Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released
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| 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) |
|---|---|---|---|
| AccI | GTMKAC | 1 cut(s) | 978 |
| AccII | CGCG | 1 cut(s) | 334 |
| AciI | CCGC | 3 cut(s) | 540, 566, 823 |
| AclWI | GGATC | 4 cut(s) | 284, 736, 983, 1655 |
| AcoI | YGGCCR | 1 cut(s) | 177 |
| AcsI | RAATTY | 3 cut(s) | 809, 1340, 1700 |
| AcuI | CTGAAG | 3 cut(s) | 187, 564, 1901 |
| AdeI | CACNNNGTG | 1 cut(s) | 1456 |
| AfaI | GTAC | 3 cut(s) | 1113, 1326, 1728 |
| AgsI | TTSAA | 6 cut(s) | 339, 673, 815, 942, 1084, 1353 |
| AjnI | CCWGG | 3 cut(s) | 182, 195, 1098 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 1700, 1732 |
| AleI | CACNNNNGTG | 1 cut(s) | 1384 |
| Alw26I | GTCTC | 4 cut(s) | 214, 647, 1416, 1742 |
| AlwI | GGATC | 4 cut(s) | 284, 736, 983, 1655 |
| AlwNI | CAGNNNCTG | 1 cut(s) | 536 |
| Ama87I | CYCGRG | 1 cut(s) | 650 |
| AoxI | GGCC | 5 cut(s) | 162, 177, 879, 1318, 1542 |
| ApoI | RAATTY | 3 cut(s) | 809, 1340, 1700 |
| ArsI | GACNNNNNNTTYG | 2 cut(s) | 646, 678 |
| Asp700I | GAANNNNTTC | 2 cut(s) | 501, 1700 |
| AspLEI | GCGC | 1 cut(s) | 1191 |
| AspS9I | GGNCC | 2 cut(s) | 162, 455 |
| AsuC2I | CCSGG | 1 cut(s) | 305 |
| AsuHPI | GGTGA | 1 cut(s) | 940 |
| AsuII | TTCGAA | 1 cut(s) | 1405 |
| AvaI | CYCGRG | 1 cut(s) | 650 |
| AvaII | GGWCC | 1 cut(s) | 455 |
| BalI | TGGCCA | 1 cut(s) | 179 |
| BanII | GRGCYC | 1 cut(s) | 310 |
| BbsI | GAAGAC | 3 cut(s) | 1181, 1519, 1805 |
| BccI | CCATC | 4 cut(s) | 227, 1761, 1781, 1819 |
| BcgI | CGANNNNNNTGC | 2 cut(s) | 1295, 1329 |
| BciT130I | CCWGG | 3 cut(s) | 184, 197, 1100 |
| BclI | TGATCA | 3 cut(s) | 1168, 1224, 1420 |
| BcnI | CCSGG | 1 cut(s) | 305 |
| BcoDI | GTCTC | 4 cut(s) | 214, 647, 1416, 1742 |
| BfaI | CTAG | 4 cut(s) | 708, 1026, 1599, 1730 |
| BfmI | CTRYAG | 2 cut(s) | 357, 492 |
| BglI | GCCNNNNNGGC | 1 cut(s) | 1148 |
| BglII | AGATCT | 2 cut(s) | 1294, 1601 |
| BlpI | GCTNAGC | 1 cut(s) | 681 |
| Bme1390I | CCNGG | 4 cut(s) | 184, 197, 305, 1100 |
| Bme18I | GGWCC | 1 cut(s) | 455 |
| BmeT110I | CYCGRG | 1 cut(s) | 650 |
| BmgT120I | GGNCC | 2 cut(s) | 162, 455 |
| BmiI | GGNNCC | 1 cut(s) | 253 |
| BmrFI | CCNGG | 4 cut(s) | 184, 197, 305, 1100 |
| BmrI | ACTGGG | 1 cut(s) | 1138 |
| BmsI | GCATC | 1 cut(s) | 1336 |
| BmuI | ACTGGG | 1 cut(s) | 1138 |
| BpiI | GAAGAC | 3 cut(s) | 1181, 1519, 1805 |
