Rw1G038460

RNA polymerase sigma factor sigE, chloroplastic

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr1
Physical Location & Seq
Forward (+)
65993953 .. 65996210
2258 bp
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UTR
Exon/CDS
Intron
Rw1G038460.1

Sequence Viewer

Length: 1494 bp
ATGGGAGTTGTGACAGTTTCTAGCTCAGTTTCTAGGACTCCGTTAGGATTGAGCCCAAAATTGGCATCAAGTCAGAGATCAACGTTGAGAAAGCCATTGATTGTTGCCTTTAGAACAGATAAATCCAATAAGAACGCGTTGGTTGCGCCTCAGGAGAAAGTACCTTTGCCAATAGAAACACGAAAGAAGGTCCAAAAACTAGGGAAGGCTCGAAAGCTCCCCGAAAGTGTAAAAGCTGCATTGATAGAGGAGGCTCCTACTTGTAATTTGGAACTGGATTACAATGAAGCTGCTGCCAAGCTGGAAAATCTGTACAAGCGCAGCCCCGAGACTGAAGCTTCGGATTTGGAAAATGTAGATGGATTGATGATCAAGAGAAGTCGCAAAAGGAGGAAGAAGATCAGTGAAGTTGATGACAAAGTAGAGAAGAGAAAAAGCGATGACATTGTGGTTGGGAGCAGGACAAAGAAGGCTAAAAGATTGAGTCTTGATAAAAGGGTTGCGTTGAAATGGAATAAGGACGAGAAAGTGGCTGCTCCAGTAGTTCGAAAGAGAAAAGATAGAAAGAGTGAGAATCAGATGATTGAGGAGCTTGTAAGGGAGTATTCGGCTTCAACTGATCTCGTCAGTTTAGACTGGAAAAAGATGAGGATTCCTCCAGTTCTTACTTCTTCTGAGCATACTTGGTTGTTCAAGCTAATGCAACCTATGAAGGCTCTTCTTCAAGTGAAAGAAACTCTGCAGAAAGATTTGGGGAGAGAACCAAATAAGGGTGAACTAGCTGAGGCGACAAGTATGAGTGTGGTTCAAGTGAAAAAACACTTGGAGGTTGGTCGAGCTGCAAGAAACAAACTCATCAAGCATAATCTCCGGCTTGTGTTATTTGTCATTAACAAATACTTTCAAGACTTTGCGAATGGTCCAAAATTTCAAGACCTTTGTCAGGCAGGAGTGAAGGGACTTATACGATTCCGGCTTTCCACATATGGTCTTTTCTGGATCAGGCATGCCATCATACGTTCCATGACACTATCAAGCTTTACTCGTGTCTCCTTTGGCCTTGAGTCTGTTAGGGCGGAAATCCAGAAAGCCAAGCTTGAAATGTTGGTTCAGCTTAAAAGAATGCCAACAGAGGACGAGATAATTGAAAAGGTTGGAATTTCCCCTGAGAGGTATCATGAAGTAATGAGGGCCTCAAAACCTGAGGAATTTATAAACGCTATTACTGATGTTGACGGCGTTGAAGGTGATAACCGGCGGAAACCTGCTCTTCTCAGGCTTGCTATCGATGATGTGCTTGATTCCCTGAAGCCAAAAGAAAGCTTGGTGATCAGGCAGAGATATGGCCTTGATGGCAAGGGTGACAGAACATTGGGGGAGATAGCTGGAAACTTGAATATTTCAAGAGAAATGGTTCGAAAGCATGAAGTTAAGGCCCTCATGAAGCTCAAGCATCCAGCTCGAGTAGACTATCTTCGCAGATACATAGTCTAA
Functional Annotation
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families

Protein Analysis

497

Amino Acids

56.7

Weight (kDa)

9.99

Isoelectric Point (pI)

