DNA-directed RNA polymerases I, II, and III subunit
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| Semialdhyde_dh | PF01118 | 53 - 189 | 1.6e-28 | Semialdehyde dehydrogenase, NAD binding domain |
| Semialdhyde_dhC_1 | PF22698 | 197 - 361 | 6.4e-58 | Semialdehyde dehydrogenase, dimerisation domain |
| Semialdhyde_dhC | PF02774 | 206 - 364 | 1.4e-20 | Semialdehyde dehydrogenase, dimerisation domain |
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AccB1I | GGYRCC | 2 cut(s) | 42, 701 |
| AccI | GTMKAC | 1 cut(s) | 451 |
| AccII | CGCG | 1 cut(s) | 568 |
| AccIII | TCCGGA | 1 cut(s) | 778 |
| AciI | CCGC | 1 cut(s) | 919 |
| AcsI | RAATTY | 3 cut(s) | 67, 121, 953 |
| AcuI | CTGAAG | 2 cut(s) | 756, 1083 |
| AfaI | GTAC | 1 cut(s) | 722 |
| AfiI | CCNNNNNNNGG | 2 cut(s) | 52, 227 |
| AgsI | TTSAA | 3 cut(s) | 126, 647, 816 |
| AjiI | CACGTC | 1 cut(s) | 698 |
| AjnI | CCWGG | 1 cut(s) | 895 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 141, 173 |
| AluBI | AGCT | 6 cut(s) | 6, 260, 521, 610, 734, 1097 |
| AluI | AGCT | 6 cut(s) | 6, 260, 521, 610, 734, 1097 |
| Alw21I | GWGCWC | 2 cut(s) | 8, 1151 |
| Ama87I | CYCGRG | 1 cut(s) | 1002 |
| Aor13HI | TCCGGA | 1 cut(s) | 778 |
| AoxI | GGCC | 1 cut(s) | 403 |
| ApeKI | GCWGC | 2 cut(s) | 205, 806 |
| ApoI | RAATTY | 3 cut(s) | 67, 121, 953 |
| ArsI | GACNNNNNNTTYG | 2 cut(s) | 526, 558 |
| AspLEI | GCGC | 2 cut(s) | 502, 568 |
| AsuC2I | CCSGG | 2 cut(s) | 585, 1050 |
| AvaI | CYCGRG | 1 cut(s) | 1002 |
| BanI | GGYRCC | 2 cut(s) | 42, 701 |
| BanII | GRGCYC | 1 cut(s) | 8 |
| Bbv12I | GWGCWC | 2 cut(s) | 8, 1151 |
| BbvI | GCAGC | 2 cut(s) | 192, 793 |
| BccI | CCATC | 3 cut(s) | 50, 310, 1126 |
| BceAI | ACGGC | 1 cut(s) | 843 |
| BcgI | CGANNNNNNTGC | 2 cut(s) | 983, 1017 |
| BciT130I | CCWGG | 1 cut(s) | 897 |
| BcnI | CCSGG | 2 cut(s) | 585, 1050 |
| BfaI | CTAG | 2 cut(s) | 572, 801 |
| BfmI | CTRYAG | 1 cut(s) | 1112 |
| BfoI | RGCGCY | 1 cut(s) | 503 |
| BglI | GCCNNNNNGGC | 1 cut(s) | 710 |
| BisI | GCNGC | 3 cut(s) | 206, 807, 920 |
| BlsI | GCNGC | 3 cut(s) | 207, 808, 921 |
| Bme1390I | CCNGG | 3 cut(s) | 585, 897, 1050 |
| BmeT110I | CYCGRG | 1 cut(s) | 1002 |
| BmgBI | CACGTC | 1 cut(s) | 698 |
| BmiI | GGNNCC | 4 cut(s) | 44, 172, 703, 894 |
| BmrFI | CCNGG | 3 cut(s) | 585, 897, 1050 |
