ribonuclease H protein
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| PPR_3 | PF13812 | 82 - 138 | 8.7e-06 | Pentatricopeptide repeat domain |
| PPR_2 | PF13041 | 91 - 139 | 8.7e-11 | PPR repeat family |
| PPR | PF01535 | 94 - 123 | 4e-06 | PPR repeat |
| PPR_2 | PF13041 | 199 - 246 | 1.2e-08 | PPR repeat family |
| PPR | PF01535 | 201 - 230 | 4.4e-07 | PPR repeat |
| E_motif | PF20431 | 316 - 378 | 3.2e-17 | E motif |
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) |
|---|---|---|---|
| Acc16I | TGCGCA | 1 cut(s) | 633 |
| Acc36I | ACCTGC | 1 cut(s) | 293 |
| AciI | CCGC | 2 cut(s) | 224, 977 |
| AclWI | GGATC | 2 cut(s) | 603, 822 |
| AcoI | YGGCCR | 1 cut(s) | 640 |
| AcsI | RAATTY | 4 cut(s) | 517, 874, 1006, 1194 |
| AcuI | CTGAAG | 1 cut(s) | 672 |
| AdeI | CACNNNGTG | 1 cut(s) | 799 |
| AfaI | GTAC | 3 cut(s) | 536, 804, 1248 |
| AfiI | CCNNNNNNNGG | 1 cut(s) | 915 |
| AflIII | ACRYGT | 2 cut(s) | 824, 1035 |
| AhdI | GACNNNNNGTC | 1 cut(s) | 1267 |
| AjnI | CCWGG | 2 cut(s) | 483, 1158 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 321, 353 |
| AloI | GAACNNNNNNTCC | 2 cut(s) | 1005, 1037 |
| AluBI | AGCT | 9 cut(s) | 21, 436, 449, 656, 869, 985, 992, 1048, 1337 |
| AluI | AGCT | 9 cut(s) | 21, 436, 449, 656, 869, 985, 992, 1048, 1337 |
| Alw21I | GWGCWC | 1 cut(s) | 795 |
| Alw26I | GTCTC | 3 cut(s) | 193, 286, 607 |
| AlwI | GGATC | 2 cut(s) | 603, 822 |
| AoxI | GGCC | 4 cut(s) | 147, 333, 374, 640 |
| ApeKI | GCWGC | 3 cut(s) | 433, 932, 1119 |
| ApoI | RAATTY | 4 cut(s) | 517, 874, 1006, 1194 |
| Asp700I | GAANNNNTTC | 1 cut(s) | 1154 |
| AspA2I | CCTAGG | 1 cut(s) | 1001 |
| AspLEI | GCGC | 1 cut(s) | 634 |
| AspS9I | GGNCC | 3 cut(s) | 334, 375, 1013 |
| AsuC2I | CCSGG | 1 cut(s) | 1116 |
| AsuHPI | GGTGA | 3 cut(s) | 83, 503, 1174 |
| AsuII | TTCGAA | 1 cut(s) | 1311 |
| AvaII | GGWCC | 1 cut(s) | 1013 |
| AvrII | CCTAGG | 1 cut(s) | 1001 |
| BalI | TGGCCA | 1 cut(s) | 642 |
| Bbv12I | GWGCWC | 1 cut(s) | 795 |
| BbvI | GCAGC | 3 cut(s) | 445, 919, 1106 |
| BccI | CCATC | 3 cut(s) | 259, 554, 1050 |
| BceAI | ACGGC | 1 cut(s) | 893 |
| BcgI | CGANNNNNNTGC | 2 cut(s) | 837, 871 |
| BciT130I | CCWGG | 2 cut(s) | 485, 1160 |
| BcnI | CCSGG | 1 cut(s) | 1116 |
| BcoDI | GTCTC | 3 cut(s) | 193, 286, 607 |
| BfaI | CTAG | 1 cut(s) | 1002 |
| BfmI | CTRYAG | 3 cut(s) | 27, 431, 1120 |
| BfuAI | ACCTGC | 1 cut(s) | 293 |
| BisI | GCNGC | 4 cut(s) | 225, 434, 933, 1120 |
| BlnI | CCTAGG | 1 cut(s) | 1001 |
