rRNA processing
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| DUF1218 | PF06749 | 61 - 157 | 1.2e-08 | Protein of unknown function (DUF1218) |
| TPPII_Ig-like-1 | PF21223 | 157 - 197 | 1.4e-07 | Tripeptidyl-peptidase II, first Ig-like domain |
| TPPII_GBD | PF21316 | 217 - 259 | 1.4e-06 | TPPII, galactose-binding domain-like |
| TPPII | PF12580 | 286 - 399 | 9.2e-40 | Tripeptidyl peptidase II |
| Peptidase_C48 | PF02902 | 420 - 484 | 7.5e-07 | Ulp1 protease family, C-terminal catalytic domain |
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) |
|---|---|---|---|
| AanI | TTATAA | 1 cut(s) | 375 |
| AarI | CACCTGC | 1 cut(s) | 889 |
| Acc36I | ACCTGC | 1 cut(s) | 889 |
| AccB1I | GGYRCC | 2 cut(s) | 695, 829 |
| AccI | GTMKAC | 1 cut(s) | 616 |
| AccII | CGCG | 1 cut(s) | 561 |
| AciI | CCGC | 5 cut(s) | 206, 255, 441, 561, 1283 |
| AclWI | GGATC | 3 cut(s) | 146, 389, 908 |
| AcsI | RAATTY | 2 cut(s) | 906, 1079 |
| AcuI | CTGAAG | 2 cut(s) | 870, 1050 |
| AdeI | CACNNNGTG | 1 cut(s) | 1383 |
| AfaI | GTAC | 3 cut(s) | 143, 313, 687 |
| AfiI | CCNNNNNNNGG | 4 cut(s) | 101, 116, 117, 560 |
| AgsI | TTSAA | 5 cut(s) | 683, 710, 845, 1012, 1158 |
| AhlI | ACTAGT | 1 cut(s) | 808 |
| AjnI | CCWGG | 3 cut(s) | 306, 655, 1413 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 675, 707 |
| Alw21I | GWGCWC | 1 cut(s) | 278 |
| Alw26I | GTCTC | 1 cut(s) | 1092 |
| AlwI | GGATC | 3 cut(s) | 146, 389, 908 |
| AlwNI | CAGNNNCTG | 1 cut(s) | 926 |
| AoxI | GGCC | 3 cut(s) | 344, 562, 658 |
| ApeKI | GCWGC | 6 cut(s) | 41, 98, 326, 329, 884, 926 |
| ApoI | RAATTY | 2 cut(s) | 906, 1079 |
| AseI | ATTAAT | 1 cut(s) | 789 |
| AspLEI | GCGC | 3 cut(s) | 407, 561, 991 |
| AspS9I | GGNCC | 1 cut(s) | 563 |
| AsuHPI | GGTGA | 6 cut(s) | 142, 289, 356, 1148, 1369, 1471 |
| AsuII | TTCGAA | 1 cut(s) | 638 |
| BanI | GGYRCC | 2 cut(s) | 695, 829 |
| BbsI | GAAGAC | 1 cut(s) | 1469 |
| Bbv12I | GWGCWC | 1 cut(s) | 278 |
| BbvI | GCAGC | 6 cut(s) | 53, 110, 316, 338, 871, 913 |
| BccI | CCATC | 3 cut(s) | 154, 812, 1016 |
| BcgI | CGANNNNNNTGC | 2 cut(s) | 857, 891 |
| BciT130I | CCWGG | 3 cut(s) | 308, 657, 1415 |
| BcoDI | GTCTC | 1 cut(s) | 1092 |
| BcuI | ACTAGT | 1 cut(s) | 808 |
| BfaI | CTAG | 2 cut(s) | 809, 860 |
| BfmI | CTRYAG | 2 cut(s) | 96, 348 |
| BfoI | RGCGCY | 2 cut(s) | 408, 992 |
| BfuAI | ACCTGC | 1 cut(s) | 889 |
| BisI | GCNGC | 7 cut(s) | 42, 99, 327, 330, 562, 885, 927 |
| BlsI | GCNGC | 7 cut(s) | 43, 100, 328, 331, 563, 886, 928 |
| Bme1390I | CCNGG | 3 cut(s) | 308, 657, 1415 |
