DNA-directed 5'-3' RNA polymerase activity
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| PPR_2 | PF13041 | 125 - 172 | 1.3e-09 | PPR repeat family |
| PPR | PF01535 | 128 - 156 | 8.3e-07 | PPR repeat |
| PPR_2 | PF13041 | 226 - 273 | 1.3e-08 | PPR repeat family |
| PPR | PF01535 | 229 - 258 | 6.3e-06 | PPR repeat |
| PPR_2 | PF13041 | 328 - 376 | 7e-10 | PPR repeat family |
| PPR | PF01535 | 330 - 358 | 1.2e-07 | PPR repeat |
| E_motif | PF20431 | 447 - 509 | 5.2e-19 | E motif |
| DYW_deaminase | PF14432 | 545 - 637 | 1.9e-38 | DYW family of nucleic acid deaminases |
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AanI | TTATAA | 1 cut(s) | 563 |
| AccII | CGCG | 1 cut(s) | 351 |
| AccIII | TCCGGA | 1 cut(s) | 294 |
| AciI | CCGC | 4 cut(s) | 64, 89, 281, 349 |
| AcoI | YGGCCR | 2 cut(s) | 393, 1237 |
| AcsI | RAATTY | 4 cut(s) | 94, 1157, 1268, 1361 |
| AcuI | CTGAAG | 2 cut(s) | 884, 1770 |
| AfaI | GTAC | 5 cut(s) | 425, 504, 517, 694, 923 |
| AfiI | CCNNNNNNNGG | 1 cut(s) | 1649 |
| AflIII | ACRYGT | 1 cut(s) | 615 |
| AgsI | TTSAA | 6 cut(s) | 164, 644, 1057, 1256, 1268, 1391 |
| AjnI | CCWGG | 2 cut(s) | 144, 1507 |
| Alw21I | GWGCWC | 2 cut(s) | 291, 357 |
| Alw26I | GTCTC | 3 cut(s) | 643, 691, 1825 |
| Alw44I | GTGCAC | 1 cut(s) | 287 |
| Ama87I | CYCGRG | 1 cut(s) | 974 |
| Aor13HI | TCCGGA | 1 cut(s) | 294 |
| AoxI | GGCC | 4 cut(s) | 166, 225, 393, 1237 |
| ApaLI | GTGCAC | 1 cut(s) | 287 |
| ApeKI | GCWGC | 3 cut(s) | 600, 830, 1301 |
| ApoI | RAATTY | 4 cut(s) | 94, 1157, 1268, 1361 |
| ArsI | GACNNNNNNTTYG | 2 cut(s) | 164, 196 |
| AseI | ATTAAT | 1 cut(s) | 1478 |
| AspS9I | GGNCC | 4 cut(s) | 225, 297, 476, 838 |
| AsuC2I | CCSGG | 1 cut(s) | 301 |
| AsuHPI | GGTGA | 3 cut(s) | 90, 1370, 1612 |
| AsuII | TTCGAA | 1 cut(s) | 183 |
| AvaI | CYCGRG | 1 cut(s) | 974 |
| AvaII | GGWCC | 3 cut(s) | 297, 476, 838 |
| BaeGI | GKGCMC | 1 cut(s) | 291 |
| BbsI | GAAGAC | 1 cut(s) | 16 |
| Bbv12I | GWGCWC | 2 cut(s) | 291, 357 |
| BbvI | GCAGC | 3 cut(s) | 612, 817, 1288 |
| BccI | CCATC | 5 cut(s) | 1147, 1165, 1443, 1578, 1711 |
| BceAI | ACGGC | 3 cut(s) | 408, 828, 1224 |
| BciT130I | CCWGG | 2 cut(s) | 146, 1509 |
| BciVI | GTATCC | 1 cut(s) | 1628 |