45.49

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Sigma70_r3 PF04539 240 - 280 9.8e-06 Sigma-70 region 3
Sigma70_r3 PF04539 359 - 400 2.3e-06 Sigma-70 region 3
Sigma70_r4 PF04545 432 - 485 9.7e-14 Sigma-70, region 4
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 1214
Acc36I ACCTGC 1 cut(s) 1273
AccI GTMKAC 1 cut(s) 1467
AccII CGCG 1 cut(s) 137
AciI CCGC 2 cut(s) 1076, 1258
AclI AACGTT 1 cut(s) 83
AclWI GGATC 1 cut(s) 1007
AcsI RAATTY 3 cut(s) 926, 1158, 1208
AcuI CTGAAG 2 cut(s) 354, 1328
AfaI GTAC 2 cut(s) 162, 314
AfiI CCNNNNNNNGG 4 cut(s) 61, 770, 943, 1170
AflIII ACRYGT 1 cut(s) 135
AjuI GAANNNNNNNTTGG 2 cut(s) 806, 838
Alw26I GTCTC 2 cut(s) 323, 1054
AlwI GGATC 1 cut(s) 1007
Ama87I CYCGRG 2 cut(s) 326, 1461
AoxI GGCC 4 cut(s) 1057, 1191, 1345, 1434
ApeKI GCWGC 6 cut(s) 236, 290, 293, 321, 533, 839
ApoI RAATTY 3 cut(s) 926, 1158, 1208
ArsI GACNNNNNNTTYG 2 cut(s) 322, 354
Asp700I GAANNNNTTC 1 cut(s) 1413
AspLEI GCGC 2 cut(s) 148, 321
AspS9I GGNCC 4 cut(s) 190, 920, 1191, 1435
AsuHPI GGTGA 4 cut(s) 785, 1259, 1339, 1373
AsuII TTCGAA 2 cut(s) 547, 1417
AvaI CYCGRG 2 cut(s) 326, 1461
AvaII GGWCC 2 cut(s) 190, 920
AxyI CCTNAGG 2 cut(s) 150, 1203
BanII GRGCYC 1 cut(s) 56
BarI GAAGNNNNNNTAC 2 cut(s) 1458, 1490
BauI CACGAG 1 cut(s) 1044
BbvCI CCTCAGC 1 cut(s) 783
BbvI GCAGC 6 cut(s) 223, 277, 280, 333, 520, 826
BccI CCATC 3 cut(s) 353, 1019, 1346
BceAI ACGGC 1 cut(s) 1252
BcgI CGANNNNNNTGC 2 cut(s) 1442, 1476
BclI TGATCA 2 cut(s) 369, 1329
BcoDI GTCTC 2 cut(s) 323, 1054
BfaI CTAG 4 cut(s) 21, 33, 200, 779
BfmI CTRYAG 1 cut(s) 740
BfuAI ACCTGC 1 cut(s) 1273
BglI GCCNNNNNGGC 1 cut(s) 1353
BisI GCNGC 6 cut(s) 237, 291, 294, 322, 534, 840
BlsI GCNGC 6 cut(s) 238, 292, 295, 323, 535, 841
Bme18I GGWCC 2 cut(s) 190, 920
BmeT110I CYCGRG 2 cut(s) 326, 1461
BmgT120I GGNCC 4 cut(s) 190, 920, 1191, 1435
BmiI GGNNCC 1 cut(s) 255
BmsI GCATC 2 cut(s) 74, 1462
BoxI GACNNNNGTC 1 cut(s) 939
BplI GAGNNNNNCTC 2 cut(s) 640, 672
BpmI CTGGAG 2 cut(s) 522, 642
Bpu10I CCTNAGC 1 cut(s) 783
Bpu14I TTCGAA 2 cut(s) 547, 1417
BpuEI CTTGAG 2 cut(s) 1082, 1433
Bsa29I ATCGAT 1 cut(s) 1287
Bsc4I CCNNNNNNNGG 4 cut(s) 61, 770, 943, 1170
Bse118I RCCGGY 1 cut(s) 1254
Bse1I ACTGG 4 cut(s) 279, 539, 641, 659
Bse21I CCTNAGG 2 cut(s) 150, 1203
BseCI ATCGAT 1 cut(s) 1287
BseGI GGATG 1 cut(s) 1453
BseLI CCNNNNNNNGG 4 cut(s) 61, 770, 943, 1170
BseMII CTCAG 7 cut(s) 39, 164, 666, 774, 1158, 1194, 1288
BseNI ACTGG 4 cut(s) 279, 539, 641, 659
BseRI GAGGAG 2 cut(s) 263, 602
BseXI GCAGC 6 cut(s) 223, 277, 280, 333, 520, 826
Bsh1236I CGCG 1 cut(s) 137
BshFI GGCC 4 cut(s) 1059, 1193, 1347, 1436
BshVI ATCGAT 1 cut(s) 1287
BsiHKCI CYCGRG 2 cut(s) 326, 1461
BsiSI CCGG 3 cut(s) 871, 973, 1255
BslFI GGGAC 1 cut(s) 972
BslI CCNNNNNNNGG 4 cut(s) 61, 770, 943, 1170
BsmAI GTCTC 2 cut(s) 323, 1054
BsmFI GGGAC 1 cut(s) 972
BsmI GAATGC 1 cut(s) 1128
BsnI GGCC 4 cut(s) 1059, 1193, 1347, 1436
BsoBI CYCGRG 2 cut(s) 326, 1461
Bsp119I TTCGAA 2 cut(s) 547, 1417
Bsp1286I GDGCHC 1 cut(s) 56
Bsp1407I TGTACA 1 cut(s) 312