| BlsI | GCNGC | 4 cut(s) | 226, 435, 934, 1121 |
| Bme1390I | CCNGG | 3 cut(s) | 485, 1116, 1160 |
| Bme18I | GGWCC | 1 cut(s) | 1013 |
| BmeRI | GACNNNNNGTC | 1 cut(s) | 1267 |
| BmgT120I | GGNCC | 3 cut(s) | 334, 375, 1013 |
| BmrFI | CCNGG | 3 cut(s) | 485, 1116, 1160 |
| BmsI | GCATC | 3 cut(s) | 159, 895, 1243 |
| Bpu14I | TTCGAA | 1 cut(s) | 1311 |
| BpuMI | CCSGG | 1 cut(s) | 1116 |
| Bsa29I | ATCGAT | 1 cut(s) | 248 |
| BsaBI | GATNNNNATC | 1 cut(s) | 173 |
| BsaI | GGTCTC | 1 cut(s) | 193 |
| BsaJI | CCNNGG | 4 cut(s) | 201, 337, 643, 1001 |
| BsaXI | ACNNNNNCTCC | 6 cut(s) | 333, 363, 971, 1001, 1045, 1075 |
| Bsc4I | CCNNNNNNNGG | 1 cut(s) | 915 |
| Bse3DI | GCAATG | 1 cut(s) | 109 |
| Bse8I | GATNNNNATC | 1 cut(s) | 173 |
| BseBI | CCWGG | 2 cut(s) | 485, 1160 |
| BseCI | ATCGAT | 1 cut(s) | 248 |
| BseDI | CCNNGG | 4 cut(s) | 201, 337, 643, 1001 |
| BseGI | GGATG | 1 cut(s) | 174 |
| BseJI | GATNNNNATC | 1 cut(s) | 173 |
| BseLI | CCNNNNNNNGG | 1 cut(s) | 915 |
| BseMI | GCAATG | 1 cut(s) | 109 |
| BseRI | GAGGAG | 1 cut(s) | 341 |
| BseXI | GCAGC | 3 cut(s) | 445, 919, 1106 |
| BshFI | GGCC | 4 cut(s) | 149, 335, 376, 642 |
| BshVI | ATCGAT | 1 cut(s) | 248 |
| BsiHKAI | GWGCWC | 1 cut(s) | 795 |
| BsiSI | CCGG | 1 cut(s) | 1115 |
| BslFI | GGGAC | 2 cut(s) | 639, 661 |
| BslI | CCNNNNNNNGG | 1 cut(s) | 915 |
| BsmAI | GTCTC | 3 cut(s) | 193, 286, 607 |
| BsmFI | GGGAC | 2 cut(s) | 639, 661 |
| BsmI | GAATGC | 2 cut(s) | 295, 616 |
| BsnI | GGCC | 4 cut(s) | 149, 335, 376, 642 |
| Bso31I | GGTCTC | 1 cut(s) | 193 |
| Bsp119I | TTCGAA | 1 cut(s) | 1311 |
| Bsp1286I | GDGCHC | 1 cut(s) | 795 |
| Bsp1407I | TGTACA | 2 cut(s) | 534, 1246 |
| Bsp143I | GATC | 5 cut(s) | 245, 427, 595, 814, 835 |
| Bsp19I | CCATGG | 2 cut(s) | 201, 643 |
| BspACI | CCGC | 2 cut(s) | 224, 977 |
| BspANI | GGCC | 4 cut(s) | 149, 335, 376, 642 |
| BspDI | ATCGAT | 1 cut(s) | 248 |
| BspMAI | CTGCAG | 3 cut(s) | 31, 435, 1124 |
| BspMI | ACCTGC | 1 cut(s) | 293 |
| BspPI | GGATC | 2 cut(s) | 603, 822 |
| BspQI | GCTCTTC | 3 cut(s) | 489, 783, 1272 |
| BspT104I | TTCGAA | 1 cut(s) | 1311 |
| BspTNI | GGTCTC | 1 cut(s) | 193 |
| BsrDI | GCAATG | 1 cut(s) | 109 |
| BsrGI | TGTACA | 2 cut(s) | 534, 1246 |
| BssECI | CCNNGG | 4 cut(s) | 201, 337, 643, 1001 |
| BssMI | GATC | 5 cut(s) | 245, 427, 595, 814, 835 |
| BssT1I | CCWWGG | 4 cut(s) | 201, 337, 643, 1001 |
| Bst2UI | CCWGG | 2 cut(s) | 485, 1160 |
| Bst6I | CTCTTC | 4 cut(s) | 324, 489, 783, 1272 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 299 |
