NB-ARC domain
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| Retrotran_gag_2 | PF14223 | 57 - 106 | 1.1e-09 | gag-polypeptide of LTR copia-type |
| Pol_BBD | PF22936 | 109 - 173 | 5.8e-12 | Pol polyprotein, beta-barrel domain |
| rve | PF00665 | 226 - 306 | 1e-11 | Integrase core domain |
| SH3_retrovirus | PF25597 | 380 - 443 | 1.4e-25 | Retroviral polymerase SH3-like domain |
| RVT_2 | PF07727 | 549 - 776 | 1.1e-66 | Reverse transcriptase (RNA-dependent DNA polymerase) |
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AanI | TTATAA | 1 cut(s) | 1710 |
| Acc36I | ACCTGC | 1 cut(s) | 2955 |
| AccB7I | CCANNNNNTGG | 1 cut(s) | 1691 |
| AccI | GTMKAC | 1 cut(s) | 2945 |
| AciI | CCGC | 1 cut(s) | 202 |
| AclWI | GGATC | 4 cut(s) | 333, 1665, 1905, 3008 |
| AcsI | RAATTY | 7 cut(s) | 121, 481, 857, 1004, 2005, 2288, 2896 |
| AcuI | CTGAAG | 2 cut(s) | 833, 2978 |
| AdeI | CACNNNGTG | 1 cut(s) | 1415 |
| AfiI | CCNNNNNNNGG | 2 cut(s) | 599, 1691 |
| AjnI | CCWGG | 6 cut(s) | 466, 713, 885, 1108, 1786, 2878 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 1419, 1451 |
| Alw21I | GWGCWC | 1 cut(s) | 513 |
| Alw26I | GTCTC | 3 cut(s) | 1165, 2164, 2372 |
| AlwI | GGATC | 4 cut(s) | 333, 1665, 1905, 3008 |
| Ama87I | CYCGRG | 1 cut(s) | 225 |
| AoxI | GGCC | 5 cut(s) | 883, 1851, 2429, 2676, 2754 |
| ApeKI | GCWGC | 5 cut(s) | 60, 1586, 1859, 2447, 2735 |
| ApoI | RAATTY | 7 cut(s) | 121, 481, 857, 1004, 2005, 2288, 2896 |
| AseI | ATTAAT | 2 cut(s) | 251, 2888 |
| AspLEI | GCGC | 1 cut(s) | 46 |
| AspS9I | GGNCC | 3 cut(s) | 1484, 1852, 2676 |
| AsuHPI | GGTGA | 6 cut(s) | 88, 851, 1279, 2171, 2195, 2941 |
| AsuII | TTCGAA | 1 cut(s) | 302 |
| AvaI | CYCGRG | 1 cut(s) | 225 |
| AvaII | GGWCC | 1 cut(s) | 1484 |
| BbsI | GAAGAC | 3 cut(s) | 103, 1082, 1938 |
| Bbv12I | GWGCWC | 1 cut(s) | 513 |
| BbvCI | CCTCAGC | 2 cut(s) | 1014, 2835 |
| BbvI | GCAGC | 5 cut(s) | 72, 1573, 1846, 2459, 2747 |
| BccI | CCATC | 8 cut(s) | 271, 499, 962, 1724, 1867, 1912, 2351, 2920 |
| BcgI | CGANNNNNNTGC | 4 cut(s) | 94, 128, 2872, 2906 |
| BciT130I | CCWGG | 6 cut(s) | 468, 715, 887, 1110, 1788, 2880 |
| BciVI | GTATCC | 1 cut(s) | 1355 |
| BclI | TGATCA | 2 cut(s) | 1465, 1498 |
| BcoDI | GTCTC | 3 cut(s) | 1165, 2164, 2372 |
| BfaI | CTAG | 2 cut(s) | 2192, 2463 |
