Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double- stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA
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| Species | Orthologous Gene IDs |
|---|---|
| arabidopsis_thaliana | AT5G26680 AT5G26680 AT5G26680 AT5G26680 AT5G26680 |
| fragaria_vesca | FvH4_6g08670 FvH4_6g08670 FvH4_6g08670 |
| malus_domestica | MD04G1184400.v1.1 |
| prunus_persica | Prupe.6G302900_v2.0.a1 Prupe.6G302900_v2.0.a1 Prupe.6G302900_v2.0.a1 Prupe.6G302900_v2.0.a1 Prupe.6G302900_v2.0.a1 Prupe.6G302900_v2.0.a1 |
| pyrus_communis | pycom04g16340 |
| rosa_chinensis | RchiOBHm_Chr3g0458811 |
| rosa_laevigata | RLG00000025134 |
| rosa_multiflora | Rmu_sc0001634.1_g000030 Rmu_sc0016560.1_g000001 Rmu_sc0022983.1_g000002 |
| rosa_roxburghii | Rroxscaffold_6G00420780 |
| rosa_rugosa | Rorug03G0031900 Rorug03G0032000 |
| rosa_samantha | Rh3AG089600 Rh3BG092500 Rh3CG092800 Rh3DG093500 |
| rosa_wichuraiana | Rw3G007670 |
| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AanI | TTATAA | 1 cut(s) | 1194 |
| Acc65I | GGTACC | 1 cut(s) | 804 |
| AccB1I | GGYRCC | 2 cut(s) | 804, 1202 |
| AccB7I | CCANNNNNTGG | 1 cut(s) | 292 |
| AccI | GTMKAC | 1 cut(s) | 778 |
| AccII | CGCG | 1 cut(s) | 211 |
| AciI | CCGC | 7 cut(s) | 32, 85, 211, 344, 754, 844, 1064 |
| AclWI | GGATC | 3 cut(s) | 584, 597, 672 |
| AcoI | YGGCCR | 2 cut(s) | 82, 824 |
| AcsI | RAATTY | 3 cut(s) | 65, 569, 620 |
| AcyI | GRCGYC | 2 cut(s) | 530, 1203 |
| AdeI | CACNNNGTG | 1 cut(s) | 491 |
| AfaI | GTAC | 3 cut(s) | 806, 1062, 1092 |
| AfiI | CCNNNNNNNGG | 3 cut(s) | 292, 616, 1108 |
| AgsI | TTSAA | 4 cut(s) | 280, 745, 955, 1039 |
| AhlI | ACTAGT | 1 cut(s) | 185 |
| AjiI | CACGTC | 1 cut(s) | 1056 |
| AjnI | CCWGG | 1 cut(s) | 195 |
| AluBI | AGCT | 8 cut(s) | 25, 233, 292, 563, 597, 649, 740, 748 |
| AluI | AGCT | 8 cut(s) | 25, 233, 292, 563, 597, 649, 740, 748 |
| Alw21I | GWGCWC | 1 cut(s) | 565 |
| AlwI | GGATC | 3 cut(s) | 584, 597, 672 |
| AoxI | GGCC | 3 cut(s) | 82, 824, 1157 |
| ApeKI | GCWGC | 2 cut(s) | 409, 995 |
| ApoI | RAATTY | 3 cut(s) | 65, 569, 620 |
| Asp718I | GGTACC | 1 cut(s) | 804 |
| AspLEI | GCGC | 1 cut(s) | 1205 |
| AspS9I | GGNCC | 1 cut(s) | 1158 |
| AsuHPI | GGTGA | 3 cut(s) | 188, 412, 949 |