| BmgT120I | GGNCC | 1 cut(s) | 563 |
| BmiI | GGNNCC | 3 cut(s) | 448, 697, 831 |
| BmrFI | CCNGG | 3 cut(s) | 308, 657, 1415 |
| BmsI | GCATC | 5 cut(s) | 266, 367, 872, 1099, 1227 |
| BpiI | GAAGAC | 1 cut(s) | 1469 |
| BpmI | CTGGAG | 1 cut(s) | 123 |
| Bpu10I | CCTNAGC | 1 cut(s) | 1293 |
| Bpu14I | TTCGAA | 1 cut(s) | 638 |
| BpuEI | CTTGAG | 2 cut(s) | 1026, 1226 |
| BsaJI | CCNNGG | 5 cut(s) | 306, 307, 554, 1213, 1413 |
| BsaXI | ACNNNNNCTCC | 2 cut(s) | 1017, 1047 |
| Bsc4I | CCNNNNNNNGG | 4 cut(s) | 101, 116, 117, 560 |
| Bse1I | ACTGG | 4 cut(s) | 271, 433, 833, 920 |
| BseBI | CCWGG | 3 cut(s) | 308, 657, 1415 |
| BseDI | CCNNGG | 5 cut(s) | 306, 307, 554, 1213, 1413 |
| BseGI | GGATG | 1 cut(s) | 863 |
| BseLI | CCNNNNNNNGG | 4 cut(s) | 101, 116, 117, 560 |
| BseMII | CTCAG | 3 cut(s) | 984, 1103, 1284 |
| BseNI | ACTGG | 4 cut(s) | 271, 433, 833, 920 |
| BseRI | GAGGAG | 1 cut(s) | 459 |
| BseXI | GCAGC | 6 cut(s) | 53, 110, 316, 338, 871, 913 |
| BsgI | GTGCAG | 1 cut(s) | 500 |
| Bsh1236I | CGCG | 1 cut(s) | 561 |
| BshFI | GGCC | 3 cut(s) | 346, 564, 660 |
| BshNI | GGYRCC | 2 cut(s) | 695, 829 |
| BsiHKAI | GWGCWC | 1 cut(s) | 278 |
| BslFI | GGGAC | 1 cut(s) | 442 |
| BslI | CCNNNNNNNGG | 4 cut(s) | 101, 116, 117, 560 |
| BsmAI | GTCTC | 1 cut(s) | 1092 |
| BsmFI | GGGAC | 1 cut(s) | 442 |
| BsnI | GGCC | 3 cut(s) | 346, 564, 660 |
| Bsp119I | TTCGAA | 1 cut(s) | 638 |
| Bsp1286I | GDGCHC | 1 cut(s) | 278 |
| Bsp143I | GATC | 5 cut(s) | 151, 394, 900, 952, 1101 |
| BspACI | CCGC | 5 cut(s) | 206, 255, 441, 561, 1283 |
| BspANI | GGCC | 3 cut(s) | 346, 564, 660 |
| BspCNI | CTCAG | 3 cut(s) | 983, 1102, 1285 |
| BspFNI | CGCG | 1 cut(s) | 561 |
| BspLI | GGNNCC | 3 cut(s) | 448, 697, 831 |
| BspMAI | CTGCAG | 1 cut(s) | 100 |
| BspMI | ACCTGC | 1 cut(s) | 889 |
| BspPI | GGATC | 3 cut(s) | 146, 389, 908 |
| BspQI | GCTCTTC | 1 cut(s) | 1159 |
| BspT104I | TTCGAA | 1 cut(s) | 638 |
| BspT107I | GGYRCC | 2 cut(s) | 695, 829 |
| BsrI | ACTGG | 4 cut(s) | 271, 433, 833, 920 |
| BssECI | CCNNGG | 5 cut(s) | 306, 307, 554, 1213, 1413 |
| BssMI | GATC | 5 cut(s) | 151, 394, 900, 952, 1101 |
| BssT1I | CCWWGG | 2 cut(s) | 554, 1213 |
| Bst2UI | CCWGG | 3 cut(s) | 308, 657, 1415 |
| Bst4CI | ACNGT | 4 cut(s) | 477, 607, 1280, 1316 |
| Bst6I | CTCTTC | 3 cut(s) | 948, 1159, 1387 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 884 |
| BstBI | TTCGAA | 1 cut(s) | 638 |
| BstC8I | GCNNGC | 2 cut(s) | 96, 162 |
| BstDEI | CTNAG | 8 cut(s) | 87, 503, 893, 970, 1089, 1196, 1293, 1366 |
| BstF5I | GGATG | 1 cut(s) | 863 |
