TABLE 4.
PRV polyadenylation signals predicted by PolyADQ
| Gene | Sequence | Locationa | Score | 3′ UTR sizeb
|
Evidencec (reference[s]) | |
|---|---|---|---|---|---|---|
| Pred. | Exptl | |||||
| ORF1.2 | AATAAA | 2262-2267 | 0.735 | 28 | Ka type 4 (3) | |
| ORF-1 | 28 | Ka type 4 (3) | ||||
| UL54 | AATAAA | 2730-2725 r | 0.525 | 25 | Ka type 4 (3) | |
| UL53 | 1,190 | Ka type 4 (3) | ||||
| UL52 | 2,083 | Ka type 4 (3) | ||||
| UL51 | AATAAA | 8433-8438 | 0.222 | 85 | Ka type 4 (3) | |
| UL50 | AATAAA | 8448-8443 r | 0.333 | 104 | ||
| Orphan | AATAAA | 9015-9020 | 0.031 | NA | —d | |
| UL49.5 | AATAAA | 10336-10341 | 0.455 | 808 | Ka type 3 (28) | |
| UL49 | 21 | Ka type 3 (28) | ||||
| UL48 | AATAAA | 16153-16158 | 0.817 | 4,533 | Ka type 3 (7, 28) | |
| UL47 | 2,180 | Ka type 3 (7) | ||||
| UL46 | 80 | 78 | TNL type 1 (35), Ka type 2 (7) | |||
| UL27 | AATAAA | 16835-16830 r | 0.322 | 44 | 46 | TNL type 1 (36), Ka type 3 (7) |
| UL28 | 2,656 | |||||
| UL29 | AATAAA | 21741-21736 r | 0.601 | 72 | 74 | TNL type 1 (35) |
| UL30 | AATAAA | 28768-28773 | 0.274 | 41 | ||
| UL31 | AATAAA | 28620-28615 r | 0.693 | 78 | 74 | TNL type 1 (35) |
| UL32 | 886 | |||||
| UL33 | AATAAA | 32565-32570 | 0.537 | 1,351 | ||
| UL34 | 404 | Ka type 3 (27) | ||||
| UL35 | 38 | |||||
| Orphan | AATAAA | 33047-33052 | 0.031 | NA | —d | |
| UL36 | AATAAA | 33061-33056 r | 0.872 | 24 | ||
| UL37 (M)g | AATAAA | 42356-42351 r | 0.395 | 22 | Ka type 3 (8) | |
| UL37 (m)g | 22 | Ka type 3 (8) | ||||
| UL38 | AATAAA | 46325-46330 | 0.180 | 76 | Ka type 3 (8) | |
| UL39 | AATAAA | 49959-49964 | 0.621 | 1,007 | NIA-3 type 4 (22) | |
| UL40 | 86 | NIA-3 type 4 (22) | ||||
| UL41 | AATAAA | 50405-50400 r | 0.382 | 21 | ||
| Orphan | AATAAA | 52778-52773 r | 0.265 | NA | ||
| UL42 | AATAAA | 52781-52786 | 0.331 | 24 | 18 | TNL type 1 (36), NIA-3 type 4 (22) |
| UL43 | ATTAAA | 53946-53951 | 0.007 | 8 | 25 | TNL type 1 (36), NIA-3 type 4 (22) |
| UL44 | AATAAA | 55500-55505 | 0.496 | 57 | 21 ± 40 | Be type 2, 4 (60), NIA-3 type 4 (22) |
| Orphan | AATAAA | 55608-55613 | 0.178 | NA | ||
| UL26.5 | AATAAA | 55659-55654 r | 0.707 | 65 | 48 ± 40 | NIA-3 type 2, 4 (10), Ka type 3 (23) |
| UL26 | 65 | 48 ± 40 | NIA-3 type 2, 4 (10), Ka type 3 (23) | |||
| UL25 | 1,673 | 1,656 ± 40 | NIA-3 type 2, 4 (10), Ka type 3 (23) | |||
| UL24 | 3,370 | Ka type 3 (23) | ||||
| UL23 | AATAAA | 60585-60590 | 0.438 | 136 | Ka type 4 (42) | |
| UL22 | AATAAA | 62652-62657 | 0.268 | 7 | Ka type 4 (42) | |
| Orphan | AATAAA | 63531-63526 r | 0.382 | NA | ||
| UL21 | AATAAA | 64502-64497 r | 0.064 | 11 | NIA-3 type 4 (22) | |
| UL20 | ATTAAA | 66653-66658 | 0.005 | 21 | ||
| UL19 (M) | ATATAAA | 70838-70844 | —e | 128 | 121 | Indiana S type 1, 4 (77) |
| UL19 (m) | AATAAA | 71841-71846 | 0.449 | 1,130 | Indiana S type 4 (77) | |
| UL18 | 83 | |||||