| BaeI | ACNNNNGTAYC | 2 cut(s) | 1044, 1077 |
| BalI | TGGCCA | 1 cut(s) | 826 |
| BamHI | GGATCC | 1 cut(s) | 589 |
| BanI | GGYRCC | 2 cut(s) | 804, 1202 |
| BanII | GRGCYC | 1 cut(s) | 565 |
| BbsI | GAAGAC | 3 cut(s) | 372, 426, 543 |
| Bbv12I | GWGCWC | 1 cut(s) | 565 |
| BbvI | GCAGC | 2 cut(s) | 421, 1007 |
| BccI | CCATC | 3 cut(s) | 104, 254, 580 |
| BceAI | ACGGC | 1 cut(s) | 357 |
| BciT130I | CCWGG | 1 cut(s) | 197 |
| BcuI | ACTAGT | 1 cut(s) | 185 |
| BfaI | CTAG | 5 cut(s) | 186, 594, 840, 1025, 1155 |
| BfmI | CTRYAG | 4 cut(s) | 424, 768, 978, 1136 |
| BfoI | RGCGCY | 1 cut(s) | 1206 |
| BglI | GCCNNNNNGGC | 1 cut(s) | 762 |
| BisI | GCNGC | 4 cut(s) | 85, 410, 845, 996 |
| BlsI | GCNGC | 4 cut(s) | 86, 411, 846, 997 |
| Bme1390I | CCNGG | 1 cut(s) | 197 |
| BmgBI | CACGTC | 1 cut(s) | 1056 |
| BmgT120I | GGNCC | 1 cut(s) | 1158 |
| BmiI | GGNNCC | 5 cut(s) | 468, 591, 806, 858, 1204 |
| BmrFI | CCNGG | 1 cut(s) | 197 |
| BmrI | ACTGGG | 1 cut(s) | 605 |
| BmsI | GCATC | 3 cut(s) | 91, 147, 310 |
| BmuI | ACTGGG | 1 cut(s) | 605 |
| BpiI | GAAGAC | 3 cut(s) | 372, 426, 543 |
| BplI | GAGNNNNNCTC | 2 cut(s) | 455, 487 |
| BpmI | CTGGAG | 4 cut(s) | 179, 255, 891, 908 |
| Bpu10I | CCTNAGC | 1 cut(s) | 633 |
| BpuEI | CTTGAG | 3 cut(s) | 312, 583, 803 |
| Bsa29I | ATCGAT | 1 cut(s) | 99 |
| BsaBI | GATNNNNATC | 1 cut(s) | 95 |
| BsaHI | GRCGYC | 2 cut(s) | 530, 1203 |
| BsaJI | CCNNGG | 1 cut(s) | 196 |
| BsaXI | ACNNNNNCTCC | 2 cut(s) | 881, 911 |
| Bsc4I | CCNNNNNNNGG | 3 cut(s) | 292, 616, 1108 |
| Bse1I | ACTGG | 5 cut(s) | 245, 611, 860, 891, 1113 |
| Bse8I | GATNNNNATC | 1 cut(s) | 95 |
| BseBI | CCWGG | 1 cut(s) | 197 |
| BseCI | ATCGAT | 1 cut(s) | 99 |
| BseDI | CCNNGG | 1 cut(s) | 196 |
| BseGI | GGATG | 2 cut(s) | 701, 750 |
| BseJI | GATNNNNATC | 1 cut(s) | 95 |
| BseLI | CCNNNNNNNGG | 3 cut(s) | 292, 616, 1108 |
| BseMII | CTCAG | 2 cut(s) | 144, 486 |
| BseNI | ACTGG | 5 cut(s) | 245, 611, 860, 891, 1113 |
| BseRI | GAGGAG | 1 cut(s) | 659 |
| BseXI | GCAGC | 2 cut(s) | 421, 1007 |
| Bsh1236I | CGCG | 1 cut(s) | 211 |
| BshFI | GGCC | 3 cut(s) | 84, 826, 1159 |
| BshNI | GGYRCC | 2 cut(s) | 804, 1202 |
| BshVI | ATCGAT | 1 cut(s) | 99 |
| BsiHKAI | GWGCWC | 1 cut(s) | 565 |
| BslFI | GGGAC | 1 cut(s) | 163 |