| BplI | GAGNNNNNCTC | 4 cut(s) | 239, 271, 279, 311 |
| BpmI | CTGGAG | 3 cut(s) | 624, 1082, 1628 |
| Bpu1102I | GCTNAGC | 1 cut(s) | 681 |
| Bpu14I | TTCGAA | 1 cut(s) | 1405 |
| BpuEI | CTTGAG | 1 cut(s) | 557 |
| BpuMI | CCSGG | 1 cut(s) | 305 |
| BsaJI | CCNNGG | 5 cut(s) | 196, 264, 431, 723, 837 |
| BsaXI | ACNNNNNCTCC | 2 cut(s) | 442, 472 |
| Bse1I | ACTGG | 6 cut(s) | 457, 641, 747, 1092, 1144, 1388 |
| Bse3DI | GCAATG | 3 cut(s) | 258, 593, 1802 |
| BseBI | CCWGG | 3 cut(s) | 184, 197, 1100 |
| BseDI | CCNNGG | 5 cut(s) | 196, 264, 431, 723, 837 |
| BseGI | GGATG | 5 cut(s) | 592, 1287, 1316, 1516, 1792 |
| BseMI | GCAATG | 3 cut(s) | 258, 593, 1802 |
| BseMII | CTCAG | 4 cut(s) | 230, 371, 456, 995 |
| BseNI | ACTGG | 6 cut(s) | 457, 641, 747, 1092, 1144, 1388 |
| BseRI | GAGGAG | 2 cut(s) | 60, 1118 |
| BseYI | CCCAGC | 1 cut(s) | 1277 |
| BsgI | GTGCAG | 2 cut(s) | 723, 1353 |
| Bsh1236I | CGCG | 1 cut(s) | 334 |
| BshFI | GGCC | 5 cut(s) | 164, 179, 881, 1320, 1544 |
| BsiHKCI | CYCGRG | 1 cut(s) | 650 |
| BsiSI | CCGG | 1 cut(s) | 304 |
| BslFI | GGGAC | 1 cut(s) | 84 |
| BsmAI | GTCTC | 4 cut(s) | 214, 647, 1416, 1742 |
| BsmFI | GGGAC | 1 cut(s) | 84 |
| BsnI | GGCC | 5 cut(s) | 164, 179, 881, 1320, 1544 |
| BsoBI | CYCGRG | 1 cut(s) | 650 |
| Bsp119I | TTCGAA | 1 cut(s) | 1405 |
| Bsp1286I | GDGCHC | 1 cut(s) | 310 |
| Bsp1407I | TGTACA | 1 cut(s) | 1111 |
| Bsp1720I | GCTNAGC | 1 cut(s) | 681 |
| Bsp19I | CCATGG | 2 cut(s) | 431, 723 |
| BspACI | CCGC | 3 cut(s) | 540, 566, 823 |
| BspANI | GGCC | 5 cut(s) | 164, 179, 881, 1320, 1544 |
| BspCNI | CTCAG | 4 cut(s) | 229, 372, 457, 996 |
| BspFNI | CGCG | 1 cut(s) | 334 |
| BspHI | TCATGA | 1 cut(s) | 1704 |
| BspLI | GGNNCC | 1 cut(s) | 253 |
| BspPI | GGATC | 4 cut(s) | 284, 736, 983, 1655 |
| BspQI | GCTCTTC | 1 cut(s) | 880 |
| BspT104I | TTCGAA | 1 cut(s) | 1405 |
| BsrDI | GCAATG | 3 cut(s) | 258, 593, 1802 |
| BsrGI | TGTACA | 1 cut(s) | 1111 |
| BsrI | ACTGG | 6 cut(s) | 457, 641, 747, 1092, 1144, 1388 |
| BssECI | CCNNGG | 5 cut(s) | 196, 264, 431, 723, 837 |
| BssT1I | CCWWGG | 3 cut(s) | 264, 431, 723 |
| Bst2UI | CCWGG | 3 cut(s) | 184, 197, 1100 |
| Bst4CI | ACNGT | 2 cut(s) | 193, 361 |
| Bst6I | CTCTTC | 4 cut(s) | 152, 510, 880, 1556 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 536 |
| BstAUI | TGTACA | 1 cut(s) | 1111 |
| BstBI | TTCGAA | 1 cut(s) | 1405 |
