transposition, RNA-mediated
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| Retrotran_gag_3 | PF14244 | 22 - 65 | 1.5e-13 | gag-polypeptide of LTR copia-type |
| Pol_BBD | PF22936 | 309 - 383 | 2.7e-14 | Pol polyprotein, beta-barrel domain |
| gag_pre-integrs | PF13976 | 416 - 452 | 5.3e-06 | GAG-pre-integrase domain |
| SH3_retrovirus | PF25597 | 551 - 592 | 1.2e-15 | Retroviral polymerase SH3-like domain |
| RVT_2 | PF07727 | 752 - 940 | 1.8e-59 | Reverse transcriptase (RNA-dependent DNA polymerase) |
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AanI | TTATAA | 4 cut(s) | 344, 1698, 1707, 2118 |
| Acc65I | GGTACC | 1 cut(s) | 1442 |
| AccB1I | GGYRCC | 2 cut(s) | 1034, 1442 |
| AccI | GTMKAC | 1 cut(s) | 2403 |
| AclI | AACGTT | 1 cut(s) | 1151 |
| AclWI | GGATC | 3 cut(s) | 240, 1206, 2576 |
| AcsI | RAATTY | 6 cut(s) | 285, 691, 818, 1499, 2123, 2277 |
| AcuI | CTGAAG | 2 cut(s) | 1269, 2115 |
| AfaI | GTAC | 7 cut(s) | 554, 874, 1444, 1492, 2167, 2443, 2667 |
| AflII | CTTAAG | 1 cut(s) | 448 |
| AflIII | ACRYGT | 2 cut(s) | 604, 1389 |
| AjnI | CCWGG | 2 cut(s) | 784, 2560 |
| AloI | GAACNNNNNNTCC | 1 cut(s) | 33 |
| Alw21I | GWGCWC | 3 cut(s) | 1409, 2158, 2751 |
| Alw26I | GTCTC | 5 cut(s) | 559, 1512, 1617, 1907, 2347 |
| Alw44I | GTGCAC | 1 cut(s) | 2154 |
| AlwI | GGATC | 3 cut(s) | 240, 1206, 2576 |
| AlwNI | CAGNNNCTG | 2 cut(s) | 842, 1973 |
| AoxI | GGCC | 1 cut(s) | 2483 |
| ApaLI | GTGCAC | 1 cut(s) | 2154 |
| ApeKI | GCWGC | 2 cut(s) | 731, 1632 |
| ApoI | RAATTY | 6 cut(s) | 285, 691, 818, 1499, 2123, 2277 |
| Asp700I | GAANNNNTTC | 2 cut(s) | 101, 2032 |
| Asp718I | GGTACC | 1 cut(s) | 1442 |
| AspS9I | GGNCC | 2 cut(s) | 153, 2048 |
| AsuHPI | GGTGA | 6 cut(s) | 688, 1198, 1235, 1566, 2537, 2792 |
| AsuII | TTCGAA | 1 cut(s) | 2275 |
| AvaII | GGWCC | 2 cut(s) | 153, 2048 |
| BaeGI | GKGCMC | 1 cut(s) | 2158 |
| BanI | GGYRCC | 2 cut(s) | 1034, 1442 |
| BarI | GAAGNNNNNNTAC | 2 cut(s) | 2586, 2618 |
| BauI | CACGAG | 3 cut(s) | 2037, 2376, 2637 |
| BbsI | GAAGAC | 1 cut(s) | 1220 |
| Bbv12I | GWGCWC | 3 cut(s) | 1409, 2158, 2751 |
| BbvCI | CCTCAGC | 1 cut(s) | 414 |
| BbvI | GCAGC | 2 cut(s) | 718, 1619 |
