TABLE 4.
Mapping of 3′UTRs of KSHV genesa
| Gene | Pol | 3′UTR cloning | ORF position | PAS sequence | PAS position | TTS from this study | TTS from other studies | Source or reference |
|---|---|---|---|---|---|---|---|---|
| ORF-K1 | + | Y | 105–974 | AAUACA | 2953–2958 | 2970 | 2972 | 64 |
| ORF4 | + | Y | 1142–2794 | AAUACA | 2953–2958 | 2972 | 64 | |
| ORF6 | + | Y | 3210–6611 | AUUAAA | 7008–7013 | 7035 | This study | |
| ORF7 | + | N | 6628–8715 | Not mapped | ||||
| ORF8 | + | N | 8699–11236 | Not mapped | ||||
| ORF9 | + | Y | 11363–14401 | AAUAAA | 17055–17060 | 17079 | This study | |
| ORF10 | + | Y | 14519–15775 | AAUAAA | 17055–17060 | 17070 | This study | |
| ORF11 | + | Y | 15790–17013 | AAUAAA | 17055–17060 | 17070 | 17080 | 69 |
| ORF-K2 | – | Y | 17875–17261 | AAUAAA | 17205–17200 | 17184 | 17182 | 70 |
| ORF2 | – | Y | 18553–17921 | AAUAAA | 17205–17200 | 17181 | This study | |
| ORF-K3 | – | Y | 19609–18608 | AUUAAA | 18612–18607 | 18593 | 18595, 18577 | 71 |
| ORF70 | – | Y | 21104–20091 | AUUAAA | 18612–18607 | 18594 | This study | |
| ORF-K4 | – | Y | 21832–21548 | AAUAAA | 21348–21343 | 21324 | This study | |
| ORF-K4.1 | – | N | 22529–22185 | AAUAAA | 21348–21343 | 21324 | 52, 72, 73 | |
| ORF-K4.2 | – | N | 23077–22745 | AAUAAA | 21348–21343 | 21324 | 21325 | 52, 73 |
| ORF-K5 | – | Y | 26483–25713 | AUUAAA | 25574–25569 | 25545 | 25538 | 74 |
| ORF-K6 | – | Y | 27424–27137 | AAUAAA | 26920–26915 | 26895 | This study | |
| ORF-K7 | + | Y | 28622–29002 | AAUAAA | 29719–29724 | 29743 | This study | |
| ORF16 | + | Y | 30145–30672 | AUUAAA/AAUGAA | 30732–30737/30736-30741 | 30753 | This study | |
| ORF17 | – | Y | 32482–30821 | AAUAAA | 30765–30760 | 30744 | This study | |
| ORF18 | + | Y | 32424–33197 | AUUAAA | 33431–33436 | 33450 | This study | |
| ORF19 | – | Y | 34843–33194 | AUUAAA | 32873–32868 | 32862 | This study | |
| ORF20 | – | N | 35573–34611 | Not mapped | ||||
| ORF21 | + | Y | 35383–37125 | AAUAAA | 39312–39317 | 39328 | This study | |
| ORF22 | + | Y | 37113–39305 | AAUAAA | 39312–39317 | 39334 | This study | |
| ORF23 | – | Y | 40516–39302 | AAGAAA | 39278–39273 | 39250 | This study | |
| ORF24 | – | Y | 42778–40520 | AAUAAA | 39251–39246 | 39227 | This study | |
| ORF25 | + | Y | 42777–46907 | AAUAAA | 48741–48746 | 48789 | This study | |
| ORF26 | + | Y | 46933–47850 | AAUAAA | 48741–48746 | 48769 | This study | |
| ORF27 | + | Y | 47873–48745 | AUUAAA | 4877–48775 | 48780 | This study | |
| ORF28 | + | N | 48991–49299 | Not mapped | ||||
| ORF29b | – | Y | 50417–49362 | AAUAAA | 49366–49361 | 49342 | 49347 | 75 |
| ORF30 | + | Y | 50623–50856 | AAUAAA | 54072–54077 | 54099 | 53 | |
| ORF31 | + | Y | 50763–51437 | AAUAAA | 54072–54077 | 54099 | 53 | |
| ORF32 | + | Y | 51404–52768 | AAUAAA | 54072–54077 | 54099 | 53 | |
| ORF33 | + | Y | 52761–53699 | AAUAAA | 54072–54077 | 54100 | 53 | |
| ORF29a | – | N | 54676–53738 | Not mapped | ||||
| ORF34 | + | Y | 54675–55658 | AAUAAA | 58853–58858 | 58878 | This study | |
| ORF35 | + | Y | 55639–56091 | AAUAAA | 58853–58858 | 58878 | 58881 | 76 |
| ORF36 | + | Y | 55976–57301 | AAUAAA | 58853–58858 | 58878 | This study | |
| ORF37 | + | Y | 57273–58733 | AAUAAA | 58853–58858 | 58878 | This study | |
| ORF38 | + | Y | 58688–58873 | Not mapped | ||||
| ORF39 | – | Y | 60175–58976 | AAUAAA | 58906–58901 | 58885 | This study | |
| ORF40 | + | Y | 60308–61681 | AAUAAA | 62540–62545 | 62561, 62559 | This study | |
