transposition, RNA-mediated
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| Retrotran_gag_2 | PF14223 | 48 - 169 | 1.6e-16 | gag-polypeptide of LTR copia-type |
| Pol_BBD | PF22936 | 555 - 629 | 6.2e-21 | Pol polyprotein, beta-barrel domain |
| rve | PF00665 | 630 - 721 | 5.9e-09 | Integrase core domain |
| SH3_retrovirus | PF25597 | 777 - 833 | 6.6e-14 | Retroviral polymerase SH3-like domain |
| RVT_2 | PF07727 | 970 - 1212 | 6.5e-73 | Reverse transcriptase (RNA-dependent DNA polymerase) |
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AanI | TTATAA | 2 cut(s) | 765, 2439 |
| AasI | GACNNNNNNGTC | 2 cut(s) | 1356, 2393 |
| Acc36I | ACCTGC | 2 cut(s) | 3220, 3881 |
| AccI | GTMKAC | 1 cut(s) | 1388 |
| AciI | CCGC | 3 cut(s) | 1743, 2162, 3007 |
| AclWI | GGATC | 4 cut(s) | 996, 1189, 2673, 3221 |
| AcuI | CTGAAG | 3 cut(s) | 2580, 2592, 3423 |
| AfaI | GTAC | 5 cut(s) | 2535, 2658, 3722, 3863, 4034 |
| AfiI | CCNNNNNNNGG | 4 cut(s) | 838, 2292, 3087, 4243 |
| AflII | CTTAAG | 1 cut(s) | 3257 |
| AflIII | ACRYGT | 2 cut(s) | 1588, 1616 |
| AhlI | ACTAGT | 2 cut(s) | 3641, 4136 |
| AjnI | CCWGG | 1 cut(s) | 1807 |
| AleI | CACNNNNGTG | 2 cut(s) | 1326, 1961 |
| Alw21I | GWGCWC | 4 cut(s) | 388, 906, 2502, 4343 |
| AlwI | GGATC | 4 cut(s) | 996, 1189, 2673, 3221 |
| Ama87I | CYCGRG | 1 cut(s) | 3943 |
| AoxI | GGCC | 1 cut(s) | 2575 |
| ApeKI | GCWGC | 4 cut(s) | 2567, 2650, 3611, 4040 |
| ArsI | GACNNNNNNTTYG | 2 cut(s) | 3410, 3442 |
| AseI | ATTAAT | 1 cut(s) | 2472 |
| Asp700I | GAANNNNTTC | 7 cut(s) | 186, 692, 1540, 2452, 3099, 3643, 4251 |
| AspS9I | GGNCC | 2 cut(s) | 4, 1376 |
| AsuHPI | GGTGA | 9 cut(s) | 229, 353, 710, 1313, 1667, 1712, 1772, 1975, 2702 |
| AsuNHI | GCTAGC | 2 cut(s) | 916, 3731 |
| AvaI | CYCGRG | 1 cut(s) | 3943 |
| AvaII | GGWCC | 2 cut(s) | 4, 1376 |
| AxyI | CCTNAGG | 1 cut(s) | 3789 |
| BanII | GRGCYC | 1 cut(s) | 388 |
| BarI | GAAGNNNNNNTAC | 2 cut(s) | 1642, 1674 |
| BbsI | GAAGAC | 4 cut(s) | 558, 660, 1556, 3098 |
| Bbv12I | GWGCWC | 4 cut(s) | 388, 906, 2502, 4343 |
| BbvI | GCAGC | 4 cut(s) | 2554, 2662, 3598, 4052 |
| BccI | CCATC | 7 cut(s) | 44, 79, 2294, 2455, 2696, 3243, 3542 |
| BcgI | CGANNNNNNTGC | 2 cut(s) | 4019, 4053 |