| BmrI | ACTGGG | 1 cut(s) | 48 |
| BmsI | GCATC | 3 cut(s) | 284, 322, 343 |
| BmuI | ACTGGG | 1 cut(s) | 48 |
| BoxI | GACNNNNGTC | 1 cut(s) | 447 |
| BpmI | CTGGAG | 1 cut(s) | 879 |
| BpuMI | CCSGG | 2 cut(s) | 585, 1050 |
| Bsa29I | ATCGAT | 1 cut(s) | 1077 |
| BsaJI | CCNNGG | 7 cut(s) | 157, 311, 583, 705, 859, 896, 1048 |
| BsaWI | WCCGGW | 1 cut(s) | 778 |
| Bsc4I | CCNNNNNNNGG | 2 cut(s) | 52, 227 |
| Bse1I | ACTGG | 3 cut(s) | 43, 174, 190 |
| BseAI | TCCGGA | 1 cut(s) | 778 |
| BseBI | CCWGG | 1 cut(s) | 897 |
| BseCI | ATCGAT | 1 cut(s) | 1077 |
| BseDI | CCNNGG | 7 cut(s) | 157, 311, 583, 705, 859, 896, 1048 |
| BseGI | GGATG | 6 cut(s) | 61, 217, 321, 337, 358, 952 |
| BseLI | CCNNNNNNNGG | 2 cut(s) | 52, 227 |
| BseMII | CTCAG | 3 cut(s) | 31, 183, 456 |
| BseNI | ACTGG | 3 cut(s) | 43, 174, 190 |
| BseRI | GAGGAG | 1 cut(s) | 566 |
| BseXI | GCAGC | 2 cut(s) | 192, 793 |
| Bsh1236I | CGCG | 1 cut(s) | 568 |
| BshFI | GGCC | 1 cut(s) | 405 |
| BshNI | GGYRCC | 2 cut(s) | 42, 701 |
| BshVI | ATCGAT | 1 cut(s) | 1077 |
| BsiHKAI | GWGCWC | 2 cut(s) | 8, 1151 |
| BsiHKCI | CYCGRG | 1 cut(s) | 1002 |
| BsiSI | CCGG | 4 cut(s) | 503, 585, 779, 1050 |
| BslFI | GGGAC | 1 cut(s) | 807 |
| BslI | CCNNNNNNNGG | 2 cut(s) | 52, 227 |
| BsmFI | GGGAC | 1 cut(s) | 807 |
| BsnI | GGCC | 1 cut(s) | 405 |
| BsoBI | CYCGRG | 1 cut(s) | 1002 |
| Bsp1286I | GDGCHC | 2 cut(s) | 8, 1151 |
| Bsp13I | TCCGGA | 1 cut(s) | 778 |
| Bsp1407I | TGTACA | 1 cut(s) | 720 |
| Bsp143I | GATC | 2 cut(s) | 430, 1039 |
| BspACI | CCGC | 1 cut(s) | 919 |
| BspANI | GGCC | 1 cut(s) | 405 |
| BspCNI | CTCAG | 3 cut(s) | 30, 184, 457 |
| BspDI | ATCGAT | 1 cut(s) | 1077 |
| BspEI | TCCGGA | 1 cut(s) | 778 |
| BspFNI | CGCG | 1 cut(s) | 568 |
| BspLI | GGNNCC | 4 cut(s) | 44, 172, 703, 894 |
| BspQI | GCTCTTC | 1 cut(s) | 1048 |
| BspT107I | GGYRCC | 2 cut(s) | 42, 701 |
| BsrGI | TGTACA | 1 cut(s) | 720 |
| BsrI | ACTGG | 3 cut(s) | 43, 174, 190 |
| BssECI | CCNNGG | 7 cut(s) | 157, 311, 583, 705, 859, 896, 1048 |
| BssMI | GATC | 2 cut(s) | 430, 1039 |
| BssT1I | CCWWGG | 3 cut(s) | 157, 311, 705 |
| Bst2UI | CCWGG | 1 cut(s) | 897 |
| Bst4CI | ACNGT | 3 cut(s) | 267, 826, 927 |
| Bst6I | CTCTTC | 1 cut(s) | 1048 |
| BstAUI | TGTACA | 1 cut(s) | 720 |
| BstC8I | GCNNGC | 2 cut(s) | 210, 992 |
| BstDEI | CTNAG | 3 cut(s) | 17, 192, 465 |
