Table 3.
Coding potential and putative transcription regulatory sequences of CoV genomesa
| CoV | ORF | Location (nt) | Length (nt) | Length (aa) | Frame | Putative TRS |
|
|---|---|---|---|---|---|---|---|
| TRS location (nt) | TRS sequence(s) (distance in bases to AUG)b | ||||||
| PorCoV HKU15 | 1ab | 540–19342 | 18,803 | 6,268 | +3, +2 | 75 | ACACCA(459)AUG |
| S | 19324–22806 | 3,483 | 1,161 | +1 | 19178 | ACACCA(145)AUG | |
| E | 22800–23051 | 252 | 84 | +3 | 22777 | ACACCG(17)AUG | |
| M | 23044–23697 | 654 | 218 | +1 | 23018 | ACACCA(20)AUG | |
| NS6 | 23697–23981 | 285 | 95 | +3 | 23645 | ACACCA(46)AUG | |
| N | 24002–25030 | 1,029 | 343 | +2 | 23989 | ACACCA(7)AUG | |
| NS7 | 24096–24698 | 603 | 201 | +3 | 24008 | GCACCA(82)AUG | |
| WECoV HKU16 | 1ab | 511–19397 | 18,887 | 6,296 | +1, +3 | 66 | ACACCA(439)AUG |
| S | 19379–22918 | 3,540 | 1,180 | +2 | 19233 | ACACCA(140)AUG | |
| E | 22912–23160 | 249 | 83 | +1 | 22886 | ACACCA(20)AUG | |
| M | 23153–23809 | 657 | 219 | +2 | 23130 | ACACCA(17)AUG | |
| NS6 | 23809–24090 | 282 | 94 | +1 | 23768 | ACAUCA(35)AUG | |
| N | 24115–25158 | 1,044 | 348 | +1 | 24101 | ACACCA(8)AUG | |
| NS7a | 24143–24811 | 669 | 223 | +2 | 24101 | ACACCA(36)AUG | |
| NS7b | 25139–25270 | 132 | 44 | +2 | 25039 | AAACCA(94)AUG | |
| SpCoV HKU17 | 1ab | 520–19352 | 18,833 | 6,278 | +1, +3 | 57 | ACACCA(452)AUG |
| S | 19334–22954 | 3,621 | 1,207 | +2 | 19188 | ACACCA(140)AUG | |
| E | 22948–23196 | 249 | 83 | +1 | 22925 | ACACCG(17)AUG | |
| M | 23189–23842 | 654 | 218 | +2 | 23166 | ACACCA(17)AUG | |
| NS6 | 23842–24129 | 288 | 96 | +1 | 23790 | ACACCA(46)AUG | |
| N | 24150–25178 | 1,029 | 343 | +3 | 24137 | ACACCA(7)AUG | |
| NS7a | 25189–25623 | 435 | 145 | +1 | 25179 | ACACCA(4)AUG | |
| NS7b | 25539–25751 | 213 | 71 | +3 | 25523 | ACUCCA(10)AUG | |
| MRCoV HKU18 | 1ab | 596–19356 | 18,761 | 6,254 | +2, +1 | 64 | ACACCA(526)AUG |
| S | 19338–22991 | 3,654 | 1,218 | +3 | 19192 | ACACCA(140)AUG | |
| E | 22985–23233 | 249 | 83 | +2 | 22945 | ACACCG(34)AUG | |
| M | 23226–23882 | 657 | 219 | +3 | 23203 | ACACCA(17)AUG | |
| NS6 | 23882–24172 | 291 | 97 | +2 | 23857 | ACGCCA(19)AUG | |
| N | 24355–25395 | 1,041 | 347 | +1 | 24340 | ACACCA(9)AUG | |
| NS7a | 25407–25580 | 174 | 58 | +3 | 25396 | ACACCA(5)AUG | |
| NS7b | 25561–25932 | 372 | 124 | +1 | |||
| NS7c | 25941–26195 | 255 | 85 | +3 | 25910 | ACACCA(25)AUG | |
| NHCoV HKU19 | 1ab | 482–19323 | 18,842 | 6,281 | +2, +1 | 67 | ACACCG(409)AUG |
| S | 19305–23069 | 3,765 | 1,255 | +3 | 19156 | ACACCG(143)AUG | |
| E | 23069–23317 | 249 | 83 | +2 | 23013 | ACACCA(50)AUG | |
| M | 23310–23960 | 651 | 217 | +3 | 23211 | ACACCG(93)AUG | |
| NS6 | 23960–24238 | 279 | 93 | +2 | 23951 | ACACCU(3)AUG | |
| N | 24248–25276 | 1,029 | 343 | +2 | 24231 | ACACCU(8)AUG | |
| NS7a | 25277–25573 | 297 | 99 | +2 | 25248 | ACACCG(23)AUG | |
| NS7b | 25583–25876 | 294 | 98 | +2 | 25560 | ACACCA(17)AUG | |
| WiCoV HKU20 | 1ab | 219–18838 | 18,620 | 6,207 | +3, +2 | 60 | ACACCA(153)AUG |
| S | 18817–22455 | 3,639 | 1,213 | +1 | 18731 | ACACCU(80)AUG | |
| E | 22455–22715 | 261 | 87 | +3 | 22380 | ACACCA(69)AUG | |
| M | 22708–23358 | 651 | 217 | +1 | 22597 | ACACCG(105)AUG | |
| NS6 | 23358–23630 | 273 | 91 | +3 | |||
| N | 23646–24698 | 1,053 | 351 | +3 | 23631 | ACACCA(9)AUG | |
| NS7a | 24695–24928 | 234 | 78 | +2 | 24609 | AAACCA(80)AUG | |
| NS7b | 25218–25466 | 249 | 83 | +3 | 25177 | ACACCG(35)AUG | |
| NS7c | 25450–25716 | 267 | 89 | +1 | 25444 | ACACCGAUG | |
| NS7d | 25752–25952 | 201 | 67 | +3 | 25735 | AAACCU(11)AUG | |
| CMCoV HKU21 | 1ab | 478–19103 | 18,626 | 6,209 | +1, +3 | 63 | ACACCA(409)AUG |
| S | 19085–22729 | 3,645 | 1,215 | +2 | 18939 | ACACCA(140)AUG | |
| E | 22723–22971 | 249 | 83 | +1 | 22697 | ACACCA(20)AUG | |
| M | 22973–23779 | 807 | 269 | +2 | 22938 | ACACCA(29)AUG | |
| NS6 | 23779–24024 | 246 | 82 | +1 | 23727 | ACACCA(46)AUG | |
| N | 24052–25107 | 1,056 | 352 | +1 | 24039 | ACACCG(7)AUG | |
| NS7a | 25107–25379 | 273 | 91 | +3 | 25036 | ACACCU(65)AUG | |
| NS7b | 25391–25576 | 186 | 62 | +2 | 25379 | ACACCU(6)AUG | |
| NS7c | 25500–25916 | 417 | 139 | +2 | |||
a
PorCoV HKU15, WECoV HKU16, SpCoV HKU17, MRCoV HKU18, NHCoV HKU19, WiCoV HKU20, and CMCoV HKU21. aa, amino acid; nt, nucleotide.
b
Boldface indicates putative TRS sequences. The nucleotide variations are in italic.