Probably involved in the RNA silencing pathway and required for the generation of small interfering RNAs (siRNAs)
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| RdRP | PF05183 | 11 - 482 | 1.7e-80 | RNA dependent RNA polymerase |
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| Acc65I | GGTACC | 1 cut(s) | 490 |
| AccB1I | GGYRCC | 1 cut(s) | 490 |
| AccB7I | CCANNNNNTGG | 1 cut(s) | 529 |
| AciI | CCGC | 3 cut(s) | 664, 981, 1578 |
| AclI | AACGTT | 1 cut(s) | 302 |
| AclWI | GGATC | 5 cut(s) | 24, 37, 269, 368, 755 |
| AcoI | YGGCCR | 1 cut(s) | 1575 |
| AcsI | RAATTY | 1 cut(s) | 500 |
| AcuI | CTGAAG | 2 cut(s) | 824, 1143 |
| AcvI | CACGTG | 1 cut(s) | 563 |
| AfaI | GTAC | 7 cut(s) | 14, 430, 492, 831, 839, 1043, 1562 |
| AfiI | CCNNNNNNNGG | 3 cut(s) | 26, 529, 1331 |
| AflIII | ACRYGT | 1 cut(s) | 560 |
| AgsI | TTSAA | 5 cut(s) | 1067, 1074, 1172, 1363, 1413 |
| AhlI | ACTAGT | 1 cut(s) | 832 |
| AjnI | CCWGG | 1 cut(s) | 1214 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 897, 929 |
| AluBI | AGCT | 8 cut(s) | 66, 322, 527, 758, 1030, 1070, 1199, 1313 |
| AluI | AGCT | 8 cut(s) | 66, 322, 527, 758, 1030, 1070, 1199, 1313 |
| Alw26I | GTCTC | 3 cut(s) | 125, 677, 1018 |
| AlwI | GGATC | 5 cut(s) | 24, 37, 269, 368, 755 |
| AoxI | GGCC | 1 cut(s) | 1575 |
| ApeKI | GCWGC | 3 cut(s) | 566, 1196, 1580 |
| ApoI | RAATTY | 1 cut(s) | 500 |
| AseI | ATTAAT | 3 cut(s) | 623, 1430, 1509 |
| Asp700I | GAANNNNTTC | 1 cut(s) | 1137 |
| Asp718I | GGTACC | 1 cut(s) | 490 |
| AspA2I | CCTAGG | 1 cut(s) | 437 |
| AspS9I | GGNCC | 3 cut(s) | 953, 1348, 1366 |
| AsuC2I | CCSGG | 2 cut(s) | 34, 849 |
| AsuHPI | GGTGA | 2 cut(s) | 605, 1010 |
| AsuNHI | GCTAGC | 1 cut(s) | 1210 |
| AvaII | GGWCC | 3 cut(s) | 953, 1348, 1366 |
| AvrII | CCTAGG | 1 cut(s) | 437 |
| BaeI | ACNNNNGTAYC | 2 cut(s) | 821, 854 |
| BamHI | GGATCC | 1 cut(s) | 29 |
| BanI | GGYRCC | 1 cut(s) | 490 |
| BbrPI | CACGTG | 1 cut(s) | 563 |
| BbsI | GAAGAC | 1 cut(s) | 1470 |
| BbvCI | CCTCAGC | 1 cut(s) | 1026 |
| BbvI | GCAGC | 3 cut(s) | 578, 1208, 1567 |
| BciT130I | CCWGG | 1 cut(s) | 1216 |
| BciVI | GTATCC | 1 cut(s) | 152 |
| BcnI | CCSGG | 2 cut(s) | 34, 849 |
| BcoDI | GTCTC | 3 cut(s) | 125, 677, 1018 |
| BcuI | ACTAGT | 1 cut(s) | 832 |
| BfaI | CTAG | 7 cut(s) | 438, 833, 1130, 1164, 1211, 1238, 1316 |
| BfmI | CTRYAG | 1 cut(s) | 1655 |
| BfuI | GTATCC | 1 cut(s) | 152 |
| BglII | AGATCT | 2 cut(s) | 1126, 1135 |
| BisI | GCNGC | 4 cut(s) | 567, 1197, 1578, 1581 |
| BlnI | CCTAGG | 1 cut(s) | 437 |