| BstAUI | TGTACA | 2 cut(s) | 534, 1246 |
| BstBI | TTCGAA | 1 cut(s) | 1311 |
| BstC8I | GCNNGC | 5 cut(s) | 19, 58, 443, 447, 930 |
| BstDEI | CTNAG | 1 cut(s) | 870 |
| BstDSI | CCRYGG | 2 cut(s) | 201, 643 |
| BstF5I | GGATG | 1 cut(s) | 174 |
| BstHHI | GCGC | 1 cut(s) | 634 |
| BstKTI | GATC | 5 cut(s) | 248, 430, 598, 817, 838 |
| BstMAI | GTCTC | 3 cut(s) | 193, 286, 607 |
| BstMBI | GATC | 5 cut(s) | 245, 427, 595, 814, 835 |
| BstMWI | GCNNNNNNNGC | 3 cut(s) | 224, 299, 442 |
| BstNI | CCWGG | 2 cut(s) | 485, 1160 |
| BstNSI | RCATGY | 4 cut(s) | 56, 632, 828, 1039 |
| BstSCI | CCNGG | 3 cut(s) | 483, 1114, 1158 |
| BstSFI | CTRYAG | 3 cut(s) | 27, 431, 1120 |
| BstV1I | GCAGC | 3 cut(s) | 445, 919, 1106 |
| Bsu15I | ATCGAT | 1 cut(s) | 248 |
| BsuRI | GGCC | 4 cut(s) | 149, 335, 376, 642 |
| BsuTUI | ATCGAT | 1 cut(s) | 248 |
| BtgI | CCRYGG | 2 cut(s) | 201, 643 |
| BtsCI | GGATG | 1 cut(s) | 174 |
| BtsI | GCAGTG | 1 cut(s) | 36 |
| BtsIMutI | CAGTG | 1 cut(s) | 36 |
| BveI | ACCTGC | 1 cut(s) | 293 |
| Cac8I | GCNNGC | 5 cut(s) | 19, 58, 443, 447, 930 |
| CfoI | GCGC | 1 cut(s) | 634 |
| Cfr13I | GGNCC | 3 cut(s) | 334, 375, 1013 |
| ClaI | ATCGAT | 1 cut(s) | 248 |
| Csp6I | GTAC | 3 cut(s) | 535, 803, 1247 |
| CviQI | GTAC | 3 cut(s) | 535, 803, 1247 |
| DdeI | CTNAG | 1 cut(s) | 870 |
| DpnI | GATC | 5 cut(s) | 247, 429, 597, 816, 837 |
| DpnII | GATC | 5 cut(s) | 245, 427, 595, 814, 835 |
| DraIII | CACNNNGTG | 1 cut(s) | 799 |
| DriI | GACNNNNNGTC | 1 cut(s) | 1267 |
| EaeI | YGGCCR | 1 cut(s) | 640 |
| Eam1104I | CTCTTC | 4 cut(s) | 324, 489, 783, 1272 |
| Eam1105I | GACNNNNNGTC | 1 cut(s) | 1267 |
| EarI | CTCTTC | 4 cut(s) | 324, 489, 783, 1272 |
| EciI | GGCGGA | 1 cut(s) | 992 |
| Eco130I | CCWWGG | 4 cut(s) | 201, 337, 643, 1001 |
| Eco31I | GGTCTC | 1 cut(s) | 193 |
| Eco47I | GGWCC | 1 cut(s) | 1013 |
| Eco57I | CTGAAG | 1 cut(s) | 672 |
| EcoO109I | RGGNCCY | 1 cut(s) | 334 |
| EcoRI | GAATTC | 1 cut(s) | 1006 |
| EcoRII | CCWGG | 2 cut(s) | 483, 1158 |
| EcoT14I | CCWWGG | 4 cut(s) | 201, 337, 643, 1001 |
| EcoT22I | ATGCAT | 1 cut(s) | 109 |
| ErhI | CCWWGG | 4 cut(s) | 201, 337, 643, 1001 |
| FalI | AAGNNNNNCTT | 2 cut(s) | 321, 353 |
| FaqI | GGGAC | 2 cut(s) | 639, 661 |
| Fnu4HI | GCNGC | 4 cut(s) | 225, 434, 933, 1120 |
| FokI | GGATG | 1 cut(s) | 181 |
| Fsp4HI | GCNGC | 4 cut(s) | 225, 434, 933, 1120 |
| FspBI | CTAG | 1 cut(s) | 1002 |
| FspI | TGCGCA | 1 cut(s) | 633 |
