | 26523 | SOX21 | MA0866.1 | 26089 | 26103 | 1 | 0.91 | AACAATTTTATTGTA |
| ORF6 | 27202 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| ORF7a | 27394 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| ORF7b | 27756 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| ORF8 | 27894 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| N | 28274 | SHOX | MA0630.1 | 28490 | 28497 | 1 | 1 | TTAATTGG |
| N | 28274 | JUN | MA0488.1 | 27290 | 27302 | 1 | 0.965 | TTTATGATGTAAT |
| ORF10 | 29558 | Bach1::Mafk | MA0591.1 | 29511 | 29525 | 1 | 0.923 | GAGTTGAGTCAGCAC |
| ORF10 | 29558 | MAFA | MA1521.1 | 29327 | 29341 | 1 | 0.923 | ATGCTTATTCAGCAA |
| S | 21563 | HOXD9 | MA0913.2 | 21578 | 21587 | 1 | 1 | GCAATAAAAC |
| S | 21563 | HOXD13 | MA0909.2 | 21578 | 21588 | 1 | 0.993 | GGCAATAAAAC |
| S | 21563 | CDX4 | MA1473.1 | 21578 | 21588 | 1 | 1 | GGCAATAAAAC |
| ORF3a | 25393 | Alx1 | MA0854.1 | 24591 | 24607 | 1 | 0.98 | AGCTCTAATTAATTGTT |
| ORF3a | 25393 | SOX21 | MA0866.1 | 26089 | 26103 | 1 | 0.91 | AACAATTTTATTGTA |
| ORF3a | 25393 | TGIF2LY | MA1572.1 | 24799 | 24810 | 1 | 0.896 | TGACAAATGGCA |
| E | 26245 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| E | 26245 | SOX21 | MA0866.1 | 26089 | 26103 | 1 | 0.91 | AACAATTTTATTGTA |
| M | 26523 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| M | 26523 | SOX21 | MA0866.1 | 26089 | 26103 | 1 | 0.91 | AACAATTTTATTGTA |
| ORF6 | 27202 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| ORF7a | 27394 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| ORF7b | 27756 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| ORF8 | 27894 | SIX1 | MA1118.1 | 27220 | 27230 | 1 | 0.995 | GTAACCTGAAA |
| N | 28274 | SHOX | MA0630.1 | 28490 | 28497 | 1 | 1 | TTAATTGG |
| N | 28274 | JUN | MA0488.1 | 27290 | 27302 | 1 | 0.965 | TTTATGATGTAAT |
| ORF10 | 29558 | Bach1::Mafk | MA0591.1 | 29511 | 29525 | 1 | 0.923 | GAGTTGAGTCAGCAC |
| ORF10 | 29558 | MAFA | MA1521.1 | 29327 | 29341 | 1 | 0.923 | ATGCTTATTCAGCAA |
Abbreviations: ISGF3, interferon-stimulated gene factor 3; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; TF, transcription factor.