Table S1.
No. | ICP27-mediated polyadenylation in intron 1 (132) | ICP27-mediated polyadenylation in intron 2 or alternative exon 2 (16) | ICP27-mediated use of alternative 5′ ss (12) | ICP27-mediated intron retention (78) | ||||||||||||
Gene | PAS sequence | PAS to TSS | PAS to 5′ ss | 5′ ss to TSS | Predicted size of novel ORF, aa | Gene | PAS sequence | PAS TO TSS | PAS TO 5′SS | Predicted size of novel ORF, aa | Gene | Affected 5′ ss to TSS | Predicted size of novel ORF, aa | Gene | Intron retained | |
1 | ABHD6 | AATAAA | 1,269 | 858 | 411 | None | CAD | AATAAA | 1,369 | 753 | <100 | DESI2 | 308 | <100 | AKT1S1 | Multiple introns |
2 | ACAD9 | AATAAA | 1,417 | 1,310 | 107 | <100 | CCT4 | AATAAA | 731 | 413 | <100 | HERPUD1 | 628 | 119 | ALAS1 | Intron 1 and 2 |
3 | ACTR3B | AATAAA | 1,696 | 1,518 | 178 | <100 | COQ4 | AATAAA | 1,046 | 410 | <100 | LEPR* | 89 | 113 | ALKBH6 | Multiple introns |
4 | ADCY1 | AATAAA | 2,375 | 1,717 | 658 | 249 | ELK1 | AATAAA | 1,847 | 1,163 | None | NSUN4 | 743 | <100 | ANKRD9 | Intron 1 and 2 |
5 | AEBP2 | ATTAAA | 1,404 | 525 | 879 | 227 | EIF4G3 | AATAAA | 1,605 | 459 | 144 | PIGG | 290 | <100 | ARFIP2 | Last intron |
6 | AFTPH | AATAAA | 2,176 | 1,868 | 308 | None | EPC1 | AATAAA | 1,944 | 1,636 | None | PPP1R8* | 151 | None) | ARMC5 | Last two introns |
7 | AGPAT5 | AATAAA | 2,197 | 1,666 | 531 | 134 | HOMEZ | AATAAA | 2,144 | 1,956 | None | RANGAP1 | 178 | None | ATPIF1 | Last intron |
8 | ALV9 | AATAAA | 1,241 | 864 | 377 | <100 | MDH2 | AATAAA | 1,147 | 939 | <100 | TACO1 | 492 | 122 | ATPIP | Multiple introns |
9 | AMMCR1 | AATAAA | 1,330 | 986 | 344 | None | MIB2 | AATAAA | 2,320 | 680 | 237 | TMEM5 | 346 | None | ATXN2L | Multiple introns |
10 | APPL1 | AATAAA | 860 | 659 | 201 | <100 | NFKBIL1 | ATTAAA | 2,002 | 413 | 121 | TRMU | 446 | 139 | BRD4 | Multiple introns |
11 | ARNTL | ATTAAA | 1,686 | 1,489 | 197 | None | SNX5 | AATAAA | 1,269 | 652 | 126 | UBE2J2 | 189 | None | CAND2 | Last two introns |
12 | ASB13 | AATAAA | 1,727 | 1,640 | 87 | <100 | STON1 | AATAAA | 886 | 225 | None | ZER1 | 349 | None | CC2D2A | Last intron |
13 | ATP6V0A2 | AATAAA | 719 | 354 | 365 | <100 | TMEM127 | AATAAA | 2,471 | 1,595 | 112 | CHMP2A | Intron 1 | |||
14 | ATR | AATAAA | 1053 | 872 | 181 | <100 | WWTR1 | ATTAAA | 1,855 | 627 | None | CHTF8 | Last intron | |||
15 | ATXN10 | AATAAA | 1134 | 752 | 382 | <100 | ZNF274 | AATAAA | 2,441 | 1,431 | None | CREBBP | Last intron | |||
16 | AVL9 | ATTAAA | 1,241 | 864 | 377 | <100 | ZNF778 | AATAAA | 554 | 347 | None | CRELD1 | Multiple introns | |||
17 | BRSK2 | AATAAA | 1,903 | 1,426 | 477 | 224 | CUL7 | Multiple introns | ||||||||
18 | BTBD2 | AATAAA | 3,542 | 3,135 | 407 | 205 | DAXX | Last intron | ||||||||
