ribonuclease H protein
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| 5_3_exonuc_N | PF02739 | 98 - 165 | 2.6e-07 | 5'-3' exonuclease, N-terminal resolvase-like domain |
| 5_3_exonuc_N | PF02739 | 180 - 288 | 1.7e-28 | 5'-3' exonuclease, N-terminal resolvase-like domain |
| 5_3_exonuc | PF01367 | 291 - 386 | 2.4e-24 | 5'-3' exonuclease, C-terminal SAM fold |
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AanI | TTATAA | 2 cut(s) | 428, 1151 |
| AarI | CACCTGC | 1 cut(s) | 1043 |
| Acc36I | ACCTGC | 1 cut(s) | 1043 |
| Acc65I | GGTACC | 1 cut(s) | 1120 |
| AccB1I | GGYRCC | 2 cut(s) | 96, 1120 |
| AciI | CCGC | 5 cut(s) | 156, 180, 464, 567, 1211 |
| AclI | AACGTT | 1 cut(s) | 951 |
| AclWI | GGATC | 2 cut(s) | 766, 1223 |
| AcoI | YGGCCR | 1 cut(s) | 361 |
| AcsI | RAATTY | 4 cut(s) | 544, 977, 994, 1175 |
| AcuI | CTGAAG | 1 cut(s) | 602 |
| AcvI | CACGTG | 1 cut(s) | 812 |
| AfaI | GTAC | 3 cut(s) | 623, 738, 1122 |
| AfeI | AGCGCT | 1 cut(s) | 417 |
| AfiI | CCNNNNNNNGG | 3 cut(s) | 284, 463, 595 |
| AgsI | TTSAA | 5 cut(s) | 35, 61, 282, 628, 1129 |
| AhlI | ACTAGT | 1 cut(s) | 503 |
| AjnI | CCWGG | 3 cut(s) | 73, 670, 928 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 376, 408 |
| AluBI | AGCT | 5 cut(s) | 57, 80, 121, 340, 683 |
| AluI | AGCT | 5 cut(s) | 57, 80, 121, 340, 683 |
| Alw21I | GWGCWC | 1 cut(s) | 82 |
| Alw26I | GTCTC | 3 cut(s) | 137, 751, 1190 |
| AlwI | GGATC | 2 cut(s) | 766, 1223 |
| AlwNI | CAGNNNCTG | 1 cut(s) | 1058 |
| Ama87I | CYCGRG | 1 cut(s) | 92 |
| Aor51HI | AGCGCT | 1 cut(s) | 417 |
| AoxI | GGCC | 4 cut(s) | 3, 70, 361, 1041 |
| ApeKI | GCWGC | 1 cut(s) | 22 |
| ApoI | RAATTY | 4 cut(s) | 544, 977, 994, 1175 |
| Asp700I | GAANNNNTTC | 1 cut(s) | 805 |
| Asp718I | GGTACC | 1 cut(s) | 1120 |
| AspLEI | GCGC | 3 cut(s) | 108, 418, 792 |
| AspS9I | GGNCC | 1 cut(s) | 71 |
| AsuC2I | CCSGG | 1 cut(s) | 204 |
| AsuHPI | GGTGA | 1 cut(s) | 920 |
| AvaI | CYCGRG | 1 cut(s) | 92 |
| AxyI | CCTNAGG | 1 cut(s) | 1158 |
| BaeGI | GKGCMC | 1 cut(s) | 99 |
| BaeI | ACNNNNGTAYC | 2 cut(s) | 591, 624 |
| BalI | TGGCCA | 1 cut(s) | 363 |
| BanI | GGYRCC | 2 cut(s) | 96, 1120 |
| BanII | GRGCYC | 1 cut(s) | 82 |
| BbrPI | CACGTG | 1 cut(s) | 812 |
| Bbv12I | GWGCWC | 1 cut(s) | 82 |
| BbvI | GCAGC | 1 cut(s) | 9 |