| BfmI | CTRYAG | 5 cut(s) | 58, 649, 786, 1365, 2712 |
| BfuAI | ACCTGC | 1 cut(s) | 2955 |
| BfuI | GTATCC | 1 cut(s) | 1355 |
| BglI | GCCNNNNNGGC | 1 cut(s) | 653 |
| BglII | AGATCT | 1 cut(s) | 549 |
| BisI | GCNGC | 5 cut(s) | 61, 1587, 1860, 2448, 2736 |
| BlsI | GCNGC | 5 cut(s) | 62, 1588, 1861, 2449, 2737 |
| BmcAI | AGTACT | 1 cut(s) | 3014 |
| Bme1390I | CCNGG | 6 cut(s) | 468, 715, 887, 1110, 1788, 2880 |
| Bme18I | GGWCC | 1 cut(s) | 1484 |
| BmeT110I | CYCGRG | 1 cut(s) | 225 |
| BmgT120I | GGNCC | 3 cut(s) | 1484, 1852, 2676 |
| BmiI | GGNNCC | 1 cut(s) | 996 |
| BmrFI | CCNGG | 6 cut(s) | 468, 715, 887, 1110, 1788, 2880 |
| BmsI | GCATC | 4 cut(s) | 1040, 1129, 2263, 2904 |
| BpiI | GAAGAC | 3 cut(s) | 103, 1082, 1938 |
| Bpu10I | CCTNAGC | 4 cut(s) | 821, 1014, 1949, 2835 |
| Bpu14I | TTCGAA | 1 cut(s) | 302 |
| BpuEI | CTTGAG | 2 cut(s) | 1496, 2303 |
| Bsa29I | ATCGAT | 4 cut(s) | 682, 1048, 1794, 3003 |
| BsaBI | GATNNNNATC | 1 cut(s) | 1497 |
| BsaJI | CCNNGG | 4 cut(s) | 72, 1590, 1845, 2212 |
| BsaXI | ACNNNNNCTCC | 2 cut(s) | 2596, 2626 |
| Bsc4I | CCNNNNNNNGG | 2 cut(s) | 599, 1691 |
| Bse118I | RCCGGY | 1 cut(s) | 2311 |
| Bse1I | ACTGG | 3 cut(s) | 382, 403, 2860 |
| Bse3DI | GCAATG | 1 cut(s) | 1524 |
| Bse8I | GATNNNNATC | 1 cut(s) | 1497 |
| BseBI | CCWGG | 6 cut(s) | 468, 715, 887, 1110, 1788, 2880 |
| BseCI | ATCGAT | 4 cut(s) | 682, 1048, 1794, 3003 |
| BseDI | CCNNGG | 4 cut(s) | 72, 1590, 1845, 2212 |
| BseGI | GGATG | 6 cut(s) | 319, 723, 1600, 1735, 1878, 2906 |
| BseJI | GATNNNNATC | 1 cut(s) | 1497 |
| BseLI | CCNNNNNNNGG | 2 cut(s) | 599, 1691 |
| BseMI | GCAATG | 1 cut(s) | 1524 |
| BseMII | CTCAG | 8 cut(s) | 502, 1005, 1446, 1793, 1963, 2139, 2507, 2849 |
| BseNI | ACTGG | 3 cut(s) | 382, 403, 2860 |
| BseRI | GAGGAG | 3 cut(s) | 849, 1497, 2641 |
| BseXI | GCAGC | 5 cut(s) | 72, 1573, 1846, 2459, 2747 |
| BsgI | GTGCAG | 5 cut(s) | 694, 1760, 1845, 2733, 2754 |
| BshFI | GGCC | 5 cut(s) | 885, 1853, 2431, 2678, 2756 |
| BshVI | ATCGAT | 4 cut(s) | 682, 1048, 1794, 3003 |
| BsiHKAI | GWGCWC | 1 cut(s) | 513 |
| BsiHKCI | CYCGRG | 1 cut(s) | 225 |
| BsiSI | CCGG | 1 cut(s) | 2312 |
| BslFI | GGGAC | 2 cut(s) | 64, 2512 |
| BslI | CCNNNNNNNGG | 2 cut(s) | 599, 1691 |
| BsmAI | GTCTC | 3 cut(s) | 1165, 2164, 2372 |
| BsmFI | GGGAC | 2 cut(s) | 64, 2512 |