| BlsI | GCNGC | 4 cut(s) | 568, 1198, 1579, 1582 |
| BmcAI | AGTACT | 1 cut(s) | 430 |
| Bme1390I | CCNGG | 3 cut(s) | 34, 849, 1216 |
| Bme18I | GGWCC | 3 cut(s) | 953, 1348, 1366 |
| BmgT120I | GGNCC | 3 cut(s) | 953, 1348, 1366 |
| BmiI | GGNNCC | 4 cut(s) | 31, 492, 1350, 1368 |
| BmrFI | CCNGG | 3 cut(s) | 34, 849, 1216 |
| BmrI | ACTGGG | 2 cut(s) | 1018, 1089 |
| BmsI | GCATC | 4 cut(s) | 526, 1309, 1462, 1513 |
| BmtI | GCTAGC | 1 cut(s) | 1214 |
| BmuI | ACTGGG | 2 cut(s) | 1018, 1089 |
| BoxI | GACNNNNGTC | 1 cut(s) | 817 |
| BpiI | GAAGAC | 1 cut(s) | 1470 |
| Bpu10I | CCTNAGC | 1 cut(s) | 1026 |
| BpuEI | CTTGAG | 1 cut(s) | 1000 |
| BpuMI | CCSGG | 2 cut(s) | 34, 849 |
| Bsa29I | ATCGAT | 2 cut(s) | 105, 600 |
| BsaAI | YACGTR | 1 cut(s) | 563 |
| BsaBI | GATNNNNATC | 3 cut(s) | 190, 999, 1452 |
| BsaI | GGTCTC | 1 cut(s) | 1018 |
| BsaJI | CCNNGG | 4 cut(s) | 90, 195, 437, 1058 |
| BsaWI | WCCGGW | 1 cut(s) | 493 |
| BsaXI | ACNNNNNCTCC | 2 cut(s) | 415, 445 |
| Bsc4I | CCNNNNNNNGG | 3 cut(s) | 26, 529, 1331 |
| Bse1I | ACTGG | 4 cut(s) | 187, 1013, 1095, 1211 |
| Bse8I | GATNNNNATC | 3 cut(s) | 190, 999, 1452 |
| BseBI | CCWGG | 1 cut(s) | 1216 |
| BseCI | ATCGAT | 2 cut(s) | 105, 600 |
| BseDI | CCNNGG | 4 cut(s) | 90, 195, 437, 1058 |
| BseGI | GGATG | 6 cut(s) | 16, 325, 790, 814, 1224, 1453 |
| BseJI | GATNNNNATC | 3 cut(s) | 190, 999, 1452 |
| BseLI | CCNNNNNNNGG | 3 cut(s) | 26, 529, 1331 |
| BseMII | CTCAG | 3 cut(s) | 573, 690, 1040 |
| BseNI | ACTGG | 4 cut(s) | 187, 1013, 1095, 1211 |
| BseRI | GAGGAG | 1 cut(s) | 423 |
| BseXI | GCAGC | 3 cut(s) | 578, 1208, 1567 |
| BsgI | GTGCAG | 1 cut(s) | 585 |
| BshFI | GGCC | 1 cut(s) | 1577 |
| BshNI | GGYRCC | 1 cut(s) | 490 |
| BshVI | ATCGAT | 2 cut(s) | 105, 600 |
| BsiSI | CCGG | 3 cut(s) | 33, 494, 848 |
| BslFI | GGGAC | 4 cut(s) | 279, 1334, 1352, 1502 |
| BslI | CCNNNNNNNGG | 3 cut(s) | 26, 529, 1331 |
| BsmAI | GTCTC | 3 cut(s) | 125, 677, 1018 |
| BsmBI | CGTCTC | 1 cut(s) | 677 |
| BsmFI | GGGAC | 4 cut(s) | 279, 1334, 1352, 1502 |
| BsnI | GGCC | 1 cut(s) | 1577 |
| Bso31I | GGTCTC | 1 cut(s) | 1018 |
| Bsp1407I | TGTACA | 1 cut(s) | 837 |
| BspACI | CCGC | 3 cut(s) | 664, 981, 1578 |
| BspANI | GGCC | 1 cut(s) | 1577 |
| BspCNI | CTCAG | 3 cut(s) | 574, 689, 1039 |
| BspDI | ATCGAT | 2 cut(s) | 105, 600 |
| BspLI | GGNNCC | 4 cut(s) | 31, 492, 1350, 1368 |
| BspOI | GCTAGC | 1 cut(s) | 1214 |
| BspPI | GGATC | 5 cut(s) | 24, 37, 269, 368, 755 |
| BspT107I | GGYRCC | 1 cut(s) | 490 |
| BspTNI | GGTCTC | 1 cut(s) | 1018 |