| BccI | CCATC | 8 cut(s) | 323, 372, 374, 476, 659, 817, 932, 1160 |
| BceAI | ACGGC | 1 cut(s) | 322 |
| BcgI | CGANNNNNNTGC | 2 cut(s) | 73, 107 |
| BciT130I | CCWGG | 3 cut(s) | 75, 672, 930 |
| BciVI | GTATCC | 1 cut(s) | 592 |
| BcnI | CCSGG | 1 cut(s) | 204 |
| BcoDI | GTCTC | 3 cut(s) | 137, 751, 1190 |
| BcuI | ACTAGT | 1 cut(s) | 503 |
| BfaI | CTAG | 2 cut(s) | 504, 1291 |
| BfmI | CTRYAG | 2 cut(s) | 322, 440 |
| BfoI | RGCGCY | 1 cut(s) | 419 |
| BfuAI | ACCTGC | 1 cut(s) | 1043 |
| BfuI | GTATCC | 1 cut(s) | 592 |
| BglII | AGATCT | 1 cut(s) | 1138 |
| BisI | GCNGC | 2 cut(s) | 23, 180 |
| BlsI | GCNGC | 2 cut(s) | 24, 181 |
| BmcAI | AGTACT | 1 cut(s) | 623 |
| Bme1390I | CCNGG | 4 cut(s) | 75, 204, 672, 930 |
| BmeT110I | CYCGRG | 1 cut(s) | 92 |
| BmgT120I | GGNCC | 1 cut(s) | 71 |
| BmiI | GGNNCC | 4 cut(s) | 98, 669, 865, 1122 |
| BmrFI | CCNGG | 4 cut(s) | 75, 204, 672, 930 |
| BmsI | GCATC | 2 cut(s) | 641, 1021 |
| BplI | GAGNNNNNCTC | 2 cut(s) | 282, 314 |
| BpuMI | CCSGG | 1 cut(s) | 204 |
| BsaAI | YACGTR | 1 cut(s) | 812 |
| BsaJI | CCNNGG | 3 cut(s) | 73, 358, 929 |
| BsaWI | WCCGGW | 1 cut(s) | 595 |
| BsaXI | ACNNNNNCTCC | 2 cut(s) | 381, 411 |
| Bsc4I | CCNNNNNNNGG | 3 cut(s) | 284, 463, 595 |
| Bse1I | ACTGG | 3 cut(s) | 107, 183, 1232 |
| Bse21I | CCTNAGG | 1 cut(s) | 1158 |
| Bse3DI | GCAATG | 1 cut(s) | 785 |
| BseBI | CCWGG | 3 cut(s) | 75, 672, 930 |
| BseDI | CCNNGG | 3 cut(s) | 73, 358, 929 |
| BseGI | GGATG | 5 cut(s) | 152, 311, 512, 632, 1168 |
| BseLI | CCNNNNNNNGG | 3 cut(s) | 284, 463, 595 |
| BseMI | GCAATG | 1 cut(s) | 785 |
| BseMII | CTCAG | 2 cut(s) | 893, 1149 |
| BseNI | ACTGG | 3 cut(s) | 107, 183, 1232 |
| BseSI | GKGCMC | 1 cut(s) | 99 |
| BseXI | GCAGC | 1 cut(s) | 9 |
| BshFI | GGCC | 4 cut(s) | 5, 72, 363, 1043 |
| BshNI | GGYRCC | 2 cut(s) | 96, 1120 |
| BsiHKAI | GWGCWC | 1 cut(s) | 82 |
| BsiHKCI | CYCGRG | 1 cut(s) | 92 |
| BsiSI | CCGG | 2 cut(s) | 204, 596 |
| BslFI | GGGAC | 2 cut(s) | 177, 627 |
| BslI | CCNNNNNNNGG | 3 cut(s) | 284, 463, 595 |
| BsmAI | GTCTC | 3 cut(s) | 137, 751, 1190 |
| BsmBI | CGTCTC | 1 cut(s) | 137 |
| BsmFI | GGGAC | 2 cut(s) | 177, 627 |
| BsnI | GGCC | 4 cut(s) | 5, 72, 363, 1043 |
| BsoBI | CYCGRG | 1 cut(s) | 92 |
| Bsp1286I | GDGCHC | 2 cut(s) | 82, 99 |