| BstDSI | CCRYGG | 1 cut(s) | 859 |
| BstF5I | GGATG | 6 cut(s) | 61, 217, 321, 337, 358, 952 |
| BstFNI | CGCG | 1 cut(s) | 568 |
| BstH2I | RGCGCY | 1 cut(s) | 503 |
| BstHHI | GCGC | 2 cut(s) | 502, 568 |
| BstKTI | GATC | 2 cut(s) | 433, 1042 |
| BstMBI | GATC | 2 cut(s) | 430, 1039 |
| BstMWI | GCNNNNNNNGC | 3 cut(s) | 497, 508, 710 |
| BstNI | CCWGG | 1 cut(s) | 897 |
| BstPAI | GACNNNNGTC | 1 cut(s) | 447 |
| BstSCI | CCNGG | 3 cut(s) | 583, 895, 1048 |
| BstSFI | CTRYAG | 1 cut(s) | 1112 |
| BstUI | CGCG | 1 cut(s) | 568 |
| BstV1I | GCAGC | 2 cut(s) | 192, 793 |
| Bsu15I | ATCGAT | 1 cut(s) | 1077 |
| BsuRI | GGCC | 1 cut(s) | 405 |
| BsuTUI | ATCGAT | 1 cut(s) | 1077 |
| BtgI | CCRYGG | 1 cut(s) | 859 |
| BtrI | CACGTC | 1 cut(s) | 698 |
| BtsCI | GGATG | 6 cut(s) | 61, 217, 321, 337, 358, 952 |
| BtsIMutI | CAGTG | 3 cut(s) | 181, 183, 723 |
| Cac8I | GCNNGC | 2 cut(s) | 210, 992 |
| CfoI | GCGC | 2 cut(s) | 502, 568 |
| ClaI | ATCGAT | 1 cut(s) | 1077 |
| CseI | GACGC | 1 cut(s) | 557 |
| Csp6I | GTAC | 1 cut(s) | 721 |
| CviAII | CATG | 2 cut(s) | 377, 773 |
| CviQI | GTAC | 1 cut(s) | 721 |
| DdeI | CTNAG | 3 cut(s) | 17, 192, 465 |
| DpnI | GATC | 2 cut(s) | 432, 1041 |
| DpnII | GATC | 2 cut(s) | 430, 1039 |
| DraI | TTTAAA | 1 cut(s) | 420 |
| Eam1104I | CTCTTC | 1 cut(s) | 1048 |
| EarI | CTCTTC | 1 cut(s) | 1048 |
| Ecl136II | GAGCTC | 1 cut(s) | 6 |
| Eco130I | CCWWGG | 3 cut(s) | 157, 311, 705 |
| Eco147I | AGGCCT | 1 cut(s) | 405 |
| Eco24I | GRGCYC | 1 cut(s) | 8 |
| Eco53kI | GAGCTC | 1 cut(s) | 6 |
| Eco57I | CTGAAG | 2 cut(s) | 756, 1083 |
| Eco88I | CYCGRG | 1 cut(s) | 1002 |
| EcoICRI | GAGCTC | 1 cut(s) | 6 |
| EcoRI | GAATTC | 1 cut(s) | 121 |
| EcoRII | CCWGG | 1 cut(s) | 895 |
| EcoT14I | CCWWGG | 3 cut(s) | 157, 311, 705 |
| EcoT38I | GRGCYC | 1 cut(s) | 8 |
| ErhI | CCWWGG | 3 cut(s) | 157, 311, 705 |
| FaeI | CATG | 2 cut(s) | 380, 776 |
| FalI | AAGNNNNNCTT | 2 cut(s) | 141, 173 |
| FaqI | GGGAC | 1 cut(s) | 807 |
| FatI | CATG | 2 cut(s) | 376, 772 |
| FblI | GTMKAC | 1 cut(s) | 451 |
| Fnu4HI | GCNGC | 3 cut(s) | 206, 807, 920 |
| FokI | GGATG | 6 cut(s) | 68, 204, 328, 344, 365, 959 |
| FriOI | GRGCYC | 1 cut(s) | 8 |
| Fsp4HI | GCNGC | 3 cut(s) | 206, 807, 920 |
| FspBI | CTAG | 2 cut(s) | 572, 801 |
| GlaI | GCGC | 2 cut(s) | 501, 567 |
