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) |
|---|---|---|---|
| Acc65I | GGTACC | 1 cut(s) | 966 |
| AccB1I | GGYRCC | 1 cut(s) | 966 |
| AciI | CCGC | 2 cut(s) | 73, 194 |
| AclI | AACGTT | 1 cut(s) | 463 |
| AclWI | GGATC | 3 cut(s) | 746, 759, 834 |
| AcoI | YGGCCR | 2 cut(s) | 244, 986 |
| AcsI | RAATTY | 2 cut(s) | 227, 782 |
| AcuI | CTGAAG | 2 cut(s) | 510, 717 |
| AcvI | CACGTG | 1 cut(s) | 10 |
| AdeI | CACNNNGTG | 1 cut(s) | 653 |
| AfaI | GTAC | 4 cut(s) | 6, 14, 968, 1224 |
| AfiI | CCNNNNNNNGG | 2 cut(s) | 778, 1233 |
| AflIII | ACRYGT | 2 cut(s) | 7, 9 |
| AgsI | TTSAA | 5 cut(s) | 442, 907, 1117, 1201, 1369 |
| AhlI | ACTAGT | 1 cut(s) | 347 |
| Alw21I | GWGCWC | 1 cut(s) | 727 |
| AlwI | GGATC | 3 cut(s) | 746, 759, 834 |
| AoxI | GGCC | 6 cut(s) | 56, 210, 244, 690, 986, 1319 |
| ApeKI | GCWGC | 5 cut(s) | 500, 503, 571, 656, 1157 |
| ApoI | RAATTY | 2 cut(s) | 227, 782 |
| Asp718I | GGTACC | 1 cut(s) | 966 |
| AspA2I | CCTAGG | 1 cut(s) | 728 |
| AspLEI | GCGC | 1 cut(s) | 1409 |
| AspS9I | GGNCC | 2 cut(s) | 375, 1320 |
| AsuC2I | CCSGG | 1 cut(s) | 373 |
| AsuHPI | GGTGA | 3 cut(s) | 350, 574, 1111 |
| AsuII | TTCGAA | 1 cut(s) | 786 |
| AsuNHI | GCTAGC | 1 cut(s) | 266 |
| AvaII | GGWCC | 1 cut(s) | 375 |
| AvrII | CCTAGG | 1 cut(s) | 728 |
| BaeI | ACNNNNGTAYC | 1 cut(s) | 29 |
| BalI | TGGCCA | 1 cut(s) | 988 |
| BamHI | GGATCC | 1 cut(s) | 751 |
| BanI | GGYRCC | 1 cut(s) | 966 |
| BanII | GRGCYC | 1 cut(s) | 727 |
| BbrPI | CACGTG | 1 cut(s) | 10 |
| BbsI | GAAGAC | 2 cut(s) | 534, 705 |
| Bbv12I | GWGCWC | 1 cut(s) | 727 |
| BbvI | GCAGC | 5 cut(s) | 512, 515, 583, 643, 1169 |
| BccI | CCATC | 1 cut(s) | 1225 |
| BciVI | GTATCC | 1 cut(s) | 887 |
| BcnI | CCSGG | 1 cut(s) | 373 |
| BcuI | ACTAGT | 1 cut(s) | 347 |
| BfaI | CTAG | 6 cut(s) | 99, 267, 348, 729, 756, 1187 |
| BfuI | GTATCC | 1 cut(s) | 887 |
| BglI | GCCNNNNNGGC | 1 cut(s) | 209 |
| BisI | GCNGC | 5 cut(s) | 501, 504, 572, 657, 1158 |
| BlnI | CCTAGG | 1 cut(s) | 728 |
| BlsI | GCNGC | 5 cut(s) | 502, 505, 573, 658, 1159 |
| Bme1390I | CCNGG | 1 cut(s) | 373 |
| Bme18I | GGWCC | 1 cut(s) | 375 |
| BmgT120I | GGNCC | 2 cut(s) | 375, 1320 |
| BmiI | GGNNCC | 5 cut(s) | 630, 753, 928, 968, 1020 |
| BmrFI | CCNGG | 1 cut(s) | 373 |
| BmrI | ACTGGG | 1 cut(s) | 767 |
| BmsI | GCATC | 4 cut(s) | 253, 285, 309, 472 |
| BmtI | GCTAGC | 1 cut(s) | 270 |
| BmuI | ACTGGG | 1 cut(s) | 767 |
