Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released
Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.
| Species | Orthologous Gene IDs |
|---|---|
| arabidopsis_thaliana | AT1G08540 |
| fragaria_vesca | FvH4_1g29160 FvH4_1g29160 |
| malus_domestica | MD12G1111900.v1.1 MD14G1100900.v1.1 |
| prunus_persica | Prupe.7G021900_v2.0.a1 Prupe.7G021900_v2.0.a1 Prupe.7G021900_v2.0.a1 Prupe.7G021900_v2.0.a1 |
| pyrus_communis | pycom12g09170 pycom14g08810 |
| rosa_chinensis | RchiOBHm_Chr3g0494351 RchiOBHm_Chr3g0494481 |
| rosa_laevigata | RLG00000022672 |
| rosa_multiflora | Rmu_sc0000152.1_g000008 |
| rosa_roxburghii | Rroxscaffold_6G00391100 |
| rosa_rugosa | Rorug03G0265600 |
| rosa_samantha | Rh3BG350900 Rh3CG347600 Rh3DG350200 |
| rosa_wichuraiana | Rw3G027560 |
| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| Acc36I | ACCTGC | 1 cut(s) | 1651 |
| AccI | GTMKAC | 1 cut(s) | 418 |
| AccII | CGCG | 1 cut(s) | 325 |
| AciI | CCGC | 5 cut(s) | 39, 168, 171, 323, 531 |
| AclWI | GGATC | 6 cut(s) | 275, 440, 478, 887, 1186, 1559 |
| AcoI | YGGCCR | 1 cut(s) | 192 |
| AcsI | RAATTY | 6 cut(s) | 389, 463, 713, 972, 1244, 1537 |
| AcuI | CTGAAG | 4 cut(s) | 555, 584, 852, 1805 |
| AdeI | CACNNNGTG | 1 cut(s) | 1360 |
| AfaI | GTAC | 2 cut(s) | 873, 1632 |
| AgsI | TTSAA | 7 cut(s) | 330, 414, 668, 719, 846, 1196, 1257 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 1604, 1636 |
| AleI | CACNNNNGTG | 1 cut(s) | 1288 |
| Alw26I | GTCTC | 1 cut(s) | 1646 |
| AlwI | GGATC | 6 cut(s) | 275, 440, 478, 887, 1186, 1559 |
| AlwNI | CAGNNNCTG | 1 cut(s) | 527 |
| AoxI | GGCC | 5 cut(s) | 165, 192, 783, 1222, 1386 |
| ApoI | RAATTY | 6 cut(s) | 389, 463, 713, 972, 1244, 1537 |
| Asp700I | GAANNNNTTC | 1 cut(s) | 492 |
| AspLEI | GCGC | 1 cut(s) | 204 |
| AspS9I | GGNCC | 4 cut(s) | 118, 165, 216, 1513 |
| AsuC2I | CCSGG | 1 cut(s) | 296 |
| AsuHPI | GGTGA | 1 cut(s) | 88 |
| AsuII | TTCGAA | 2 cut(s) | 1309, 1777 |
| AvaII | GGWCC | 3 cut(s) | 118, 216, 1513 |
| AxyI | CCTNAGG | 1 cut(s) | 212 |
| BaeGI | GKGCMC | 1 cut(s) | 301 |
| BalI | TGGCCA | 1 cut(s) | 194 |
| BbsI | GAAGAC | 4 cut(s) | 660, 1085, 1423, 1709 |
| BccI | CCATC | 4 cut(s) | 114, 1665, 1685, 1723 |
| BceAI | ACGGC | 3 cut(s) | 29, 158, 768 |
| BcgI | CGANNNNNNTGC | 2 cut(s) | 1199, 1233 |
| BclI | TGATCA | 2 cut(s) | 1072, 1128 |
| BcnI | CCSGG | 1 cut(s) | 296 |
| BcoDI | GTCTC | 1 cut(s) | 1646 |