19 | CACHD1 | AATAAA | 1,952 | 1,802 | 150 | <100 | DMPK | Multiple introns | ||||||||
20 | CACNA2D1 | AATAAA | 813 | 371 | 442 | <100 | DLG3 | Intron 1 | ||||||||
21 | CAMSAP3 | AATAAA | 2,646 | 2,397 | 249 | 141 | DLX4 | Intron 1 | ||||||||
22 | CCDC85C | ATTAAA | 4,804 | 3,922 | 882 | 379 | DPP8 | Intron 1 | ||||||||
23 | CCDC113 | AATAAA | 2,073 | 1,893 | 180 | <100 | DYRK1B | Last intron | ||||||||
24 | CD99L2 | AATAAA | 1,071 | 776 | 295 | <100 | EMC6 | Intron 1 | ||||||||
25 | CEP85L | AATAAA | 2,586 | 1,925 | 661 | 240 | ERF | Multiple introns | ||||||||
26 | CLSTN1 | AATAAA | 2,122 | 1,238 | 884 | <100 | FBXO31 | Last intron | ||||||||
27 | CMTM4 | AATAAA | 1,715 | 1,347 | 368 | <100 | GTPBP3 | Intron 1 | ||||||||
28 | C6ORF89 | AATAAA | 2,775 | 2,611 | 164 | None) | IFT88 | Intron 1 | ||||||||
29 | CPSF6 | AATAAA | 1,100 | 930 | 170 | 127 | ILK | Intron 1 | ||||||||
30 | CTNNBIP1 | AATAAA | 1,274 | 1,100 | 174 | None | JRK | Intron 1 | ||||||||
31 | CYP2U1 | AATAAA | 1,160 | 521 | 639 | 205 | KLC2 | Last two introns | ||||||||
32 | DCAF10 | AATAAA | 979 | 339 | 640 | 180 | LINC00476 | Last intron | ||||||||
33 | DGCR2 | AATAAA | 1,188 | 861 | 327 | 185 | LPHN1 | Multiple introns | ||||||||
34 | DHRS4 | AATAAA | 1,113 | 931 | 182 | <100 | LPPR3 | Multiple introns | ||||||||
35 | DHX35 | AATAAA | 638 | 568 | 70 | 111 | LRFN4 | Intron 1 | ||||||||
36 | DUSP22 | AATAAA | 1,887 | 1,383 | 504 | <100 | MAP3K12 | Multiple introns | ||||||||
37 | DNMT3A | AATAAA | 5,653 | 5,492 | 161 | None | MFSD5 | Intron 1 | ||||||||
38 | DYNC1I1 | AATAAA | 1,547 | 1,279 | 268 | None) | MID1IP1 | Intron 1 | ||||||||
39 | EFCAB5 | AATAAA | 1,902 | 1,789 | 113 | None | MIDN | Multiple introns | ||||||||
40 | ENDOD1 | AATAAA | 1,085 | 667 | 418 | 157 | MIEF2 | Last intron | ||||||||
41 | EPN2 | ATTAAA | 2,214 | 2,059 | 155 | None | NADK | Multiple introns | ||||||||
42 | ERCC6 | AATAAA | 1,057 | 895 | 162 | None) | NFS1 | Intron1 | ||||||||
43 | ERLEC1 | AATAAA | 1,186 | 754 | 432 | 118 | PHF12 | Intron 1 and Last intron | ||||||||
44 | EXTL3 | AATAAA | 1,036 | 849 | 187 | None | P4HTM | Intron 1 | ||||||||
45 | FAM175A | AATAAA | 641 | 463 | 178 | 128 | PI4KB | Last intron | ||||||||
46 | FAM178A | AATAAA | 1,297 | 615 | 682 | <100 | PLEKH3 | Multiple introns | ||||||||
47 | FBXL5 | AATAAA | 1,952 | 1,743 | 209 | <100 | PMEL | Middle intron | ||||||||
48 | FBXW11 | AATAAA | 1,430 | 1,014 | 416 | 117 | PML | Multiple introns | ||||||||
49 | FNIP1 | AATAAA | 1,248 | 1,014 | 234 | <100 | POLR2A | Last intron | ||||||||
50 | FYCO1 | AATAAA | 1,520 | 1,417 | 103 | None | PPPDE1 | Intron 1 | ||||||||
51 | GIT1 | AATAAA | 3,257 | 2,991 | 266 | 205 | PPP1R7 | Last intron | ||||||||
52 | GLCCI1 | AATAAA | 2,978 | 1,921 | 1,057 | 249 | PRMT2 | Intron 1 | ||||||||
