gag-polypeptide of LTR copia-type
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| Retrotran_gag_2 | PF14223 | 27 - 202 | 4.1e-32 | gag-polypeptide of LTR copia-type |
| Pol_BBD | PF22936 | 342 - 421 | 1.8e-21 | Pol polyprotein, beta-barrel domain |
| gag_pre-integrs | PF13976 | 473 - 524 | 1.2e-16 | GAG-pre-integrase domain |
| rve | PF00665 | 538 - 639 | 4.6e-15 | Integrase core domain |
| SH3_retrovirus | PF25597 | 713 - 757 | 7.1e-16 | Retroviral polymerase SH3-like domain |
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AccI | GTMKAC | 1 cut(s) | 794 |
| AciI | CCGC | 1 cut(s) | 1916 |
| AclWI | GGATC | 2 cut(s) | 131, 137 |
| AcsI | RAATTY | 5 cut(s) | 113, 459, 612, 836, 1225 |
| AcuI | CTGAAG | 1 cut(s) | 972 |
| AfaI | GTAC | 7 cut(s) | 736, 763, 1005, 1153, 1844, 2026, 2216 |
| AfiI | CCNNNNNNNGG | 1 cut(s) | 1216 |
| AflII | CTTAAG | 1 cut(s) | 2122 |
| Alw21I | GWGCWC | 2 cut(s) | 214, 1629 |
| Alw26I | GTCTC | 5 cut(s) | 507, 1572, 1732, 1885, 2164 |
| AlwI | GGATC | 2 cut(s) | 131, 137 |
| AlwNI | CAGNNNCTG | 1 cut(s) | 1001 |
| ApeKI | GCWGC | 2 cut(s) | 995, 1918 |
| ApoI | RAATTY | 5 cut(s) | 113, 459, 612, 836, 1225 |
| AseI | ATTAAT | 1 cut(s) | 432 |
| Asp700I | GAANNNNTTC | 1 cut(s) | 2107 |
| AspS9I | GGNCC | 1 cut(s) | 1649 |
| AsuHPI | GGTGA | 7 cut(s) | 62, 403, 464, 1108, 1345, 1357, 1850 |
| AvaII | GGWCC | 1 cut(s) | 1649 |
| BaeI | ACNNNNGTAYC | 6 cut(s) | 507, 540, 1080, 1113, 1143, 1176 |
| BanII | GRGCYC | 2 cut(s) | 214, 1629 |
| BbsI | GAAGAC | 1 cut(s) | 34 |
| Bbv12I | GWGCWC | 2 cut(s) | 214, 1629 |
| BbvI | GCAGC | 2 cut(s) | 1007, 1930 |
| BccI | CCATC | 3 cut(s) | 1108, 1115, 1777 |
| BceAI | ACGGC | 1 cut(s) | 1074 |
| BclI | TGATCA | 4 cut(s) | 598, 967, 1015, 2221 |
| BcoDI | GTCTC | 5 cut(s) | 507, 1572, 1732, 1885, 2164 |
| BfaI | CTAG | 5 cut(s) | 15, 375, 1130, 1536, 1713 |
| BfmI | CTRYAG | 1 cut(s) | 2236 |
| BfrI | CTTAAG | 1 cut(s) | 2122 |
| BglII | AGATCT | 1 cut(s) | 246 |
| BisI | GCNGC | 2 cut(s) | 996, 1919 |
| BlpI | GCTNAGC | 1 cut(s) | 621 |
| BlsI | GCNGC | 2 cut(s) | 997, 1920 |
| BmcAI | AGTACT | 1 cut(s) | 2026 |
| Bme18I | GGWCC | 1 cut(s) | 1649 |
| BmgT120I | GGNCC | 1 cut(s) | 1649 |
| BmrI | ACTGGG | 1 cut(s) | 32 |
| BmsI | GCATC | 7 cut(s) | 154, 193, 274, 358, 1391, 1495, 2211 |
| BmuI | ACTGGG | 1 cut(s) | 32 |
| BoxI | GACNNNNGTC | 1 cut(s) | 1955 |