| BciT130I | CCWGG | 1 cut(s) | 1809 |
| BciVI | GTATCC | 1 cut(s) | 1823 |
| BclI | TGATCA | 3 cut(s) | 2074, 2527, 3682 |
| BcuI | ACTAGT | 2 cut(s) | 3641, 4136 |
| BfmI | CTRYAG | 2 cut(s) | 2344, 3213 |
| BfrI | CTTAAG | 1 cut(s) | 3257 |
| BfuAI | ACCTGC | 2 cut(s) | 3220, 3881 |
| BfuI | GTATCC | 1 cut(s) | 1823 |
| BglII | AGATCT | 1 cut(s) | 436 |
| BisI | GCNGC | 4 cut(s) | 2568, 2651, 3612, 4041 |
| BlpI | GCTNAGC | 1 cut(s) | 408 |
| BlsI | GCNGC | 4 cut(s) | 2569, 2652, 3613, 4042 |
| Bme1390I | CCNGG | 1 cut(s) | 1809 |
| Bme18I | GGWCC | 2 cut(s) | 4, 1376 |
| BmeT110I | CYCGRG | 1 cut(s) | 3943 |
| BmgT120I | GGNCC | 2 cut(s) | 4, 1376 |
| BmiI | GGNNCC | 2 cut(s) | 2151, 2928 |
| BmrFI | CCNGG | 1 cut(s) | 1809 |
| BmsI | GCATC | 8 cut(s) | 631, 1978, 2365, 2785, 2802, 3598, 3828, 4216 |
| BmtI | GCTAGC | 2 cut(s) | 920, 3735 |
| BpiI | GAAGAC | 4 cut(s) | 558, 660, 1556, 3098 |
| BplI | GAGNNNNNCTC | 4 cut(s) | 905, 937, 2024, 2056 |
| BpmI | CTGGAG | 1 cut(s) | 1275 |
| Bpu1102I | GCTNAGC | 1 cut(s) | 408 |
| BpuEI | CTTGAG | 8 cut(s) | 87, 417, 1137, 3015, 3027, 3387, 4089, 4259 |
| Bsa29I | ATCGAT | 1 cut(s) | 636 |
| BsaBI | GATNNNNATC | 1 cut(s) | 567 |
| BsaI | GGTCTC | 1 cut(s) | 3557 |
| BsaJI | CCNNGG | 3 cut(s) | 909, 3633, 3942 |
| BsaWI | WCCGGW | 1 cut(s) | 2935 |
| BsaXI | ACNNNNNCTCC | 4 cut(s) | 793, 823, 3535, 3565 |
| Bsc4I | CCNNNNNNNGG | 4 cut(s) | 838, 2292, 3087, 4243 |
| Bse1I | ACTGG | 4 cut(s) | 1715, 2630, 2647, 3673 |
| Bse21I | CCTNAGG | 1 cut(s) | 3789 |
| Bse3DI | GCAATG | 5 cut(s) | 1608, 2278, 2766, 3117, 4035 |
| Bse8I | GATNNNNATC | 1 cut(s) | 567 |
| BseBI | CCWGG | 1 cut(s) | 1809 |
| BseCI | ATCGAT | 1 cut(s) | 636 |
| BseDI | CCNNGG | 3 cut(s) | 909, 3633, 3942 |
| BseJI | GATNNNNATC | 1 cut(s) | 567 |
| BseLI | CCNNNNNNNGG | 4 cut(s) | 838, 2292, 3087, 4243 |
| BseMI | GCAATG | 5 cut(s) | 1608, 2278, 2766, 3117, 4035 |
| BseMII | CTCAG | 5 cut(s) | 836, 894, 966, 1381, 1907 |
| BseNI | ACTGG | 4 cut(s) | 1715, 2630, 2647, 3673 |
| BseRI | GAGGAG | 3 cut(s) | 27, 926, 1255 |
| BseXI | GCAGC | 4 cut(s) | 2554, 2662, 3598, 4052 |
| BshFI | GGCC | 1 cut(s) | 2577 |
| BshVI | ATCGAT | 1 cut(s) | 636 |