53 | GREB1l | AATAAA | 1,505 | 1,178 | 327 | None | RELA | Last intron | ||||||||
54 | GSKIP | AATAAA | 1,551 | 1,434 | 117 | None | RFT1 | Last intron | ||||||||
55 | GSR | AATAAA | 1,500 | 1,060 | 440 | 190 | SETD1A | Middle intron | ||||||||
56 | HDAC7 | AATAAA | 2,709 | 2,262 | 447 | 160 | SHISA5 | Last intron | ||||||||
57 | HILPDA | AATAAA | 581 | 387 | 194 | None | SLC10A3 | Last intron | ||||||||
58 | HNRNPLL | AATAAA | 1,728 | 1548 | 180 | None | SLC35A2 | Last intron | ||||||||
59 | HSDL1 | AATAAA | 1,040 | 924 | 116 | None | SPATA2 | Last intron | ||||||||
60 | IFNAR2 | AATAAA | 2,418 | 2,096 | 322 | None | STIM1 | Last intron | ||||||||
61 | INSR | AATAAA | 1,899 | 1,690 | 209 | 173 | STC2 | Last intron | ||||||||
62 | KLC1 | AATAAA | 1,060 | 753 | 307 | None | TAPBP | Intron 1 and 2 | ||||||||
63 | LEPR | AATAAA | 1,117 | 987 | 130 | 113 | TCF3 | Multiple introns | ||||||||
64 | LRRC47 | AATAAA | 1,751 | 1,108 | 643 | 234 | TMEM129 | Multiple introns | ||||||||
65 | MAML1 | AATAAA | 1,984 | 1,406 | 578 | 127 | TMEM173 | Intron 2 | ||||||||
66 | MAP3K3 | AATAAA | 1,581 | 1,026 | 555 | 183 | TJAP1 | Last intron | ||||||||
67 | MAP3K7 | AATAAA | 1,291 | 753 | 538 | <100 | TSC22D4 | Multiple introns | ||||||||
68 | MBP | AATAAA | 2,715 | 2,477 | 238 | None | VARS | First intron | ||||||||
69 | MCCC1 | AATAAA | 1,659 | 1,423 | 236 | <100 | WBP1L | Last intron | ||||||||
70 | MEGF8 | AATAAA | 1,564 | 742 | 822 | <100 | WDR5 | Intron 1 | ||||||||
71 | MKL1 | AATAAA | 2,983 | 2,741 | 242 | None | YPEL3 | Multiple introns | ||||||||
72 | MLLT1 | AATAAA | 5,612 | 5,436 | 176 | <100 | ZC3H10 | Intron 1 | ||||||||
73 | MOB1B | AATAAA | 1,586 | 1,378 | 208 | <100 | ZNF107 | Last intron | ||||||||
74 | NAA16 | AATAAA | 887 | 509 | 378 | 118 | ZNF200 | Intron 1 | ||||||||
75 | NFKB1 | AATAAA | 1,164 | 704 | 460 | None | ZNF416 | Last intron | ||||||||
76 | NUTM2B-AS1 | AATAAA | 1,804 | 1,407 | 397 | None | ZNF580 | Intron 1 | ||||||||
77 | PAFAH1B1 | AATAAA | 2,027 | 1,649 | 378 | None | ZNF598 | Multiple introns | ||||||||
78 | PFKFB3 | AATAAA | 4,212 | 4,078 | 134 | 203 | ZNF668 | Last intron | ||||||||
79 | PIP4K2B | ATTAAA | 3,766 | 3,066 | 700 | <100 | ||||||||||
80 | PLAG1 | AATAAA | 1,047 | 915 | 132 | None | ||||||||||
81 | PPM1E | AATAAA | 2,143 | 1,550 | 593 | 154 | ||||||||||
82 | PPP6C | AATAAA | 953 | 575 | 378 | 118 | ||||||||||
83 | PPP1R8 | AATAAA | 780 | 629 | 151 | None | ||||||||||
84 | PPTC7 | AATAAA | 1,351 | 900 | 451 | 291 | ||||||||||
85 | PRDM10 | AATAAA | 2,249 | 1917 | 332 | None | ||||||||||
86 | PRDM15 | AATAAA | 1,050 | 837 | 213 | 226 | ||||||||||
87 | PRKACB | AATAAA | 1,255 | 858 | 397 | None | ||||||||||
88 | QSOX2 | AATAAA | 2,650 | 2,284 | 366 | 186 | ||||||||||