| BpiI | GAAGAC | 2 cut(s) | 534, 705 |
| BplI | GAGNNNNNCTC | 2 cut(s) | 617, 649 |
| BpmI | CTGGAG | 3 cut(s) | 417, 965, 1053 |
| Bpu14I | TTCGAA | 1 cut(s) | 786 |
| BpuEI | CTTGAG | 2 cut(s) | 745, 1070 |
| BpuMI | CCSGG | 1 cut(s) | 373 |
| BsaAI | YACGTR | 1 cut(s) | 10 |
| BsaJI | CCNNGG | 3 cut(s) | 728, 795, 880 |
| BsaWI | WCCGGW | 1 cut(s) | 854 |
| Bsc4I | CCNNNNNNNGG | 2 cut(s) | 778, 1233 |
| Bse1I | ACTGG | 3 cut(s) | 773, 948, 1022 |
| BseDI | CCNNGG | 3 cut(s) | 728, 795, 880 |
| BseGI | GGATG | 2 cut(s) | 86, 912 |
| BseLI | CCNNNNNNNGG | 2 cut(s) | 778, 1233 |
| BseMII | CTCAG | 2 cut(s) | 306, 648 |
| BseNI | ACTGG | 3 cut(s) | 773, 948, 1022 |
| BseRI | GAGGAG | 1 cut(s) | 821 |
| BseXI | GCAGC | 5 cut(s) | 512, 515, 583, 643, 1169 |
| BsgI | GTGCAG | 1 cut(s) | 642 |
| BshFI | GGCC | 6 cut(s) | 58, 212, 246, 692, 988, 1321 |
| BshNI | GGYRCC | 1 cut(s) | 966 |
| BsiHKAI | GWGCWC | 1 cut(s) | 727 |
| BsiSI | CCGG | 2 cut(s) | 373, 855 |
| BslFI | GGGAC | 2 cut(s) | 63, 325 |
| BslI | CCNNNNNNNGG | 2 cut(s) | 778, 1233 |
| BsmFI | GGGAC | 2 cut(s) | 63, 325 |
| BsmI | GAATGC | 1 cut(s) | 846 |
| BsnI | GGCC | 6 cut(s) | 58, 212, 246, 692, 988, 1321 |
| Bsp119I | TTCGAA | 1 cut(s) | 786 |
| Bsp1286I | GDGCHC | 1 cut(s) | 727 |
| Bsp143I | GATC | 2 cut(s) | 751, 826 |
| BspACI | CCGC | 2 cut(s) | 73, 194 |
| BspANI | GGCC | 6 cut(s) | 58, 212, 246, 692, 988, 1321 |
| BspCNI | CTCAG | 2 cut(s) | 307, 647 |
| BspLI | GGNNCC | 5 cut(s) | 630, 753, 928, 968, 1020 |
| BspOI | GCTAGC | 1 cut(s) | 270 |
| BspPI | GGATC | 3 cut(s) | 746, 759, 834 |
| BspQI | GCTCTTC | 1 cut(s) | 1035 |
| BspT104I | TTCGAA | 1 cut(s) | 786 |
| BspT107I | GGYRCC | 1 cut(s) | 966 |
| BsrI | ACTGG | 3 cut(s) | 773, 948, 1022 |
| BssECI | CCNNGG | 3 cut(s) | 728, 795, 880 |
| BssMI | GATC | 2 cut(s) | 751, 826 |
| BssT1I | CCWWGG | 2 cut(s) | 728, 795 |
| Bst4CI | ACNGT | 6 cut(s) | 160, 556, 651, 875, 1121, 1327 |
| Bst6I | CTCTTC | 1 cut(s) | 1035 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 653 |
| BstBAI | YACGTR | 1 cut(s) | 10 |
| BstBI | TTCGAA | 1 cut(s) | 786 |
| BstC8I | GCNNGC | 2 cut(s) | 268, 456 |
| BstDEI | CTNAG | 4 cut(s) | 151, 315, 599, 634 |
| BstF5I | GGATG | 2 cut(s) | 86, 912 |
| BstHHI | GCGC | 1 cut(s) | 1409 |
| BstKTI | GATC | 2 cut(s) | 754, 829 |
| BstMBI | GATC | 2 cut(s) | 751, 826 |
| BstMWI | GCNNNNNNNGC | 6 cut(s) | 200, 209, 243, 263, 653, 1378 |
| BstNSI | RCATGY | 1 cut(s) | 367 |