| BsiHKAI | GWGCWC | 4 cut(s) | 388, 906, 2502, 4343 |
| BsiHKCI | CYCGRG | 1 cut(s) | 3943 |
| BsiSI | CCGG | 1 cut(s) | 2936 |
| BslI | CCNNNNNNNGG | 4 cut(s) | 838, 2292, 3087, 4243 |
| BsmI | GAATGC | 1 cut(s) | 1087 |
| BsnI | GGCC | 1 cut(s) | 2577 |
| Bso31I | GGTCTC | 1 cut(s) | 3557 |
| BsoBI | CYCGRG | 1 cut(s) | 3943 |
| Bsp1286I | GDGCHC | 4 cut(s) | 388, 906, 2502, 4343 |
| Bsp1407I | TGTACA | 1 cut(s) | 3861 |
| Bsp1720I | GCTNAGC | 1 cut(s) | 408 |
| Bsp19I | CCATGG | 1 cut(s) | 3633 |
| BspACI | CCGC | 3 cut(s) | 1743, 2162, 3007 |
| BspANI | GGCC | 1 cut(s) | 2577 |
| BspCNI | CTCAG | 5 cut(s) | 835, 893, 967, 1380, 1908 |
| BspDI | ATCGAT | 1 cut(s) | 636 |
| BspHI | TCATGA | 3 cut(s) | 199, 1399, 3471 |
| BspLI | GGNNCC | 2 cut(s) | 2151, 2928 |
| BspMAI | CTGCAG | 1 cut(s) | 3217 |
| BspMI | ACCTGC | 2 cut(s) | 3220, 3881 |
| BspOI | GCTAGC | 2 cut(s) | 920, 3735 |
| BspPI | GGATC | 4 cut(s) | 996, 1189, 2673, 3221 |
| BspQI | GCTCTTC | 2 cut(s) | 393, 591 |
| BspTI | CTTAAG | 1 cut(s) | 3257 |
| BspTNI | GGTCTC | 1 cut(s) | 3557 |
| BsrDI | GCAATG | 5 cut(s) | 1608, 2278, 2766, 3117, 4035 |
| BsrGI | TGTACA | 1 cut(s) | 3861 |
| BsrI | ACTGG | 4 cut(s) | 1715, 2630, 2647, 3673 |
| BssECI | CCNNGG | 3 cut(s) | 909, 3633, 3942 |
| BssT1I | CCWWGG | 1 cut(s) | 3633 |
| Bst2UI | CCWGG | 1 cut(s) | 1809 |
| Bst4CI | ACNGT | 4 cut(s) | 8, 600, 4004, 4348 |
| Bst6I | CTCTTC | 9 cut(s) | 393, 591, 831, 1645, 1890, 2047, 2209, 2680, 2947 |
| BstAFI | CTTAAG | 1 cut(s) | 3257 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 2277 |
| BstAUI | TGTACA | 1 cut(s) | 3861 |
| BstC8I | GCNNGC | 3 cut(s) | 918, 2278, 3733 |
| BstDSI | CCRYGG | 1 cut(s) | 3633 |
| BstMWI | GCNNNNNNNGC | 9 cut(s) | 749, 857, 1634, 2240, 2277, 2846, 3083, 3293, 3617 |
| BstNI | CCWGG | 1 cut(s) | 1809 |
| BstNSI | RCATGY | 3 cut(s) | 1592, 1620, 3126 |
| BstSCI | CCNGG | 1 cut(s) | 1807 |
| BstSFI | CTRYAG | 2 cut(s) | 2344, 3213 |
| BstV1I | GCAGC | 4 cut(s) | 2554, 2662, 3598, 4052 |
| BstV2I | GAAGAC | 4 cut(s) | 558, 660, 1556, 3098 |
| BstX2I | RGATCY | 3 cut(s) | 436, 1181, 3226 |
| BstYI | RGATCY | 3 cut(s) | 436, 1181, 3226 |
| Bsu15I | ATCGAT | 1 cut(s) | 636 |
| Bsu36I | CCTNAGG | 1 cut(s) | 3789 |