| BsmI | GAATGC | 5 cut(s) | 143, 298, 1324, 2082, 2645 |
| BsnI | GGCC | 5 cut(s) | 885, 1853, 2431, 2678, 2756 |
| BsoBI | CYCGRG | 1 cut(s) | 225 |
| Bsp119I | TTCGAA | 1 cut(s) | 302 |
| Bsp1286I | GDGCHC | 1 cut(s) | 513 |
| Bsp1407I | TGTACA | 2 cut(s) | 1035, 1941 |
| Bsp19I | CCATGG | 1 cut(s) | 72 |
| BspACI | CCGC | 1 cut(s) | 202 |
| BspANI | GGCC | 5 cut(s) | 885, 1853, 2431, 2678, 2756 |
| BspCNI | CTCAG | 8 cut(s) | 501, 1006, 1447, 1792, 1962, 2140, 2508, 2848 |
| BspDI | ATCGAT | 4 cut(s) | 682, 1048, 1794, 3003 |
| BspHI | TCATGA | 1 cut(s) | 24 |
| BspLI | GGNNCC | 1 cut(s) | 996 |
| BspMAI | CTGCAG | 3 cut(s) | 62, 1369, 2716 |
| BspMI | ACCTGC | 1 cut(s) | 2955 |
| BspPI | GGATC | 4 cut(s) | 333, 1665, 1905, 3008 |
| BspQI | GCTCTTC | 1 cut(s) | 2954 |
| BspT104I | TTCGAA | 1 cut(s) | 302 |
| BsrDI | GCAATG | 1 cut(s) | 1524 |
| BsrFI | RCCGGY | 1 cut(s) | 2311 |
| BsrGI | TGTACA | 2 cut(s) | 1035, 1941 |
| BsrI | ACTGG | 3 cut(s) | 382, 403, 2860 |
| BssAI | RCCGGY | 1 cut(s) | 2311 |
| BssECI | CCNNGG | 4 cut(s) | 72, 1590, 1845, 2212 |
| BssNAI | GTATAC | 1 cut(s) | 2946 |
| BssT1I | CCWWGG | 4 cut(s) | 72, 1590, 1845, 2212 |
| Bst1107I | GTATAC | 1 cut(s) | 2946 |
| Bst2UI | CCWGG | 6 cut(s) | 468, 715, 887, 1110, 1788, 2880 |
| Bst6I | CTCTTC | 3 cut(s) | 1422, 1575, 2954 |
| BstAUI | TGTACA | 2 cut(s) | 1035, 1941 |
| BstBI | TTCGAA | 1 cut(s) | 302 |
| BstC8I | GCNNGC | 2 cut(s) | 1192, 2452 |
| BstDSI | CCRYGG | 1 cut(s) | 72 |
| BstF5I | GGATG | 6 cut(s) | 319, 723, 1600, 1735, 1878, 2906 |
| BstHHI | GCGC | 1 cut(s) | 46 |
| BstMAI | GTCTC | 3 cut(s) | 1165, 2164, 2372 |
| BstMWI | GCNNNNNNNGC | 5 cut(s) | 653, 1820, 1859, 1985, 2741 |
| BstNI | CCWGG | 6 cut(s) | 468, 715, 887, 1110, 1788, 2880 |
| BstNSI | RCATGY | 1 cut(s) | 1308 |
| BstSCI | CCNGG | 6 cut(s) | 466, 713, 885, 1108, 1786, 2878 |
| BstSFI | CTRYAG | 5 cut(s) | 58, 649, 786, 1365, 2712 |
| BstV1I | GCAGC | 5 cut(s) | 72, 1573, 1846, 2459, 2747 |
| BstV2I | GAAGAC | 3 cut(s) | 103, 1082, 1938 |
| BstX2I | RGATCY | 3 cut(s) | 325, 549, 1657 |
| BstXI | CCANNNNNNTGG | 2 cut(s) | 1989, 2213 |
| BstYI | RGATCY | 3 cut(s) | 325, 549, 1657 |
| BstZ17I | GTATAC | 1 cut(s) | 2946 |
| Bsu15I | ATCGAT | 4 cut(s) | 682, 1048, 1794, 3003 |
| BsuI | GTATCC | 1 cut(s) | 1355 |
