DNA-directed RNA polymerases I, II, and III subunit
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| RNA_pol_Rpb5_N | PF03871 | 5 - 90 | 6.3e-29 | RNA polymerase Rpb5, N-terminal 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) |
|---|---|---|---|
| AccB7I | CCANNNNNTGG | 1 cut(s) | 233 |
| AclWI | GGATC | 1 cut(s) | 99 |
| AfaI | GTAC | 1 cut(s) | 362 |
| AfiI | CCNNNNNNNGG | 1 cut(s) | 233 |
| AgsI | TTSAA | 2 cut(s) | 357, 370 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 216, 248 |
| Alw26I | GTCTC | 1 cut(s) | 69 |
| AlwI | GGATC | 1 cut(s) | 99 |
| AspS9I | GGNCC | 1 cut(s) | 157 |
| AsuHPI | GGTGA | 1 cut(s) | 197 |
| AsuII | TTCGAA | 1 cut(s) | 43 |
| AvaII | GGWCC | 1 cut(s) | 157 |
| BclI | TGATCA | 1 cut(s) | 196 |
| BcoDI | GTCTC | 1 cut(s) | 69 |
| Bme18I | GGWCC | 1 cut(s) | 157 |
| BmgT120I | GGNCC | 1 cut(s) | 157 |
| BmsI | GCATC | 1 cut(s) | 45 |
| Bpu14I | TTCGAA | 1 cut(s) | 43 |
| BsaBI | GATNNNNATC | 1 cut(s) | 96 |
| Bsc4I | CCNNNNNNNGG | 1 cut(s) | 233 |
| Bse8I | GATNNNNATC | 1 cut(s) | 96 |
| BseJI | GATNNNNATC | 1 cut(s) | 96 |
| BseLI | CCNNNNNNNGG | 1 cut(s) | 233 |
| BseMII | CTCAG | 1 cut(s) | 287 |
| BslI | CCNNNNNNNGG | 1 cut(s) | 233 |
| BsmAI | GTCTC | 1 cut(s) | 69 |
| Bsp119I | TTCGAA | 1 cut(s) | 43 |
| Bsp143I | GATC | 4 cut(s) | 70, 91, 97, 196 |
| BspCNI | CTCAG | 1 cut(s) | 286 |
| BspHI | TCATGA | 1 cut(s) | 94 |
| BspPI | GGATC | 1 cut(s) | 99 |
| BspT104I | TTCGAA | 1 cut(s) | 43 |
| BssMI | GATC | 4 cut(s) | 70, 91, 97, 196 |
| Bst4CI | ACNGT | 2 cut(s) | 52, 120 |
| Bst6I | CTCTTC | 2 cut(s) | 173, 245 |
| BstBI | TTCGAA | 1 cut(s) | 43 |
| BstDEI | CTNAG | 2 cut(s) | 273, 298 |
| BstKTI | GATC | 4 cut(s) | 73, 94, 100, 199 |
| BstMAI | GTCTC | 1 cut(s) | 69 |
| BstMBI | GATC | 4 cut(s) | 70, 91, 97, 196 |
| BtsIMutI | CAGTG | 1 cut(s) | 57 |
| CciI | TCATGA | 1 cut(s) | 94 |
| Cfr13I | GGNCC | 1 cut(s) | 157 |
| Csp6I | GTAC | 1 cut(s) | 361 |
| CviAII | CATG | 3 cut(s) | 95, 134, 268 |
| CviJI | RGCY | 1 cut(s) | 31 |
| CviKI_1 | RGCY | 1 cut(s) | 31 |
| CviQI | GTAC | 1 cut(s) | 361 |
| DdeI | CTNAG | 2 cut(s) | 273, 298 |
| DpnI | GATC | 4 cut(s) | 72, 93, 99, 198 |
| DpnII | GATC | 4 cut(s) | 70, 91, 97, 196 |
| DraI | TTTAAA | 1 cut(s) | 124 |
| Eam1104I | CTCTTC | 2 cut(s) | 173, 245 |
| EarI | CTCTTC | 2 cut(s) | 173, 245 |
| Eco47I | GGWCC | 1 cut(s) | 157 |
| EcoO109I | RGGNCCY | 1 cut(s) | 157 |
| FaeI | CATG | 3 cut(s) | 98, 137, 271 |
| FaiI | YATR | 4 cut(s) | 96, 135, 207, 269 |
| FalI | AAGNNNNNCTT | 1 cut(s) | 350 |
| FatI | CATG | 3 cut(s) | 94, 133, 267 |