| Bsp143I | GATC | 5 cut(s) | 326, 771, 1102, 1138, 1228 |
| Bsp19I | CCATGG | 1 cut(s) | 358 |
| BspACI | CCGC | 5 cut(s) | 156, 180, 464, 567, 1211 |
| BspANI | GGCC | 4 cut(s) | 5, 72, 363, 1043 |
| BspCNI | CTCAG | 2 cut(s) | 892, 1150 |
| BspHI | TCATGA | 1 cut(s) | 214 |
| BspLI | GGNNCC | 4 cut(s) | 98, 669, 865, 1122 |
| BspMI | ACCTGC | 1 cut(s) | 1043 |
| BspPI | GGATC | 2 cut(s) | 766, 1223 |
| BspQI | GCTCTTC | 1 cut(s) | 1237 |
| BspT107I | GGYRCC | 2 cut(s) | 96, 1120 |
| BsrDI | GCAATG | 1 cut(s) | 785 |
| BsrI | ACTGG | 3 cut(s) | 107, 183, 1232 |
| BssECI | CCNNGG | 3 cut(s) | 73, 358, 929 |
| BssMI | GATC | 5 cut(s) | 326, 771, 1102, 1138, 1228 |
| BssT1I | CCWWGG | 1 cut(s) | 358 |
| Bst2UI | CCWGG | 3 cut(s) | 75, 672, 930 |
| Bst4CI | ACNGT | 2 cut(s) | 444, 658 |
| Bst6I | CTCTTC | 2 cut(s) | 22, 1237 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 1009 |
| BstBAI | YACGTR | 1 cut(s) | 812 |
| BstC8I | GCNNGC | 2 cut(s) | 7, 82 |
| BstDEI | CTNAG | 2 cut(s) | 879, 1158 |
| BstDSI | CCRYGG | 1 cut(s) | 358 |
| BstF5I | GGATG | 5 cut(s) | 152, 311, 512, 632, 1168 |
| BstH2I | RGCGCY | 1 cut(s) | 419 |
| BstHHI | GCGC | 3 cut(s) | 108, 418, 792 |
| BstKTI | GATC | 5 cut(s) | 329, 774, 1105, 1141, 1231 |
| BstMAI | GTCTC | 3 cut(s) | 137, 751, 1190 |
| BstMBI | GATC | 5 cut(s) | 326, 771, 1102, 1138, 1228 |
| BstMWI | GCNNNNNNNGC | 5 cut(s) | 103, 1009, 1049, 1064, 1202 |
| BstNI | CCWGG | 3 cut(s) | 75, 672, 930 |
| BstNSI | RCATGY | 1 cut(s) | 377 |
| BstSCI | CCNGG | 4 cut(s) | 73, 202, 670, 928 |
| BstSFI | CTRYAG | 2 cut(s) | 322, 440 |
| BstSLI | GKGCMC | 1 cut(s) | 99 |
| BstV1I | GCAGC | 1 cut(s) | 9 |
| BstX2I | RGATCY | 2 cut(s) | 771, 1138 |
| BstYI | RGATCY | 2 cut(s) | 771, 1138 |
| Bsu36I | CCTNAGG | 1 cut(s) | 1158 |
| BsuI | GTATCC | 1 cut(s) | 592 |
| BsuRI | GGCC | 4 cut(s) | 5, 72, 363, 1043 |
| BtgI | CCRYGG | 1 cut(s) | 358 |
| BtsCI | GGATG | 5 cut(s) | 152, 311, 512, 632, 1168 |
| BtsI | GCAGTG | 1 cut(s) | 1010 |
| BtsIMutI | CAGTG | 3 cut(s) | 100, 190, 1010 |
| BveI | ACCTGC | 1 cut(s) | 1043 |
| Cac8I | GCNNGC | 2 cut(s) | 7, 82 |
| CaiI | CAGNNNCTG | 1 cut(s) | 1058 |
| CciI | TCATGA | 1 cut(s) | 214 |
| CfoI | GCGC | 3 cut(s) | 108, 418, 792 |
| Cfr13I | GGNCC | 1 cut(s) | 71 |
| Csp6I | GTAC | 3 cut(s) | 622, 737, 1121 |
