transposition, RNA-mediated
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| Retrotran_gag_2 | PF14223 | 20 - 148 | 2.2e-20 | gag-polypeptide of LTR copia-type |
| Pol_BBD | PF22936 | 602 - 675 | 2.7e-21 | Pol polyprotein, beta-barrel domain |
| SH3_retrovirus | PF25597 | 788 - 830 | 5.3e-12 | Retroviral polymerase SH3-like domain |
| RVT_2 | PF07727 | 962 - 1190 | 5.5e-65 | Reverse transcriptase (RNA-dependent DNA polymerase) |
Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.
| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| Acc36I | ACCTGC | 1 cut(s) | 3812 |
| AccI | GTMKAC | 6 cut(s) | 62, 3014, 3365, 3457, 3646, 3667 |
| AciI | CCGC | 2 cut(s) | 764, 3959 |
| AclI | AACGTT | 1 cut(s) | 1403 |
| AclWI | GGATC | 8 cut(s) | 284, 317, 933, 1648, 2553, 2597, 2652, 3587 |
| AcoI | YGGCCR | 1 cut(s) | 765 |
| AcuI | CTGAAG | 5 cut(s) | 164, 573, 936, 1314, 2640 |
| AcyI | GRCGYC | 1 cut(s) | 1072 |
| AfaI | GTAC | 9 cut(s) | 1087, 1808, 2155, 2435, 2553, 2613, 3772, 3988, 4185 |
| AfiI | CCNNNNNNNGG | 1 cut(s) | 1491 |
| AflIII | ACRYGT | 2 cut(s) | 1880, 2319 |
| AhdI | GACNNNNNGTC | 1 cut(s) | 835 |
| AjnI | CCWGG | 3 cut(s) | 1488, 1948, 3903 |
| AleI | CACNNNNGTG | 2 cut(s) | 1434, 3398 |
| Alw21I | GWGCWC | 2 cut(s) | 3572, 3703 |
| Alw26I | GTCTC | 7 cut(s) | 1612, 2582, 2664, 2779, 3038, 3769, 3797 |
| AlwI | GGATC | 8 cut(s) | 284, 317, 933, 1648, 2553, 2597, 2652, 3587 |
| AlwNI | CAGNNNCTG | 2 cut(s) | 2336, 3548 |
| AoxI | GGCC | 2 cut(s) | 765, 807 |
| ApeKI | GCWGC | 3 cut(s) | 884, 2705, 3971 |
| ArsI | GACNNNNNNTTYG | 2 cut(s) | 3341, 3373 |
| AseI | ATTAAT | 1 cut(s) | 2847 |
| Asp700I | GAANNNNTTC | 2 cut(s) | 3075, 3389 |
| AspA2I | CCTAGG | 3 cut(s) | 283, 1460, 3266 |
| AspLEI | GCGC | 1 cut(s) | 3750 |
| AspS9I | GGNCC | 3 cut(s) | 127, 330, 376 |
| AsuC2I | CCSGG | 1 cut(s) | 3056 |
| AsuHPI | GGTGA | 6 cut(s) | 299, 959, 1853, 2582, 2612, 3532 |
| AvaII | GGWCC | 3 cut(s) | 127, 330, 376 |
| AvrII | CCTAGG | 3 cut(s) | 283, 1460, 3266 |
| AxyI | CCTNAGG | 1 cut(s) | 326 |
| BaeI | ACNNNNGTAYC | 2 cut(s) | 3366, 3399 |
| BarI | GAAGNNNNNNTAC | 2 cut(s) | 3970, 4002 |
| Bbv12I | GWGCWC | 2 cut(s) | 3572, 3703 |
| BbvI | GCAGC | 3 cut(s) | 871, 2717, 3983 |
| BccI | CCATC | 8 cut(s) | 926, 1361, 1898, 2072, 2234, 3397, 3529, 4082 |