| BsuI | GTATCC | 1 cut(s) | 1823 |
| BsuRI | GGCC | 1 cut(s) | 2577 |
| BsuTUI | ATCGAT | 1 cut(s) | 636 |
| BtgI | CCRYGG | 1 cut(s) | 3633 |
| BtsIMutI | CAGTG | 1 cut(s) | 4257 |
| BveI | ACCTGC | 2 cut(s) | 3220, 3881 |
| Cac8I | GCNNGC | 3 cut(s) | 918, 2278, 3733 |
| CciI | TCATGA | 3 cut(s) | 199, 1399, 3471 |
| Cfr13I | GGNCC | 2 cut(s) | 4, 1376 |
| ClaI | ATCGAT | 1 cut(s) | 636 |
| Csp6I | GTAC | 5 cut(s) | 2534, 2657, 3721, 3862, 4033 |
| CspCI | CAANNNNNGTGG | 2 cut(s) | 1764, 1799 |
| CviQI | GTAC | 5 cut(s) | 2534, 2657, 3721, 3862, 4033 |
| DraI | TTTAAA | 4 cut(s) | 790, 1516, 1824, 3174 |
| DrdI | GACNNNNNNGTC | 2 cut(s) | 1356, 2393 |
| DseDI | GACNNNNNNGTC | 2 cut(s) | 1356, 2393 |
| Eam1104I | CTCTTC | 9 cut(s) | 393, 591, 831, 1645, 1890, 2047, 2209, 2680, 2947 |
| EarI | CTCTTC | 9 cut(s) | 393, 591, 831, 1645, 1890, 2047, 2209, 2680, 2947 |
| Ecl136II | GAGCTC | 1 cut(s) | 386 |
| Eco130I | CCWWGG | 1 cut(s) | 3633 |
| Eco24I | GRGCYC | 1 cut(s) | 388 |
| Eco31I | GGTCTC | 1 cut(s) | 3557 |
| Eco32I | GATATC | 2 cut(s) | 3776, 4202 |
| Eco47I | GGWCC | 2 cut(s) | 4, 1376 |
| Eco53kI | GAGCTC | 1 cut(s) | 386 |
| Eco57I | CTGAAG | 3 cut(s) | 2580, 2592, 3423 |
| Eco81I | CCTNAGG | 1 cut(s) | 3789 |
| Eco88I | CYCGRG | 1 cut(s) | 3943 |
| EcoICRI | GAGCTC | 1 cut(s) | 386 |
| EcoRI | GAATTC | 1 cut(s) | 3458 |
| EcoRII | CCWGG | 1 cut(s) | 1807 |
| EcoRV | GATATC | 2 cut(s) | 3776, 4202 |
| EcoT14I | CCWWGG | 1 cut(s) | 3633 |
| EcoT22I | ATGCAT | 2 cut(s) | 1045, 2057 |
| EcoT38I | GRGCYC | 1 cut(s) | 388 |
| ErhI | CCWWGG | 1 cut(s) | 3633 |
| FalI | AAGNNNNNCTT | 4 cut(s) | 1845, 1877, 3006, 3038 |
| FauI | CCCGC | 1 cut(s) | 3014 |
| FbaI | TGATCA | 3 cut(s) | 2074, 2527, 3682 |
| FblI | GTMKAC | 1 cut(s) | 1388 |
| Fnu4HI | GCNGC | 4 cut(s) | 2568, 2651, 3612, 4041 |
| FriOI | GRGCYC | 1 cut(s) | 388 |
| Fsp4HI | GCNGC | 4 cut(s) | 2568, 2651, 3612, 4041 |
| GluI | GCNGC | 4 cut(s) | 2568, 2651, 3612, 4041 |
| GsuI | CTGGAG | 1 cut(s) | 1275 |
| HaeIII | GGCC | 1 cut(s) | 2577 |
| HapII | CCGG | 1 cut(s) | 2936 |
| HindIII | AAGCTT | 3 cut(s) | 171, 2592, 3712 |
| HpaII | CCGG | 1 cut(s) | 2936 |
| HphI | GGTGA | 9 cut(s) | 229, 353, 710, 1313, 1667, 1712, 1772, 1975, 2702 |