| BfaI | CTAG | 5 cut(s) | 276, 852, 1503, 1634, 1650 |
| BfmI | CTRYAG | 6 cut(s) | 348, 483, 725, 966, 1001, 1056 |
| BfuAI | ACCTGC | 1 cut(s) | 1651 |
| BglII | AGATCT | 4 cut(s) | 911, 1198, 1505, 1588 |
| Bme1390I | CCNGG | 1 cut(s) | 296 |
| Bme18I | GGWCC | 3 cut(s) | 118, 216, 1513 |
| BmgT120I | GGNCC | 4 cut(s) | 118, 165, 216, 1513 |
| BmiI | GGNNCC | 2 cut(s) | 119, 218 |
| BmrFI | CCNGG | 1 cut(s) | 296 |
| BpiI | GAAGAC | 4 cut(s) | 660, 1085, 1423, 1709 |
| Bpu14I | TTCGAA | 2 cut(s) | 1309, 1777 |
| BpuEI | CTTGAG | 1 cut(s) | 928 |
| BpuMI | CCSGG | 1 cut(s) | 296 |
| BsaJI | CCNNGG | 3 cut(s) | 422, 627, 741 |
| BsaXI | ACNNNNNCTCC | 4 cut(s) | 171, 201, 1355, 1385 |
| Bse1I | ACTGG | 3 cut(s) | 996, 1292, 1327 |
| Bse21I | CCTNAGG | 1 cut(s) | 212 |
| Bse3DI | GCAATG | 2 cut(s) | 1041, 1706 |
| BseDI | CCNNGG | 3 cut(s) | 422, 627, 741 |
| BseGI | GGATG | 6 cut(s) | 583, 1191, 1220, 1420, 1696, 1704 |
| BseMI | GCAATG | 2 cut(s) | 1041, 1706 |
| BseMII | CTCAG | 4 cut(s) | 226, 385, 447, 1575 |
| BseNI | ACTGG | 3 cut(s) | 996, 1292, 1327 |
| BseRI | GAGGAG | 4 cut(s) | 175, 195, 198, 1022 |
| BseSI | GKGCMC | 1 cut(s) | 301 |
| BseYI | CCCAGC | 1 cut(s) | 124 |
| BsgI | GTGCAG | 2 cut(s) | 1226, 1257 |
| Bsh1236I | CGCG | 1 cut(s) | 325 |
| BshFI | GGCC | 5 cut(s) | 167, 194, 785, 1224, 1388 |
| BsiSI | CCGG | 1 cut(s) | 295 |
| BsmAI | GTCTC | 1 cut(s) | 1646 |
| BsnI | GGCC | 5 cut(s) | 167, 194, 785, 1224, 1388 |
| Bsp119I | TTCGAA | 2 cut(s) | 1309, 1777 |
| Bsp1286I | GDGCHC | 1 cut(s) | 301 |
| Bsp19I | CCATGG | 1 cut(s) | 627 |
| BspACI | CCGC | 5 cut(s) | 39, 168, 171, 323, 531 |
| BspANI | GGCC | 5 cut(s) | 167, 194, 785, 1224, 1388 |
| BspCNI | CTCAG | 4 cut(s) | 225, 384, 448, 1574 |
| BspFNI | CGCG | 1 cut(s) | 325 |
| BspLI | GGNNCC | 2 cut(s) | 119, 218 |
| BspMAI | CTGCAG | 4 cut(s) | 729, 970, 1005, 1060 |
| BspMI | ACCTGC | 1 cut(s) | 1651 |
| BspPI | GGATC | 6 cut(s) | 275, 440, 478, 887, 1186, 1559 |
| BspT104I | TTCGAA | 2 cut(s) | 1309, 1777 |
| BsrDI | GCAATG | 2 cut(s) | 1041, 1706 |
| BsrI | ACTGG | 3 cut(s) | 996, 1292, 1327 |
| BssECI | CCNNGG | 3 cut(s) | 422, 627, 741 |
| BssT1I | CCWWGG | 2 cut(s) | 627, 741 |
| Bst4CI | ACNGT | 5 cut(s) | 208, 257, 352, 423, 1103 |
| Bst6I | CTCTTC | 3 cut(s) | 152, 498, 501 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 527 |
| BstBI | TTCGAA | 2 cut(s) | 1309, 1777 |