| BclI | TGATCA | 1 cut(s) | 261 |
| BcnI | CCSGG | 1 cut(s) | 301 |
| BcoDI | GTCTC | 3 cut(s) | 643, 691, 1825 |
| BfaI | CTAG | 2 cut(s) | 1382, 1700 |
| BfmI | CTRYAG | 2 cut(s) | 452, 1440 |
| BfuI | GTATCC | 1 cut(s) | 1628 |
| BisI | GCNGC | 4 cut(s) | 349, 601, 831, 1302 |
| BlsI | GCNGC | 4 cut(s) | 350, 602, 832, 1303 |
| BmcAI | AGTACT | 1 cut(s) | 504 |
| Bme1390I | CCNGG | 3 cut(s) | 146, 301, 1509 |
| Bme18I | GGWCC | 3 cut(s) | 297, 476, 838 |
| BmeT110I | CYCGRG | 1 cut(s) | 974 |
| BmgT120I | GGNCC | 4 cut(s) | 225, 297, 476, 838 |
| BmiI | GGNNCC | 4 cut(s) | 299, 477, 1315, 1506 |
| BmrFI | CCNGG | 3 cut(s) | 146, 301, 1509 |
| BmsI | GCATC | 2 cut(s) | 331, 1272 |
| BpiI | GAAGAC | 1 cut(s) | 16 |
| Bpu14I | TTCGAA | 1 cut(s) | 183 |
| BpuEI | CTTGAG | 3 cut(s) | 250, 934, 1226 |
| BpuMI | CCSGG | 1 cut(s) | 301 |
| BsaJI | CCNNGG | 2 cut(s) | 144, 841 |
| BsaWI | WCCGGW | 1 cut(s) | 294 |
| BsaXI | ACNNNNNCTCC | 2 cut(s) | 1026, 1056 |
| Bsc4I | CCNNNNNNNGG | 1 cut(s) | 1649 |
| Bse118I | RCCGGY | 2 cut(s) | 100, 283 |
| Bse1I | ACTGG | 4 cut(s) | 523, 801, 1760, 1913 |
| Bse3DI | GCAATG | 1 cut(s) | 1008 |
| BseAI | TCCGGA | 1 cut(s) | 294 |
| BseBI | CCWGG | 2 cut(s) | 146, 1509 |
| BseDI | CCNNGG | 2 cut(s) | 144, 841 |
| BseGI | GGATG | 6 cut(s) | 80, 685, 1158, 1223, 1570, 1678 |
| BseLI | CCNNNNNNNGG | 1 cut(s) | 1649 |
| BseMI | GCAATG | 1 cut(s) | 1008 |
| BseMII | CTCAG | 3 cut(s) | 125, 362, 1281 |
| BseNI | ACTGG | 4 cut(s) | 523, 801, 1760, 1913 |
| BseRI | GAGGAG | 1 cut(s) | 1691 |
| BseSI | GKGCMC | 1 cut(s) | 291 |
| BseXI | GCAGC | 3 cut(s) | 612, 817, 1288 |
| BseYI | CCCAGC | 2 cut(s) | 717, 1403 |
| Bsh1236I | CGCG | 1 cut(s) | 351 |
| BshFI | GGCC | 4 cut(s) | 168, 227, 395, 1239 |
| BsiHKAI | GWGCWC | 2 cut(s) | 291, 357 |
| BsiHKCI | CYCGRG | 1 cut(s) | 974 |
| BsiSI | CCGG | 5 cut(s) | 101, 284, 295, 301, 754 |
| BslFI | GGGAC | 1 cut(s) | 489 |
| BslI | CCNNNNNNNGG | 1 cut(s) | 1649 |
| BsmAI | GTCTC | 3 cut(s) | 643, 691, 1825 |
| BsmBI | CGTCTC | 1 cut(s) | 643 |
| BsmFI | GGGAC | 1 cut(s) | 489 |
| BsmI | GAATGC | 2 cut(s) | 642, 1003 |
| BsnI | GGCC | 4 cut(s) | 168, 227, 395, 1239 |
| BsoBI | CYCGRG | 1 cut(s) | 974 |
| Bsp119I | TTCGAA | 1 cut(s) | 183 |