| BslI | CCNNNNNNNGG | 3 cut(s) | 292, 616, 1108 |
| BsmFI | GGGAC | 1 cut(s) | 163 |
| BsmI | GAATGC | 1 cut(s) | 714 |
| BsnI | GGCC | 3 cut(s) | 84, 826, 1159 |
| Bsp1286I | GDGCHC | 1 cut(s) | 565 |
| Bsp143I | GATC | 2 cut(s) | 589, 664 |
| BspACI | CCGC | 7 cut(s) | 32, 85, 211, 344, 754, 844, 1064 |
| BspANI | GGCC | 3 cut(s) | 84, 826, 1159 |
| BspCNI | CTCAG | 2 cut(s) | 145, 485 |
| BspDI | ATCGAT | 1 cut(s) | 99 |
| BspFNI | CGCG | 1 cut(s) | 211 |
| BspLI | GGNNCC | 5 cut(s) | 468, 591, 806, 858, 1204 |
| BspMAI | CTGCAG | 1 cut(s) | 428 |
| BspPI | GGATC | 3 cut(s) | 584, 597, 672 |
| BspT107I | GGYRCC | 2 cut(s) | 804, 1202 |
| BsrI | ACTGG | 5 cut(s) | 245, 611, 860, 891, 1113 |
| BssECI | CCNNGG | 1 cut(s) | 196 |
| BssMI | GATC | 2 cut(s) | 589, 664 |
| BssNAI | GTATAC | 1 cut(s) | 779 |
| BssNI | GRCGYC | 2 cut(s) | 530, 1203 |
| Bst1107I | GTATAC | 1 cut(s) | 779 |
| Bst2UI | CCWGG | 1 cut(s) | 197 |
| Bst4CI | ACNGT | 3 cut(s) | 394, 489, 707 |
| Bst6I | CTCTTC | 1 cut(s) | 828 |
| BstACI | GRCGYC | 2 cut(s) | 530, 1203 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 491 |
| BstC8I | GCNNGC | 3 cut(s) | 106, 294, 1184 |
| BstDEI | CTNAG | 4 cut(s) | 153, 472, 633, 1178 |
| BstF5I | GGATG | 2 cut(s) | 701, 750 |
| BstFNI | CGCG | 1 cut(s) | 211 |
| BstH2I | RGCGCY | 1 cut(s) | 1206 |
| BstHHI | GCGC | 1 cut(s) | 1205 |
| BstKTI | GATC | 2 cut(s) | 592, 667 |
| BstMBI | GATC | 2 cut(s) | 589, 664 |
| BstMWI | GCNNNNNNNGC | 6 cut(s) | 38, 101, 298, 491, 762, 1179 |
| BstNI | CCWGG | 1 cut(s) | 197 |
| BstNSI | RCATGY | 1 cut(s) | 205 |
| BstSCI | CCNGG | 1 cut(s) | 195 |
| BstSFI | CTRYAG | 4 cut(s) | 424, 768, 978, 1136 |
| BstUI | CGCG | 1 cut(s) | 211 |
| BstV1I | GCAGC | 2 cut(s) | 421, 1007 |
| BstV2I | GAAGAC | 3 cut(s) | 372, 426, 543 |
| BstX2I | RGATCY | 1 cut(s) | 589 |
| BstXI | CCANNNNNNTGG | 1 cut(s) | 822 |
| BstYI | RGATCY | 1 cut(s) | 589 |
| BstZ17I | GTATAC | 1 cut(s) | 779 |
| Bsu15I | ATCGAT | 1 cut(s) | 99 |
| BsuRI | GGCC | 3 cut(s) | 84, 826, 1159 |
| BsuTUI | ATCGAT | 1 cut(s) | 99 |
| BtrI | CACGTC | 1 cut(s) | 1056 |
| BtsCI | GGATG | 2 cut(s) | 701, 750 |
| BtsIMutI | CAGTG | 1 cut(s) | 494 |
| Cac8I | GCNNGC | 3 cut(s) | 106, 294, 1184 |
| CfoI | GCGC | 1 cut(s) | 1205 |