| BsrGI | TGTACA | 1 cut(s) | 837 |
| BsrI | ACTGG | 4 cut(s) | 187, 1013, 1095, 1211 |
| BssECI | CCNNGG | 4 cut(s) | 90, 195, 437, 1058 |
| BssT1I | CCWWGG | 3 cut(s) | 90, 437, 1058 |
| Bst2UI | CCWGG | 1 cut(s) | 1216 |
| Bst4CI | ACNGT | 6 cut(s) | 119, 704, 819, 932, 1469, 1560 |
| BstAUI | TGTACA | 1 cut(s) | 837 |
| BstBAI | YACGTR | 1 cut(s) | 563 |
| BstC8I | GCNNGC | 2 cut(s) | 1212, 1528 |
| BstDEI | CTNAG | 4 cut(s) | 582, 676, 707, 1026 |
| BstF5I | GGATG | 6 cut(s) | 16, 325, 790, 814, 1224, 1453 |
| BstMAI | GTCTC | 3 cut(s) | 125, 677, 1018 |
| BstMWI | GCNNNNNNNGC | 1 cut(s) | 1319 |
| BstNI | CCWGG | 1 cut(s) | 1216 |
| BstPAI | GACNNNNGTC | 1 cut(s) | 817 |
| BstSCI | CCNGG | 3 cut(s) | 32, 847, 1214 |
| BstSFI | CTRYAG | 1 cut(s) | 1655 |
| BstV1I | GCAGC | 3 cut(s) | 578, 1208, 1567 |
| BstV2I | GAAGAC | 1 cut(s) | 1470 |
| BstX2I | RGATCY | 4 cut(s) | 29, 373, 1126, 1135 |
| BstYI | RGATCY | 4 cut(s) | 29, 373, 1126, 1135 |
| Bsu15I | ATCGAT | 2 cut(s) | 105, 600 |
| BsuI | GTATCC | 1 cut(s) | 152 |
| BsuRI | GGCC | 1 cut(s) | 1577 |
| BsuTUI | ATCGAT | 2 cut(s) | 105, 600 |
| BtsCI | GGATG | 6 cut(s) | 16, 325, 790, 814, 1224, 1453 |
| Cac8I | GCNNGC | 2 cut(s) | 1212, 1528 |
| Cfr13I | GGNCC | 3 cut(s) | 953, 1348, 1366 |
| ClaI | ATCGAT | 2 cut(s) | 105, 600 |
| Csp6I | GTAC | 7 cut(s) | 13, 429, 491, 830, 838, 1042, 1561 |
| CviAII | CATG | 7 cut(s) | 259, 482, 508, 542, 872, 1371, 1387 |
| CviQI | GTAC | 7 cut(s) | 13, 429, 491, 830, 838, 1042, 1561 |
| DdeI | CTNAG | 4 cut(s) | 582, 676, 707, 1026 |
| DraI | TTTAAA | 1 cut(s) | 777 |
| EaeI | YGGCCR | 1 cut(s) | 1575 |
| Eco130I | CCWWGG | 3 cut(s) | 90, 437, 1058 |
| Eco31I | GGTCTC | 1 cut(s) | 1018 |
| Eco32I | GATATC | 1 cut(s) | 845 |
| Eco47I | GGWCC | 3 cut(s) | 953, 1348, 1366 |
| Eco57I | CTGAAG | 2 cut(s) | 824, 1143 |
| Eco72I | CACGTG | 1 cut(s) | 563 |
| EcoO109I | RGGNCCY | 1 cut(s) | 1366 |
| EcoRII | CCWGG | 1 cut(s) | 1214 |
| EcoRV | GATATC | 1 cut(s) | 845 |
| EcoT14I | CCWWGG | 3 cut(s) | 90, 437, 1058 |
| EcoT22I | ATGCAT | 1 cut(s) | 483 |
| ErhI | CCWWGG | 3 cut(s) | 90, 437, 1058 |
| Esp3I | CGTCTC | 1 cut(s) | 677 |
| FaeI | CATG | 7 cut(s) | 262, 485, 511, 545, 875, 1374, 1390 |
| FalI | AAGNNNNNCTT | 2 cut(s) | 1042, 1074 |
| FaqI | GGGAC | 4 cut(s) | 279, 1334, 1352, 1502 |
| FatI | CATG | 7 cut(s) | 258, 481, 507, 541, 871, 1370, 1386 |
| Fnu4HI | GCNGC | 4 cut(s) | 567, 1197, 1578, 1581 |
| FokI | GGATG | 6 cut(s) | 3, 312, 797, 821, 1231, 1460 |