| Bsp1286I | GDGCHC | 2 cut(s) | 291, 357 |
| Bsp13I | TCCGGA | 1 cut(s) | 294 |
| Bsp1407I | TGTACA | 1 cut(s) | 692 |
| Bsp143I | GATC | 5 cut(s) | 261, 442, 464, 1228, 1561 |
| BspACI | CCGC | 4 cut(s) | 64, 89, 281, 349 |
| BspANI | GGCC | 4 cut(s) | 168, 227, 395, 1239 |
| BspCNI | CTCAG | 3 cut(s) | 126, 363, 1282 |
| BspEI | TCCGGA | 1 cut(s) | 294 |
| BspFNI | CGCG | 1 cut(s) | 351 |
| BspLI | GGNNCC | 4 cut(s) | 299, 477, 1315, 1506 |
| BspMAI | CTGCAG | 1 cut(s) | 1444 |
| BspT104I | TTCGAA | 1 cut(s) | 183 |
| BsrDI | GCAATG | 1 cut(s) | 1008 |
| BsrFI | RCCGGY | 2 cut(s) | 100, 283 |
| BsrGI | TGTACA | 1 cut(s) | 692 |
| BsrI | ACTGG | 4 cut(s) | 523, 801, 1760, 1913 |
| BssAI | RCCGGY | 2 cut(s) | 100, 283 |
| BssECI | CCNNGG | 2 cut(s) | 144, 841 |
| BssMI | GATC | 5 cut(s) | 261, 442, 464, 1228, 1561 |
| BssT1I | CCWWGG | 1 cut(s) | 841 |
| Bst2UI | CCWGG | 2 cut(s) | 146, 1509 |
| Bst6I | CTCTTC | 4 cut(s) | 729, 1032, 1578, 1831 |
| BstAUI | TGTACA | 1 cut(s) | 692 |
| BstBI | TTCGAA | 1 cut(s) | 183 |
| BstC8I | GCNNGC | 7 cut(s) | 346, 353, 545, 605, 668, 828, 848 |
| BstDEI | CTNAG | 6 cut(s) | 22, 134, 371, 414, 941, 1290 |
| BstF5I | GGATG | 6 cut(s) | 80, 685, 1158, 1223, 1570, 1678 |
| BstFNI | CGCG | 1 cut(s) | 351 |
| BstKTI | GATC | 5 cut(s) | 264, 445, 467, 1231, 1564 |
| BstMAI | GTCTC | 3 cut(s) | 643, 691, 1825 |
| BstMBI | GATC | 5 cut(s) | 261, 442, 464, 1228, 1561 |
| BstMWI | GCNNNNNNNGC | 5 cut(s) | 345, 434, 754, 1057, 1291 |
| BstNI | CCWGG | 2 cut(s) | 146, 1509 |
| BstNSI | RCATGY | 1 cut(s) | 619 |
| BstSCI | CCNGG | 3 cut(s) | 144, 299, 1507 |
| BstSFI | CTRYAG | 2 cut(s) | 452, 1440 |
| BstSLI | GKGCMC | 1 cut(s) | 291 |
| BstUI | CGCG | 1 cut(s) | 351 |
| BstV1I | GCAGC | 3 cut(s) | 612, 817, 1288 |
| BstV2I | GAAGAC | 1 cut(s) | 16 |
| BstXI | CCANNNNNNTGG | 1 cut(s) | 1808 |
| BsuI | GTATCC | 1 cut(s) | 1628 |
| BsuRI | GGCC | 4 cut(s) | 168, 227, 395, 1239 |
| BtgZI | GCGATG | 1 cut(s) | 354 |
| BtsCI | GGATG | 6 cut(s) | 80, 685, 1158, 1223, 1570, 1678 |
| BtsIMutI | CAGTG | 3 cut(s) | 808, 1099, 1714 |
| Cac8I | GCNNGC | 7 cut(s) | 346, 353, 545, 605, 668, 828, 848 |
| Cfr10I | RCCGGY | 2 cut(s) | 100, 283 |
| Cfr13I | GGNCC | 4 cut(s) | 225, 297, 476, 838 |
