Table 1.
New viral features in the KSHV genome including, Upstream and Small ORFs, Alternate start codon usage and Internal ORFs, derived from Next-generation sequencing studies adapted from KSHV 2.0 [57]. All annotation coordinates are based on GQ 994935.1.
| Gene | Strand | Start–Stop | Small Open Reading Frame (sORF) | Upstream Open Reading Frame (uORF) | New Features |
|---|---|---|---|---|---|
| ORF6.1 | + | 3027–3203 | - | uORF | - |
| ORF6.2 | + | 3150–3203 | - | uORF | - |
| ORF10.1 | + | 14,451–14,531 | - | uORF | - |
| ORF10.2 | + | 15,574–15,756 | - | - | Internal ORF |
| ORF11.1 | + | 15,633–15,722 | - | uORF | - |
| ORF11.2 | + | 15,648–15,722 | - | uORF | - |
| ORF11.3 | + | 15,693–15,722 | - | uORF | - |
| ORF11.4 | + | 15,745–15,756 | - | uORF | - |
| ORF11.5 | + | 15,926–15,991 | - | - | Internal ORF |
| vIL6.6 | − | 17,873–17,862 | - | uORF | - |
| vIL6.5 | − | 17,915–17,877 | - | uORF | - |
| vIL6.4 | − | 18,003–17,902 | - | uORF | - |
| vIL6.3 | − | 18,047–17,985 | - | uORF | - |
| vIL6.2 | − | 18,086–18,057 | - | uORF | - |
| vIL6.1 | − | 18,116–18,057 | - | uORF | - |
| ORFK3A | − | 19,128–18,589 | - | - | Internal ORF |
| ORF70A | − | 21,099–20,038 | - | - | Alternate start |
| ORFK4A | − | 21,820–21,743 | - | uORF | - |
| ORFK4.1a | − | 22,517–22,416 | sORF | - | - |
| ORFK4.1d | − | 22,610–22,545 | sORF | - | - |
| ORFK4.1e | − | 22,653–22,627 | sORF | - | - |
| ORFK4.1c | − | 22,806–22,723 | sORF | - | - |
| ORFK4.1b | − | 22,850–22,545 | sORF | - | - |
| 1.4KbB | + | 24,871–24,915 | sORF | - | - |
| 1.4KbC | + | 24,921–25,058 | sORF | - | - |
| ORFK5.1 | − | 26,569–26,555 | - | uORF | - |
| ORFK6.1 | − | 27,647–27,615 | - | uORF | - |
| ORFK6A | − | 27,443–27,087 | - | - | Alternate start |
| ORFK6B | − | 27,422–27,087 | - | - | Alternate start |
| PAN1.1 | + | 28,655–28,768 | sORF | - | - |
| PAN1.2 | + | 28,831–28,965 | sORF | - | - |
| PAN1.3 | + | 28,888–28,965 | sORF | - | - |
| ORF20A | − | 35,322–34,429 | - | - | Internal ORF |
| ORF20B | − | 35,202–34,429 | - | - | Internal ORF |
| ORF21.1 | + | 35,151–35,177 | - | uORF | - |
| ORF25.1 | + | 42,345–42,380 | - | uORF | - |
| ORF28.1 | + | 48,758–48,811 | - | uORF | - |
| ORF30.1 | + | 50,317–50,358 | - | uORF | - |
| ORF34.1 | + | 54,399–54,485 | - | uORF | - |
| ORF35.1 | + | 55,419–55,445 | - | uORF | - |
| ORF35.2 | + | 55,442–55,474 | - | uORF | - |
| ORF37.1 | + | 57,040–57,126 | - | uORF | - |
| ORF38.1 | + | 58,251–58,259 | - | uORF | - |
| ORF38.2 | + | 58,455–58,589 | - | uORF | - |
| 43.1-AS | + | 63,214–63,228 | sORFs | - | - |
| ORF43.2-AS | + | 63,254–63,295 | sORFs | - | - |
| ORF45.1 | − | 68,447–68,364 | - | uORF | - |
| ORF49.1 | − | 72,425–72,384 | - | uORF | - |
| ORF50AS | − | 74,222–74,130 | sORF | - | - |
| k8.1 short | + | 75,890–75,971 | - | - | Internal ORF |
| ORF54A | + | 77,552–78,439 | - | - | Alternate start |
| ORF55.1 | − | 79,501–79,340 | - | uORF | - |
| ORF57A | + | 81,464–83,453 | - | - | Splice variant |
| ORF61.2 | − | 100,071–100,018 | - | uORF | - |
| ORF61.1 | − | 100,095–100,018 | - | uORF | - |
| ORF62B | − | 101,019–100,018 | - | - | Alternate start |
| ORF62A | − | 101,061–100,018 | - | - | Alternate start |
| ORF65.1 | − | 112,321–112,289 | - | uORF | - |
| ORF69.1 | + | 116,043–116,138 | - | uORF | - |
| Kaposin C2 | − | 119,084–117,738 | - | - | Alternate start |
| ORF72.1 | − | 124,182–124,108 | - | uORF | - |
| ORF75.1 | − | 134,809–134,729 | - | uORF | - |
| ORF75.2 | − | 134,894–134,817 | - | uORF | - |
| K15.1 | − | 135,938–135,846 | sORF | - | - |