| Cfr13I | GGNCC | 1 cut(s) | 1158 |
| ClaI | ATCGAT | 1 cut(s) | 99 |
| CseI | GACGC | 1 cut(s) | 519 |
| Csp6I | GTAC | 3 cut(s) | 805, 1061, 1091 |
| CviAII | CATG | 8 cut(s) | 52, 109, 202, 445, 541, 616, 761, 1248 |
| CviQI | GTAC | 3 cut(s) | 805, 1061, 1091 |
| DdeI | CTNAG | 4 cut(s) | 153, 472, 633, 1178 |
| DinI | GGCGCC | 1 cut(s) | 1204 |
| DpnI | GATC | 2 cut(s) | 591, 666 |
| DpnII | GATC | 2 cut(s) | 589, 664 |
| DraIII | CACNNNGTG | 1 cut(s) | 491 |
| EaeI | YGGCCR | 2 cut(s) | 82, 824 |
| Eam1104I | CTCTTC | 1 cut(s) | 828 |
| EarI | CTCTTC | 1 cut(s) | 828 |
| EciI | GGCGGA | 2 cut(s) | 47, 743 |
| Ecl136II | GAGCTC | 1 cut(s) | 563 |
| Eco24I | GRGCYC | 1 cut(s) | 565 |
| Eco53kI | GAGCTC | 1 cut(s) | 563 |
| EcoICRI | GAGCTC | 1 cut(s) | 563 |
| EcoRII | CCWGG | 1 cut(s) | 195 |
| EcoT22I | ATGCAT | 1 cut(s) | 53 |
| EcoT38I | GRGCYC | 1 cut(s) | 565 |
| EgeI | GGCGCC | 1 cut(s) | 1204 |
| EheI | GGCGCC | 1 cut(s) | 1204 |
| FaeI | CATG | 8 cut(s) | 55, 112, 205, 448, 544, 619, 764, 1251 |
| FaqI | GGGAC | 1 cut(s) | 163 |
| FatI | CATG | 8 cut(s) | 51, 108, 201, 444, 540, 615, 760, 1247 |
| FauNDI | CATATG | 1 cut(s) | 829 |
| FblI | GTMKAC | 1 cut(s) | 778 |
| Fnu4HI | GCNGC | 4 cut(s) | 85, 410, 845, 996 |
| FokI | GGATG | 2 cut(s) | 708, 737 |
| FriOI | GRGCYC | 1 cut(s) | 565 |
| Fsp4HI | GCNGC | 4 cut(s) | 85, 410, 845, 996 |
| FspBI | CTAG | 5 cut(s) | 186, 594, 840, 1025, 1155 |
| GlaI | GCGC | 1 cut(s) | 1204 |
| GluI | GCNGC | 4 cut(s) | 85, 410, 845, 996 |
| GsuI | CTGGAG | 4 cut(s) | 179, 255, 891, 908 |
| HaeII | RGCGCY | 1 cut(s) | 1206 |
| HaeIII | GGCC | 3 cut(s) | 84, 826, 1159 |
| HgaI | GACGC | 1 cut(s) | 519 |
| HhaI | GCGC | 1 cut(s) | 1205 |
| Hin1I | GRCGYC | 2 cut(s) | 530, 1203 |
| Hin1II | CATG | 8 cut(s) | 55, 112, 205, 448, 544, 619, 764, 1251 |
| Hin6I | GCGC | 1 cut(s) | 1203 |
| HinP1I | GCGC | 1 cut(s) | 1203 |
| HinfI | GANTC | 5 cut(s) | 350, 545, 951, 1028, 1120 |
| HphI | GGTGA | 3 cut(s) | 188, 412, 949 |
| Hpy166II | GTNNAC | 5 cut(s) | 386, 779, 900, 1013, 1091 |
| Hpy188I | TCNGA | 4 cut(s) | 475, 535, 735, 1125 |
| Hpy8I | GTNNAC | 5 cut(s) | 386, 779, 900, 1013, 1091 |
| Hpy99I | CGWCG | 1 cut(s) | 343 |
| HpyAV | CCTTC | 3 cut(s) | 49, 911, 1069 |