| BceAI | ACGGC | 1 cut(s) | 81 |
| BcgI | CGANNNNNNTGC | 2 cut(s) | 3810, 3844 |
| BciT130I | CCWGG | 3 cut(s) | 1490, 1950, 3905 |
| BciVI | GTATCC | 1 cut(s) | 1964 |
| BclI | TGATCA | 2 cut(s) | 949, 2004 |
| BcnI | CCSGG | 1 cut(s) | 3056 |
| BcoDI | GTCTC | 7 cut(s) | 1612, 2582, 2664, 2779, 3038, 3769, 3797 |
| BfmI | CTRYAG | 4 cut(s) | 1323, 3396, 3549, 4260 |
| BfuAI | ACCTGC | 1 cut(s) | 3812 |
| BfuI | GTATCC | 1 cut(s) | 1964 |
| BglI | GCCNNNNNGGC | 1 cut(s) | 3269 |
| BisI | GCNGC | 4 cut(s) | 765, 885, 2706, 3972 |
| BlnI | CCTAGG | 3 cut(s) | 283, 1460, 3266 |
| BlpI | GCTNAGC | 1 cut(s) | 1578 |
| BlsI | GCNGC | 4 cut(s) | 766, 886, 2707, 3973 |
| Bme1390I | CCNGG | 4 cut(s) | 1490, 1950, 3056, 3905 |
| Bme18I | GGWCC | 3 cut(s) | 127, 330, 376 |
| BmeRI | GACNNNNNGTC | 1 cut(s) | 835 |
| BmgT120I | GGNCC | 3 cut(s) | 127, 330, 376 |
| BmiI | GGNNCC | 1 cut(s) | 128 |
| BmrFI | CCNGG | 4 cut(s) | 1490, 1950, 3056, 3905 |
| BmrI | ACTGGG | 1 cut(s) | 1105 |
| BmsI | GCATC | 7 cut(s) | 607, 901, 2180, 2362, 3759, 4002, 4253 |
| BmuI | ACTGGG | 1 cut(s) | 1105 |
| BplI | GAGNNNNNCTC | 4 cut(s) | 827, 859, 2096, 2128 |
| BpmI | CTGGAG | 2 cut(s) | 2328, 2592 |
| Bpu1102I | GCTNAGC | 1 cut(s) | 1578 |
| BpuEI | CTTGAG | 5 cut(s) | 889, 2777, 2991, 3318, 3755 |
| BpuMI | CCSGG | 1 cut(s) | 3056 |
| BsaAI | YACGTR | 1 cut(s) | 2124 |
| BsaHI | GRCGYC | 1 cut(s) | 1072 |
| Bsc4I | CCNNNNNNNGG | 1 cut(s) | 1491 |
| Bse1I | ACTGG | 4 cut(s) | 58, 1100, 2609, 4094 |
| Bse21I | CCTNAGG | 1 cut(s) | 326 |
| Bse3DI | GCAATG | 3 cut(s) | 468, 2859, 2929 |
| BseBI | CCWGG | 3 cut(s) | 1490, 1950, 3905 |
| BseGI | GGATG | 8 cut(s) | 502, 895, 1416, 3136, 3352, 3540, 3862, 4008 |
| BseLI | CCNNNNNNNGG | 1 cut(s) | 1491 |
| BseMI | GCAATG | 3 cut(s) | 468, 2859, 2929 |
| BseNI | ACTGG | 4 cut(s) | 58, 1100, 2609, 4094 |
| BseRI | GAGGAG | 1 cut(s) | 619 |
| BseX3I | CGGCCG | 1 cut(s) | 765 |
| BseXI | GCAGC | 3 cut(s) | 871, 2717, 3983 |
| BseYI | CCCAGC | 1 cut(s) | 1067 |
| BsgI | GTGCAG | 1 cut(s) | 1003 |
| Bsh1285I | CGRYCG | 1 cut(s) | 768 |
| BshFI | GGCC | 2 cut(s) | 767, 809 |
| BsiEI | CGRYCG | 1 cut(s) | 768 |
| BsiHKAI | GWGCWC | 2 cut(s) | 3572, 3703 |
| BsiSI | CCGG | 1 cut(s) | 3056 |
| BslFI | GGGAC | 3 cut(s) | 140, 1313, 3539 |