| BstFNI | CGCG | 1 cut(s) | 561 |
| BstH2I | RGCGCY | 2 cut(s) | 408, 992 |
| BstHHI | GCGC | 3 cut(s) | 407, 561, 991 |
| BstKTI | GATC | 5 cut(s) | 154, 397, 903, 955, 1104 |
| BstMAI | GTCTC | 1 cut(s) | 1092 |
| BstMBI | GATC | 5 cut(s) | 151, 394, 900, 952, 1101 |
| BstMWI | GCNNNNNNNGC | 4 cut(s) | 240, 411, 860, 884 |
| BstNI | CCWGG | 3 cut(s) | 308, 657, 1415 |
| BstNSI | RCATGY | 1 cut(s) | 414 |
| BstSCI | CCNGG | 3 cut(s) | 306, 655, 1413 |
| BstSFI | CTRYAG | 2 cut(s) | 96, 348 |
| BstUI | CGCG | 1 cut(s) | 561 |
| BstV1I | GCAGC | 6 cut(s) | 53, 110, 316, 338, 871, 913 |
| BstV2I | GAAGAC | 1 cut(s) | 1469 |
| BstX2I | RGATCY | 1 cut(s) | 394 |
| BstXI | CCANNNNNNTGG | 1 cut(s) | 307 |
| BstYI | RGATCY | 1 cut(s) | 394 |
| BsuRI | GGCC | 3 cut(s) | 346, 564, 660 |
| BtgZI | GCGATG | 1 cut(s) | 453 |
| BtsCI | GGATG | 1 cut(s) | 863 |
| BtsIMutI | CAGTG | 2 cut(s) | 278, 603 |
| BveI | ACCTGC | 1 cut(s) | 889 |
| Cac8I | GCNNGC | 2 cut(s) | 96, 162 |
| CaiI | CAGNNNCTG | 1 cut(s) | 926 |
| CfoI | GCGC | 3 cut(s) | 407, 561, 991 |
| Cfr13I | GGNCC | 1 cut(s) | 563 |
| CseI | GACGC | 1 cut(s) | 364 |
| Csp6I | GTAC | 3 cut(s) | 142, 312, 686 |
| CspCI | CAANNNNNGTGG | 4 cut(s) | 688, 723, 1297, 1332 |
| CviAII | CATG | 6 cut(s) | 127, 411, 454, 702, 718, 782 |
| CviQI | GTAC | 3 cut(s) | 142, 312, 686 |
| DdeI | CTNAG | 8 cut(s) | 87, 503, 893, 970, 1089, 1196, 1293, 1366 |
| DpnI | GATC | 5 cut(s) | 153, 396, 902, 954, 1103 |
| DpnII | GATC | 5 cut(s) | 151, 394, 900, 952, 1101 |
| DraIII | CACNNNGTG | 1 cut(s) | 1383 |
| Eam1104I | CTCTTC | 3 cut(s) | 948, 1159, 1387 |
| EarI | CTCTTC | 3 cut(s) | 948, 1159, 1387 |
| EciI | GGCGGA | 1 cut(s) | 456 |
| Eco130I | CCWWGG | 2 cut(s) | 554, 1213 |
| Eco57I | CTGAAG | 2 cut(s) | 870, 1050 |
| EcoRI | GAATTC | 1 cut(s) | 906 |
| EcoRII | CCWGG | 3 cut(s) | 306, 655, 1413 |
| EcoT14I | CCWWGG | 2 cut(s) | 554, 1213 |
| ErhI | CCWWGG | 2 cut(s) | 554, 1213 |
| FaeI | CATG | 6 cut(s) | 130, 414, 457, 705, 721, 785 |
| FalI | AAGNNNNNCTT | 2 cut(s) | 675, 707 |
| FaqI | GGGAC | 1 cut(s) | 442 |
| FatI | CATG | 6 cut(s) | 126, 410, 453, 701, 717, 781 |
| FauI | CCCGC | 2 cut(s) | 262, 1276 |
| FblI | GTMKAC | 1 cut(s) | 616 |
| Fnu4HI | GCNGC | 7 cut(s) | 42, 99, 327, 330, 562, 885, 927 |
| FokI | GGATG | 1 cut(s) | 850 |
| Fsp4HI | GCNGC | 7 cut(s) | 42, 99, 327, 330, 562, 885, 927 |
| FspBI | CTAG | 2 cut(s) | 809, 860 |
| GlaI | GCGC | 3 cut(s) | 406, 560, 990 |
| GluI | GCNGC | 7 cut(s) | 42, 99, 327, 330, 562, 885, 927 |
| GsuI | CTGGAG | 1 cut(s) | 123 |