| BstC8I | GCNNGC | 2 cut(s) | 960, 1569 |
| BstDEI | CTNAG | 5 cut(s) | 216, 380, 465, 681, 1004 |
| BstDSI | CCRYGG | 2 cut(s) | 431, 723 |
| BstF5I | GGATG | 5 cut(s) | 592, 1287, 1316, 1516, 1792 |
| BstFNI | CGCG | 1 cut(s) | 334 |
| BstHHI | GCGC | 1 cut(s) | 1191 |
| BstMAI | GTCTC | 4 cut(s) | 214, 647, 1416, 1742 |
| BstNI | CCWGG | 3 cut(s) | 184, 197, 1100 |
| BstSCI | CCNGG | 4 cut(s) | 182, 195, 303, 1098 |
| BstSFI | CTRYAG | 2 cut(s) | 357, 492 |
| BstUI | CGCG | 1 cut(s) | 334 |
| BstV2I | GAAGAC | 3 cut(s) | 1181, 1519, 1805 |
| BstX2I | RGATCY | 5 cut(s) | 289, 728, 1294, 1601, 1660 |
| BstYI | RGATCY | 5 cut(s) | 289, 728, 1294, 1601, 1660 |
| BsuRI | GGCC | 5 cut(s) | 164, 179, 881, 1320, 1544 |
| BtgI | CCRYGG | 2 cut(s) | 431, 723 |
| BtgZI | GCGATG | 1 cut(s) | 315 |
| BtsCI | GGATG | 5 cut(s) | 592, 1287, 1316, 1516, 1792 |
| BtsI | GCAGTG | 1 cut(s) | 116 |
| BtsIMutI | CAGTG | 5 cut(s) | 116, 462, 740, 1151, 1381 |
| Cac8I | GCNNGC | 2 cut(s) | 960, 1569 |
| CaiI | CAGNNNCTG | 1 cut(s) | 536 |
| CciI | TCATGA | 1 cut(s) | 1704 |
| CfoI | GCGC | 1 cut(s) | 1191 |
| Cfr13I | GGNCC | 2 cut(s) | 162, 455 |
| Csp6I | GTAC | 3 cut(s) | 1112, 1325, 1727 |
| CspCI | CAANNNNNGTGG | 2 cut(s) | 570, 605 |
| CviAII | CATG | 6 cut(s) | 175, 432, 724, 1453, 1705, 1863 |
| CviQI | GTAC | 3 cut(s) | 1112, 1325, 1727 |
| DdeI | CTNAG | 5 cut(s) | 216, 380, 465, 681, 1004 |
| DraIII | CACNNNGTG | 1 cut(s) | 1456 |
| EaeI | YGGCCR | 1 cut(s) | 177 |
| Eam1104I | CTCTTC | 4 cut(s) | 152, 510, 880, 1556 |
| EarI | CTCTTC | 4 cut(s) | 152, 510, 880, 1556 |
| Eco130I | CCWWGG | 3 cut(s) | 264, 431, 723 |
| Eco147I | AGGCCT | 1 cut(s) | 1320 |
| Eco24I | GRGCYC | 1 cut(s) | 310 |
| Eco47I | GGWCC | 1 cut(s) | 455 |
| Eco57I | CTGAAG | 3 cut(s) | 187, 564, 1901 |
| Eco88I | CYCGRG | 1 cut(s) | 650 |
| EcoRII | CCWGG | 3 cut(s) | 182, 195, 1098 |
| EcoT14I | CCWWGG | 3 cut(s) | 264, 431, 723 |
| EcoT38I | GRGCYC | 1 cut(s) | 310 |
| ErhI | CCWWGG | 3 cut(s) | 264, 431, 723 |
| FaeI | CATG | 6 cut(s) | 178, 435, 727, 1456, 1708, 1866 |
| FaqI | GGGAC | 1 cut(s) | 84 |
| FatI | CATG | 6 cut(s) | 174, 431, 723, 1452, 1704, 1862 |
| FauI | CCCGC | 1 cut(s) | 816 |
| FauNDI | CATATG | 1 cut(s) | 687 |
| FbaI | TGATCA | 3 cut(s) | 1168, 1224, 1420 |
| FblI | GTMKAC | 1 cut(s) | 978 |
| FokI | GGATG | 5 cut(s) | 599, 1294, 1323, 1503, 1799 |
| FriOI | GRGCYC | 1 cut(s) | 310 |