| Hpy166II | GTNNAC | 6 cut(s) | 1389, 1956, 2635, 3862, 3864, 4284 |
| Hpy8I | GTNNAC | 6 cut(s) | 1389, 1956, 2635, 3862, 3864, 4284 |
| HpyCH4III | ACNGT | 4 cut(s) | 8, 600, 4004, 4348 |
| HpyF10VI | GCNNNNNNNGC | 9 cut(s) | 749, 857, 1634, 2240, 2277, 2846, 3083, 3293, 3617 |
| Ksp22I | TGATCA | 3 cut(s) | 2074, 2527, 3682 |
| LguI | GCTCTTC | 2 cut(s) | 393, 591 |
| LmnI | GCTCC | 4 cut(s) | 913, 1268, 1810, 2155 |
| Lsp1109I | GCAGC | 4 cut(s) | 2554, 2662, 3598, 4052 |
| LweI | GCATC | 8 cut(s) | 631, 1978, 2365, 2785, 2802, 3598, 3828, 4216 |
| MaeIII | GTNAC | 9 cut(s) | 206, 316, 1319, 1750, 1760, 1798, 2336, 2384, 4127 |
| MfeI | CAATTG | 6 cut(s) | 522, 1176, 1877, 2493, 3351, 4268 |
| MflI | RGATCY | 3 cut(s) | 436, 1181, 3226 |
| MhlI | GDGCHC | 4 cut(s) | 388, 906, 2502, 4343 |
| MmeI | TCCRAC | 4 cut(s) | 185, 488, 852, 3559 |
| Mph1103I | ATGCAT | 2 cut(s) | 1045, 2057 |
| MroXI | GAANNNNTTC | 7 cut(s) | 186, 692, 1540, 2452, 3099, 3643, 4251 |
| MslI | CAYNNNNRTG | 3 cut(s) | 1326, 1961, 4061 |
| MspA1I | CMGCKG | 2 cut(s) | 1743, 4043 |
| MspCI | CTTAAG | 1 cut(s) | 3257 |
| MspI | CCGG | 1 cut(s) | 2936 |
| MspR9I | CCNGG | 1 cut(s) | 1809 |
| MunI | CAATTG | 6 cut(s) | 522, 1176, 1877, 2493, 3351, 4268 |
| Mva1269I | GAATGC | 1 cut(s) | 1087 |
| MvaI | CCWGG | 1 cut(s) | 1809 |
| MwoI | GCNNNNNNNGC | 9 cut(s) | 749, 857, 1634, 2240, 2277, 2846, 3083, 3293, 3617 |
| NcoI | CCATGG | 1 cut(s) | 3633 |
| NheI | GCTAGC | 2 cut(s) | 916, 3731 |
| NlaIV | GGNNCC | 2 cut(s) | 2151, 2928 |
| NmeAIII | GCCGAG | 2 cut(s) | 2126, 4054 |
| NmuCI | GTSAC | 5 cut(s) | 1319, 1750, 1760, 2384, 4127 |
| NsiI | ATGCAT | 2 cut(s) | 1045, 2057 |
| NspI | RCATGY | 3 cut(s) | 1592, 1620, 3126 |
| OliI | CACNNNNGTG | 2 cut(s) | 1326, 1961 |
| PagI | TCATGA | 3 cut(s) | 199, 1399, 3471 |
| PciI | ACATGT | 2 cut(s) | 1588, 1616 |
| PciSI | GCTCTTC | 2 cut(s) | 393, 591 |
| PctI | GAATGC | 1 cut(s) | 1087 |
| PdmI | GAANNNNTTC | 7 cut(s) | 186, 692, 1540, 2452, 3099, 3643, 4251 |
| PkrI | GCNGC | 4 cut(s) | 2569, 2652, 3613, 4042 |
| PscI | ACATGT | 2 cut(s) | 1588, 1616 |
| PshBI | ATTAAT | 1 cut(s) | 2472 |
| PsiI | TTATAA | 2 cut(s) | 765, 2439 |