89 | RABL6 | AATAAA | 2,076 | 1,671 | 405 | 148 | ||||||||||
90 | RBL1 | AATAAA | 891 | 663 | 228 | 133 | ||||||||||
91 | R3HDM1 | AATAAA | 1,096 | 917 | 179 | None | ||||||||||
92 | RFX2 | AATAAA | 2,944 | 2683 | 261 | None | ||||||||||
93 | RIC1 | AATAAA | 2,009 | 1585 | 424 | 220 | ||||||||||
94 | RMND5A | AATAAA | 1,285 | 766 | 519 | None | ||||||||||
95 | RRP1B | AATAAA | 3,066 | 2,822 | 244 | None | ||||||||||
96 | SCRN1 | AATAAA | 1,460 | 1,352 | 108 | <100 | ||||||||||
97 | SGSM2 | AATAAA | 1,155 | 921 | 234 | 180 | ||||||||||
98 | SLC4A4 | AATAAA | 2,154 | 2,036 | 118 | None | ||||||||||
99 | SLC22A5 | AATAAA | 1,115 | 453 | 662 | 139 | ||||||||||
100 | SLC46A3 | AATAAA | 1,235 | 717 | 518 | None | ||||||||||
101 | SNX25 | AATAAA | 754 | 528 | 226 | None | ||||||||||
102 | SP3 | ATTAAA | 912 | 454 | 458 | <100 | ||||||||||
103 | SPTAN1 | AATAAA | 759 | 620 | 139 | None | ||||||||||
104 | SSH2 | AATAAA | 1,069 | 767 | 302 | <100 | ||||||||||
105 | STXBP3 | AATAAA | 1,864 | 1,750 | 114 | <100 | ||||||||||
106 | SUPT16H | AATAAA | 1,640 | 862 | 778 | <100 | ||||||||||
107 | TBC1D2B | ATTAAA | 884 | 473 | 411 | 231 | ||||||||||
108 | TIAM1 | AATAAA | 2,475 | 2,425 | 50 | None | ||||||||||
109 | TIPRL | AATAAA | 815 | 478 | 337 | <100 | ||||||||||
110 | TMEM116 | AATAAA | 2,772 | 2,554 | 218 | None | ||||||||||
111 | TMEM170B | AATAAA | 2,283 | 2,186 | 97 | None | ||||||||||
112 | TMEM245 | AATAAA | 1,588 | 973 | 615 | 245 | ||||||||||
113 | TRAF6 | AATAAA | 1,047 | 781 | 266 | None | ||||||||||
114 | TSHZ3 | AATAAA | 1,054 | 949 | 105 | None | ||||||||||
115 | TTC13 | AATAAA | 1,039 | 726 | 313 | 166 | ||||||||||
116 | UBE2J1 | AATAAA | 1,117 | 755 | 362 | <100 | ||||||||||
117 | UNK | AATAAA | 1,535 | 1,389 | 146 | 139 | ||||||||||
118 | URI1 | AATAAA | 1,053 | 627 | 426 | None | ||||||||||
119 | USP31 | ATTAAA | 1,098 | 465 | 633 | 280 | ||||||||||
120 | WDYHV1 | AATAAA | 1,118 | 910 | 208 | None | ||||||||||
121 | YWHAG | AATAAA | 1,078 | 770 | 308 | 203 | ||||||||||
122 | ZAK | AATAAA | 1,459 | 1,293 | 166 | None | ||||||||||
123 | ZC3H6 | AATAAA | 909 | 441 | 468 | None | ||||||||||
124 | ZFP90 | AATAAA | 1,044 | 853 | 191 | None | ||||||||||
125 | ZKSCAN1 | AATAAA | 981 | 826 | 155 | None | ||||||||||
126 | ZMIZ2 | AATAAA | 4,051 | 3,667 | 384 | None | ||||||||||
127 | ZNF75A | AATAAA | 935 | 697 | 238 | None | ||||||||||
128 | ZNF250 | AATAAA | 2,426 | 1,869 | 557 | None | ||||||||||
129 | ZNF254 | AATAAA | 498 | 320 | 178 | None | ||||||||||
130 | ZNF273 | AATAAA | 537 | 359 | 178 | None | ||||||||||
131 | ZNF627 | AATAAA | 1,025 | 814 | 211 | None | ||||||||||
132 | ZSCAN32 | AATAAA | 452 | 360 | 92 | None |
Use of both alternative 5′ splice sites (ss) and intronic PAS were observed for these genes.