| BpiI | GAAGAC | 1 cut(s) | 34 |
| BplI | GAGNNNNNCTC | 2 cut(s) | 1832, 1864 |
| BpmI | CTGGAG | 1 cut(s) | 320 |
| Bpu10I | CCTNAGC | 1 cut(s) | 1329 |
| Bpu1102I | GCTNAGC | 1 cut(s) | 621 |
| BpuEI | CTTGAG | 7 cut(s) | 737, 1125, 1643, 1756, 1840, 1907, 2264 |
| Bsa29I | ATCGAT | 1 cut(s) | 1701 |
| BsaBI | GATNNNNATC | 2 cut(s) | 141, 1125 |
| BsaJI | CCNNGG | 1 cut(s) | 254 |
| BsaXI | ACNNNNNCTCC | 2 cut(s) | 2004, 2034 |
| Bsc4I | CCNNNNNNNGG | 1 cut(s) | 1216 |
| Bse1I | ACTGG | 4 cut(s) | 38, 186, 731, 2322 |
| Bse3DI | GCAATG | 1 cut(s) | 1879 |
| Bse8I | GATNNNNATC | 2 cut(s) | 141, 1125 |
| BseCI | ATCGAT | 1 cut(s) | 1701 |
| BseDI | CCNNGG | 1 cut(s) | 254 |
| BseGI | GGATG | 4 cut(s) | 208, 298, 384, 1119 |
| BseJI | GATNNNNATC | 2 cut(s) | 141, 1125 |
| BseLI | CCNNNNNNNGG | 1 cut(s) | 1216 |
| BseMI | GCAATG | 1 cut(s) | 1879 |
| BseMII | CTCAG | 6 cut(s) | 138, 612, 675, 710, 1212, 2159 |
| BseNI | ACTGG | 4 cut(s) | 38, 186, 731, 2322 |
| BseXI | GCAGC | 2 cut(s) | 1007, 1930 |
| BseYI | CCCAGC | 1 cut(s) | 1456 |
| BsgI | GTGCAG | 1 cut(s) | 1578 |
| BshVI | ATCGAT | 1 cut(s) | 1701 |
| BsiHKAI | GWGCWC | 2 cut(s) | 214, 1629 |
| BslFI | GGGAC | 5 cut(s) | 1193, 1473, 1896, 2037, 2328 |
| BslI | CCNNNNNNNGG | 1 cut(s) | 1216 |
| BsmAI | GTCTC | 5 cut(s) | 507, 1572, 1732, 1885, 2164 |
| BsmFI | GGGAC | 5 cut(s) | 1193, 1473, 1896, 2037, 2328 |
| Bsp1286I | GDGCHC | 2 cut(s) | 214, 1629 |
| Bsp1407I | TGTACA | 1 cut(s) | 1003 |
| Bsp143I | GATC | 8 cut(s) | 136, 142, 246, 466, 598, 967, 1015, 2221 |
| Bsp1720I | GCTNAGC | 1 cut(s) | 621 |
| BspACI | CCGC | 1 cut(s) | 1916 |
| BspCNI | CTCAG | 6 cut(s) | 139, 613, 676, 709, 1213, 2160 |
| BspDI | ATCGAT | 1 cut(s) | 1701 |
| BspPI | GGATC | 2 cut(s) | 131, 137 |
| BspTI | CTTAAG | 1 cut(s) | 2122 |
| BsrDI | GCAATG | 1 cut(s) | 1879 |
| BsrGI | TGTACA | 1 cut(s) | 1003 |
| BsrI | ACTGG | 4 cut(s) | 38, 186, 731, 2322 |
| BssECI | CCNNGG | 1 cut(s) | 254 |
| BssMI | GATC | 8 cut(s) | 136, 142, 246, 466, 598, 967, 1015, 2221 |
| BssT1I | CCWWGG | 1 cut(s) | 254 |
| Bst4CI | ACNGT | 4 cut(s) | 887, 1003, 1037, 2219 |
| Bst6I | CTCTTC | 3 cut(s) | 95, 352, 725 |
| BstAFI | CTTAAG | 1 cut(s) | 2122 |
| BstAUI | TGTACA | 1 cut(s) | 1003 |
| BstC8I | GCNNGC | 3 cut(s) | 869, 939, 1568 |
| BstF5I | GGATG | 4 cut(s) | 208, 298, 384, 1119 |