| HaeII | RGCGCY | 2 cut(s) | 408, 992 |
| HaeIII | GGCC | 3 cut(s) | 346, 564, 660 |
| HgaI | GACGC | 1 cut(s) | 364 |
| HhaI | GCGC | 3 cut(s) | 407, 561, 991 |
| Hin1II | CATG | 6 cut(s) | 130, 414, 457, 705, 721, 785 |
| Hin6I | GCGC | 3 cut(s) | 405, 559, 989 |
| HinP1I | GCGC | 3 cut(s) | 405, 559, 989 |
| HincII | GTYRAC | 2 cut(s) | 617, 760 |
| HindII | GTYRAC | 2 cut(s) | 617, 760 |
| HindIII | AAGCTT | 1 cut(s) | 1140 |
| HinfI | GANTC | 4 cut(s) | 388, 576, 761, 1085 |
| HphI | GGTGA | 6 cut(s) | 142, 289, 356, 1148, 1369, 1471 |
| Hpy166II | GTNNAC | 2 cut(s) | 617, 760 |
| Hpy188I | TCNGA | 8 cut(s) | 151, 575, 771, 868, 905, 973, 1108, 1436 |
| Hpy188III | TCNNGA | 5 cut(s) | 392, 729, 956, 1243, 1292 |
| Hpy8I | GTNNAC | 2 cut(s) | 617, 760 |
| Hpy99I | CGWCG | 1 cut(s) | 358 |
| HpyAV | CCTTC | 5 cut(s) | 292, 301, 460, 503, 1336 |
| HpyCH4III | ACNGT | 4 cut(s) | 477, 607, 1280, 1316 |
| HpyCH4IV | ACGT | 1 cut(s) | 979 |
| HpyF10VI | GCNNNNNNNGC | 4 cut(s) | 240, 411, 860, 884 |
| HpyF3I | CTNAG | 8 cut(s) | 87, 503, 893, 970, 1089, 1196, 1293, 1366 |
| HpySE526I | ACGT | 1 cut(s) | 979 |
| Hsp92II | CATG | 6 cut(s) | 130, 414, 457, 705, 721, 785 |
| HspAI | GCGC | 3 cut(s) | 405, 559, 989 |
| Kzo9I | GATC | 5 cut(s) | 151, 394, 900, 952, 1101 |
| LguI | GCTCTTC | 1 cut(s) | 1159 |
| LmnI | GCTCC | 3 cut(s) | 256, 446, 1025 |
| Lsp1109I | GCAGC | 6 cut(s) | 53, 110, 316, 338, 871, 913 |
| LweI | GCATC | 5 cut(s) | 266, 367, 872, 1099, 1227 |
| MaeI | CTAG | 2 cut(s) | 809, 860 |
| MaeII | ACGT | 1 cut(s) | 979 |
| MaeIII | GTNAC | 1 cut(s) | 956 |
| MalI | GATC | 5 cut(s) | 153, 396, 902, 954, 1103 |
| MboI | GATC | 5 cut(s) | 151, 394, 900, 952, 1101 |
| MflI | RGATCY | 1 cut(s) | 394 |
| MhlI | GDGCHC | 1 cut(s) | 278 |
| MluCI | AATT | 7 cut(s) | 370, 582, 641, 840, 906, 1013, 1079 |
| MlyI | GAGTC | 2 cut(s) | 755, 1094 |
| MmeI | TCCRAC | 2 cut(s) | 179, 971 |
| MseI | TTAA | 4 cut(s) | 789, 795, 998, 1056 |
| MslI | CAYNNNNRTG | 1 cut(s) | 522 |
| MspA1I | CMGCKG | 2 cut(s) | 101, 329 |
| MspR9I | CCNGG | 3 cut(s) | 308, 657, 1415 |
| MvaI | CCWGG | 3 cut(s) | 308, 657, 1415 |
| MvnI | CGCG | 1 cut(s) | 561 |
| MwoI | GCNNNNNNNGC | 4 cut(s) | 240, 411, 860, 884 |
| NdeII | GATC | 5 cut(s) | 151, 394, 900, 952, 1101 |
| NlaIII | CATG | 6 cut(s) | 130, 414, 457, 705, 721, 785 |
| NlaIV | GGNNCC | 3 cut(s) | 448, 697, 831 |
| NmeAIII | GCCGAG | 1 cut(s) | 417 |
| NmuCI | GTSAC | 1 cut(s) | 956 |
| NspI | RCATGY | 1 cut(s) | 414 |
| NspV | TTCGAA | 1 cut(s) | 638 |
| PaqCI | CACCTGC | 1 cut(s) | 889 |