| BslI | CCNNNNNNNGG | 1 cut(s) | 1491 |
| BsmAI | GTCTC | 7 cut(s) | 1612, 2582, 2664, 2779, 3038, 3769, 3797 |
| BsmFI | GGGAC | 3 cut(s) | 140, 1313, 3539 |
| BsmI | GAATGC | 2 cut(s) | 16, 484 |
| BsnI | GGCC | 2 cut(s) | 767, 809 |
| Bsp1286I | GDGCHC | 2 cut(s) | 3572, 3703 |
| Bsp1407I | TGTACA | 2 cut(s) | 2433, 3986 |
| Bsp1720I | GCTNAGC | 1 cut(s) | 1578 |
| Bsp19I | CCATGG | 1 cut(s) | 213 |
| BspACI | CCGC | 2 cut(s) | 764, 3959 |
| BspANI | GGCC | 2 cut(s) | 767, 809 |
| BspLI | GGNNCC | 1 cut(s) | 128 |
| BspMAI | CTGCAG | 3 cut(s) | 1327, 3400, 3553 |
| BspMI | ACCTGC | 1 cut(s) | 3812 |
| BspPI | GGATC | 8 cut(s) | 284, 317, 933, 1648, 2553, 2597, 2652, 3587 |
| BsrDI | GCAATG | 3 cut(s) | 468, 2859, 2929 |
| BsrGI | TGTACA | 2 cut(s) | 2433, 3986 |
| BsrI | ACTGG | 4 cut(s) | 58, 1100, 2609, 4094 |
| BssNAI | GTATAC | 2 cut(s) | 63, 3015 |
| BssNI | GRCGYC | 1 cut(s) | 1072 |
| BssT1I | CCWWGG | 8 cut(s) | 213, 283, 957, 1460, 2730, 3266, 3720, 4036 |
| Bst1107I | GTATAC | 2 cut(s) | 63, 3015 |
| Bst2UI | CCWGG | 3 cut(s) | 1490, 1950, 3905 |
| Bst4CI | ACNGT | 4 cut(s) | 579, 1436, 1486, 1777 |
| Bst6I | CTCTTC | 2 cut(s) | 366, 2119 |
| BstACI | GRCGYC | 1 cut(s) | 1072 |
| BstAUI | TGTACA | 2 cut(s) | 2433, 3986 |
| BstBAI | YACGTR | 1 cut(s) | 2124 |
| BstC8I | GCNNGC | 5 cut(s) | 6, 1327, 1712, 3090, 4047 |
| BstDSI | CCRYGG | 1 cut(s) | 213 |
| BstF5I | GGATG | 8 cut(s) | 502, 895, 1416, 3136, 3352, 3540, 3862, 4008 |
| BstHHI | GCGC | 1 cut(s) | 3750 |
| BstMAI | GTCTC | 7 cut(s) | 1612, 2582, 2664, 2779, 3038, 3769, 3797 |
| BstMCI | CGRYCG | 1 cut(s) | 768 |
| BstMWI | GCNNNNNNNGC | 8 cut(s) | 119, 479, 881, 1793, 2177, 2863, 3059, 3269 |
| BstNI | CCWGG | 3 cut(s) | 1490, 1950, 3905 |
| BstNSI | RCATGY | 3 cut(s) | 1884, 2323, 3430 |
| BstSCI | CCNGG | 4 cut(s) | 1488, 1948, 3054, 3903 |
| BstSFI | CTRYAG | 4 cut(s) | 1323, 3396, 3549, 4260 |
| BstV1I | GCAGC | 3 cut(s) | 871, 2717, 3983 |
| BstX2I | RGATCY | 2 cut(s) | 925, 3592 |
| BstXI | CCANNNNNNTGG | 1 cut(s) | 214 |
| BstYI | RGATCY | 2 cut(s) | 925, 3592 |
| BstZ17I | GTATAC | 2 cut(s) | 63, 3015 |
| BstZI | CGGCCG | 1 cut(s) | 765 |
| Bsu36I | CCTNAGG | 1 cut(s) | 326 |
| BsuI | GTATCC | 1 cut(s) | 1964 |
| BsuRI | GGCC | 2 cut(s) | 767, 809 |
| BtgI | CCRYGG | 1 cut(s) | 213 |