| BstKTI | GATC | 8 cut(s) | 139, 145, 249, 469, 601, 970, 1018, 2224 |
| BstMAI | GTCTC | 5 cut(s) | 507, 1572, 1732, 1885, 2164 |
| BstMBI | GATC | 8 cut(s) | 136, 142, 246, 466, 598, 967, 1015, 2221 |
| BstMWI | GCNNNNNNNGC | 7 cut(s) | 284, 706, 992, 1252, 1453, 1607, 1624 |
| BstNSI | RCATGY | 2 cut(s) | 178, 905 |
| BstPAI | GACNNNNGTC | 1 cut(s) | 1955 |
| BstSFI | CTRYAG | 1 cut(s) | 2236 |
| BstV1I | GCAGC | 2 cut(s) | 1007, 1930 |
| BstV2I | GAAGAC | 1 cut(s) | 34 |
| BstX2I | RGATCY | 2 cut(s) | 136, 246 |
| BstYI | RGATCY | 2 cut(s) | 136, 246 |
| Bsu15I | ATCGAT | 1 cut(s) | 1701 |
| BsuTUI | ATCGAT | 1 cut(s) | 1701 |
| BtsCI | GGATG | 4 cut(s) | 208, 298, 384, 1119 |
| BtsI | GCAGTG | 1 cut(s) | 2070 |
| BtsIMutI | CAGTG | 3 cut(s) | 1042, 2070, 2224 |
| Cac8I | GCNNGC | 3 cut(s) | 869, 939, 1568 |
| CaiI | CAGNNNCTG | 1 cut(s) | 1001 |
| Cfr13I | GGNCC | 1 cut(s) | 1649 |
| ClaI | ATCGAT | 1 cut(s) | 1701 |
| Csp6I | GTAC | 7 cut(s) | 735, 762, 1004, 1152, 1843, 2025, 2215 |
| CspCI | CAANNNNNGTGG | 2 cut(s) | 811, 846 |
| CviQI | GTAC | 7 cut(s) | 735, 762, 1004, 1152, 1843, 2025, 2215 |
| DpnI | GATC | 8 cut(s) | 138, 144, 248, 468, 600, 969, 1017, 2223 |
| DpnII | GATC | 8 cut(s) | 136, 142, 246, 466, 598, 967, 1015, 2221 |
| DraI | TTTAAA | 1 cut(s) | 1768 |
| Eam1104I | CTCTTC | 3 cut(s) | 95, 352, 725 |
| EarI | CTCTTC | 3 cut(s) | 95, 352, 725 |
| Ecl136II | GAGCTC | 2 cut(s) | 212, 1627 |
| Eco130I | CCWWGG | 1 cut(s) | 254 |
| Eco24I | GRGCYC | 2 cut(s) | 214, 1629 |
| Eco47I | GGWCC | 1 cut(s) | 1649 |
| Eco53kI | GAGCTC | 2 cut(s) | 212, 1627 |
| Eco57I | CTGAAG | 1 cut(s) | 972 |
| EcoICRI | GAGCTC | 2 cut(s) | 212, 1627 |
| EcoT14I | CCWWGG | 1 cut(s) | 254 |
| EcoT22I | ATGCAT | 1 cut(s) | 2204 |
| EcoT38I | GRGCYC | 2 cut(s) | 214, 1629 |
| ErhI | CCWWGG | 1 cut(s) | 254 |
| FalI | AAGNNNNNCTT | 2 cut(s) | 2092, 2124 |
| FaqI | GGGAC | 5 cut(s) | 1193, 1473, 1896, 2037, 2328 |
| FauI | CCCGC | 1 cut(s) | 1923 |
| FauNDI | CATATG | 2 cut(s) | 448, 1053 |
| FbaI | TGATCA | 4 cut(s) | 598, 967, 1015, 2221 |
| FblI | GTMKAC | 1 cut(s) | 794 |
| Fnu4HI | GCNGC | 2 cut(s) | 996, 1919 |
| FokI | GGATG | 4 cut(s) | 215, 305, 391, 1126 |
| FriOI | GRGCYC | 2 cut(s) | 214, 1629 |
| Fsp4HI | GCNGC | 2 cut(s) | 996, 1919 |
| FspBI | CTAG | 5 cut(s) | 15, 375, 1130, 1536, 1713 |
| GluI | GCNGC | 2 cut(s) | 996, 1919 |