| BsuRI | GGCC | 5 cut(s) | 885, 1853, 2431, 2678, 2756 |
| BsuTUI | ATCGAT | 4 cut(s) | 682, 1048, 1794, 3003 |
| BtgI | CCRYGG | 1 cut(s) | 72 |
| BtsCI | GGATG | 6 cut(s) | 319, 723, 1600, 1735, 1878, 2906 |
| BtsI | GCAGTG | 2 cut(s) | 2580, 2701 |
| BveI | ACCTGC | 1 cut(s) | 2955 |
| Cac8I | GCNNGC | 2 cut(s) | 1192, 2452 |
| CciI | TCATGA | 1 cut(s) | 24 |
| CfoI | GCGC | 1 cut(s) | 46 |
| Cfr10I | RCCGGY | 1 cut(s) | 2311 |
| Cfr13I | GGNCC | 3 cut(s) | 1484, 1852, 2676 |
| ClaI | ATCGAT | 4 cut(s) | 682, 1048, 1794, 3003 |
| CviAII | CATG | 6 cut(s) | 25, 47, 73, 1154, 1305, 1602 |
| DraI | TTTAAA | 2 cut(s) | 769, 2155 |
| DraIII | CACNNNGTG | 1 cut(s) | 1415 |
| Eam1104I | CTCTTC | 3 cut(s) | 1422, 1575, 2954 |
| EarI | CTCTTC | 3 cut(s) | 1422, 1575, 2954 |
| Eco130I | CCWWGG | 4 cut(s) | 72, 1590, 1845, 2212 |
| Eco147I | AGGCCT | 1 cut(s) | 885 |
| Eco47I | GGWCC | 1 cut(s) | 1484 |
| Eco57I | CTGAAG | 2 cut(s) | 833, 2978 |
| Eco88I | CYCGRG | 1 cut(s) | 225 |
| EcoRI | GAATTC | 1 cut(s) | 1004 |
| EcoRII | CCWGG | 6 cut(s) | 466, 713, 885, 1108, 1786, 2878 |
| EcoT14I | CCWWGG | 4 cut(s) | 72, 1590, 1845, 2212 |
| EcoT22I | ATGCAT | 1 cut(s) | 2647 |
| ErhI | CCWWGG | 4 cut(s) | 72, 1590, 1845, 2212 |
| FaeI | CATG | 6 cut(s) | 28, 50, 76, 1157, 1308, 1605 |
| FalI | AAGNNNNNCTT | 4 cut(s) | 396, 428, 2040, 2072 |
| FaqI | GGGAC | 2 cut(s) | 64, 2512 |
| FatI | CATG | 6 cut(s) | 24, 46, 72, 1153, 1304, 1601 |
| FauNDI | CATATG | 1 cut(s) | 2493 |
| FbaI | TGATCA | 2 cut(s) | 1465, 1498 |
| FblI | GTMKAC | 1 cut(s) | 2945 |
| Fnu4HI | GCNGC | 5 cut(s) | 61, 1587, 1860, 2448, 2736 |
| FokI | GGATG | 6 cut(s) | 326, 730, 1607, 1742, 1885, 2893 |
| Fsp4HI | GCNGC | 5 cut(s) | 61, 1587, 1860, 2448, 2736 |
| FspBI | CTAG | 2 cut(s) | 2192, 2463 |
| GlaI | GCGC | 1 cut(s) | 45 |
| GluI | GCNGC | 5 cut(s) | 61, 1587, 1860, 2448, 2736 |
| HaeIII | GGCC | 5 cut(s) | 885, 1853, 2431, 2678, 2756 |
| HapII | CCGG | 1 cut(s) | 2312 |
| HhaI | GCGC | 1 cut(s) | 46 |
| Hin1II | CATG | 6 cut(s) | 28, 50, 76, 1157, 1308, 1605 |
| Hin6I | GCGC | 1 cut(s) | 44 |
| HinP1I | GCGC | 1 cut(s) | 44 |
| HincII | GTYRAC | 1 cut(s) | 1166 |
| HindII | GTYRAC | 1 cut(s) | 1166 |
| HindIII | AAGCTT | 5 cut(s) | 818, 1089, 1956, 2452, 2987 |
| HpaII | CCGG | 1 cut(s) | 2312 |