| BstC8I | GCNNGC | 1 cut(s) | 1031 |
| BstDEI | CTNAG | 5 cut(s) | 212, 371, 385, 456, 1561 |
| BstDSI | CCRYGG | 2 cut(s) | 422, 627 |
| BstF5I | GGATG | 6 cut(s) | 583, 1191, 1220, 1420, 1696, 1704 |
| BstFNI | CGCG | 1 cut(s) | 325 |
| BstHHI | GCGC | 1 cut(s) | 204 |
| BstMAI | GTCTC | 1 cut(s) | 1646 |
| BstSCI | CCNGG | 1 cut(s) | 294 |
| BstSFI | CTRYAG | 6 cut(s) | 348, 483, 725, 966, 1001, 1056 |
| BstSLI | GKGCMC | 1 cut(s) | 301 |
| BstUI | CGCG | 1 cut(s) | 325 |
| BstV2I | GAAGAC | 4 cut(s) | 660, 1085, 1423, 1709 |
| BstX2I | RGATCY | 7 cut(s) | 280, 911, 1178, 1198, 1505, 1564, 1588 |
| BstXI | CCANNNNNNTGG | 2 cut(s) | 113, 1523 |
| BstYI | RGATCY | 7 cut(s) | 280, 911, 1178, 1198, 1505, 1564, 1588 |
| Bsu36I | CCTNAGG | 1 cut(s) | 212 |
| BsuRI | GGCC | 5 cut(s) | 167, 194, 785, 1224, 1388 |
| BtgI | CCRYGG | 2 cut(s) | 422, 627 |
| BtsCI | GGATG | 6 cut(s) | 583, 1191, 1220, 1420, 1696, 1704 |
| BtsIMutI | CAGTG | 4 cut(s) | 262, 357, 453, 1285 |
| BveI | ACCTGC | 1 cut(s) | 1651 |
| Cac8I | GCNNGC | 1 cut(s) | 1031 |
| CaiI | CAGNNNCTG | 1 cut(s) | 527 |
| CfoI | GCGC | 1 cut(s) | 204 |
| Cfr13I | GGNCC | 4 cut(s) | 118, 165, 216, 1513 |
| CseI | GACGC | 2 cut(s) | 1259, 1580 |
| Csp6I | GTAC | 2 cut(s) | 872, 1631 |
| CspCI | CAANNNNNGTGG | 2 cut(s) | 561, 596 |
| CviAII | CATG | 4 cut(s) | 190, 628, 1357, 1767 |
| CviQI | GTAC | 2 cut(s) | 872, 1631 |
| DdeI | CTNAG | 5 cut(s) | 212, 371, 385, 456, 1561 |
| DraI | TTTAAA | 2 cut(s) | 1410, 1543 |
| DraIII | CACNNNGTG | 1 cut(s) | 1360 |
| EaeI | YGGCCR | 1 cut(s) | 192 |
| Eam1104I | CTCTTC | 3 cut(s) | 152, 498, 501 |
| EarI | CTCTTC | 3 cut(s) | 152, 498, 501 |
| Eco130I | CCWWGG | 2 cut(s) | 627, 741 |
| Eco147I | AGGCCT | 1 cut(s) | 1224 |
| Eco47I | GGWCC | 3 cut(s) | 118, 216, 1513 |
| Eco57I | CTGAAG | 4 cut(s) | 555, 584, 852, 1805 |
| Eco81I | CCTNAGG | 1 cut(s) | 212 |
| EcoO109I | RGGNCCY | 1 cut(s) | 216 |
| EcoRI | GAATTC | 1 cut(s) | 972 |
| EcoT14I | CCWWGG | 2 cut(s) | 627, 741 |
| ErhI | CCWWGG | 2 cut(s) | 627, 741 |
| FaeI | CATG | 4 cut(s) | 193, 631, 1360, 1770 |
| FatI | CATG | 4 cut(s) | 189, 627, 1356, 1766 |
| FbaI | TGATCA | 2 cut(s) | 1072, 1128 |
| FblI | GTMKAC | 1 cut(s) | 418 |
| FokI | GGATG | 6 cut(s) | 590, 1198, 1227, 1407, 1703, 1711 |
| FspBI | CTAG | 5 cut(s) | 276, 852, 1503, 1634, 1650 |
| GlaI | GCGC | 1 cut(s) | 203 |
| GsaI | CCCAGC | 1 cut(s) | 128 |