| ORF41 | + | Y | 61827–62444 | AAUAAA | 62540–62545 | 62559 | This study | |
| ORF42 | – | Y | 63272–62436 | AAUAAA | 62440–62435 | 62416 | This study | |
| ORF43 | – | Y | 64953–63136 | AAUAAA | 62440–62435 | 62416 | This study | |
| ORF44 | + | Y | 64892–67258 | AAUAAA | 67295–67300 | 67319 | This study | |
| ORF45 | – | Y | 68576–67353 | AAUAAA | 67350–67345 | 67323 | 67329 | 52 |
| ORF46 | – | Y | 69404–68637 | AAUAAA | 67350–67345 | 67323 | This study | |
| ORF47 | – | Y | 69915–69412 | AAUAAA | 67350–67345 | 67328 | This study | |
| ORF48 | – | Y | 71381–70173 | AAUAAA | 67350–67345 | 67333 | This study | |
| ORF49 | – | Y | 72538–71630 | AAUAAA | 71634–71629 | 71615 | 71618 | 77 |
| ORF50 | + | Y | 72734–74629 | AAUAAA | 76714–76719 | 76737 | 76737 | 52 |
| ORF-K8 | + | Y | 74850–75569 | AAUAAA | 76714–76719 | 76737 | 76737 | 52 |
| ORF-K8.1 | + | N | 75785–76690 | AAUAAA | 76714–76719 | 76737 | 76737 | 52 |
| ORF52 | – | Y | 77197–76802 | AAUAAA | 76729–76724 | 76706 | This study | |
| ORF53 | – | Y | 77665–77333 | AAUAAA | 76729–76724 | 76706 | This study | |
| ORF54 | + | Y | 77667–78623 | AAUAAA | 78753–78778 | 78778 | This study | |
| ORF55 | – | Y | 79448–78765 | AAUAAA | 78724–78719 | 78706 | This study | |
| ORF56 | + | Y | 79436–81967 | AAUAAA | 83608–83613 | 83631 | 83628, 83631, 82634 | 48 |
| ORF57 | + | Y | 83717–83544 | AAUAAA | 83608–83613 | 83630 | 83628, 83631, 82634 | 48 |
| ORF-K9 | – | Y | 85209–83860 | AAUAAA | 83808–83803 | 83789 | 83787, 83788, 83789 | 47 |
| ORF-K10 | – | Y | 88164–86074 | AAUAAA | 86030–86025 | 86004 | 86006, 86007, 86008 | 47 |
| ORF-K10.5 | – | Y | 91394–89600 | AAUAAA | 89392–89387 | 89372 | 89373 | 47 |
| ORF-K11 | – | N | 93367–91964 | AAUAAA | 91753–91748 | 91751, 91756 | 47 | |
| ORF58 | – | Y | 95544–94471 | AAUAAA | 94488–94483 | 94466 | 94469, 94477 | 48 |
| ORF59 | – | Y | 96939–95549 | AAUAAA | 94492–94487 | 94466 | 94469, 94477 | 48 |
| ORF60 | – | Y | 97787–96870 | AAUAAA | 94492–94487 | 94466 | This study | |
| ORF61 | – | Y | 100194–97816 | AAUAAA | 94492–94487 | 94471 | This study | |
| ORF62 | – | Y | 101194–100199 | AAUAAA | 98298–98293 | 98723 | This study | |
| ORF63 | + | N | 01208–103994 | Not mapped | ||||
| ORF64 | + | Y | 104000–111907 | AAUAAA | 111886–111891 | 111912 | This study | |
| ORF65 | – | Y | 112443–111931 | AAUAAA | 111826–111807 | 111807 | This study | |
| ORF66 | – | Y | 113759–112470 | AAUAAA | 111826–111807 | 111809 | This study | |
| ORF67 | – | Y | 114508–113693 | AAUAAA | 111826–111807 | 111809 | This study | |
| ORF68 | + | N | 114768–116405 | Not mapped | ||||
| ORF69 | + | Y | 116669–117346 | AAUAAA | 117403–117408 | 117424 | 117425 | 78 |
| ORF-K12 | – | Y | 118101–117919 | AAUAAA | 117447–117442 | 117432 | 117432 | 79 |
| ORF71 | – | Y | 122710–122145 | AAUAAA | 122094–122089 | 122068 | 122070 | 50 |
| ORF72 | – | Y | 123566–122793 | AAUAAA | 122094–122089 | 122068 | 122070 | 50 |
| ORF73 | – | Y | 127296–123808 | AAUAAA | 122094–122089 | 122065 | 122070 | 50 |
| ORF-K14 | + | Y | 127883–128929 | AUUAAA | 130518–130523 | 130547 | 130545 | 80 |
| ORF74 | + | Y | 129371–130399 | AUUAAA | 130518–130523 | 130547 | 130545 | 80 |
| ORF75 | – | Y | 134440–130550 | AUUAAA | 130518–130523 | 130499 | This study | |
| ORF-K15 | – | N | 136279–135997 | Not mapped |
a
Pol, the direction of RNA Pol II transcription; PAS, poly(A) signal.; TTS, transcription termination site.