| GsaI | CCCAGC | 1 cut(s) | 1460 |
| GsuI | CTGGAG | 1 cut(s) | 320 |
| HincII | GTYRAC | 1 cut(s) | 2116 |
| HindII | GTYRAC | 1 cut(s) | 2116 |
| HindIII | AAGCTT | 4 cut(s) | 776, 1354, 2177, 2305 |
| HinfI | GANTC | 7 cut(s) | 11, 129, 554, 686, 849, 1099, 1580 |
| HphI | GGTGA | 7 cut(s) | 62, 403, 464, 1108, 1345, 1357, 1850 |
| Hpy166II | GTNNAC | 5 cut(s) | 795, 1154, 1649, 1994, 2116 |
| Hpy188I | TCNGA | 8 cut(s) | 241, 466, 744, 1428, 1476, 1590, 1639, 1750 |
| Hpy8I | GTNNAC | 5 cut(s) | 795, 1154, 1649, 1994, 2116 |
| HpyCH4III | ACNGT | 4 cut(s) | 887, 1003, 1037, 2219 |
| HpyCH4V | TGCA | 9 cut(s) | 167, 822, 918, 995, 1382, 1510, 1559, 1872, 2202 |
| HpyF10VI | GCNNNNNNNGC | 7 cut(s) | 284, 706, 992, 1252, 1453, 1607, 1624 |
| Ksp22I | TGATCA | 4 cut(s) | 598, 967, 1015, 2221 |
| Kzo9I | GATC | 8 cut(s) | 136, 142, 246, 466, 598, 967, 1015, 2221 |
| LmnI | GCTCC | 2 cut(s) | 495, 668 |
| Lsp1109I | GCAGC | 2 cut(s) | 1007, 1930 |
| LweI | GCATC | 7 cut(s) | 154, 193, 274, 358, 1391, 1495, 2211 |
| MaeI | CTAG | 5 cut(s) | 15, 375, 1130, 1536, 1713 |
| MaeIII | GTNAC | 3 cut(s) | 1096, 1727, 1977 |
| MalI | GATC | 8 cut(s) | 138, 144, 248, 468, 600, 969, 1017, 2223 |
| MboI | GATC | 8 cut(s) | 136, 142, 246, 466, 598, 967, 1015, 2221 |
| MfeI | CAATTG | 1 cut(s) | 519 |
| MflI | RGATCY | 2 cut(s) | 136, 246 |
| MhlI | GDGCHC | 2 cut(s) | 214, 1629 |
| MlyI | GAGTC | 4 cut(s) | 5, 695, 1093, 1574 |
| MmeI | TCCRAC | 2 cut(s) | 906, 2072 |
| Mph1103I | ATGCAT | 1 cut(s) | 2204 |
| MroXI | GAANNNNTTC | 1 cut(s) | 2107 |
| MseI | TTAA | 9 cut(s) | 75, 339, 432, 525, 588, 1370, 1767, 1812, 2123 |
| MslI | CAYNNNNRTG | 3 cut(s) | 227, 1638, 2207 |
| MspCI | CTTAAG | 1 cut(s) | 2122 |
| MunI | CAATTG | 1 cut(s) | 519 |
| MwoI | GCNNNNNNNGC | 7 cut(s) | 284, 706, 992, 1252, 1453, 1607, 1624 |
| NdeI | CATATG | 2 cut(s) | 448, 1053 |
| NdeII | GATC | 8 cut(s) | 136, 142, 246, 466, 598, 967, 1015, 2221 |
| NmuCI | GTSAC | 1 cut(s) | 1096 |
| NsiI | ATGCAT | 1 cut(s) | 2204 |
| NspI | RCATGY | 2 cut(s) | 178, 905 |
| PdmI | GAANNNNTTC | 1 cut(s) | 2107 |
| PfeI | GAWTC | 3 cut(s) | 129, 554, 849 |
| PkrI | GCNGC | 2 cut(s) | 997, 1920 |
| PleI | GAGTC | 4 cut(s) | 5, 694, 1093, 1574 |
| PpsI | GAGTC | 4 cut(s) | 5, 694, 1093, 1574 |
| PshAI | GACNNNNGTC | 1 cut(s) | 1955 |
| PshBI | ATTAAT | 1 cut(s) | 432 |