| Psp124BI | GAGCTC | 1 cut(s) | 388 |
| Psp6I | CCWGG | 1 cut(s) | 1807 |
| PspGI | CCWGG | 1 cut(s) | 1807 |
| PspN4I | GGNNCC | 2 cut(s) | 2151, 2928 |
| PspPI | GGNCC | 2 cut(s) | 4, 1376 |
| PstI | CTGCAG | 1 cut(s) | 3217 |
| PsuI | RGATCY | 3 cut(s) | 436, 1181, 3226 |
| PvuII | CAGCTG | 1 cut(s) | 4043 |
| RsaI | GTAC | 5 cut(s) | 2535, 2658, 3722, 3863, 4034 |
| RsaNI | GTAC | 5 cut(s) | 2534, 2657, 3721, 3862, 4033 |
| RseI | CAYNNNNRTG | 3 cut(s) | 1326, 1961, 4061 |
| SacI | GAGCTC | 1 cut(s) | 388 |
| SapI | GCTCTTC | 2 cut(s) | 393, 591 |
| SatI | GCNGC | 4 cut(s) | 2568, 2651, 3612, 4041 |
| Sau96I | GGNCC | 2 cut(s) | 4, 1376 |
| SbfI | CCTGCAGG | 1 cut(s) | 3217 |
| ScrFI | CCNGG | 1 cut(s) | 1809 |
| SdaI | CCTGCAGG | 1 cut(s) | 3217 |
| SduI | GDGCHC | 4 cut(s) | 388, 906, 2502, 4343 |
| SfaNI | GCATC | 8 cut(s) | 631, 1978, 2365, 2785, 2802, 3598, 3828, 4216 |
| SfcI | CTRYAG | 2 cut(s) | 2344, 3213 |
| SinI | GGWCC | 2 cut(s) | 4, 1376 |
| SmiMI | CAYNNNNRTG | 3 cut(s) | 1326, 1961, 4061 |
| SmlI | CTYRAG | 9 cut(s) | 102, 432, 1152, 3030, 3042, 3257, 3402, 4104, 4238 |
| SmoI | CTYRAG | 9 cut(s) | 102, 432, 1152, 3030, 3042, 3257, 3402, 4104, 4238 |
| SpeI | ACTAGT | 2 cut(s) | 3641, 4136 |
| Sse8387I | CCTGCAGG | 1 cut(s) | 3217 |
| SsiI | CCGC | 3 cut(s) | 1743, 2162, 3007 |
| SstI | GAGCTC | 1 cut(s) | 388 |
| StyD4I | CCNGG | 1 cut(s) | 1807 |
| StyI | CCWWGG | 1 cut(s) | 3633 |
| TaaI | ACNGT | 4 cut(s) | 8, 600, 4004, 4348 |
| TaqI | TCGA | 6 cut(s) | 382, 636, 1938, 2541, 3931, 4198 |
| TatI | WGTACW | 3 cut(s) | 2656, 3861, 4032 |
| TscAI | CASTG | 1 cut(s) | 4264 |
| TseFI | GTSAC | 5 cut(s) | 1319, 1750, 1760, 2384, 4127 |
| TseI | GCWGC | 4 cut(s) | 2567, 2650, 3611, 4040 |
| Tsp45I | GTSAC | 5 cut(s) | 1319, 1750, 1760, 2384, 4127 |
| TspGWI | ACGGA | 2 cut(s) | 1241, 1779 |
| TspRI | CASTG | 1 cut(s) | 4264 |
| Vha464I | CTTAAG | 1 cut(s) | 3257 |
| VpaK11BI | GGWCC | 2 cut(s) | 4, 1376 |
| VspI | ATTAAT | 1 cut(s) | 2472 |
| XbaI | TCTAGA | 2 cut(s) | 571, 1646 |
| XceI | RCATGY | 3 cut(s) | 1592, 1620, 3126 |
| XmiI | GTMKAC | 1 cut(s) | 1388 |
| XmnI | GAANNNNTTC | 7 cut(s) | 186, 692, 1540, 2452, 3099, 3643, 4251 |
| Zsp2I | ATGCAT | 2 cut(s) | 1045, 2057 |