| BtsCI | GGATG | 8 cut(s) | 502, 895, 1416, 3136, 3352, 3540, 3862, 4008 |
| BtsI | GCAGTG | 4 cut(s) | 2343, 3393, 3405, 3948 |
| BveI | ACCTGC | 1 cut(s) | 3812 |
| Cac8I | GCNNGC | 5 cut(s) | 6, 1327, 1712, 3090, 4047 |
| CaiI | CAGNNNCTG | 2 cut(s) | 2336, 3548 |
| CfoI | GCGC | 1 cut(s) | 3750 |
| Cfr13I | GGNCC | 3 cut(s) | 127, 330, 376 |
| CseI | GACGC | 1 cut(s) | 1061 |
| CsiI | ACCWGGT | 2 cut(s) | 1948, 3903 |
| Csp6I | GTAC | 9 cut(s) | 1086, 1807, 2154, 2434, 2552, 2612, 3771, 3987, 4184 |
| CviQI | GTAC | 9 cut(s) | 1086, 1807, 2154, 2434, 2552, 2612, 3771, 3987, 4184 |
| DraI | TTTAAA | 4 cut(s) | 2100, 2164, 3115, 3150 |
| DriI | GACNNNNNGTC | 1 cut(s) | 835 |
| EaeI | YGGCCR | 1 cut(s) | 765 |
| EagI | CGGCCG | 1 cut(s) | 765 |
| Eam1104I | CTCTTC | 2 cut(s) | 366, 2119 |
| Eam1105I | GACNNNNNGTC | 1 cut(s) | 835 |
| EarI | CTCTTC | 2 cut(s) | 366, 2119 |
| EclXI | CGGCCG | 1 cut(s) | 765 |
| Eco130I | CCWWGG | 8 cut(s) | 213, 283, 957, 1460, 2730, 3266, 3720, 4036 |
| Eco32I | GATATC | 1 cut(s) | 4133 |
| Eco47I | GGWCC | 3 cut(s) | 127, 330, 376 |
| Eco52I | CGGCCG | 1 cut(s) | 765 |
| Eco57I | CTGAAG | 5 cut(s) | 164, 573, 936, 1314, 2640 |
| Eco81I | CCTNAGG | 1 cut(s) | 326 |
| EcoO109I | RGGNCCY | 2 cut(s) | 127, 330 |
| EcoRI | GAATTC | 2 cut(s) | 1726, 3309 |
| EcoRII | CCWGG | 3 cut(s) | 1488, 1948, 3903 |
| EcoRV | GATATC | 1 cut(s) | 4133 |
| EcoT14I | CCWWGG | 8 cut(s) | 213, 283, 957, 1460, 2730, 3266, 3720, 4036 |
| EcoT22I | ATGCAT | 3 cut(s) | 2173, 2211, 2859 |
| ErhI | CCWWGG | 8 cut(s) | 213, 283, 957, 1460, 2730, 3266, 3720, 4036 |
| FaqI | GGGAC | 3 cut(s) | 140, 1313, 3539 |
| FbaI | TGATCA | 2 cut(s) | 949, 2004 |
| FblI | GTMKAC | 6 cut(s) | 62, 3014, 3365, 3457, 3646, 3667 |
| Fnu4HI | GCNGC | 4 cut(s) | 765, 885, 2706, 3972 |
| FokI | GGATG | 8 cut(s) | 509, 882, 1403, 3143, 3359, 3547, 3869, 4015 |
| Fsp4HI | GCNGC | 4 cut(s) | 765, 885, 2706, 3972 |
| GlaI | GCGC | 1 cut(s) | 3749 |
| GluI | GCNGC | 4 cut(s) | 765, 885, 2706, 3972 |
| GsaI | CCCAGC | 1 cut(s) | 1071 |
| GsuI | CTGGAG | 2 cut(s) | 2328, 2592 |
| HaeIII | GGCC | 2 cut(s) | 767, 809 |
| HapII | CCGG | 1 cut(s) | 3056 |
| HgaI | GACGC | 1 cut(s) | 1061 |
| HhaI | GCGC | 1 cut(s) | 3750 |
| Hin1I | GRCGYC | 1 cut(s) | 1072 |
| Hin6I | GCGC | 1 cut(s) | 3748 |