| GlaI | GCGC | 1 cut(s) | 633 |
| GluI | GCNGC | 4 cut(s) | 225, 434, 933, 1120 |
| HaeIII | GGCC | 4 cut(s) | 149, 335, 376, 642 |
| HapII | CCGG | 1 cut(s) | 1115 |
| HhaI | GCGC | 1 cut(s) | 634 |
| Hin6I | GCGC | 1 cut(s) | 632 |
| HinP1I | GCGC | 1 cut(s) | 632 |
| HincII | GTYRAC | 2 cut(s) | 1086, 1108 |
| HindII | GTYRAC | 2 cut(s) | 1086, 1108 |
| HinfI | GANTC | 4 cut(s) | 342, 365, 1268, 1289 |
| HpaII | CCGG | 1 cut(s) | 1115 |
| HphI | GGTGA | 3 cut(s) | 83, 503, 1174 |
| Hpy166II | GTNNAC | 3 cut(s) | 255, 1086, 1108 |
| Hpy188I | TCNGA | 5 cut(s) | 179, 193, 578, 1149, 1327 |
| Hpy188III | TCNNGA | 3 cut(s) | 355, 659, 1011 |
| Hpy8I | GTNNAC | 3 cut(s) | 255, 1086, 1108 |
| HpyAV | CCTTC | 6 cut(s) | 32, 147, 752, 805, 1071, 1183 |
| HpyF10VI | GCNNNNNNNGC | 3 cut(s) | 224, 299, 442 |
| HpyF3I | CTNAG | 1 cut(s) | 870 |
| HspAI | GCGC | 1 cut(s) | 632 |
| Kzo9I | GATC | 5 cut(s) | 245, 427, 595, 814, 835 |
| LguI | GCTCTTC | 3 cut(s) | 489, 783, 1272 |
| LmnI | GCTCC | 1 cut(s) | 691 |
| Lsp1109I | GCAGC | 3 cut(s) | 445, 919, 1106 |
| LweI | GCATC | 3 cut(s) | 159, 895, 1243 |
| MaeI | CTAG | 1 cut(s) | 1002 |
| MaeIII | GTNAC | 3 cut(s) | 305, 706, 1259 |
| MalI | GATC | 5 cut(s) | 247, 429, 597, 816, 837 |
| MboI | GATC | 5 cut(s) | 245, 427, 595, 814, 835 |
| MboII | GAAGA | 8 cut(s) | 341, 506, 569, 767, 800, 1016, 1289, 1340 |
| MfeI | CAATTG | 1 cut(s) | 806 |
| MhlI | GDGCHC | 1 cut(s) | 795 |
| MlsI | TGGCCA | 1 cut(s) | 642 |
| MluCI | AATT | 7 cut(s) | 479, 517, 766, 806, 874, 1006, 1194 |
| MluNI | TGGCCA | 1 cut(s) | 642 |
| MlyI | GAGTC | 3 cut(s) | 336, 374, 1277 |
| MmeI | TCCRAC | 3 cut(s) | 493, 567, 1106 |
| MnlI | CCTC | 9 cut(s) | 139, 214, 264, 325, 362, 842, 877, 1067, 1083 |
| Mox20I | TGGCCA | 1 cut(s) | 642 |
| Mph1103I | ATGCAT | 1 cut(s) | 109 |
| MroXI | GAANNNNTTC | 1 cut(s) | 1154 |
| MscI | TGGCCA | 1 cut(s) | 642 |
| MseI | TTAA | 2 cut(s) | 878, 957 |
| MslI | CAYNNNNRTG | 3 cut(s) | 893, 1149, 1242 |
| Msp20I | TGGCCA | 1 cut(s) | 642 |
| MspI | CCGG | 1 cut(s) | 1115 |
| MspR9I | CCNGG | 3 cut(s) | 485, 1116, 1160 |
| MunI | CAATTG | 1 cut(s) | 806 |
| Mva1269I | GAATGC | 2 cut(s) | 295, 616 |
| MvaI | CCWGG | 2 cut(s) | 485, 1160 |
| MwoI | GCNNNNNNNGC | 3 cut(s) | 224, 299, 442 |
| NciI | CCSGG | 1 cut(s) | 1116 |
| NcoI | CCATGG | 2 cut(s) | 201, 643 |
| NdeII | GATC | 5 cut(s) | 245, 427, 595, 814, 835 |
| NmuCI | GTSAC | 1 cut(s) | 1259 |
| NsbI | TGCGCA | 1 cut(s) | 633 |
| NsiI | ATGCAT | 1 cut(s) | 109 |