| BccI | CCATC | 4 cut(s) | 893, 2062, 2156, 2333 |
| BcgI | CGANNNNNNTGC | 2 cut(s) | 2618, 2652 |
| BciT130I | CCWGG | 2 cut(s) | 786, 2562 |
| BcoDI | GTCTC | 5 cut(s) | 559, 1512, 1617, 1907, 2347 |
| BfmI | CTRYAG | 3 cut(s) | 2010, 2023, 2298 |
| BfrI | CTTAAG | 1 cut(s) | 448 |
| BisI | GCNGC | 2 cut(s) | 732, 1633 |
| BlpI | GCTNAGC | 1 cut(s) | 1992 |
| BlsI | GCNGC | 2 cut(s) | 733, 1634 |
| BmcAI | AGTACT | 2 cut(s) | 2443, 2667 |
| Bme1390I | CCNGG | 2 cut(s) | 786, 2562 |
| Bme18I | GGWCC | 2 cut(s) | 153, 2048 |
| BmgT120I | GGNCC | 2 cut(s) | 153, 2048 |
| BmiI | GGNNCC | 2 cut(s) | 1036, 1444 |
| BmrFI | CCNGG | 2 cut(s) | 786, 2562 |
| BmsI | GCATC | 4 cut(s) | 322, 509, 744, 1273 |
| BpiI | GAAGAC | 1 cut(s) | 1220 |
| Bpu10I | CCTNAGC | 2 cut(s) | 414, 636 |
| Bpu1102I | GCTNAGC | 1 cut(s) | 1992 |
| Bpu14I | TTCGAA | 1 cut(s) | 2275 |
| BpuEI | CTTGAG | 5 cut(s) | 1423, 1494, 1923, 2690, 2792 |
| BsaAI | YACGTR | 1 cut(s) | 1530 |
| BsaBI | GATNNNNATC | 3 cut(s) | 1254, 1678, 1794 |
| BsaI | GGTCTC | 2 cut(s) | 559, 1512 |
| BsaJI | CCNNGG | 5 cut(s) | 264, 785, 811, 2223, 2560 |
| Bse1I | ACTGG | 2 cut(s) | 1997, 2782 |
| Bse3DI | GCAATG | 1 cut(s) | 2701 |
| Bse8I | GATNNNNATC | 3 cut(s) | 1254, 1678, 1794 |
| BseBI | CCWGG | 2 cut(s) | 786, 2562 |
| BseDI | CCNNGG | 5 cut(s) | 264, 785, 811, 2223, 2560 |
| BseGI | GGATG | 3 cut(s) | 1279, 1747, 2566 |
| BseJI | GATNNNNATC | 3 cut(s) | 1254, 1678, 1794 |
| BseMI | GCAATG | 1 cut(s) | 2701 |
| BseNI | ACTGG | 2 cut(s) | 1997, 2782 |
| BseRI | GAGGAG | 3 cut(s) | 431, 780, 2625 |
| BseSI | GKGCMC | 1 cut(s) | 2158 |
| BseXI | GCAGC | 2 cut(s) | 718, 1619 |
| BseYI | CCCAGC | 1 cut(s) | 5 |
| BsgI | GTGCAG | 1 cut(s) | 1618 |
| BshFI | GGCC | 1 cut(s) | 2485 |
| BshNI | GGYRCC | 2 cut(s) | 1034, 1442 |
| BsiHKAI | GWGCWC | 3 cut(s) | 1409, 2158, 2751 |
| BsmAI | GTCTC | 5 cut(s) | 559, 1512, 1617, 1907, 2347 |
| BsmI | GAATGC | 2 cut(s) | 1246, 2515 |
| BsnI | GGCC | 1 cut(s) | 2485 |
| Bso31I | GGTCTC | 2 cut(s) | 559, 1512 |
| Bsp119I | TTCGAA | 1 cut(s) | 2275 |
| Bsp1286I | GDGCHC | 3 cut(s) | 1409, 2158, 2751 |
| Bsp1407I | TGTACA | 1 cut(s) | 552 |
| Bsp143I | GATC | 7 cut(s) | 232, 1198, 1249, 1606, 2527, 2581, 2796 |