| HinP1I | GCGC | 1 cut(s) | 3748 |
| HincII | GTYRAC | 4 cut(s) | 1174, 1567, 2341, 3613 |
| HindII | GTYRAC | 4 cut(s) | 1174, 1567, 2341, 3613 |
| HindIII | AAGCTT | 3 cut(s) | 1580, 3240, 4043 |
| HpaI | GTTAAC | 2 cut(s) | 1174, 1567 |
| HpaII | CCGG | 1 cut(s) | 3056 |
| HphI | GGTGA | 6 cut(s) | 299, 959, 1853, 2582, 2612, 3532 |
| Hpy99I | CGWCG | 1 cut(s) | 3867 |
| HpyCH4III | ACNGT | 4 cut(s) | 579, 1436, 1486, 1777 |
| HpyCH4IV | ACGT | 7 cut(s) | 91, 1403, 1895, 2123, 3773, 3865, 3966 |
| HpyF10VI | GCNNNNNNNGC | 8 cut(s) | 119, 479, 881, 1793, 2177, 2863, 3059, 3269 |
| HpySE526I | ACGT | 7 cut(s) | 91, 1403, 1895, 2123, 3773, 3865, 3966 |
| Hsp92I | GRCGYC | 1 cut(s) | 1072 |
| HspAI | GCGC | 1 cut(s) | 3748 |
| Ksp22I | TGATCA | 2 cut(s) | 949, 2004 |
| KspAI | GTTAAC | 2 cut(s) | 1174, 1567 |
| Lsp1109I | GCAGC | 3 cut(s) | 871, 2717, 3983 |
| LweI | GCATC | 7 cut(s) | 607, 901, 2180, 2362, 3759, 4002, 4253 |
| MabI | ACCWGGT | 2 cut(s) | 1948, 3903 |
| MaeII | ACGT | 7 cut(s) | 91, 1403, 1895, 2123, 3773, 3865, 3966 |
| MfeI | CAATTG | 1 cut(s) | 1689 |
| MflI | RGATCY | 2 cut(s) | 925, 3592 |
| MhlI | GDGCHC | 2 cut(s) | 3572, 3703 |
| Mph1103I | ATGCAT | 3 cut(s) | 2173, 2211, 2859 |
| MroXI | GAANNNNTTC | 2 cut(s) | 3075, 3389 |
| MslI | CAYNNNNRTG | 5 cut(s) | 212, 260, 1434, 3398, 3563 |
| MspA1I | CMGCKG | 1 cut(s) | 3974 |
| MspI | CCGG | 1 cut(s) | 3056 |
| MspR9I | CCNGG | 4 cut(s) | 1490, 1950, 3056, 3905 |
| MunI | CAATTG | 1 cut(s) | 1689 |
| Mva1269I | GAATGC | 2 cut(s) | 16, 484 |
| MvaI | CCWGG | 3 cut(s) | 1490, 1950, 3905 |
| MwoI | GCNNNNNNNGC | 8 cut(s) | 119, 479, 881, 1793, 2177, 2863, 3059, 3269 |
| NciI | CCSGG | 1 cut(s) | 3056 |
| NcoI | CCATGG | 1 cut(s) | 213 |
| NlaIV | GGNNCC | 1 cut(s) | 128 |
| NsiI | ATGCAT | 3 cut(s) | 2173, 2211, 2859 |
| NspI | RCATGY | 3 cut(s) | 1884, 2323, 3430 |
| OliI | CACNNNNGTG | 2 cut(s) | 1434, 3398 |
| PciI | ACATGT | 2 cut(s) | 1880, 2319 |
| PctI | GAATGC | 2 cut(s) | 16, 484 |
| PdmI | GAANNNNTTC | 2 cut(s) | 3075, 3389 |
| PkrI | GCNGC | 4 cut(s) | 766, 886, 2707, 3973 |
| Ppu21I | YACGTR | 1 cut(s) | 2124 |
| PpuMI | RGGWCCY | 2 cut(s) | 127, 330 |
| PscI | ACATGT | 2 cut(s) | 1880, 2319 |
| PshBI | ATTAAT | 1 cut(s) | 2847 |
| Psp1406I | AACGTT | 1 cut(s) | 1403 |