| Fsp4HI | GCNGC | 4 cut(s) | 567, 1197, 1578, 1581 |
| FspBI | CTAG | 7 cut(s) | 438, 833, 1130, 1164, 1211, 1238, 1316 |
| GluI | GCNGC | 4 cut(s) | 567, 1197, 1578, 1581 |
| HaeIII | GGCC | 1 cut(s) | 1577 |
| HapII | CCGG | 3 cut(s) | 33, 494, 848 |
| Hin1II | CATG | 7 cut(s) | 262, 485, 511, 545, 875, 1374, 1390 |
| HindIII | AAGCTT | 2 cut(s) | 525, 1068 |
| HpaII | CCGG | 3 cut(s) | 33, 494, 848 |
| HphI | GGTGA | 2 cut(s) | 605, 1010 |
| Hpy166II | GTNNAC | 4 cut(s) | 838, 854, 956, 1055 |
| Hpy188I | TCNGA | 3 cut(s) | 196, 330, 1111 |
| Hpy8I | GTNNAC | 4 cut(s) | 838, 854, 956, 1055 |
| HpyAV | CCTTC | 6 cut(s) | 256, 799, 820, 889, 1357, 1419 |
| HpyCH4III | ACNGT | 6 cut(s) | 119, 704, 819, 932, 1469, 1560 |
| HpyCH4IV | ACGT | 3 cut(s) | 302, 562, 958 |
| HpyCH4V | TGCA | 8 cut(s) | 470, 481, 511, 555, 566, 948, 1288, 1322 |
| HpyF10VI | GCNNNNNNNGC | 1 cut(s) | 1319 |
| HpyF3I | CTNAG | 4 cut(s) | 582, 676, 707, 1026 |
| HpySE526I | ACGT | 3 cut(s) | 302, 562, 958 |
| Hsp92II | CATG | 7 cut(s) | 262, 485, 511, 545, 875, 1374, 1390 |
| KpnI | GGTACC | 1 cut(s) | 494 |
| LmnI | GCTCC | 1 cut(s) | 327 |
| Lsp1109I | GCAGC | 3 cut(s) | 578, 1208, 1567 |
| LweI | GCATC | 4 cut(s) | 526, 1309, 1462, 1513 |
| MaeI | CTAG | 7 cut(s) | 438, 833, 1130, 1164, 1211, 1238, 1316 |
| MaeII | ACGT | 3 cut(s) | 302, 562, 958 |
| MaeIII | GTNAC | 1 cut(s) | 1247 |
| MboII | GAAGA | 9 cut(s) | 122, 509, 545, 931, 1130, 1136, 1145, 1291, 1475 |
| MflI | RGATCY | 4 cut(s) | 29, 373, 1126, 1135 |
| MlyI | GAGTC | 3 cut(s) | 728, 1111, 1228 |
| MmeI | TCCRAC | 3 cut(s) | 401, 788, 895 |
| MnlI | CCTC | 9 cut(s) | 190, 444, 450, 479, 654, 685, 1035, 1186, 1537 |
| Mph1103I | ATGCAT | 1 cut(s) | 483 |
| MroXI | GAANNNNTTC | 1 cut(s) | 1137 |
| MslI | CAYNNNNRTG | 2 cut(s) | 150, 174 |
| MspA1I | CMGCKG | 2 cut(s) | 1199, 1580 |
| MspI | CCGG | 3 cut(s) | 33, 494, 848 |
| MspR9I | CCNGG | 3 cut(s) | 34, 849, 1216 |
| MvaI | CCWGG | 1 cut(s) | 1216 |
| MwoI | GCNNNNNNNGC | 1 cut(s) | 1319 |
| NciI | CCSGG | 2 cut(s) | 34, 849 |
| NheI | GCTAGC | 1 cut(s) | 1210 |
| NlaIII | CATG | 7 cut(s) | 262, 485, 511, 545, 875, 1374, 1390 |
| NlaIV | GGNNCC | 4 cut(s) | 31, 492, 1350, 1368 |
| NmuCI | GTSAC | 1 cut(s) | 1247 |
| NsiI | ATGCAT | 1 cut(s) | 483 |
| PdmI | GAANNNNTTC | 1 cut(s) | 1137 |
| PfeI | GAWTC | 7 cut(s) | 4, 128, 186, 343, 653, 905, 1651 |
| PflMI | CCANNNNNTGG | 1 cut(s) | 529 |
| PkrI | GCNGC | 4 cut(s) | 568, 1198, 1579, 1582 |
| PleI | GAGTC | 3 cut(s) | 728, 1110, 1228 |
| PmaCI | CACGTG | 1 cut(s) | 563 |