| PasI | CCCWGGG | 1 cut(s) | 307 |
| PciSI | GCTCTTC | 1 cut(s) | 1159 |
| PfeI | GAWTC | 2 cut(s) | 388, 576 |
| PkrI | GCNGC | 7 cut(s) | 43, 100, 328, 331, 563, 886, 928 |
| PleI | GAGTC | 2 cut(s) | 755, 1093 |
| PpsI | GAGTC | 2 cut(s) | 755, 1093 |
| PshBI | ATTAAT | 1 cut(s) | 789 |
| PsiI | TTATAA | 1 cut(s) | 375 |
| Psp6I | CCWGG | 3 cut(s) | 306, 655, 1413 |
| PspGI | CCWGG | 3 cut(s) | 306, 655, 1413 |
| PspN4I | GGNNCC | 3 cut(s) | 448, 697, 831 |
| PspPI | GGNCC | 1 cut(s) | 563 |
| PstI | CTGCAG | 1 cut(s) | 100 |
| PstNI | CAGNNNCTG | 1 cut(s) | 926 |
| PsuI | RGATCY | 1 cut(s) | 394 |
| PvuII | CAGCTG | 2 cut(s) | 101, 329 |
| RsaI | GTAC | 3 cut(s) | 143, 313, 687 |
| RsaNI | GTAC | 3 cut(s) | 142, 312, 686 |
| RseI | CAYNNNNRTG | 1 cut(s) | 522 |
| SalI | GTCGAC | 1 cut(s) | 615 |
| SapI | GCTCTTC | 1 cut(s) | 1159 |
| SaqAI | TTAA | 4 cut(s) | 789, 795, 998, 1056 |
| SatI | GCNGC | 7 cut(s) | 42, 99, 327, 330, 562, 885, 927 |
| Sau3AI | GATC | 5 cut(s) | 151, 394, 900, 952, 1101 |
| Sau96I | GGNCC | 1 cut(s) | 563 |
| SchI | GAGTC | 2 cut(s) | 755, 1094 |
| ScrFI | CCNGG | 3 cut(s) | 308, 657, 1415 |
| SduI | GDGCHC | 1 cut(s) | 278 |
| SfaNI | GCATC | 5 cut(s) | 266, 367, 872, 1099, 1227 |
| SfcI | CTRYAG | 2 cut(s) | 96, 348 |
| SfuI | TTCGAA | 1 cut(s) | 638 |
| SmiMI | CAYNNNNRTG | 1 cut(s) | 522 |
| SmlI | CTYRAG | 2 cut(s) | 1041, 1241 |
| SmoI | CTYRAG | 2 cut(s) | 1041, 1241 |
| SpeI | ACTAGT | 1 cut(s) | 808 |
| Sse9I | AATT | 7 cut(s) | 370, 582, 641, 840, 906, 1013, 1079 |
| SsiI | CCGC | 5 cut(s) | 206, 255, 441, 561, 1283 |
| SspMI | CTAG | 2 cut(s) | 809, 860 |
| StyD4I | CCNGG | 3 cut(s) | 306, 655, 1413 |
| StyI | CCWWGG | 2 cut(s) | 554, 1213 |
| TaaI | ACNGT | 4 cut(s) | 477, 607, 1280, 1316 |
| TaiI | ACGT | 1 cut(s) | 982 |
| TaqI | TCGA | 3 cut(s) | 616, 638, 916 |
| TasI | AATT | 7 cut(s) | 370, 582, 641, 840, 906, 1013, 1079 |
| TauI | GCSGC | 1 cut(s) | 564 |
| TfiI | GAWTC | 2 cut(s) | 388, 576 |
| Tru1I | TTAA | 4 cut(s) | 789, 795, 998, 1056 |
| Tru9I | TTAA | 4 cut(s) | 789, 795, 998, 1056 |
| TscAI | CASTG | 2 cut(s) | 278, 610 |
| TseFI | GTSAC | 1 cut(s) | 956 |
| TseI | GCWGC | 6 cut(s) | 41, 98, 326, 329, 884, 926 |
| Tsp45I | GTSAC | 1 cut(s) | 956 |
| TspDTI | ATGAA | 6 cut(s) | 32, 442, 540, 621, 770, 1355 |
| TspGWI | ACGGA | 1 cut(s) | 1319 |
| TspRI | CASTG | 2 cut(s) | 278, 610 |
| VspI | ATTAAT | 1 cut(s) | 789 |
| XapI | RAATTY | 2 cut(s) | 906, 1079 |
| XceI | RCATGY | 1 cut(s) | 414 |
| XmiI | GTMKAC | 1 cut(s) | 616 |
| XspI | CTAG | 2 cut(s) | 809, 860 |