| NspI | RCATGY | 4 cut(s) | 56, 632, 828, 1039 |
| NspV | TTCGAA | 1 cut(s) | 1311 |
| PciI | ACATGT | 2 cut(s) | 824, 1035 |
| PciSI | GCTCTTC | 3 cut(s) | 489, 783, 1272 |
| PctI | GAATGC | 2 cut(s) | 295, 616 |
| PdmI | GAANNNNTTC | 1 cut(s) | 1154 |
| PfeI | GAWTC | 1 cut(s) | 1289 |
| PkrI | GCNGC | 4 cut(s) | 226, 435, 934, 1121 |
| PleI | GAGTC | 3 cut(s) | 336, 373, 1276 |
| PpsI | GAGTC | 3 cut(s) | 336, 373, 1276 |
| PscI | ACATGT | 2 cut(s) | 824, 1035 |
| Psp6I | CCWGG | 2 cut(s) | 483, 1158 |
| PspGI | CCWGG | 2 cut(s) | 483, 1158 |
| PspPI | GGNCC | 3 cut(s) | 334, 375, 1013 |
| PstI | CTGCAG | 3 cut(s) | 31, 435, 1124 |
| RsaI | GTAC | 3 cut(s) | 536, 804, 1248 |
| RsaNI | GTAC | 3 cut(s) | 535, 803, 1247 |
| RseI | CAYNNNNRTG | 3 cut(s) | 893, 1149, 1242 |
| SapI | GCTCTTC | 3 cut(s) | 489, 783, 1272 |
| SaqAI | TTAA | 2 cut(s) | 878, 957 |
| SatI | GCNGC | 4 cut(s) | 225, 434, 933, 1120 |
| Sau3AI | GATC | 5 cut(s) | 245, 427, 595, 814, 835 |
| Sau96I | GGNCC | 3 cut(s) | 334, 375, 1013 |
| SchI | GAGTC | 3 cut(s) | 336, 374, 1277 |
| ScrFI | CCNGG | 3 cut(s) | 485, 1116, 1160 |
| SduI | GDGCHC | 1 cut(s) | 795 |
| SfaNI | GCATC | 3 cut(s) | 159, 895, 1243 |
| SfcI | CTRYAG | 3 cut(s) | 27, 431, 1120 |
| SfuI | TTCGAA | 1 cut(s) | 1311 |
| SinI | GGWCC | 1 cut(s) | 1013 |
| SmiMI | CAYNNNNRTG | 3 cut(s) | 893, 1149, 1242 |
| Sse9I | AATT | 7 cut(s) | 479, 517, 766, 806, 874, 1006, 1194 |
| SsiI | CCGC | 2 cut(s) | 224, 977 |
| SspI | AATATT | 2 cut(s) | 666, 955 |
| SspMI | CTAG | 1 cut(s) | 1002 |
| StyD4I | CCNGG | 3 cut(s) | 483, 1114, 1158 |
| StyI | CCWWGG | 4 cut(s) | 201, 337, 643, 1001 |
| TaqI | TCGA | 3 cut(s) | 248, 847, 1311 |
| TasI | AATT | 7 cut(s) | 479, 517, 766, 806, 874, 1006, 1194 |
| TatI | WGTACW | 2 cut(s) | 534, 1246 |
| TauI | GCSGC | 1 cut(s) | 227 |
| TfiI | GAWTC | 1 cut(s) | 1289 |
| Tru1I | TTAA | 2 cut(s) | 878, 957 |
| Tru9I | TTAA | 2 cut(s) | 878, 957 |
| TscAI | CASTG | 1 cut(s) | 36 |
| TseFI | GTSAC | 1 cut(s) | 1259 |
| TseI | GCWGC | 3 cut(s) | 433, 932, 1119 |
| Tsp45I | GTSAC | 1 cut(s) | 1259 |
| TspDTI | ATGAA | 9 cut(s) | 80, 342, 554, 797, 801, 935, 1244, 1290, 1293 |
| TspRI | CASTG | 1 cut(s) | 36 |
| VpaK11BI | GGWCC | 1 cut(s) | 1013 |
| XapI | RAATTY | 4 cut(s) | 517, 874, 1006, 1194 |
| XceI | RCATGY | 4 cut(s) | 56, 632, 828, 1039 |
| XmaJI | CCTAGG | 1 cut(s) | 1001 |
| XmnI | GAANNNNTTC | 1 cut(s) | 1154 |
| XspI | CTAG | 1 cut(s) | 1002 |
| Zsp2I | ATGCAT | 1 cut(s) | 109 |