| HpyCH4III | ACNGT | 3 cut(s) | 394, 489, 707 |
| HpyCH4IV | ACGT | 1 cut(s) | 1055 |
| HpyCH4V | TGCA | 5 cut(s) | 51, 323, 426, 504, 684 |
| HpyF10VI | GCNNNNNNNGC | 6 cut(s) | 38, 101, 298, 491, 762, 1179 |
| HpyF3I | CTNAG | 4 cut(s) | 153, 472, 633, 1178 |
| HpySE526I | ACGT | 1 cut(s) | 1055 |
| Hsp92I | GRCGYC | 2 cut(s) | 530, 1203 |
| Hsp92II | CATG | 8 cut(s) | 55, 112, 205, 448, 544, 619, 764, 1251 |
| HspAI | GCGC | 1 cut(s) | 1203 |
| KasI | GGCGCC | 1 cut(s) | 1202 |
| KpnI | GGTACC | 1 cut(s) | 808 |
| Kzo9I | GATC | 2 cut(s) | 589, 664 |
| LmnI | GCTCC | 6 cut(s) | 58, 472, 560, 568, 646, 910 |
| Lsp1109I | GCAGC | 2 cut(s) | 421, 1007 |
| LweI | GCATC | 3 cut(s) | 91, 147, 310 |
| MaeI | CTAG | 5 cut(s) | 186, 594, 840, 1025, 1155 |
| MaeII | ACGT | 1 cut(s) | 1055 |
| MaeIII | GTNAC | 6 cut(s) | 74, 181, 302, 400, 707, 1145 |
| MalI | GATC | 2 cut(s) | 591, 666 |
| MboI | GATC | 2 cut(s) | 589, 664 |
| MboII | GAAGA | 7 cut(s) | 153, 377, 431, 548, 566, 845, 926 |
| MflI | RGATCY | 1 cut(s) | 589 |
| MhlI | GDGCHC | 1 cut(s) | 565 |
| MlsI | TGGCCA | 1 cut(s) | 826 |
| MluNI | TGGCCA | 1 cut(s) | 826 |
| Mly113I | GGCGCC | 1 cut(s) | 1203 |
| MlyI | GAGTC | 1 cut(s) | 359 |
| Mox20I | TGGCCA | 1 cut(s) | 826 |
| Mph1103I | ATGCAT | 1 cut(s) | 53 |
| MscI | TGGCCA | 1 cut(s) | 826 |
| MseI | TTAA | 9 cut(s) | 17, 240, 852, 869, 894, 972, 990, 1068, 1095 |
| MslI | CAYNNNNRTG | 1 cut(s) | 449 |
| Msp20I | TGGCCA | 1 cut(s) | 826 |
| MspR9I | CCNGG | 1 cut(s) | 197 |
| Mva1269I | GAATGC | 1 cut(s) | 714 |
| MvaI | CCWGG | 1 cut(s) | 197 |
| MvnI | CGCG | 1 cut(s) | 211 |
| MwoI | GCNNNNNNNGC | 6 cut(s) | 38, 101, 298, 491, 762, 1179 |
| NarI | GGCGCC | 1 cut(s) | 1203 |
| NdeI | CATATG | 1 cut(s) | 829 |
| NdeII | GATC | 2 cut(s) | 589, 664 |
| NlaIII | CATG | 8 cut(s) | 55, 112, 205, 448, 544, 619, 764, 1251 |
| NlaIV | GGNNCC | 5 cut(s) | 468, 591, 806, 858, 1204 |
| NmuCI | GTSAC | 2 cut(s) | 400, 707 |
| NsiI | ATGCAT | 1 cut(s) | 53 |
| NspI | RCATGY | 1 cut(s) | 205 |
| PctI | GAATGC | 1 cut(s) | 714 |
| PfeI | GAWTC | 4 cut(s) | 545, 951, 1028, 1120 |
| PflMI | CCANNNNNTGG | 1 cut(s) | 292 |
| PkrI | GCNGC | 4 cut(s) | 86, 411, 846, 997 |
| PleI | GAGTC | 1 cut(s) | 358 |
| PluTI | GGCGCC | 1 cut(s) | 1206 |