| CviAII | CATG | 8 cut(s) | 215, 359, 374, 458, 479, 541, 956, 1117 |
| CviQI | GTAC | 3 cut(s) | 622, 737, 1121 |
| DdeI | CTNAG | 2 cut(s) | 879, 1158 |
| DpnI | GATC | 5 cut(s) | 328, 773, 1104, 1140, 1230 |
| DpnII | GATC | 5 cut(s) | 326, 771, 1102, 1138, 1228 |
| EaeI | YGGCCR | 1 cut(s) | 361 |
| Eam1104I | CTCTTC | 2 cut(s) | 22, 1237 |
| EarI | CTCTTC | 2 cut(s) | 22, 1237 |
| Ecl136II | GAGCTC | 1 cut(s) | 80 |
| Eco130I | CCWWGG | 1 cut(s) | 358 |
| Eco147I | AGGCCT | 1 cut(s) | 1043 |
| Eco24I | GRGCYC | 1 cut(s) | 82 |
| Eco47III | AGCGCT | 1 cut(s) | 417 |
| Eco53kI | GAGCTC | 1 cut(s) | 80 |
| Eco57I | CTGAAG | 1 cut(s) | 602 |
| Eco72I | CACGTG | 1 cut(s) | 812 |
| Eco81I | CCTNAGG | 1 cut(s) | 1158 |
| Eco88I | CYCGRG | 1 cut(s) | 92 |
| EcoICRI | GAGCTC | 1 cut(s) | 80 |
| EcoRII | CCWGG | 3 cut(s) | 73, 670, 928 |
| EcoT14I | CCWWGG | 1 cut(s) | 358 |
| EcoT38I | GRGCYC | 1 cut(s) | 82 |
| ErhI | CCWWGG | 1 cut(s) | 358 |
| Esp3I | CGTCTC | 1 cut(s) | 137 |
| FaeI | CATG | 8 cut(s) | 218, 362, 377, 461, 482, 544, 959, 1120 |
| FaqI | GGGAC | 2 cut(s) | 177, 627 |
| FatI | CATG | 8 cut(s) | 214, 358, 373, 457, 478, 540, 955, 1116 |
| FauI | CCCGC | 1 cut(s) | 574 |
| Fnu4HI | GCNGC | 2 cut(s) | 23, 180 |
| FokI | GGATG | 5 cut(s) | 139, 298, 499, 619, 1175 |
| FriOI | GRGCYC | 1 cut(s) | 82 |
| Fsp4HI | GCNGC | 2 cut(s) | 23, 180 |
| FspBI | CTAG | 2 cut(s) | 504, 1291 |
| GlaI | GCGC | 3 cut(s) | 107, 417, 791 |
| GluI | GCNGC | 2 cut(s) | 23, 180 |
| HaeII | RGCGCY | 1 cut(s) | 419 |
| HaeIII | GGCC | 4 cut(s) | 5, 72, 363, 1043 |
| HapII | CCGG | 2 cut(s) | 204, 596 |
| HhaI | GCGC | 3 cut(s) | 108, 418, 792 |
| Hin1II | CATG | 8 cut(s) | 218, 362, 377, 461, 482, 544, 959, 1120 |
| Hin6I | GCGC | 3 cut(s) | 106, 416, 790 |
| HinP1I | GCGC | 3 cut(s) | 106, 416, 790 |
| HindIII | AAGCTT | 2 cut(s) | 55, 338 |
| HinfI | GANTC | 3 cut(s) | 239, 1032, 1183 |
| HpaII | CCGG | 2 cut(s) | 204, 596 |
| HphI | GGTGA | 1 cut(s) | 920 |
| Hpy166II | GTNNAC | 1 cut(s) | 190 |
| Hpy188I | TCNGA | 4 cut(s) | 369, 771, 1037, 1102 |
| Hpy188III | TCNNGA | 3 cut(s) | 215, 1180, 1189 |
| Hpy8I | GTNNAC | 1 cut(s) | 190 |
| HpyAV | CCTTC | 5 cut(s) | 288, 462, 792, 803, 1208 |
| HpyCH4III | ACNGT | 2 cut(s) | 444, 658 |
| HpyCH4IV | ACGT | 3 cut(s) | 811, 951, 1096 |