| Bsp1720I | GCTNAGC | 1 cut(s) | 1992 |
| Bsp19I | CCATGG | 2 cut(s) | 264, 2223 |
| BspANI | GGCC | 1 cut(s) | 2485 |
| BspHI | TCATGA | 2 cut(s) | 2170, 2578 |
| BspLI | GGNNCC | 2 cut(s) | 1036, 1444 |
| BspMAI | CTGCAG | 2 cut(s) | 2014, 2027 |
| BspPI | GGATC | 3 cut(s) | 240, 1206, 2576 |
| BspT104I | TTCGAA | 1 cut(s) | 2275 |
| BspT107I | GGYRCC | 2 cut(s) | 1034, 1442 |
| BspTI | CTTAAG | 1 cut(s) | 448 |
| BspTNI | GGTCTC | 2 cut(s) | 559, 1512 |
| BsrDI | GCAATG | 1 cut(s) | 2701 |
| BsrGI | TGTACA | 1 cut(s) | 552 |
| BsrI | ACTGG | 2 cut(s) | 1997, 2782 |
| BssECI | CCNNGG | 5 cut(s) | 264, 785, 811, 2223, 2560 |
| BssMI | GATC | 7 cut(s) | 232, 1198, 1249, 1606, 2527, 2581, 2796 |
| BssSI | CACGAG | 3 cut(s) | 2037, 2376, 2637 |
| BssT1I | CCWWGG | 3 cut(s) | 264, 811, 2223 |
| Bst2BI | CACGAG | 3 cut(s) | 2037, 2376, 2637 |
| Bst2UI | CCWGG | 2 cut(s) | 786, 2562 |
| Bst4CI | ACNGT | 3 cut(s) | 778, 1960, 2446 |
| Bst6I | CTCTTC | 5 cut(s) | 208, 2134, 2532, 2710, 2787 |
| BstAFI | CTTAAG | 1 cut(s) | 448 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 2818 |
| BstAUI | TGTACA | 1 cut(s) | 552 |
| BstBAI | YACGTR | 1 cut(s) | 1530 |
| BstBI | TTCGAA | 1 cut(s) | 2275 |
| BstC8I | GCNNGC | 3 cut(s) | 445, 2220, 2600 |
| BstDSI | CCRYGG | 2 cut(s) | 264, 2223 |
| BstF5I | GGATG | 3 cut(s) | 1279, 1747, 2566 |
| BstKTI | GATC | 7 cut(s) | 235, 1201, 1252, 1609, 2530, 2584, 2799 |
| BstMAI | GTCTC | 5 cut(s) | 559, 1512, 1617, 1907, 2347 |
| BstMBI | GATC | 7 cut(s) | 232, 1198, 1249, 1606, 2527, 2581, 2796 |
| BstMWI | GCNNNNNNNGC | 4 cut(s) | 1413, 2429, 2648, 2818 |
| BstNI | CCWGG | 2 cut(s) | 786, 2562 |
| BstNSI | RCATGY | 2 cut(s) | 608, 1393 |
| BstSCI | CCNGG | 2 cut(s) | 784, 2560 |
| BstSFI | CTRYAG | 3 cut(s) | 2010, 2023, 2298 |
| BstSLI | GKGCMC | 1 cut(s) | 2158 |
| BstV1I | GCAGC | 2 cut(s) | 718, 1619 |
| BstV2I | GAAGAC | 1 cut(s) | 1220 |
| BstX2I | RGATCY | 1 cut(s) | 1198 |
| BstYI | RGATCY | 1 cut(s) | 1198 |
| BsuRI | GGCC | 1 cut(s) | 2485 |
| BtgI | CCRYGG | 2 cut(s) | 264, 2223 |
| BtsCI | GGATG | 3 cut(s) | 1279, 1747, 2566 |
| Cac8I | GCNNGC | 3 cut(s) | 445, 2220, 2600 |
| CaiI | CAGNNNCTG | 2 cut(s) | 842, 1973 |