| GluI | GCNGC | 3 cut(s) | 206, 807, 920 |
| GsuI | CTGGAG | 1 cut(s) | 879 |
| HaeII | RGCGCY | 1 cut(s) | 503 |
| HaeIII | GGCC | 1 cut(s) | 405 |
| HapII | CCGG | 4 cut(s) | 503, 585, 779, 1050 |
| HgaI | GACGC | 1 cut(s) | 557 |
| HhaI | GCGC | 2 cut(s) | 502, 568 |
| Hin1II | CATG | 2 cut(s) | 380, 776 |
| Hin6I | GCGC | 2 cut(s) | 500, 566 |
| HinP1I | GCGC | 2 cut(s) | 500, 566 |
| HincII | GTYRAC | 1 cut(s) | 873 |
| HindII | GTYRAC | 1 cut(s) | 873 |
| HinfI | GANTC | 4 cut(s) | 668, 812, 1044, 1117 |
| HpaII | CCGG | 4 cut(s) | 503, 585, 779, 1050 |
| Hpy166II | GTNNAC | 4 cut(s) | 371, 452, 723, 873 |
| Hpy188I | TCNGA | 4 cut(s) | 193, 346, 466, 597 |
| Hpy188III | TCNNGA | 3 cut(s) | 779, 1037, 1142 |
| Hpy8I | GTNNAC | 4 cut(s) | 371, 452, 723, 873 |
| HpyAV | CCTTC | 5 cut(s) | 46, 91, 416, 731, 968 |
| HpyCH4III | ACNGT | 3 cut(s) | 267, 826, 927 |
| HpyCH4IV | ACGT | 1 cut(s) | 697 |
| HpyCH4V | TGCA | 6 cut(s) | 11, 92, 275, 356, 511, 868 |
| HpyF10VI | GCNNNNNNNGC | 3 cut(s) | 497, 508, 710 |
| HpyF3I | CTNAG | 3 cut(s) | 17, 192, 465 |
| HpySE526I | ACGT | 1 cut(s) | 697 |
| Hsp92II | CATG | 2 cut(s) | 380, 776 |
| HspAI | GCGC | 2 cut(s) | 500, 566 |
| Kpn2I | TCCGGA | 1 cut(s) | 778 |
| Kzo9I | GATC | 2 cut(s) | 430, 1039 |
| LguI | GCTCTTC | 1 cut(s) | 1048 |
| LmnI | GCTCC | 4 cut(s) | 170, 689, 898, 1094 |
| Lsp1109I | GCAGC | 2 cut(s) | 192, 793 |
| LweI | GCATC | 3 cut(s) | 284, 322, 343 |
| MaeI | CTAG | 2 cut(s) | 572, 801 |
| MaeII | ACGT | 1 cut(s) | 697 |
| MaeIII | GTNAC | 1 cut(s) | 820 |
| MalI | GATC | 2 cut(s) | 432, 1041 |
| MboI | GATC | 2 cut(s) | 430, 1039 |
| MboII | GAAGA | 4 cut(s) | 76, 485, 962, 1065 |
| MfeI | CAATTG | 1 cut(s) | 270 |
| MhlI | GDGCHC | 2 cut(s) | 8, 1151 |
| MlyI | GAGTC | 1 cut(s) | 662 |
| MmeI | TCCRAC | 2 cut(s) | 620, 948 |
| MroI | TCCGGA | 1 cut(s) | 778 |
| MseI | TTAA | 6 cut(s) | 239, 419, 558, 630, 1122, 1180 |
| MslI | CAYNNNNRTG | 1 cut(s) | 771 |
| MspI | CCGG | 4 cut(s) | 503, 585, 779, 1050 |
| MspR9I | CCNGG | 3 cut(s) | 585, 897, 1050 |
| MunI | CAATTG | 1 cut(s) | 270 |
| MvaI | CCWGG | 1 cut(s) | 897 |
| MvnI | CGCG | 1 cut(s) | 568 |
| MwoI | GCNNNNNNNGC | 3 cut(s) | 497, 508, 710 |
| NciI | CCSGG | 2 cut(s) | 585, 1050 |
| NdeII | GATC | 2 cut(s) | 430, 1039 |
| NlaIII | CATG | 2 cut(s) | 380, 776 |