| Psp124BI | GAGCTC | 2 cut(s) | 214, 1629 |
| PspFI | CCCAGC | 1 cut(s) | 1456 |
| PspPI | GGNCC | 1 cut(s) | 1649 |
| PstNI | CAGNNNCTG | 1 cut(s) | 1001 |
| PsuI | RGATCY | 2 cut(s) | 136, 246 |
| RsaI | GTAC | 7 cut(s) | 736, 763, 1005, 1153, 1844, 2026, 2216 |
| RsaNI | GTAC | 7 cut(s) | 735, 762, 1004, 1152, 1843, 2025, 2215 |
| RseI | CAYNNNNRTG | 3 cut(s) | 227, 1638, 2207 |
| SacI | GAGCTC | 2 cut(s) | 214, 1629 |
| SaqAI | TTAA | 9 cut(s) | 75, 339, 432, 525, 588, 1370, 1767, 1812, 2123 |
| SatI | GCNGC | 2 cut(s) | 996, 1919 |
| Sau3AI | GATC | 8 cut(s) | 136, 142, 246, 466, 598, 967, 1015, 2221 |
| Sau96I | GGNCC | 1 cut(s) | 1649 |
| ScaI | AGTACT | 1 cut(s) | 2026 |
| SchI | GAGTC | 4 cut(s) | 5, 695, 1093, 1574 |
| SduI | GDGCHC | 2 cut(s) | 214, 1629 |
| SfaNI | GCATC | 7 cut(s) | 154, 193, 274, 358, 1391, 1495, 2211 |
| SfcI | CTRYAG | 1 cut(s) | 2236 |
| SinI | GGWCC | 1 cut(s) | 1649 |
| SmiMI | CAYNNNNRTG | 3 cut(s) | 227, 1638, 2207 |
| SmlI | CTYRAG | 8 cut(s) | 716, 1140, 1622, 1735, 1819, 1886, 2122, 2279 |
| SmoI | CTYRAG | 8 cut(s) | 716, 1140, 1622, 1735, 1819, 1886, 2122, 2279 |
| SsiI | CCGC | 1 cut(s) | 1916 |
| SspMI | CTAG | 5 cut(s) | 15, 375, 1130, 1536, 1713 |
| SstI | GAGCTC | 2 cut(s) | 214, 1629 |
| StyI | CCWWGG | 1 cut(s) | 254 |
| TaaI | ACNGT | 4 cut(s) | 887, 1003, 1037, 2219 |
| TaqI | TCGA | 6 cut(s) | 567, 584, 1032, 1701, 1860, 1959 |
| TaqII | GACCGA | 1 cut(s) | 1666 |
| TatI | WGTACW | 4 cut(s) | 734, 1003, 1842, 2024 |
| TfiI | GAWTC | 3 cut(s) | 129, 554, 849 |
| Tru1I | TTAA | 9 cut(s) | 75, 339, 432, 525, 588, 1370, 1767, 1812, 2123 |
| Tru9I | TTAA | 9 cut(s) | 75, 339, 432, 525, 588, 1370, 1767, 1812, 2123 |
| TscAI | CASTG | 3 cut(s) | 1042, 2070, 2224 |
| TseFI | GTSAC | 1 cut(s) | 1096 |
| TseI | GCWGC | 2 cut(s) | 995, 1918 |
| Tsp45I | GTSAC | 1 cut(s) | 1096 |
| TspGWI | ACGGA | 1 cut(s) | 1941 |
| TspRI | CASTG | 3 cut(s) | 1042, 2070, 2224 |
| Vha464I | CTTAAG | 1 cut(s) | 2122 |
| VpaK11BI | GGWCC | 1 cut(s) | 1649 |
| VspI | ATTAAT | 1 cut(s) | 432 |
| XapI | RAATTY | 5 cut(s) | 113, 459, 612, 836, 1225 |
| XbaI | TCTAGA | 1 cut(s) | 1712 |
| XceI | RCATGY | 2 cut(s) | 178, 905 |
| XmiI | GTMKAC | 1 cut(s) | 794 |
| XmnI | GAANNNNTTC | 1 cut(s) | 2107 |
| XspI | CTAG | 5 cut(s) | 15, 375, 1130, 1536, 1713 |
| ZrmI | AGTACT | 1 cut(s) | 2026 |
| Zsp2I | ATGCAT | 1 cut(s) | 2204 |