| HphI | GGTGA | 6 cut(s) | 88, 851, 1279, 2171, 2195, 2941 |
| Hpy166II | GTNNAC | 5 cut(s) | 1036, 1166, 1487, 1942, 2946 |
| Hpy8I | GTNNAC | 5 cut(s) | 1036, 1166, 1487, 1942, 2946 |
| HpyAV | CCTTC | 6 cut(s) | 592, 1225, 1321, 1329, 1379, 1603 |
| HpyF10VI | GCNNNNNNNGC | 5 cut(s) | 653, 1820, 1859, 1985, 2741 |
| Hsp92II | CATG | 6 cut(s) | 28, 50, 76, 1157, 1308, 1605 |
| HspAI | GCGC | 1 cut(s) | 44 |
| Ksp22I | TGATCA | 2 cut(s) | 1465, 1498 |
| LguI | GCTCTTC | 1 cut(s) | 2954 |
| LmnI | GCTCC | 4 cut(s) | 204, 508, 1984, 2570 |
| Lsp1109I | GCAGC | 5 cut(s) | 72, 1573, 1846, 2459, 2747 |
| LweI | GCATC | 4 cut(s) | 1040, 1129, 2263, 2904 |
| MaeI | CTAG | 2 cut(s) | 2192, 2463 |
| MaeIII | GTNAC | 8 cut(s) | 352, 394, 624, 1267, 1450, 1477, 2094, 2536 |
| MfeI | CAATTG | 1 cut(s) | 2840 |
| MflI | RGATCY | 3 cut(s) | 325, 549, 1657 |
| MhlI | GDGCHC | 1 cut(s) | 513 |
| MlyI | GAGTC | 1 cut(s) | 1704 |
| MmeI | TCCRAC | 3 cut(s) | 597, 704, 963 |
| Mph1103I | ATGCAT | 1 cut(s) | 2647 |
| MseI | TTAA | 8 cut(s) | 98, 251, 768, 861, 1116, 1293, 2154, 2888 |
| MslI | CAYNNNNRTG | 4 cut(s) | 716, 747, 851, 1358 |
| MspA1I | CMGCKG | 1 cut(s) | 674 |
| MspI | CCGG | 1 cut(s) | 2312 |
| MspR9I | CCNGG | 6 cut(s) | 468, 715, 887, 1110, 1788, 2880 |
| MunI | CAATTG | 1 cut(s) | 2840 |
| Mva1269I | GAATGC | 5 cut(s) | 143, 298, 1324, 2082, 2645 |
| MvaI | CCWGG | 6 cut(s) | 468, 715, 887, 1110, 1788, 2880 |
| MwoI | GCNNNNNNNGC | 5 cut(s) | 653, 1820, 1859, 1985, 2741 |
| NcoI | CCATGG | 1 cut(s) | 72 |
| NdeI | CATATG | 1 cut(s) | 2493 |
| NlaIII | CATG | 6 cut(s) | 28, 50, 76, 1157, 1308, 1605 |
| NlaIV | GGNNCC | 1 cut(s) | 996 |
| NmuCI | GTSAC | 5 cut(s) | 352, 1267, 1477, 2094, 2536 |
| NsiI | ATGCAT | 1 cut(s) | 2647 |
| NspI | RCATGY | 1 cut(s) | 1308 |
| NspV | TTCGAA | 1 cut(s) | 302 |
| PaeR7I | CTCGAG | 1 cut(s) | 225 |
| PagI | TCATGA | 1 cut(s) | 24 |
| PceI | AGGCCT | 1 cut(s) | 885 |
| PciSI | GCTCTTC | 1 cut(s) | 2954 |
| PctI | GAATGC | 5 cut(s) | 143, 298, 1324, 2082, 2645 |
| PflMI | CCANNNNNTGG | 1 cut(s) | 1691 |
| PkrI | GCNGC | 5 cut(s) | 62, 1588, 1861, 2449, 2737 |
| PleI | GAGTC | 1 cut(s) | 1703 |
| PpsI | GAGTC | 1 cut(s) | 1703 |
| PshBI | ATTAAT | 2 cut(s) | 251, 2888 |
| PsiI | TTATAA | 1 cut(s) | 1710 |
| Psp6I | CCWGG | 6 cut(s) | 466, 713, 885, 1108, 1786, 2878 |