| FspBI | CTAG | 4 cut(s) | 708, 1026, 1599, 1730 |
| GlaI | GCGC | 1 cut(s) | 1190 |
| GsaI | CCCAGC | 1 cut(s) | 1281 |
| GsuI | CTGGAG | 3 cut(s) | 624, 1082, 1628 |
| HaeIII | GGCC | 5 cut(s) | 164, 179, 881, 1320, 1544 |
| HapII | CCGG | 1 cut(s) | 304 |
| HhaI | GCGC | 1 cut(s) | 1191 |
| Hin1II | CATG | 6 cut(s) | 178, 435, 727, 1456, 1708, 1866 |
| Hin6I | GCGC | 1 cut(s) | 1189 |
| HinP1I | GCGC | 1 cut(s) | 1189 |
| HincII | GTYRAC | 1 cut(s) | 798 |
| HindII | GTYRAC | 1 cut(s) | 798 |
| HpaII | CCGG | 1 cut(s) | 304 |
| HphI | GGTGA | 1 cut(s) | 940 |
| Hpy166II | GTNNAC | 2 cut(s) | 798, 979 |
| Hpy188III | TCNNGA | 9 cut(s) | 365, 650, 708, 806, 1228, 1428, 1607, 1664, 1705 |
| Hpy8I | GTNNAC | 2 cut(s) | 798, 979 |
| HpyAV | CCTTC | 7 cut(s) | 399, 714, 871, 898, 1058, 1653, 1717 |
| HpyCH4III | ACNGT | 2 cut(s) | 193, 361 |
| HpyF3I | CTNAG | 5 cut(s) | 216, 380, 465, 681, 1004 |
| Hsp92II | CATG | 6 cut(s) | 178, 435, 727, 1456, 1708, 1866 |
| HspAI | GCGC | 1 cut(s) | 1189 |
| Ksp22I | TGATCA | 3 cut(s) | 1168, 1224, 1420 |
| LguI | GCTCTTC | 1 cut(s) | 880 |
| LmnI | GCTCC | 8 cut(s) | 479, 716, 826, 1101, 1105, 1274, 1609, 1819 |
| LweI | GCATC | 1 cut(s) | 1336 |
| MaeI | CTAG | 4 cut(s) | 708, 1026, 1599, 1730 |
| MaeIII | GTNAC | 2 cut(s) | 550, 998 |
| MfeI | CAATTG | 4 cut(s) | 673, 1137, 1254, 1493 |
| MflI | RGATCY | 5 cut(s) | 289, 728, 1294, 1601, 1660 |
| MhlI | GDGCHC | 1 cut(s) | 310 |
| MlsI | TGGCCA | 1 cut(s) | 179 |
| MluNI | TGGCCA | 1 cut(s) | 179 |
| MlyI | GAGTC | 7 cut(s) | 180, 208, 788, 803, 868, 1579, 1868 |
| Mox20I | TGGCCA | 1 cut(s) | 179 |
| MroXI | GAANNNNTTC | 2 cut(s) | 501, 1700 |
| MscI | TGGCCA | 1 cut(s) | 179 |
| MseI | TTAA | 6 cut(s) | 92, 243, 402, 1362, 1392, 1638 |
| MslI | CAYNNNNRTG | 2 cut(s) | 1384, 1521 |
| Msp20I | TGGCCA | 1 cut(s) | 179 |
| MspA1I | CMGCKG | 2 cut(s) | 533, 542 |
| MspI | CCGG | 1 cut(s) | 304 |
| MspR9I | CCNGG | 4 cut(s) | 184, 197, 305, 1100 |
| MunI | CAATTG | 4 cut(s) | 673, 1137, 1254, 1493 |
| MvaI | CCWGG | 3 cut(s) | 184, 197, 1100 |
| MvnI | CGCG | 1 cut(s) | 334 |
| NciI | CCSGG | 1 cut(s) | 305 |
| NcoI | CCATGG | 2 cut(s) | 431, 723 |
| NdeI | CATATG | 1 cut(s) | 687 |
| NlaIII | CATG | 6 cut(s) | 178, 435, 727, 1456, 1708, 1866 |
| NlaIV | GGNNCC | 1 cut(s) | 253 |
| NspV | TTCGAA | 1 cut(s) | 1405 |
| OliI | CACNNNNGTG | 1 cut(s) | 1384 |
| PagI | TCATGA | 1 cut(s) | 1704 |
| PceI | AGGCCT | 1 cut(s) | 1320 |