| Csp6I | GTAC | 5 cut(s) | 424, 503, 516, 693, 922 |
| CviQI | GTAC | 5 cut(s) | 424, 503, 516, 693, 922 |
| DdeI | CTNAG | 6 cut(s) | 22, 134, 371, 414, 941, 1290 |
| DpnI | GATC | 5 cut(s) | 263, 444, 466, 1230, 1563 |
| DpnII | GATC | 5 cut(s) | 261, 442, 464, 1228, 1561 |
| EaeI | YGGCCR | 2 cut(s) | 393, 1237 |
| Eam1104I | CTCTTC | 4 cut(s) | 729, 1032, 1578, 1831 |
| EarI | CTCTTC | 4 cut(s) | 729, 1032, 1578, 1831 |
| EciI | GGCGGA | 2 cut(s) | 53, 270 |
| Eco130I | CCWWGG | 1 cut(s) | 841 |
| Eco147I | AGGCCT | 1 cut(s) | 168 |
| Eco32I | GATATC | 1 cut(s) | 1611 |
| Eco47I | GGWCC | 3 cut(s) | 297, 476, 838 |
| Eco57I | CTGAAG | 2 cut(s) | 884, 1770 |
| Eco88I | CYCGRG | 1 cut(s) | 974 |
| EcoO109I | RGGNCCY | 2 cut(s) | 225, 476 |
| EcoRI | GAATTC | 2 cut(s) | 1157, 1268 |
| EcoRII | CCWGG | 2 cut(s) | 144, 1507 |
| EcoRV | GATATC | 1 cut(s) | 1611 |
| EcoT14I | CCWWGG | 1 cut(s) | 841 |
| ErhI | CCWWGG | 1 cut(s) | 841 |
| Esp3I | CGTCTC | 1 cut(s) | 643 |
| FaqI | GGGAC | 1 cut(s) | 489 |
| FauI | CCCGC | 1 cut(s) | 96 |
| FauNDI | CATATG | 1 cut(s) | 889 |
| FbaI | TGATCA | 1 cut(s) | 261 |
| Fnu4HI | GCNGC | 4 cut(s) | 349, 601, 831, 1302 |
| FokI | GGATG | 6 cut(s) | 67, 692, 1165, 1230, 1557, 1685 |
| Fsp4HI | GCNGC | 4 cut(s) | 349, 601, 831, 1302 |
| FspBI | CTAG | 2 cut(s) | 1382, 1700 |
| GluI | GCNGC | 4 cut(s) | 349, 601, 831, 1302 |
| GsaI | CCCAGC | 2 cut(s) | 721, 1407 |
| HaeIII | GGCC | 4 cut(s) | 168, 227, 395, 1239 |
| HapII | CCGG | 5 cut(s) | 101, 284, 295, 301, 754 |
| HincII | GTYRAC | 1 cut(s) | 131 |
| HindII | GTYRAC | 1 cut(s) | 131 |
| HindIII | AAGCTT | 1 cut(s) | 1049 |
| HinfI | GANTC | 2 cut(s) | 246, 581 |
| HpaII | CCGG | 5 cut(s) | 101, 284, 295, 301, 754 |
| HphI | GGTGA | 3 cut(s) | 90, 1370, 1612 |
| Hpy166II | GTNNAC | 7 cut(s) | 131, 289, 390, 489, 856, 1022, 1339 |
| Hpy188I | TCNGA | 6 cut(s) | 372, 433, 469, 903, 1085, 1291 |
| Hpy188III | TCNNGA | 9 cut(s) | 295, 611, 728, 951, 1382, 1643, 1700, 1748, 1822 |
| Hpy8I | GTNNAC | 7 cut(s) | 131, 289, 390, 489, 856, 1022, 1339 |
| HpyCH4IV | ACGT | 1 cut(s) | 491 |
| HpyF10VI | GCNNNNNNNGC | 5 cut(s) | 345, 434, 754, 1057, 1291 |
| HpyF3I | CTNAG | 6 cut(s) | 22, 134, 371, 414, 941, 1290 |