| PspGI | CCWGG | 6 cut(s) | 466, 713, 885, 1108, 1786, 2878 |
| PspN4I | GGNNCC | 1 cut(s) | 996 |
| PspPI | GGNCC | 3 cut(s) | 1484, 1852, 2676 |
| PstI | CTGCAG | 3 cut(s) | 62, 1369, 2716 |
| PsuI | RGATCY | 3 cut(s) | 325, 549, 1657 |
| PvuII | CAGCTG | 1 cut(s) | 674 |
| RseI | CAYNNNNRTG | 4 cut(s) | 716, 747, 851, 1358 |
| SapI | GCTCTTC | 1 cut(s) | 2954 |
| SaqAI | TTAA | 8 cut(s) | 98, 251, 768, 861, 1116, 1293, 2154, 2888 |
| SatI | GCNGC | 5 cut(s) | 61, 1587, 1860, 2448, 2736 |
| Sau96I | GGNCC | 3 cut(s) | 1484, 1852, 2676 |
| ScaI | AGTACT | 1 cut(s) | 3014 |
| SchI | GAGTC | 1 cut(s) | 1704 |
| ScrFI | CCNGG | 6 cut(s) | 468, 715, 887, 1110, 1788, 2880 |
| SduI | GDGCHC | 1 cut(s) | 513 |
| SfaNI | GCATC | 4 cut(s) | 1040, 1129, 2263, 2904 |
| SfcI | CTRYAG | 5 cut(s) | 58, 649, 786, 1365, 2712 |
| Sfr274I | CTCGAG | 1 cut(s) | 225 |
| SfuI | TTCGAA | 1 cut(s) | 302 |
| SinI | GGWCC | 1 cut(s) | 1484 |
| SlaI | CTCGAG | 1 cut(s) | 225 |
| SmiMI | CAYNNNNRTG | 4 cut(s) | 716, 747, 851, 1358 |
| SmlI | CTYRAG | 3 cut(s) | 225, 1511, 2282 |
| SmoI | CTYRAG | 3 cut(s) | 225, 1511, 2282 |
| SseBI | AGGCCT | 1 cut(s) | 885 |
| SsiI | CCGC | 1 cut(s) | 202 |
| SspMI | CTAG | 2 cut(s) | 2192, 2463 |
| StuI | AGGCCT | 1 cut(s) | 885 |
| StyD4I | CCNGG | 6 cut(s) | 466, 713, 885, 1108, 1786, 2878 |
| StyI | CCWWGG | 4 cut(s) | 72, 1590, 1845, 2212 |
| TaqI | TCGA | 9 cut(s) | 226, 302, 607, 682, 832, 1048, 1182, 1794, 3003 |
| TatI | WGTACW | 7 cut(s) | 1035, 1515, 1941, 2630, 2724, 2773, 3012 |
| Tru1I | TTAA | 8 cut(s) | 98, 251, 768, 861, 1116, 1293, 2154, 2888 |
| Tru9I | TTAA | 8 cut(s) | 98, 251, 768, 861, 1116, 1293, 2154, 2888 |
| TseFI | GTSAC | 5 cut(s) | 352, 1267, 1477, 2094, 2536 |
| TseI | GCWGC | 5 cut(s) | 60, 1586, 1859, 2447, 2735 |
| Tsp45I | GTSAC | 5 cut(s) | 352, 1267, 1477, 2094, 2536 |
| Van91I | CCANNNNNTGG | 1 cut(s) | 1691 |
| VpaK11BI | GGWCC | 1 cut(s) | 1484 |
| VspI | ATTAAT | 2 cut(s) | 251, 2888 |
| XapI | RAATTY | 7 cut(s) | 121, 481, 857, 1004, 2005, 2288, 2896 |
| XceI | RCATGY | 1 cut(s) | 1308 |
| XcmI | CCANNNNNNNNNTGG | 3 cut(s) | 961, 1005, 2491 |
| XhoI | CTCGAG | 1 cut(s) | 225 |
| XmiI | GTMKAC | 1 cut(s) | 2945 |
| XspI | CTAG | 2 cut(s) | 2192, 2463 |
| ZrmI | AGTACT | 1 cut(s) | 3014 |
| Zsp2I | ATGCAT | 1 cut(s) | 2647 |