| CciI | TCATGA | 2 cut(s) | 2170, 2578 |
| Cfr13I | GGNCC | 2 cut(s) | 153, 2048 |
| Csp6I | GTAC | 7 cut(s) | 553, 873, 1443, 1491, 2166, 2442, 2666 |
| CviQI | GTAC | 7 cut(s) | 553, 873, 1443, 1491, 2166, 2442, 2666 |
| DpnI | GATC | 7 cut(s) | 234, 1200, 1251, 1608, 2529, 2583, 2798 |
| DpnII | GATC | 7 cut(s) | 232, 1198, 1249, 1606, 2527, 2581, 2796 |
| Eam1104I | CTCTTC | 5 cut(s) | 208, 2134, 2532, 2710, 2787 |
| EarI | CTCTTC | 5 cut(s) | 208, 2134, 2532, 2710, 2787 |
| Eco130I | CCWWGG | 3 cut(s) | 264, 811, 2223 |
| Eco31I | GGTCTC | 2 cut(s) | 559, 1512 |
| Eco32I | GATATC | 1 cut(s) | 2093 |
| Eco47I | GGWCC | 2 cut(s) | 153, 2048 |
| Eco57I | CTGAAG | 2 cut(s) | 1269, 2115 |
| EcoO109I | RGGNCCY | 1 cut(s) | 2048 |
| EcoRI | GAATTC | 1 cut(s) | 2277 |
| EcoRII | CCWGG | 2 cut(s) | 784, 2560 |
| EcoRV | GATATC | 1 cut(s) | 2093 |
| EcoT14I | CCWWGG | 3 cut(s) | 264, 811, 2223 |
| EcoT22I | ATGCAT | 3 cut(s) | 315, 502, 759 |
| ErhI | CCWWGG | 3 cut(s) | 264, 811, 2223 |
| FalI | AAGNNNNNCTT | 4 cut(s) | 1503, 1535, 2801, 2833 |
| FauNDI | CATATG | 4 cut(s) | 517, 1786, 2097, 2395 |
| FblI | GTMKAC | 1 cut(s) | 2403 |
| Fnu4HI | GCNGC | 2 cut(s) | 732, 1633 |
| FokI | GGATG | 3 cut(s) | 1266, 1754, 2553 |
| Fsp4HI | GCNGC | 2 cut(s) | 732, 1633 |
| GluI | GCNGC | 2 cut(s) | 732, 1633 |
| GsaI | CCCAGC | 1 cut(s) | 9 |
| HaeIII | GGCC | 1 cut(s) | 2485 |
| HincII | GTYRAC | 1 cut(s) | 2473 |
| HindII | GTYRAC | 1 cut(s) | 2473 |
| HindIII | AAGCTT | 5 cut(s) | 195, 445, 864, 2327, 2600 |
| HinfI | GANTC | 8 cut(s) | 59, 215, 302, 935, 1469, 1762, 1790, 2702 |
| HphI | GGTGA | 6 cut(s) | 688, 1198, 1235, 1566, 2537, 2792 |
| Hpy166II | GTNNAC | 4 cut(s) | 553, 2156, 2404, 2473 |
| Hpy188I | TCNGA | 9 cut(s) | 52, 301, 457, 505, 1288, 1360, 1816, 1912, 2721 |
| Hpy8I | GTNNAC | 4 cut(s) | 553, 2156, 2404, 2473 |
| HpyAV | CCTTC | 7 cut(s) | 144, 656, 745, 1014, 1220, 1293, 2043 |
| HpyCH4III | ACNGT | 3 cut(s) | 778, 1960, 2446 |
| HpyCH4IV | ACGT | 4 cut(s) | 76, 1151, 1529, 2757 |
| HpyF10VI | GCNNNNNNNGC | 4 cut(s) | 1413, 2429, 2648, 2818 |
| HpySE526I | ACGT | 4 cut(s) | 76, 1151, 1529, 2757 |
| KpnI | GGTACC | 1 cut(s) | 1446 |