| HpySE526I | ACGT | 1 cut(s) | 491 |
| Kpn2I | TCCGGA | 1 cut(s) | 294 |
| Ksp22I | TGATCA | 1 cut(s) | 261 |
| Kzo9I | GATC | 5 cut(s) | 261, 442, 464, 1228, 1561 |
| LmnI | GCTCC | 5 cut(s) | 125, 745, 1504, 1571, 1678 |
| Lsp1109I | GCAGC | 3 cut(s) | 612, 817, 1288 |
| LweI | GCATC | 2 cut(s) | 331, 1272 |
| MaeI | CTAG | 2 cut(s) | 1382, 1700 |
| MaeII | ACGT | 1 cut(s) | 491 |
| MaeIII | GTNAC | 5 cut(s) | 35, 214, 790, 944, 1096 |
| MalI | GATC | 5 cut(s) | 263, 444, 466, 1230, 1563 |
| MboI | GATC | 5 cut(s) | 261, 442, 464, 1228, 1561 |
| MhlI | GDGCHC | 2 cut(s) | 291, 357 |
| MlyI | GAGTC | 1 cut(s) | 255 |
| MmeI | TCCRAC | 4 cut(s) | 147, 1499, 1612, 1861 |
| MroI | TCCGGA | 1 cut(s) | 294 |
| MseI | TTAA | 8 cut(s) | 107, 203, 461, 1047, 1275, 1350, 1478, 1622 |
| MslI | CAYNNNNRTG | 4 cut(s) | 115, 861, 1344, 1557 |
| MspI | CCGG | 5 cut(s) | 101, 284, 295, 301, 754 |
| MspR9I | CCNGG | 3 cut(s) | 146, 301, 1509 |
| Mva1269I | GAATGC | 2 cut(s) | 642, 1003 |
| MvaI | CCWGG | 2 cut(s) | 146, 1509 |
| MvnI | CGCG | 1 cut(s) | 351 |
| MwoI | GCNNNNNNNGC | 5 cut(s) | 345, 434, 754, 1057, 1291 |
| NciI | CCSGG | 1 cut(s) | 301 |
| NdeI | CATATG | 1 cut(s) | 889 |
| NdeII | GATC | 5 cut(s) | 261, 442, 464, 1228, 1561 |
| NlaIV | GGNNCC | 4 cut(s) | 299, 477, 1315, 1506 |
| NmuCI | GTSAC | 2 cut(s) | 790, 1096 |
| NspI | RCATGY | 1 cut(s) | 619 |
| NspV | TTCGAA | 1 cut(s) | 183 |
| PceI | AGGCCT | 1 cut(s) | 168 |
| PciI | ACATGT | 1 cut(s) | 615 |
| PcsI | WCGNNNNNNNCGW | 1 cut(s) | 156 |
| PctI | GAATGC | 2 cut(s) | 642, 1003 |
| PfeI | GAWTC | 1 cut(s) | 581 |
| PflFI | GACNNNGTC | 1 cut(s) | 1094 |
| PkrI | GCNGC | 4 cut(s) | 350, 602, 832, 1303 |
| PleI | GAGTC | 1 cut(s) | 254 |
| PpsI | GAGTC | 1 cut(s) | 254 |
| PpuMI | RGGWCCY | 1 cut(s) | 476 |
| PscI | ACATGT | 1 cut(s) | 615 |
| PshBI | ATTAAT | 1 cut(s) | 1478 |
| PsiI | TTATAA | 1 cut(s) | 563 |
| Psp5II | RGGWCCY | 1 cut(s) | 476 |
| Psp6I | CCWGG | 2 cut(s) | 144, 1507 |
| PspFI | CCCAGC | 2 cut(s) | 717, 1403 |
| PspGI | CCWGG | 2 cut(s) | 144, 1507 |
| PspN4I | GGNNCC | 4 cut(s) | 299, 477, 1315, 1506 |
| PspPI | GGNCC | 4 cut(s) | 225, 297, 476, 838 |
| PspPPI | RGGWCCY | 1 cut(s) | 476 |