| HpyCH4V | TGCA | 4 cut(s) | 871, 964, 1003, 1012 |
| HpyF10VI | GCNNNNNNNGC | 5 cut(s) | 103, 1009, 1049, 1064, 1202 |
| HpyF3I | CTNAG | 2 cut(s) | 879, 1158 |
| HpySE526I | ACGT | 3 cut(s) | 811, 951, 1096 |
| Hsp92II | CATG | 8 cut(s) | 218, 362, 377, 461, 482, 544, 959, 1120 |
| HspAI | GCGC | 3 cut(s) | 106, 416, 790 |
| KpnI | GGTACC | 1 cut(s) | 1124 |
| Kzo9I | GATC | 5 cut(s) | 326, 771, 1102, 1138, 1228 |
| LguI | GCTCTTC | 1 cut(s) | 1237 |
| LmnI | GCTCC | 1 cut(s) | 77 |
| Lsp1109I | GCAGC | 1 cut(s) | 9 |
| LweI | GCATC | 2 cut(s) | 641, 1021 |
| MaeI | CTAG | 2 cut(s) | 504, 1291 |
| MaeII | ACGT | 3 cut(s) | 811, 951, 1096 |
| MaeIII | GTNAC | 5 cut(s) | 272, 351, 728, 897, 908 |
| MalI | GATC | 5 cut(s) | 328, 773, 1104, 1140, 1230 |
| MboI | GATC | 5 cut(s) | 326, 771, 1102, 1138, 1228 |
| MboII | GAAGA | 5 cut(s) | 9, 266, 1037, 1097, 1254 |
| MflI | RGATCY | 2 cut(s) | 771, 1138 |
| MhlI | GDGCHC | 2 cut(s) | 82, 99 |
| MlsI | TGGCCA | 1 cut(s) | 363 |
| MluCI | AATT | 9 cut(s) | 172, 261, 429, 544, 801, 942, 977, 994, 1175 |
| MluNI | TGGCCA | 1 cut(s) | 363 |
| MlyI | GAGTC | 1 cut(s) | 1192 |
| Mox20I | TGGCCA | 1 cut(s) | 363 |
| MroXI | GAANNNNTTC | 1 cut(s) | 805 |
| MscI | TGGCCA | 1 cut(s) | 363 |
| MseI | TTAA | 1 cut(s) | 1073 |
| MslI | CAYNNNNRTG | 2 cut(s) | 219, 378 |
| Msp20I | TGGCCA | 1 cut(s) | 363 |
| MspI | CCGG | 2 cut(s) | 204, 596 |
| MspR9I | CCNGG | 4 cut(s) | 75, 204, 672, 930 |
| MvaI | CCWGG | 3 cut(s) | 75, 672, 930 |
| MwoI | GCNNNNNNNGC | 5 cut(s) | 103, 1009, 1049, 1064, 1202 |
| NciI | CCSGG | 1 cut(s) | 204 |
| NcoI | CCATGG | 1 cut(s) | 358 |
| NdeII | GATC | 5 cut(s) | 326, 771, 1102, 1138, 1228 |
| NlaIII | CATG | 8 cut(s) | 218, 362, 377, 461, 482, 544, 959, 1120 |
| NlaIV | GGNNCC | 4 cut(s) | 98, 669, 865, 1122 |
| NmeAIII | GCCGAG | 1 cut(s) | 173 |
| NmuCI | GTSAC | 2 cut(s) | 897, 908 |
| NspI | RCATGY | 1 cut(s) | 377 |
| PagI | TCATGA | 1 cut(s) | 214 |
| PaqCI | CACCTGC | 1 cut(s) | 1043 |
| PceI | AGGCCT | 1 cut(s) | 1043 |
| PciSI | GCTCTTC | 1 cut(s) | 1237 |
| PdmI | GAANNNNTTC | 1 cut(s) | 805 |
| PfeI | GAWTC | 2 cut(s) | 239, 1032 |
| PkrI | GCNGC | 2 cut(s) | 24, 181 |
| PleI | GAGTC | 1 cut(s) | 1191 |
| PmaCI | CACGTG | 1 cut(s) | 812 |
| PmlI | CACGTG | 1 cut(s) | 812 |
| PpsI | GAGTC | 1 cut(s) | 1191 |