| NlaIV | GGNNCC | 4 cut(s) | 44, 172, 703, 894 |
| PaeR7I | CTCGAG | 1 cut(s) | 1002 |
| PceI | AGGCCT | 1 cut(s) | 405 |
| PciSI | GCTCTTC | 1 cut(s) | 1048 |
| PfeI | GAWTC | 3 cut(s) | 812, 1044, 1117 |
| PkrI | GCNGC | 3 cut(s) | 207, 808, 921 |
| PleI | GAGTC | 1 cut(s) | 662 |
| PpsI | GAGTC | 1 cut(s) | 662 |
| PshAI | GACNNNNGTC | 1 cut(s) | 447 |
| Psp124BI | GAGCTC | 1 cut(s) | 8 |
| Psp6I | CCWGG | 1 cut(s) | 895 |
| PspGI | CCWGG | 1 cut(s) | 895 |
| PspN4I | GGNNCC | 4 cut(s) | 44, 172, 703, 894 |
| PspXI | VCTCGAGB | 1 cut(s) | 1002 |
| RsaI | GTAC | 1 cut(s) | 722 |
| RsaNI | GTAC | 1 cut(s) | 721 |
| RseI | CAYNNNNRTG | 1 cut(s) | 771 |
| SacI | GAGCTC | 1 cut(s) | 8 |
| SapI | GCTCTTC | 1 cut(s) | 1048 |
| SaqAI | TTAA | 6 cut(s) | 239, 419, 558, 630, 1122, 1180 |
| SatI | GCNGC | 3 cut(s) | 206, 807, 920 |
| Sau3AI | GATC | 2 cut(s) | 430, 1039 |
| SchI | GAGTC | 1 cut(s) | 662 |
| ScrFI | CCNGG | 3 cut(s) | 585, 897, 1050 |
| SduI | GDGCHC | 2 cut(s) | 8, 1151 |
| SfaNI | GCATC | 3 cut(s) | 284, 322, 343 |
| SfcI | CTRYAG | 1 cut(s) | 1112 |
| Sfr274I | CTCGAG | 1 cut(s) | 1002 |
| SlaI | CTCGAG | 1 cut(s) | 1002 |
| SmiMI | CAYNNNNRTG | 1 cut(s) | 771 |
| SmlI | CTYRAG | 1 cut(s) | 1002 |
| SmoI | CTYRAG | 1 cut(s) | 1002 |
| SseBI | AGGCCT | 1 cut(s) | 405 |
| SsiI | CCGC | 1 cut(s) | 919 |
| SspMI | CTAG | 2 cut(s) | 572, 801 |
| SstI | GAGCTC | 1 cut(s) | 8 |
| StuI | AGGCCT | 1 cut(s) | 405 |
| StyD4I | CCNGG | 3 cut(s) | 583, 895, 1048 |
| StyI | CCWWGG | 3 cut(s) | 157, 311, 705 |
| TaaI | ACNGT | 3 cut(s) | 267, 826, 927 |
| TaiI | ACGT | 1 cut(s) | 700 |
| TaqI | TCGA | 5 cut(s) | 666, 786, 1003, 1042, 1077 |
| TatI | WGTACW | 1 cut(s) | 720 |
| TauI | GCSGC | 1 cut(s) | 922 |
| TfiI | GAWTC | 3 cut(s) | 812, 1044, 1117 |
| Tru1I | TTAA | 6 cut(s) | 239, 419, 558, 630, 1122, 1180 |
| Tru9I | TTAA | 6 cut(s) | 239, 419, 558, 630, 1122, 1180 |
| TscAI | CASTG | 3 cut(s) | 181, 190, 730 |
| TseI | GCWGC | 2 cut(s) | 205, 806 |
| TspDTI | ATGAA | 3 cut(s) | 486, 963, 1012 |
| TspGWI | ACGGA | 1 cut(s) | 437 |
| TspRI | CASTG | 3 cut(s) | 181, 190, 730 |
| XapI | RAATTY | 3 cut(s) | 67, 121, 953 |
| XcmI | CCANNNNNNNNNTGG | 1 cut(s) | 53 |
| XhoI | CTCGAG | 1 cut(s) | 1002 |
| XmiI | GTMKAC | 1 cut(s) | 451 |
| XspI | CTAG | 2 cut(s) | 572, 801 |