| PstI | CTGCAG | 1 cut(s) | 1444 |
| PsyI | GACNNNGTC | 1 cut(s) | 1094 |
| RsaI | GTAC | 5 cut(s) | 425, 504, 517, 694, 923 |
| RsaNI | GTAC | 5 cut(s) | 424, 503, 516, 693, 922 |
| RseI | CAYNNNNRTG | 4 cut(s) | 115, 861, 1344, 1557 |
| SaqAI | TTAA | 8 cut(s) | 107, 203, 461, 1047, 1275, 1350, 1478, 1622 |
| SatI | GCNGC | 4 cut(s) | 349, 601, 831, 1302 |
| Sau3AI | GATC | 5 cut(s) | 261, 442, 464, 1228, 1561 |
| Sau96I | GGNCC | 4 cut(s) | 225, 297, 476, 838 |
| ScaI | AGTACT | 1 cut(s) | 504 |
| SchI | GAGTC | 1 cut(s) | 255 |
| ScrFI | CCNGG | 3 cut(s) | 146, 301, 1509 |
| SduI | GDGCHC | 2 cut(s) | 291, 357 |
| SfaNI | GCATC | 2 cut(s) | 331, 1272 |
| SfcI | CTRYAG | 2 cut(s) | 452, 1440 |
| SfuI | TTCGAA | 1 cut(s) | 183 |
| SgrAI | CRCCGGYG | 1 cut(s) | 283 |
| SinI | GGWCC | 3 cut(s) | 297, 476, 838 |
| SmiMI | CAYNNNNRTG | 4 cut(s) | 115, 861, 1344, 1557 |
| SmlI | CTYRAG | 3 cut(s) | 229, 949, 1205 |
| SmoI | CTYRAG | 3 cut(s) | 229, 949, 1205 |
| SseBI | AGGCCT | 1 cut(s) | 168 |
| SsiI | CCGC | 4 cut(s) | 64, 89, 281, 349 |
| SspMI | CTAG | 2 cut(s) | 1382, 1700 |
| StuI | AGGCCT | 1 cut(s) | 168 |
| StyD4I | CCNGG | 3 cut(s) | 144, 299, 1507 |
| StyI | CCWWGG | 1 cut(s) | 841 |
| TaiI | ACGT | 1 cut(s) | 494 |
| TaqI | TCGA | 5 cut(s) | 150, 183, 357, 1249, 1823 |
| TatI | WGTACW | 4 cut(s) | 502, 515, 692, 921 |
| TauI | GCSGC | 1 cut(s) | 351 |
| TfiI | GAWTC | 1 cut(s) | 581 |
| Tru1I | TTAA | 8 cut(s) | 107, 203, 461, 1047, 1275, 1350, 1478, 1622 |
| Tru9I | TTAA | 8 cut(s) | 107, 203, 461, 1047, 1275, 1350, 1478, 1622 |
| TscAI | CASTG | 3 cut(s) | 808, 1099, 1714 |
| TseFI | GTSAC | 2 cut(s) | 790, 1096 |
| TseI | GCWGC | 3 cut(s) | 600, 830, 1301 |
| Tsp45I | GTSAC | 2 cut(s) | 790, 1096 |
| TspGWI | ACGGA | 1 cut(s) | 1754 |
| TspRI | CASTG | 3 cut(s) | 808, 1099, 1714 |
| Tth111I | GACNNNGTC | 1 cut(s) | 1094 |
| VneI | GTGCAC | 1 cut(s) | 287 |
| VpaK11BI | GGWCC | 3 cut(s) | 297, 476, 838 |
| VspI | ATTAAT | 1 cut(s) | 1478 |
| XapI | RAATTY | 4 cut(s) | 94, 1157, 1268, 1361 |
| XbaI | TCTAGA | 2 cut(s) | 1381, 1699 |
| XceI | RCATGY | 1 cut(s) | 619 |
| XcmI | CCANNNNNNNNNTGG | 1 cut(s) | 1515 |
| XspI | CTAG | 2 cut(s) | 1382, 1700 |
| ZrmI | AGTACT | 1 cut(s) | 504 |