| Psp5II | RGGWCCY | 2 cut(s) | 127, 330 |
| Psp6I | CCWGG | 3 cut(s) | 1488, 1948, 3903 |
| PspFI | CCCAGC | 1 cut(s) | 1067 |
| PspGI | CCWGG | 3 cut(s) | 1488, 1948, 3903 |
| PspN4I | GGNNCC | 1 cut(s) | 128 |
| PspPI | GGNCC | 3 cut(s) | 127, 330, 376 |
| PspPPI | RGGWCCY | 2 cut(s) | 127, 330 |
| PstI | CTGCAG | 3 cut(s) | 1327, 3400, 3553 |
| PstNI | CAGNNNCTG | 2 cut(s) | 2336, 3548 |
| PsuI | RGATCY | 2 cut(s) | 925, 3592 |
| PvuII | CAGCTG | 1 cut(s) | 3974 |
| RsaI | GTAC | 9 cut(s) | 1087, 1808, 2155, 2435, 2553, 2613, 3772, 3988, 4185 |
| RsaNI | GTAC | 9 cut(s) | 1086, 1807, 2154, 2434, 2552, 2612, 3771, 3987, 4184 |
| RseI | CAYNNNNRTG | 5 cut(s) | 212, 260, 1434, 3398, 3563 |
| SatI | GCNGC | 4 cut(s) | 765, 885, 2706, 3972 |
| Sau96I | GGNCC | 3 cut(s) | 127, 330, 376 |
| ScrFI | CCNGG | 4 cut(s) | 1490, 1950, 3056, 3905 |
| SduI | GDGCHC | 2 cut(s) | 3572, 3703 |
| SexAI | ACCWGGT | 2 cut(s) | 1948, 3903 |
| SfaNI | GCATC | 7 cut(s) | 607, 901, 2180, 2362, 3759, 4002, 4253 |
| SfcI | CTRYAG | 4 cut(s) | 1323, 3396, 3549, 4260 |
| SinI | GGWCC | 3 cut(s) | 127, 330, 376 |
| SmiMI | CAYNNNNRTG | 5 cut(s) | 212, 260, 1434, 3398, 3563 |
| SmlI | CTYRAG | 5 cut(s) | 904, 2756, 3006, 3333, 3734 |
| SmoI | CTYRAG | 5 cut(s) | 904, 2756, 3006, 3333, 3734 |
| SsiI | CCGC | 2 cut(s) | 764, 3959 |
| SspI | AATATT | 4 cut(s) | 43, 1156, 2216, 3357 |
| StyD4I | CCNGG | 4 cut(s) | 1488, 1948, 3054, 3903 |
| StyI | CCWWGG | 8 cut(s) | 213, 283, 957, 1460, 2730, 3266, 3720, 4036 |
| TaaI | ACNGT | 4 cut(s) | 579, 1436, 1486, 1777 |
| TaiI | ACGT | 7 cut(s) | 94, 1406, 1898, 2126, 3776, 3868, 3969 |
| TaqI | TCGA | 8 cut(s) | 1456, 2419, 2701, 3069, 3079, 3628, 3703, 3862 |
| TaqII | GACCGA | 2 cut(s) | 743, 786 |
| TatI | WGTACW | 4 cut(s) | 1085, 2433, 2611, 3986 |
| TauI | GCSGC | 1 cut(s) | 767 |
| TseI | GCWGC | 3 cut(s) | 884, 2705, 3971 |
| TspGWI | ACGGA | 1 cut(s) | 2697 |
| VpaK11BI | GGWCC | 3 cut(s) | 127, 330, 376 |
| VspI | ATTAAT | 1 cut(s) | 2847 |
| XbaI | TCTAGA | 5 cut(s) | 385, 572, 1201, 1826, 4225 |
| XceI | RCATGY | 3 cut(s) | 1884, 2323, 3430 |
| XmaJI | CCTAGG | 3 cut(s) | 283, 1460, 3266 |
| XmiI | GTMKAC | 6 cut(s) | 62, 3014, 3365, 3457, 3646, 3667 |
| XmnI | GAANNNNTTC | 2 cut(s) | 3075, 3389 |
| Zsp2I | ATGCAT | 3 cut(s) | 2173, 2211, 2859 |