| HaeIII | GGCC | 5 cut(s) | 167, 194, 785, 1224, 1388 |
| HapII | CCGG | 1 cut(s) | 295 |
| HgaI | GACGC | 2 cut(s) | 1259, 1580 |
| HhaI | GCGC | 1 cut(s) | 204 |
| Hin1II | CATG | 4 cut(s) | 193, 631, 1360, 1770 |
| Hin6I | GCGC | 1 cut(s) | 202 |
| HinP1I | GCGC | 1 cut(s) | 202 |
| HinfI | GANTC | 8 cut(s) | 51, 186, 401, 683, 763, 1189, 1489, 1763 |
| HpaII | CCGG | 1 cut(s) | 295 |
| HphI | GGTGA | 1 cut(s) | 88 |
| Hpy166II | GTNNAC | 4 cut(s) | 121, 419, 426, 1099 |
| Hpy188III | TCNNGA | 7 cut(s) | 214, 977, 1132, 1196, 1332, 1511, 1568 |
| Hpy8I | GTNNAC | 4 cut(s) | 121, 419, 426, 1099 |
| Hpy99I | CGWCG | 5 cut(s) | 31, 34, 37, 1372, 1574 |
| HpyAV | CCTTC | 8 cut(s) | 69, 86, 390, 559, 775, 1557, 1621, 1689 |
| HpyCH4III | ACNGT | 5 cut(s) | 208, 257, 352, 423, 1103 |
| HpyCH4IV | ACGT | 1 cut(s) | 1370 |
| HpyF3I | CTNAG | 5 cut(s) | 212, 371, 385, 456, 1561 |
| HpySE526I | ACGT | 1 cut(s) | 1370 |
| Hsp92II | CATG | 4 cut(s) | 193, 631, 1360, 1770 |
| HspAI | GCGC | 1 cut(s) | 202 |
| Ksp22I | TGATCA | 2 cut(s) | 1072, 1128 |
| LmnI | GCTCC | 6 cut(s) | 620, 632, 697, 730, 1009, 1723 |
| MaeI | CTAG | 5 cut(s) | 276, 852, 1503, 1634, 1650 |
| MaeII | ACGT | 1 cut(s) | 1370 |
| MaeIII | GTNAC | 3 cut(s) | 131, 541, 902 |
| MfeI | CAATTG | 3 cut(s) | 441, 1158, 1397 |
| MflI | RGATCY | 7 cut(s) | 280, 911, 1178, 1198, 1505, 1564, 1588 |
| MhlI | GDGCHC | 1 cut(s) | 301 |
| MlsI | TGGCCA | 1 cut(s) | 194 |
| MluNI | TGGCCA | 1 cut(s) | 194 |
| MlyI | GAGTC | 5 cut(s) | 195, 692, 772, 1483, 1772 |
| MmeI | TCCRAC | 4 cut(s) | 28, 157, 666, 1347 |
| Mox20I | TGGCCA | 1 cut(s) | 194 |
| MroXI | GAANNNNTTC | 1 cut(s) | 492 |
| MscI | TGGCCA | 1 cut(s) | 194 |
| MseI | TTAA | 8 cut(s) | 249, 393, 1266, 1296, 1380, 1409, 1530, 1542 |
| MslI | CAYNNNNRTG | 2 cut(s) | 1288, 1425 |
| Msp20I | TGGCCA | 1 cut(s) | 194 |
| MspA1I | CMGCKG | 2 cut(s) | 524, 533 |
| MspI | CCGG | 1 cut(s) | 295 |
| MspR9I | CCNGG | 1 cut(s) | 296 |
| MunI | CAATTG | 3 cut(s) | 441, 1158, 1397 |
| MvnI | CGCG | 1 cut(s) | 325 |
| NciI | CCSGG | 1 cut(s) | 296 |
| NcoI | CCATGG | 1 cut(s) | 627 |
| NlaIII | CATG | 4 cut(s) | 193, 631, 1360, 1770 |
| NlaIV | GGNNCC | 2 cut(s) | 119, 218 |
| NmeAIII | GCCGAG | 1 cut(s) | 910 |
| NmuCI | GTSAC | 1 cut(s) | 131 |
| NspV | TTCGAA | 2 cut(s) | 1309, 1777 |
| OliI | CACNNNNGTG | 1 cut(s) | 1288 |
| PceI | AGGCCT | 1 cut(s) | 1224 |