| BstSCI | CCNGG | 1 cut(s) | 371 |
| BstV1I | GCAGC | 5 cut(s) | 512, 515, 583, 643, 1169 |
| BstV2I | GAAGAC | 2 cut(s) | 534, 705 |
| BstX2I | RGATCY | 1 cut(s) | 751 |
| BstXI | CCANNNNNNTGG | 2 cut(s) | 802, 984 |
| BstYI | RGATCY | 1 cut(s) | 751 |
| BsuI | GTATCC | 1 cut(s) | 887 |
| BsuRI | GGCC | 6 cut(s) | 58, 212, 246, 692, 988, 1321 |
| BtsCI | GGATG | 2 cut(s) | 86, 912 |
| BtsI | GCAGTG | 1 cut(s) | 513 |
| BtsIMutI | CAGTG | 5 cut(s) | 513, 656, 1126, 1323, 1336 |
| Cac8I | GCNNGC | 2 cut(s) | 268, 456 |
| CfoI | GCGC | 1 cut(s) | 1409 |
| Cfr13I | GGNCC | 2 cut(s) | 375, 1320 |
| Csp6I | GTAC | 4 cut(s) | 5, 13, 967, 1223 |
| CviAII | CATG | 8 cut(s) | 214, 271, 364, 607, 703, 778, 923, 1410 |
| CviQI | GTAC | 4 cut(s) | 5, 13, 967, 1223 |
| DdeI | CTNAG | 4 cut(s) | 151, 315, 599, 634 |
| DpnI | GATC | 2 cut(s) | 753, 828 |
| DpnII | GATC | 2 cut(s) | 751, 826 |
| DraIII | CACNNNGTG | 1 cut(s) | 653 |
| EaeI | YGGCCR | 2 cut(s) | 244, 986 |
| Eam1104I | CTCTTC | 1 cut(s) | 1035 |
| EarI | CTCTTC | 1 cut(s) | 1035 |
| EciI | GGCGGA | 1 cut(s) | 209 |
| Ecl136II | GAGCTC | 1 cut(s) | 725 |
| Eco130I | CCWWGG | 2 cut(s) | 728, 795 |
| Eco24I | GRGCYC | 1 cut(s) | 727 |
| Eco47I | GGWCC | 1 cut(s) | 375 |
| Eco53kI | GAGCTC | 1 cut(s) | 725 |
| Eco57I | CTGAAG | 2 cut(s) | 510, 717 |
| Eco72I | CACGTG | 1 cut(s) | 10 |
| EcoICRI | GAGCTC | 1 cut(s) | 725 |
| EcoRI | GAATTC | 1 cut(s) | 782 |
| EcoT14I | CCWWGG | 2 cut(s) | 728, 795 |
| EcoT38I | GRGCYC | 1 cut(s) | 727 |
| ErhI | CCWWGG | 2 cut(s) | 728, 795 |
| FaeI | CATG | 8 cut(s) | 217, 274, 367, 610, 706, 781, 926, 1413 |
| FalI | AAGNNNNNCTT | 2 cut(s) | 1032, 1064 |
| FaqI | GGGAC | 2 cut(s) | 63, 325 |
| FatI | CATG | 8 cut(s) | 213, 270, 363, 606, 702, 777, 922, 1409 |
| FauI | CCCGC | 1 cut(s) | 66 |
| Fnu4HI | GCNGC | 5 cut(s) | 501, 504, 572, 657, 1158 |
| FokI | GGATG | 2 cut(s) | 73, 899 |
| FriOI | GRGCYC | 1 cut(s) | 727 |
| Fsp4HI | GCNGC | 5 cut(s) | 501, 504, 572, 657, 1158 |
| FspBI | CTAG | 6 cut(s) | 99, 267, 348, 729, 756, 1187 |
| GlaI | GCGC | 1 cut(s) | 1408 |
| GluI | GCNGC | 5 cut(s) | 501, 504, 572, 657, 1158 |
| GsuI | CTGGAG | 3 cut(s) | 417, 965, 1053 |
| HaeIII | GGCC | 6 cut(s) | 58, 212, 246, 692, 988, 1321 |
| HapII | CCGG | 2 cut(s) | 373, 855 |
| HhaI | GCGC | 1 cut(s) | 1409 |
| Hin1II | CATG | 8 cut(s) | 217, 274, 367, 610, 706, 781, 926, 1413 |
| Hin6I | GCGC | 1 cut(s) | 1407 |