| Ppu21I | YACGTR | 1 cut(s) | 812 |
| PsiI | TTATAA | 2 cut(s) | 428, 1151 |
| Psp124BI | GAGCTC | 1 cut(s) | 82 |
| Psp1406I | AACGTT | 1 cut(s) | 951 |
| Psp6I | CCWGG | 3 cut(s) | 73, 670, 928 |
| PspCI | CACGTG | 1 cut(s) | 812 |
| PspGI | CCWGG | 3 cut(s) | 73, 670, 928 |
| PspN4I | GGNNCC | 4 cut(s) | 98, 669, 865, 1122 |
| PspPI | GGNCC | 1 cut(s) | 71 |
| PstNI | CAGNNNCTG | 1 cut(s) | 1058 |
| PsuI | RGATCY | 2 cut(s) | 771, 1138 |
| RsaI | GTAC | 3 cut(s) | 623, 738, 1122 |
| RsaNI | GTAC | 3 cut(s) | 622, 737, 1121 |
| RseI | CAYNNNNRTG | 2 cut(s) | 219, 378 |
| SacI | GAGCTC | 1 cut(s) | 82 |
| SapI | GCTCTTC | 1 cut(s) | 1237 |
| SaqAI | TTAA | 1 cut(s) | 1073 |
| SatI | GCNGC | 2 cut(s) | 23, 180 |
| Sau3AI | GATC | 5 cut(s) | 326, 771, 1102, 1138, 1228 |
| Sau96I | GGNCC | 1 cut(s) | 71 |
| ScaI | AGTACT | 1 cut(s) | 623 |
| SchI | GAGTC | 1 cut(s) | 1192 |
| ScrFI | CCNGG | 4 cut(s) | 75, 204, 672, 930 |
| SduI | GDGCHC | 2 cut(s) | 82, 99 |
| SfaNI | GCATC | 2 cut(s) | 641, 1021 |
| SfcI | CTRYAG | 2 cut(s) | 322, 440 |
| SmiMI | CAYNNNNRTG | 2 cut(s) | 219, 378 |
| SpeI | ACTAGT | 1 cut(s) | 503 |
| Sse9I | AATT | 9 cut(s) | 172, 261, 429, 544, 801, 942, 977, 994, 1175 |
| SseBI | AGGCCT | 1 cut(s) | 1043 |
| SsiI | CCGC | 5 cut(s) | 156, 180, 464, 567, 1211 |
| SspMI | CTAG | 2 cut(s) | 504, 1291 |
| SstI | GAGCTC | 1 cut(s) | 82 |
| StuI | AGGCCT | 1 cut(s) | 1043 |
| StyD4I | CCNGG | 4 cut(s) | 73, 202, 670, 928 |
| StyI | CCWWGG | 1 cut(s) | 358 |
| TaaI | ACNGT | 2 cut(s) | 444, 658 |
| TaiI | ACGT | 3 cut(s) | 814, 954, 1099 |
| TasI | AATT | 9 cut(s) | 172, 261, 429, 544, 801, 942, 977, 994, 1175 |
| TatI | WGTACW | 1 cut(s) | 621 |
| TauI | GCSGC | 1 cut(s) | 182 |
| TfiI | GAWTC | 2 cut(s) | 239, 1032 |
| Tru1I | TTAA | 1 cut(s) | 1073 |
| Tru9I | TTAA | 1 cut(s) | 1073 |
| TscAI | CASTG | 3 cut(s) | 107, 190, 1010 |
| TseFI | GTSAC | 2 cut(s) | 897, 908 |
| TseI | GCWGC | 1 cut(s) | 22 |
| Tsp45I | GTSAC | 2 cut(s) | 897, 908 |
| TspDTI | ATGAA | 7 cut(s) | 203, 480, 501, 557, 774, 819, 944 |
| TspRI | CASTG | 3 cut(s) | 107, 190, 1010 |
| XapI | RAATTY | 4 cut(s) | 544, 977, 994, 1175 |
| XceI | RCATGY | 1 cut(s) | 377 |
| XmnI | GAANNNNTTC | 1 cut(s) | 805 |
| XspI | CTAG | 2 cut(s) | 504, 1291 |
| ZrmI | AGTACT | 1 cut(s) | 623 |