| Kzo9I | GATC | 7 cut(s) | 232, 1198, 1249, 1606, 2527, 2581, 2796 |
| LmnI | GCTCC | 3 cut(s) | 266, 441, 941 |
| Lsp1109I | GCAGC | 2 cut(s) | 718, 1619 |
| LweI | GCATC | 4 cut(s) | 322, 509, 744, 1273 |
| MaeII | ACGT | 4 cut(s) | 76, 1151, 1529, 2757 |
| MaeIII | GTNAC | 6 cut(s) | 130, 1392, 1759, 1954, 2773, 2780 |
| MalI | GATC | 7 cut(s) | 234, 1200, 1251, 1608, 2529, 2583, 2798 |
| MboI | GATC | 7 cut(s) | 232, 1198, 1249, 1606, 2527, 2581, 2796 |
| MflI | RGATCY | 1 cut(s) | 1198 |
| MhlI | GDGCHC | 3 cut(s) | 1409, 2158, 2751 |
| MlyI | GAGTC | 5 cut(s) | 68, 929, 1463, 1756, 2696 |
| MmeI | TCCRAC | 2 cut(s) | 580, 1114 |
| Mph1103I | ATGCAT | 3 cut(s) | 315, 502, 759 |
| MroXI | GAANNNNTTC | 2 cut(s) | 101, 2032 |
| MseI | TTAA | 8 cut(s) | 404, 449, 716, 1619, 1883, 2150, 2624, 2768 |
| MslI | CAYNNNNRTG | 2 cut(s) | 2253, 2337 |
| MspCI | CTTAAG | 1 cut(s) | 448 |
| MspR9I | CCNGG | 2 cut(s) | 786, 2562 |
| Mva1269I | GAATGC | 2 cut(s) | 1246, 2515 |
| MvaI | CCWGG | 2 cut(s) | 786, 2562 |
| MwoI | GCNNNNNNNGC | 4 cut(s) | 1413, 2429, 2648, 2818 |
| NcoI | CCATGG | 2 cut(s) | 264, 2223 |
| NdeI | CATATG | 4 cut(s) | 517, 1786, 2097, 2395 |
| NdeII | GATC | 7 cut(s) | 232, 1198, 1249, 1606, 2527, 2581, 2796 |
| NlaIV | GGNNCC | 2 cut(s) | 1036, 1444 |
| NmuCI | GTSAC | 4 cut(s) | 1392, 1759, 2773, 2780 |
| NsiI | ATGCAT | 3 cut(s) | 315, 502, 759 |
| NspI | RCATGY | 2 cut(s) | 608, 1393 |
| NspV | TTCGAA | 1 cut(s) | 2275 |
| PagI | TCATGA | 2 cut(s) | 2170, 2578 |
| PciI | ACATGT | 2 cut(s) | 604, 1389 |
| PctI | GAATGC | 2 cut(s) | 1246, 2515 |
| PdmI | GAANNNNTTC | 2 cut(s) | 101, 2032 |
| PfeI | GAWTC | 3 cut(s) | 215, 302, 1790 |
| PkrI | GCNGC | 2 cut(s) | 733, 1634 |
| PleI | GAGTC | 5 cut(s) | 67, 929, 1463, 1756, 2696 |
| PpsI | GAGTC | 5 cut(s) | 67, 929, 1463, 1756, 2696 |
| Ppu21I | YACGTR | 1 cut(s) | 1530 |
| PpuMI | RGGWCCY | 1 cut(s) | 2048 |
| PscI | ACATGT | 2 cut(s) | 604, 1389 |
| PsiI | TTATAA | 4 cut(s) | 344, 1698, 1707, 2118 |
| Psp1406I | AACGTT | 1 cut(s) | 1151 |
| Psp5II | RGGWCCY | 1 cut(s) | 2048 |
| Psp6I | CCWGG | 2 cut(s) | 784, 2560 |
| PspFI | CCCAGC | 1 cut(s) | 5 |
| PspGI | CCWGG | 2 cut(s) | 784, 2560 |
| PspN4I | GGNNCC | 2 cut(s) | 1036, 1444 |