| FbaI | TGATCA | 1 cut(s) | 196 |
| Hin1II | CATG | 3 cut(s) | 98, 137, 271 |
| HinfI | GANTC | 3 cut(s) | 191, 271, 319 |
| HphI | GGTGA | 1 cut(s) | 197 |
| Hpy188I | TCNGA | 3 cut(s) | 196, 201, 318 |
| Hpy188III | TCNNGA | 6 cut(s) | 74, 95, 218, 241, 275, 370 |
| HpyAV | CCTTC | 1 cut(s) | 168 |
| HpyCH4III | ACNGT | 2 cut(s) | 52, 120 |
| HpyCH4V | TGCA | 2 cut(s) | 58, 329 |
| HpyF3I | CTNAG | 2 cut(s) | 273, 298 |
| Hsp92II | CATG | 3 cut(s) | 98, 137, 271 |
| Ksp22I | TGATCA | 1 cut(s) | 196 |
| Kzo9I | GATC | 4 cut(s) | 70, 91, 97, 196 |
| LpnPI | CCDG | 3 cut(s) | 91, 231, 260 |
| LweI | GCATC | 1 cut(s) | 45 |
| MaeIII | GTNAC | 4 cut(s) | 114, 185, 238, 254 |
| MalI | GATC | 4 cut(s) | 72, 93, 99, 198 |
| MboI | GATC | 4 cut(s) | 70, 91, 97, 196 |
| MboII | GAAGA | 2 cut(s) | 190, 262 |
| MluCI | AATT | 2 cut(s) | 21, 84 |
| MlyI | GAGTC | 3 cut(s) | 200, 265, 313 |
| MnlI | CCTC | 4 cut(s) | 21, 148, 174, 346 |
| MseI | TTAA | 1 cut(s) | 123 |
| MslI | CAYNNNNRTG | 2 cut(s) | 245, 266 |
| NdeII | GATC | 4 cut(s) | 70, 91, 97, 196 |
| NlaIII | CATG | 3 cut(s) | 98, 137, 271 |
| NmuCI | GTSAC | 3 cut(s) | 114, 185, 238 |
| NspV | TTCGAA | 1 cut(s) | 43 |
| PagI | TCATGA | 1 cut(s) | 94 |
| PflFI | GACNNNGTC | 1 cut(s) | 112 |
| PflMI | CCANNNNNTGG | 1 cut(s) | 233 |
| PleI | GAGTC | 3 cut(s) | 199, 265, 313 |
| PpsI | GAGTC | 3 cut(s) | 199, 265, 313 |
| PpuMI | RGGWCCY | 1 cut(s) | 157 |
| Psp5II | RGGWCCY | 1 cut(s) | 157 |
| PspPI | GGNCC | 1 cut(s) | 157 |
| PspPPI | RGGWCCY | 1 cut(s) | 157 |
| PsyI | GACNNNGTC | 1 cut(s) | 112 |
| RsaI | GTAC | 1 cut(s) | 362 |
| RsaNI | GTAC | 1 cut(s) | 361 |
| RseI | CAYNNNNRTG | 2 cut(s) | 245, 266 |
| SaqAI | TTAA | 1 cut(s) | 123 |
| Sau3AI | GATC | 4 cut(s) | 70, 91, 97, 196 |
| Sau96I | GGNCC | 1 cut(s) | 157 |
| SchI | GAGTC | 3 cut(s) | 200, 265, 313 |
| SetI | ASST | 2 cut(s) | 162, 338 |
| SfaNI | GCATC | 1 cut(s) | 45 |
| SfuI | TTCGAA | 1 cut(s) | 43 |
| SinI | GGWCC | 1 cut(s) | 157 |
| SmiMI | CAYNNNNRTG | 2 cut(s) | 245, 266 |
| Sse9I | AATT | 2 cut(s) | 21, 84 |
| TaaI | ACNGT | 2 cut(s) | 52, 120 |
| TaqI | TCGA | 2 cut(s) | 43, 73 |
| TasI | AATT | 2 cut(s) | 21, 84 |
| Tru1I | TTAA | 1 cut(s) | 123 |
| Tru9I | TTAA | 1 cut(s) | 123 |
| TscAI | CASTG | 1 cut(s) | 57 |
| TseFI | GTSAC | 3 cut(s) | 114, 185, 238 |
| Tsp45I | GTSAC | 3 cut(s) | 114, 185, 238 |
| TspDTI | ATGAA | 2 cut(s) | 161, 263 |
| TspRI | CASTG | 1 cut(s) | 57 |
| Tth111I | GACNNNGTC | 1 cut(s) | 112 |
| Van91I | CCANNNNNTGG | 1 cut(s) | 233 |
| VpaK11BI | GGWCC | 1 cut(s) | 157 |