| PcsI | WCGNNNNNNNCGW | 2 cut(s) | 32, 758 |
| PdmI | GAANNNNTTC | 1 cut(s) | 492 |
| PfeI | GAWTC | 3 cut(s) | 51, 401, 1189 |
| PleI | GAGTC | 5 cut(s) | 194, 691, 771, 1483, 1771 |
| PpsI | GAGTC | 5 cut(s) | 194, 691, 771, 1483, 1771 |
| PpuMI | RGGWCCY | 1 cut(s) | 216 |
| Psp5II | RGGWCCY | 1 cut(s) | 216 |
| PspFI | CCCAGC | 1 cut(s) | 124 |
| PspN4I | GGNNCC | 2 cut(s) | 119, 218 |
| PspPI | GGNCC | 4 cut(s) | 118, 165, 216, 1513 |
| PspPPI | RGGWCCY | 1 cut(s) | 216 |
| PstI | CTGCAG | 4 cut(s) | 729, 970, 1005, 1060 |
| PstNI | CAGNNNCTG | 1 cut(s) | 527 |
| PsuI | RGATCY | 7 cut(s) | 280, 911, 1178, 1198, 1505, 1564, 1588 |
| PvuII | CAGCTG | 1 cut(s) | 524 |
| RsaI | GTAC | 2 cut(s) | 873, 1632 |
| RsaNI | GTAC | 2 cut(s) | 872, 1631 |
| RseI | CAYNNNNRTG | 2 cut(s) | 1288, 1425 |
| SaqAI | TTAA | 8 cut(s) | 249, 393, 1266, 1296, 1380, 1409, 1530, 1542 |
| Sau96I | GGNCC | 4 cut(s) | 118, 165, 216, 1513 |
| SchI | GAGTC | 5 cut(s) | 195, 692, 772, 1483, 1772 |
| ScrFI | CCNGG | 1 cut(s) | 296 |
| SduI | GDGCHC | 1 cut(s) | 301 |
| SfcI | CTRYAG | 6 cut(s) | 348, 483, 725, 966, 1001, 1056 |
| SfuI | TTCGAA | 2 cut(s) | 1309, 1777 |
| SinI | GGWCC | 3 cut(s) | 118, 216, 1513 |
| SmiMI | CAYNNNNRTG | 2 cut(s) | 1288, 1425 |
| SmlI | CTYRAG | 1 cut(s) | 907 |
| SmoI | CTYRAG | 1 cut(s) | 907 |
| SseBI | AGGCCT | 1 cut(s) | 1224 |
| SsiI | CCGC | 5 cut(s) | 39, 168, 171, 323, 531 |
| SspMI | CTAG | 5 cut(s) | 276, 852, 1503, 1634, 1650 |
| StuI | AGGCCT | 1 cut(s) | 1224 |
| StyD4I | CCNGG | 1 cut(s) | 294 |
| StyI | CCWWGG | 2 cut(s) | 627, 741 |
| TaaI | ACNGT | 5 cut(s) | 208, 257, 352, 423, 1103 |
| TaiI | ACGT | 1 cut(s) | 1373 |
| TaqI | TCGA | 4 cut(s) | 761, 1219, 1309, 1777 |
| TatI | WGTACW | 1 cut(s) | 871 |
| TauI | GCSGC | 3 cut(s) | 170, 173, 533 |
| TfiI | GAWTC | 3 cut(s) | 51, 401, 1189 |
| Tru1I | TTAA | 8 cut(s) | 249, 393, 1266, 1296, 1380, 1409, 1530, 1542 |
| Tru9I | TTAA | 8 cut(s) | 249, 393, 1266, 1296, 1380, 1409, 1530, 1542 |
| TscAI | CASTG | 4 cut(s) | 262, 357, 460, 1292 |
| TseFI | GTSAC | 1 cut(s) | 131 |
| Tsp45I | GTSAC | 1 cut(s) | 131 |
| TspRI | CASTG | 4 cut(s) | 262, 357, 460, 1292 |
| VpaK11BI | GGWCC | 3 cut(s) | 118, 216, 1513 |
| XapI | RAATTY | 6 cut(s) | 389, 463, 713, 972, 1244, 1537 |
| XmiI | GTMKAC | 1 cut(s) | 418 |
| XmnI | GAANNNNTTC | 1 cut(s) | 492 |
| XspI | CTAG | 5 cut(s) | 276, 852, 1503, 1634, 1650 |