| PspPI | GGNCC | 2 cut(s) | 153, 2048 |
| PspPPI | RGGWCCY | 1 cut(s) | 2048 |
| PstI | CTGCAG | 2 cut(s) | 2014, 2027 |
| PstNI | CAGNNNCTG | 2 cut(s) | 842, 1973 |
| PsuI | RGATCY | 1 cut(s) | 1198 |
| RsaI | GTAC | 7 cut(s) | 554, 874, 1444, 1492, 2167, 2443, 2667 |
| RsaNI | GTAC | 7 cut(s) | 553, 873, 1443, 1491, 2166, 2442, 2666 |
| RseI | CAYNNNNRTG | 2 cut(s) | 2253, 2337 |
| SaqAI | TTAA | 8 cut(s) | 404, 449, 716, 1619, 1883, 2150, 2624, 2768 |
| SatI | GCNGC | 2 cut(s) | 732, 1633 |
| Sau3AI | GATC | 7 cut(s) | 232, 1198, 1249, 1606, 2527, 2581, 2796 |
| Sau96I | GGNCC | 2 cut(s) | 153, 2048 |
| ScaI | AGTACT | 2 cut(s) | 2443, 2667 |
| SchI | GAGTC | 5 cut(s) | 68, 929, 1463, 1756, 2696 |
| ScrFI | CCNGG | 2 cut(s) | 786, 2562 |
| SduI | GDGCHC | 3 cut(s) | 1409, 2158, 2751 |
| SfaNI | GCATC | 4 cut(s) | 322, 509, 744, 1273 |
| SfcI | CTRYAG | 3 cut(s) | 2010, 2023, 2298 |
| SfuI | TTCGAA | 1 cut(s) | 2275 |
| SinI | GGWCC | 2 cut(s) | 153, 2048 |
| SmiMI | CAYNNNNRTG | 2 cut(s) | 2253, 2337 |
| SmlI | CTYRAG | 6 cut(s) | 448, 1402, 1509, 1938, 2669, 2807 |
| SmoI | CTYRAG | 6 cut(s) | 448, 1402, 1509, 1938, 2669, 2807 |
| SspI | AATATT | 1 cut(s) | 2803 |
| StyD4I | CCNGG | 2 cut(s) | 784, 2560 |
| StyI | CCWWGG | 3 cut(s) | 264, 811, 2223 |
| TaaI | ACNGT | 3 cut(s) | 778, 1960, 2446 |
| TaiI | ACGT | 4 cut(s) | 79, 1154, 1532, 2760 |
| TaqI | TCGA | 2 cut(s) | 387, 2275 |
| TatI | WGTACW | 3 cut(s) | 552, 2441, 2665 |
| TfiI | GAWTC | 3 cut(s) | 215, 302, 1790 |
| Tru1I | TTAA | 8 cut(s) | 404, 449, 716, 1619, 1883, 2150, 2624, 2768 |
| Tru9I | TTAA | 8 cut(s) | 404, 449, 716, 1619, 1883, 2150, 2624, 2768 |
| TseFI | GTSAC | 4 cut(s) | 1392, 1759, 2773, 2780 |
| TseI | GCWGC | 2 cut(s) | 731, 1632 |
| Tsp45I | GTSAC | 4 cut(s) | 1392, 1759, 2773, 2780 |
| Vha464I | CTTAAG | 1 cut(s) | 448 |
| VneI | GTGCAC | 1 cut(s) | 2154 |
| VpaK11BI | GGWCC | 2 cut(s) | 153, 2048 |
| XapI | RAATTY | 6 cut(s) | 285, 691, 818, 1499, 2123, 2277 |
| XceI | RCATGY | 2 cut(s) | 608, 1393 |
| XmiI | GTMKAC | 1 cut(s) | 2403 |
| XmnI | GAANNNNTTC | 2 cut(s) | 101, 2032 |
| ZrmI | AGTACT | 2 cut(s) | 2443, 2667 |
| Zsp2I | ATGCAT | 3 cut(s) | 315, 502, 759 |