| PpsI | GAGTC | 1 cut(s) | 358 |
| PsiI | TTATAA | 1 cut(s) | 1194 |
| Psp124BI | GAGCTC | 1 cut(s) | 565 |
| Psp6I | CCWGG | 1 cut(s) | 195 |
| PspGI | CCWGG | 1 cut(s) | 195 |
| PspN4I | GGNNCC | 5 cut(s) | 468, 591, 806, 858, 1204 |
| PspPI | GGNCC | 1 cut(s) | 1158 |
| PstI | CTGCAG | 1 cut(s) | 428 |
| PsuI | RGATCY | 1 cut(s) | 589 |
| RsaI | GTAC | 3 cut(s) | 806, 1062, 1092 |
| RsaNI | GTAC | 3 cut(s) | 805, 1061, 1091 |
| RseI | CAYNNNNRTG | 1 cut(s) | 449 |
| SacI | GAGCTC | 1 cut(s) | 565 |
| SaqAI | TTAA | 9 cut(s) | 17, 240, 852, 869, 894, 972, 990, 1068, 1095 |
| SatI | GCNGC | 4 cut(s) | 85, 410, 845, 996 |
| Sau3AI | GATC | 2 cut(s) | 589, 664 |
| Sau96I | GGNCC | 1 cut(s) | 1158 |
| SchI | GAGTC | 1 cut(s) | 359 |
| ScrFI | CCNGG | 1 cut(s) | 197 |
| SduI | GDGCHC | 1 cut(s) | 565 |
| SfaNI | GCATC | 3 cut(s) | 91, 147, 310 |
| SfcI | CTRYAG | 4 cut(s) | 424, 768, 978, 1136 |
| SfoI | GGCGCC | 1 cut(s) | 1204 |
| SmiMI | CAYNNNNRTG | 1 cut(s) | 449 |
| SmlI | CTYRAG | 3 cut(s) | 327, 598, 782 |
| SmoI | CTYRAG | 3 cut(s) | 327, 598, 782 |
| SpeI | ACTAGT | 1 cut(s) | 185 |
| SsiI | CCGC | 7 cut(s) | 32, 85, 211, 344, 754, 844, 1064 |
| SspDI | GGCGCC | 1 cut(s) | 1202 |
| SspMI | CTAG | 5 cut(s) | 186, 594, 840, 1025, 1155 |
| SstI | GAGCTC | 1 cut(s) | 565 |
| StyD4I | CCNGG | 1 cut(s) | 195 |
| TaaI | ACNGT | 3 cut(s) | 394, 489, 707 |
| TaiI | ACGT | 1 cut(s) | 1058 |
| TaqI | TCGA | 5 cut(s) | 69, 99, 258, 308, 718 |
| TatI | WGTACW | 1 cut(s) | 1090 |
| TauI | GCSGC | 2 cut(s) | 87, 847 |
| TfiI | GAWTC | 4 cut(s) | 545, 951, 1028, 1120 |
| Tru1I | TTAA | 9 cut(s) | 17, 240, 852, 869, 894, 972, 990, 1068, 1095 |
| Tru9I | TTAA | 9 cut(s) | 17, 240, 852, 869, 894, 972, 990, 1068, 1095 |
| TscAI | CASTG | 1 cut(s) | 494 |
| TseFI | GTSAC | 2 cut(s) | 400, 707 |
| TseI | GCWGC | 2 cut(s) | 409, 995 |
| Tsp45I | GTSAC | 2 cut(s) | 400, 707 |
| TspDTI | ATGAA | 6 cut(s) | 68, 432, 661, 846, 927, 957 |
| TspGWI | ACGGA | 3 cut(s) | 403, 963, 1087 |
| TspRI | CASTG | 1 cut(s) | 494 |
| Van91I | CCANNNNNTGG | 1 cut(s) | 292 |
| XapI | RAATTY | 3 cut(s) | 65, 569, 620 |
| XceI | RCATGY | 1 cut(s) | 205 |
| XmiI | GTMKAC | 1 cut(s) | 778 |
| XspI | CTAG | 5 cut(s) | 186, 594, 840, 1025, 1155 |
| Zsp2I | ATGCAT | 1 cut(s) | 53 |