| UL17 | AATAAA | 75957-75962 | 0.381 | 1,023 | ||
| UL16 | 10 | |||||
| UL15 | AATAAA | 71897-71892 r | 0.663 | 107 | ||
| Orphan | AATAAA | 78325-78320r | 0.018 | NA | —d | |
| UL14 | AATAAA | 80280-80285 | 0.874 | 2,762 | NIA-3 type 4 (22) | |
| UL13 | 1,596 | NIA-3 type 4 (22) | ||||
| UL12 | 179 | 180 | TNL type 1 (37), NIA-3 type 4 (22) | |||
| UL11 | 30 | |||||
| UL10 | AATAAA | 80758-80753 r | 0.475 | 21 | Ka type 3 (24) | |
| UL9 | AATAAA | 86516-86521 | 0.797 | 2,076 | Ka type 4 (24) | |
| UL8.5 | 2,076 | Ka type 4 (24) | ||||
| UL8 | 28 | Ka type 4 (24) | ||||
| UL7 | AATAAA | 86532-86527 r | 0.098 | 172 | Ka type 4 (24) | |
| UL6 | 863 | Ka type 4 (24) | ||||
| UL5 | AATAAA | 91895-91900 | 0.478 | 116 | Not functionald,f | |
| UL5 | AATAAA | 92394-92399 | 0.109 | 615 | In-Fh type 4 (21) | |
| UL4 | 119 | In-Fh type 4 (21) | ||||
| UL3.5 | AATAAA | 92475-92480 | 0.058 | 21 | In-Fh type 3 (20) | |
| UL3 | 692 | In-Fh type 3 (20)/PICK> | ||||
| UL2 | 1,461 | In-Fh type 3 (20) | ||||
| UL1 | 2,389 | In-Fh type 3 (20) | ||||
| EP0 | AATAAA | 96273-96268 r | 0.559 | 233 | 234 | In-Fh type 1, 4 (13) |
| LLT (IRS) | AATAAA | 109092-109097 | 0.665 | NA | Be type 1, 4 (13) | |
| Orphan (TRS) | AATAAA | 135510-135505 r | 0.665 | NA | ||
| IE180 (IRS) | AATAAA | 102719-102714 r | 0.672 | 477 | 475 | In-Fh type 1, 4 (14), Ka type 2 (11) |
| IE180 (TRS) | AATAAA | 141883-141888 | 0.672 | 477 | 475 | In-Fh type 1, 4 (15), Ka type 2 (11) |
| US1 (IRS) | AATAAA | 117191-117196 | 0.560 | 126 | 125 | TNL type 1 (36), Ka type 3 (27) |
| US1 (TRS) | AATAAA | 127411-127406 r | 0.560 | 126 | 125 | TNL type 1 (36), Ka type 3 (27) |
| Orphan (IRS) | AATAAA | 117733-117728 r | 0.424 | NA | ||
| Orphan (TRS) | AATAAA | 126869-126874 | 0.424 | NA | ||
| Orphan | AATAAA | 118239-118244 | 0.717 | NA | ||
| US3 (M) | AATAAA | 120951-120956 | 0.431 | 1,580 | Ka type 3 (78), NIA-3 type 3 (74) | |
| US3 (m) | ||||||
| US4 | 84 | Ka type 3 (78), NIA-3 type 4 (74) | ||||
| US6 | AATAAA | 123394-123399 | 0.673 | 1,142 | 1,105 ± 90 | In-Fh type 2 (43) |
| US7 | 21 | |||||
| US8 | AATAAA | 125697-125702 | 0.189 | 487 | 497 | TNL type 1 (35) |
| US9 | 133 | 143 | TNL type 1 (35) | |||
| US2 | AATAAA | 126628-126633 | 0.452 | 72 | 59 ± 12 | In-Fh type 2 (43), NIA-3 type 3 (74) |
a
Numbering starts at +1 on the UL end of the genome. r indicates reverse strand direction.
b
Predicted (Pred.) polyadenylation sites were set at 20 bases downstream of the poly(A) signal sequence. Exptl, experimental; NA, not applicable, no protein-coding RNA.
c
Evidence abbreviations: type 1, 3′ cDNA sequence; type 2, S1 mapping; type 3, mRNA size and sense; type 4, mRNA size only.
d
Not included in annotated sequence.
e
Experimentally determined, not found as a predicted poly(A) site.
f
Contradicted by UL5 mRNA size and UL4 TSS.
g
M, major transcript; m, minor transcript.