| HinP1I | GCGC | 1 cut(s) | 1407 |
| HincII | GTYRAC | 1 cut(s) | 920 |
| HindII | GTYRAC | 1 cut(s) | 920 |
| HinfI | GANTC | 3 cut(s) | 707, 1113, 1190 |
| HpaII | CCGG | 2 cut(s) | 373, 855 |
| HphI | GGTGA | 3 cut(s) | 350, 574, 1111 |
| Hpy166II | GTNNAC | 4 cut(s) | 7, 13, 548, 920 |
| Hpy188I | TCNGA | 4 cut(s) | 637, 697, 881, 1005 |
| Hpy188III | TCNNGA | 7 cut(s) | 232, 389, 434, 672, 762, 995, 1070 |
| Hpy8I | GTNNAC | 4 cut(s) | 7, 13, 548, 920 |
| HpyAV | CCTTC | 3 cut(s) | 211, 1073, 1231 |
| HpyCH4III | ACNGT | 6 cut(s) | 160, 556, 651, 875, 1121, 1327 |
| HpyCH4IV | ACGT | 2 cut(s) | 9, 463 |
| HpyCH4V | TGCA | 7 cut(s) | 128, 358, 588, 659, 666, 846, 1300 |
| HpyF10VI | GCNNNNNNNGC | 6 cut(s) | 200, 209, 243, 263, 653, 1378 |
| HpyF3I | CTNAG | 4 cut(s) | 151, 315, 599, 634 |
| HpySE526I | ACGT | 2 cut(s) | 9, 463 |
| Hsp92II | CATG | 8 cut(s) | 217, 274, 367, 610, 706, 781, 926, 1413 |
| HspAI | GCGC | 1 cut(s) | 1407 |
| KpnI | GGTACC | 1 cut(s) | 970 |
| Kzo9I | GATC | 2 cut(s) | 751, 826 |
| LguI | GCTCTTC | 1 cut(s) | 1035 |
| LmnI | GCTCC | 7 cut(s) | 220, 634, 722, 730, 808, 932, 1072 |
| Lsp1109I | GCAGC | 5 cut(s) | 512, 515, 583, 643, 1169 |
| LweI | GCATC | 4 cut(s) | 253, 285, 309, 472 |
| MaeI | CTAG | 6 cut(s) | 99, 267, 348, 729, 756, 1187 |
| MaeII | ACGT | 2 cut(s) | 9, 463 |
| MaeIII | GTNAC | 7 cut(s) | 343, 464, 562, 869, 1121, 1129, 1173 |
| MalI | GATC | 2 cut(s) | 753, 828 |
| MboI | GATC | 2 cut(s) | 751, 826 |
| MboII | GAAGA | 9 cut(s) | 315, 454, 503, 539, 710, 728, 1052, 1088, 1254 |
| MflI | RGATCY | 1 cut(s) | 751 |
| MhlI | GDGCHC | 1 cut(s) | 727 |
| MlsI | TGGCCA | 1 cut(s) | 988 |
| MluCI | AATT | 8 cut(s) | 227, 399, 621, 782, 830, 1149, 1309, 1350 |
| MluNI | TGGCCA | 1 cut(s) | 988 |
| Mox20I | TGGCCA | 1 cut(s) | 988 |
| MscI | TGGCCA | 1 cut(s) | 988 |
| MslI | CAYNNNNRTG | 1 cut(s) | 611 |
| Msp20I | TGGCCA | 1 cut(s) | 988 |
| MspI | CCGG | 2 cut(s) | 373, 855 |
| MspR9I | CCNGG | 1 cut(s) | 373 |
| Mva1269I | GAATGC | 1 cut(s) | 846 |
| MwoI | GCNNNNNNNGC | 6 cut(s) | 200, 209, 243, 263, 653, 1378 |
| NciI | CCSGG | 1 cut(s) | 373 |
| NdeII | GATC | 2 cut(s) | 751, 826 |
| NheI | GCTAGC | 1 cut(s) | 266 |
| NlaIII | CATG | 8 cut(s) | 217, 274, 367, 610, 706, 781, 926, 1413 |
| NlaIV | GGNNCC | 5 cut(s) | 630, 753, 928, 968, 1020 |
| NmuCI | GTSAC | 5 cut(s) | 562, 869, 1121, 1129, 1173 |
| NspI | RCATGY | 1 cut(s) | 367 |
| NspV | TTCGAA | 1 cut(s) | 786 |