| PmlI | CACGTG | 1 cut(s) | 563 |
| PpsI | GAGTC | 3 cut(s) | 728, 1110, 1228 |
| Ppu21I | YACGTR | 1 cut(s) | 563 |
| PpuMI | RGGWCCY | 1 cut(s) | 1366 |
| PshAI | GACNNNNGTC | 1 cut(s) | 817 |
| PshBI | ATTAAT | 3 cut(s) | 623, 1430, 1509 |
| Psp1406I | AACGTT | 1 cut(s) | 302 |
| Psp5II | RGGWCCY | 1 cut(s) | 1366 |
| Psp6I | CCWGG | 1 cut(s) | 1214 |
| PspCI | CACGTG | 1 cut(s) | 563 |
| PspGI | CCWGG | 1 cut(s) | 1214 |
| PspN4I | GGNNCC | 4 cut(s) | 31, 492, 1350, 1368 |
| PspPI | GGNCC | 3 cut(s) | 953, 1348, 1366 |
| PspPPI | RGGWCCY | 1 cut(s) | 1366 |
| PsrI | GAACNNNNNNTAC | 2 cut(s) | 1388, 1420 |
| PsuI | RGATCY | 4 cut(s) | 29, 373, 1126, 1135 |
| PvuII | CAGCTG | 1 cut(s) | 1199 |
| RsaI | GTAC | 7 cut(s) | 14, 430, 492, 831, 839, 1043, 1562 |
| RsaNI | GTAC | 7 cut(s) | 13, 429, 491, 830, 838, 1042, 1561 |
| RseI | CAYNNNNRTG | 2 cut(s) | 150, 174 |
| SatI | GCNGC | 4 cut(s) | 567, 1197, 1578, 1581 |
| Sau96I | GGNCC | 3 cut(s) | 953, 1348, 1366 |
| ScaI | AGTACT | 1 cut(s) | 430 |
| SchI | GAGTC | 3 cut(s) | 728, 1111, 1228 |
| ScrFI | CCNGG | 3 cut(s) | 34, 849, 1216 |
| SfaNI | GCATC | 4 cut(s) | 526, 1309, 1462, 1513 |
| SfcI | CTRYAG | 1 cut(s) | 1655 |
| SinI | GGWCC | 3 cut(s) | 953, 1348, 1366 |
| SmiMI | CAYNNNNRTG | 2 cut(s) | 150, 174 |
| SmlI | CTYRAG | 1 cut(s) | 1015 |
| SmoI | CTYRAG | 1 cut(s) | 1015 |
| SpeI | ACTAGT | 1 cut(s) | 832 |
| SsiI | CCGC | 3 cut(s) | 664, 981, 1578 |
| SspMI | CTAG | 7 cut(s) | 438, 833, 1130, 1164, 1211, 1238, 1316 |
| StyD4I | CCNGG | 3 cut(s) | 32, 847, 1214 |
| StyI | CCWWGG | 3 cut(s) | 90, 437, 1058 |
| TaaI | ACNGT | 6 cut(s) | 119, 704, 819, 932, 1469, 1560 |
| TaiI | ACGT | 3 cut(s) | 305, 565, 961 |
| TaqI | TCGA | 5 cut(s) | 105, 123, 346, 600, 1485 |
| TatI | WGTACW | 3 cut(s) | 428, 837, 1560 |
| TauI | GCSGC | 1 cut(s) | 1580 |
| TfiI | GAWTC | 7 cut(s) | 4, 128, 186, 343, 653, 905, 1651 |
| TseFI | GTSAC | 1 cut(s) | 1247 |
| TseI | GCWGC | 3 cut(s) | 566, 1196, 1580 |
| Tsp45I | GTSAC | 1 cut(s) | 1247 |
| TspGWI | ACGGA | 2 cut(s) | 312, 1408 |
| Van91I | CCANNNNNTGG | 1 cut(s) | 529 |
| VpaK11BI | GGWCC | 3 cut(s) | 953, 1348, 1366 |
| VspI | ATTAAT | 3 cut(s) | 623, 1430, 1509 |
| XapI | RAATTY | 1 cut(s) | 500 |
| XbaI | TCTAGA | 2 cut(s) | 1129, 1315 |
| XcmI | CCANNNNNNNNNTGG | 1 cut(s) | 1056 |
| XmaJI | CCTAGG | 1 cut(s) | 437 |
| XmnI | GAANNNNTTC | 1 cut(s) | 1137 |
| XspI | CTAG | 7 cut(s) | 438, 833, 1130, 1164, 1211, 1238, 1316 |
| ZrmI | AGTACT | 1 cut(s) | 430 |
| Zsp2I | ATGCAT | 1 cut(s) | 483 |