| PciSI | GCTCTTC | 1 cut(s) | 880 |
| PcsI | WCGNNNNNNNCGW | 1 cut(s) | 1662 |
| PdmI | GAANNNNTTC | 2 cut(s) | 501, 1700 |
| PfeI | GAWTC | 3 cut(s) | 410, 1285, 1633 |
| PfoI | TCCNGGA | 1 cut(s) | 1098 |
| PleI | GAGTC | 7 cut(s) | 179, 208, 787, 802, 867, 1579, 1867 |
| PpsI | GAGTC | 7 cut(s) | 179, 208, 787, 802, 867, 1579, 1867 |
| Psp6I | CCWGG | 3 cut(s) | 182, 195, 1098 |
| PspFI | CCCAGC | 1 cut(s) | 1277 |
| PspGI | CCWGG | 3 cut(s) | 182, 195, 1098 |
| PspN4I | GGNNCC | 1 cut(s) | 253 |
| PspPI | GGNCC | 2 cut(s) | 162, 455 |
| PstNI | CAGNNNCTG | 1 cut(s) | 536 |
| PsuI | RGATCY | 5 cut(s) | 289, 728, 1294, 1601, 1660 |
| PvuII | CAGCTG | 1 cut(s) | 533 |
| RsaI | GTAC | 3 cut(s) | 1113, 1326, 1728 |
| RsaNI | GTAC | 3 cut(s) | 1112, 1325, 1727 |
| RseI | CAYNNNNRTG | 2 cut(s) | 1384, 1521 |
| SapI | GCTCTTC | 1 cut(s) | 880 |
| SaqAI | TTAA | 6 cut(s) | 92, 243, 402, 1362, 1392, 1638 |
| Sau96I | GGNCC | 2 cut(s) | 162, 455 |
| SchI | GAGTC | 7 cut(s) | 180, 208, 788, 803, 868, 1579, 1868 |
| ScrFI | CCNGG | 4 cut(s) | 184, 197, 305, 1100 |
| SduI | GDGCHC | 1 cut(s) | 310 |
| SfaNI | GCATC | 1 cut(s) | 1336 |
| SfcI | CTRYAG | 2 cut(s) | 357, 492 |
| SfuI | TTCGAA | 1 cut(s) | 1405 |
| SinI | GGWCC | 1 cut(s) | 455 |
| SmiMI | CAYNNNNRTG | 2 cut(s) | 1384, 1521 |
| SmlI | CTYRAG | 1 cut(s) | 572 |
| SmoI | CTYRAG | 1 cut(s) | 572 |
| SseBI | AGGCCT | 1 cut(s) | 1320 |
| SsiI | CCGC | 3 cut(s) | 540, 566, 823 |
| SspMI | CTAG | 4 cut(s) | 708, 1026, 1599, 1730 |
| StuI | AGGCCT | 1 cut(s) | 1320 |
| StyD4I | CCNGG | 4 cut(s) | 182, 195, 303, 1098 |
| StyI | CCWWGG | 3 cut(s) | 264, 431, 723 |
| TaaI | ACNGT | 2 cut(s) | 193, 361 |
| TaqI | TCGA | 3 cut(s) | 857, 1315, 1405 |
| TatI | WGTACW | 1 cut(s) | 1111 |
| TauI | GCSGC | 2 cut(s) | 542, 569 |
| TfiI | GAWTC | 3 cut(s) | 410, 1285, 1633 |
| Tru1I | TTAA | 6 cut(s) | 92, 243, 402, 1362, 1392, 1638 |
| Tru9I | TTAA | 6 cut(s) | 92, 243, 402, 1362, 1392, 1638 |
| TscAI | CASTG | 5 cut(s) | 123, 469, 747, 1151, 1388 |
| TspGWI | ACGGA | 2 cut(s) | 981, 1862 |
| TspRI | CASTG | 5 cut(s) | 123, 469, 747, 1151, 1388 |
| VpaK11BI | GGWCC | 1 cut(s) | 455 |
| XapI | RAATTY | 3 cut(s) | 809, 1340, 1700 |
| XbaI | TCTAGA | 1 cut(s) | 707 |
| XcmI | CCANNNNNNNNNTGG | 1 cut(s) | 172 |
| XmiI | GTMKAC | 1 cut(s) | 978 |
| XmnI | GAANNNNTTC | 2 cut(s) | 501, 1700 |
| XspI | CTAG | 4 cut(s) | 708, 1026, 1599, 1730 |