| PciSI | GCTCTTC | 1 cut(s) | 1035 |
| PctI | GAATGC | 1 cut(s) | 846 |
| PfeI | GAWTC | 3 cut(s) | 707, 1113, 1190 |
| PfoI | TCCNGGA | 1 cut(s) | 371 |
| PkrI | GCNGC | 5 cut(s) | 502, 505, 573, 658, 1159 |
| PmaCI | CACGTG | 1 cut(s) | 10 |
| PmlI | CACGTG | 1 cut(s) | 10 |
| Ppu21I | YACGTR | 1 cut(s) | 10 |
| Psp124BI | GAGCTC | 1 cut(s) | 727 |
| Psp1406I | AACGTT | 1 cut(s) | 463 |
| PspCI | CACGTG | 1 cut(s) | 10 |
| PspN4I | GGNNCC | 5 cut(s) | 630, 753, 928, 968, 1020 |
| PspPI | GGNCC | 2 cut(s) | 375, 1320 |
| PsuI | RGATCY | 1 cut(s) | 751 |
| RsaI | GTAC | 4 cut(s) | 6, 14, 968, 1224 |
| RsaNI | GTAC | 4 cut(s) | 5, 13, 967, 1223 |
| RseI | CAYNNNNRTG | 1 cut(s) | 611 |
| SacI | GAGCTC | 1 cut(s) | 727 |
| SapI | GCTCTTC | 1 cut(s) | 1035 |
| SatI | GCNGC | 5 cut(s) | 501, 504, 572, 657, 1158 |
| Sau3AI | GATC | 2 cut(s) | 751, 826 |
| Sau96I | GGNCC | 2 cut(s) | 375, 1320 |
| ScrFI | CCNGG | 1 cut(s) | 373 |
| SduI | GDGCHC | 1 cut(s) | 727 |
| SfaNI | GCATC | 4 cut(s) | 253, 285, 309, 472 |
| SfuI | TTCGAA | 1 cut(s) | 786 |
| SinI | GGWCC | 1 cut(s) | 375 |
| SmiMI | CAYNNNNRTG | 1 cut(s) | 611 |
| SmlI | CTYRAG | 2 cut(s) | 760, 1049 |
| SmoI | CTYRAG | 2 cut(s) | 760, 1049 |
| SpeI | ACTAGT | 1 cut(s) | 347 |
| Sse9I | AATT | 8 cut(s) | 227, 399, 621, 782, 830, 1149, 1309, 1350 |
| SsiI | CCGC | 2 cut(s) | 73, 194 |
| SspMI | CTAG | 6 cut(s) | 99, 267, 348, 729, 756, 1187 |
| SstI | GAGCTC | 1 cut(s) | 727 |
| StyD4I | CCNGG | 1 cut(s) | 371 |
| StyI | CCWWGG | 2 cut(s) | 728, 795 |
| TaaI | ACNGT | 6 cut(s) | 160, 556, 651, 875, 1121, 1327 |
| TaiI | ACGT | 2 cut(s) | 12, 466 |
| TaqI | TCGA | 2 cut(s) | 231, 786 |
| TasI | AATT | 8 cut(s) | 227, 399, 621, 782, 830, 1149, 1309, 1350 |
| TfiI | GAWTC | 3 cut(s) | 707, 1113, 1190 |
| TscAI | CASTG | 5 cut(s) | 513, 656, 1126, 1330, 1336 |
| TseFI | GTSAC | 5 cut(s) | 562, 869, 1121, 1129, 1173 |
| TseI | GCWGC | 5 cut(s) | 500, 503, 571, 656, 1157 |
| Tsp45I | GTSAC | 5 cut(s) | 562, 869, 1121, 1129, 1173 |
| TspDTI | ATGAA | 7 cut(s) | 75, 230, 823, 1053, 1089, 1119, 1302 |
| TspGWI | ACGGA | 3 cut(s) | 565, 905, 1249 |
| TspRI | CASTG | 5 cut(s) | 513, 656, 1126, 1330, 1336 |
| VpaK11BI | GGWCC | 1 cut(s) | 375 |
| XapI | RAATTY | 2 cut(s) | 227, 782 |
| XceI | RCATGY | 1 cut(s) | 367 |
| XcmI | CCANNNNNNNNNTGG | 1 cut(s) | 385 |
| XmaJI | CCTAGG | 1 cut(s) | 728 |
| XspI | CTAG | 6 cut(s) | 99, 267, 348, 729, 756, 1187 |