Bsp143I GATC 6 cut(s) 77, 369, 399, 619, 999, 1329
BspACI CCGC 2 cut(s) 1076, 1258
BspANI GGCC 4 cut(s) 1059, 1193, 1347, 1436
BspCNI CTCAG 7 cut(s) 38, 163, 667, 775, 1159, 1195, 1287
BspDI ATCGAT 1 cut(s) 1287
BspFNI CGCG 1 cut(s) 137
BspHI TCATGA 2 cut(s) 1177, 1440
BspLI GGNNCC 1 cut(s) 255
BspMAI CTGCAG 1 cut(s) 744
BspMI ACCTGC 1 cut(s) 1273
BspPI GGATC 1 cut(s) 1007
BspQI GCTCTTC 2 cut(s) 723, 1275
BspT104I TTCGAA 2 cut(s) 547, 1417
BsrFI RCCGGY 1 cut(s) 1254
BsrGI TGTACA 1 cut(s) 312
BsrI ACTGG 4 cut(s) 279, 539, 641, 659
BssAI RCCGGY 1 cut(s) 1254
BssMI GATC 6 cut(s) 77, 369, 399, 619, 999, 1329
BssSI CACGAG 1 cut(s) 1044
Bst2BI CACGAG 1 cut(s) 1044
Bst4CI ACNGT 1 cut(s) 16
Bst6I CTCTTC 3 cut(s) 422, 723, 1275
BstAUI TGTACA 1 cut(s) 312
BstBI TTCGAA 2 cut(s) 547, 1417
BstC8I GCNNGC 2 cut(s) 1008, 1281
BstDEI CTNAG 7 cut(s) 25, 150, 675, 783, 1167, 1203, 1274
BstENI CCTNNNNNAGG 1 cut(s) 941
BstF5I GGATG 1 cut(s) 1453
BstFNI CGCG 1 cut(s) 137
BstHHI GCGC 2 cut(s) 148, 321
BstKTI GATC 6 cut(s) 80, 372, 402, 622, 1002, 1332
BstMAI GTCTC 2 cut(s) 323, 1054
BstMBI GATC 6 cut(s) 77, 369, 399, 619, 999, 1329
BstMWI GCNNNNNNNGC 2 cut(s) 143, 1353
BstNSI RCATGY 1 cut(s) 1010
BstPAI GACNNNNGTC 1 cut(s) 939
BstSFI CTRYAG 1 cut(s) 740
BstUI CGCG 1 cut(s) 137
BstV1I GCAGC 6 cut(s) 223, 277, 280, 333, 520, 826
Bsu15I ATCGAT 1 cut(s) 1287
Bsu36I CCTNAGG 2 cut(s) 150, 1203
BsuRI GGCC 4 cut(s) 1059, 1193, 1347, 1436
BsuTUI ATCGAT 1 cut(s) 1287
BtgZI GCGATG 1 cut(s) 453
BtsCI GGATG 1 cut(s) 1453
BtsIMutI CAGTG 1 cut(s) 409
BveI ACCTGC 1 cut(s) 1273
Cac8I GCNNGC 2 cut(s) 1008, 1281
CciI TCATGA 2 cut(s) 1177, 1440
CfoI GCGC 2 cut(s) 148, 321
Cfr10I RCCGGY 1 cut(s) 1254
Cfr13I GGNCC 4 cut(s) 190, 920, 1191, 1435
ClaI ATCGAT 1 cut(s) 1287
Csp6I GTAC 2 cut(s) 161, 313
CviAII CATG 5 cut(s) 1007, 1024, 1178, 1424, 1441
CviQI GTAC 2 cut(s) 161, 313
DdeI CTNAG 7 cut(s) 25, 150, 675, 783, 1167, 1203, 1274
DpnI GATC 6 cut(s) 79, 371, 401, 621, 1001, 1331
DpnII GATC 6 cut(s) 77, 369, 399, 619, 999, 1329
Eam1104I CTCTTC 3 cut(s) 422, 723, 1275
EarI CTCTTC 3 cut(s) 422, 723, 1275
EciI GGCGGA 2 cut(s) 1091, 1273
Eco24I GRGCYC 1 cut(s) 56
Eco47I GGWCC 2 cut(s) 190, 920
Eco57I CTGAAG 2 cut(s) 354, 1328
Eco81I CCTNAGG 2 cut(s) 150, 1203
Eco88I CYCGRG 2 cut(s) 326, 1461
EcoNI CCTNNNNNAGG 1 cut(s) 941
EcoO109I RGGNCCY 2 cut(s) 1191, 1435
EcoT38I GRGCYC 1 cut(s) 56
FaeI CATG 5 cut(s) 1010, 1027, 1181, 1427, 1444
FalI AAGNNNNNCTT 2 cut(s) 1080, 1112
FaqI GGGAC 1 cut(s) 972
FatI CATG 5 cut(s) 1006, 1023, 1177, 1423, 1440
FauNDI CATATG 1 cut(s) 985
FbaI TGATCA 2 cut(s) 369, 1329
FblI GTMKAC 1 cut(s) 1467
Fnu4HI GCNGC 6 cut(s) 237, 291, 294, 322, 534, 840
FokI GGATG 1 cut(s) 1440
FriOI GRGCYC 1 cut(s) 56
Fsp4HI GCNGC 6 cut(s) 237, 291, 294, 322, 534, 840
FspBI CTAG 4 cut(s) 21, 33, 200, 779
GlaI GCGC 2 cut(s) 147, 320
GluI GCNGC 6 cut(s) 237, 291, 294, 322, 534, 840
GsuI CTGGAG 2 cut(s) 522, 642
HaeIII GGCC 4 cut(s) 1059, 1193, 1347, 1436
HapII CCGG 3 cut(s) 871, 973, 1255
HhaI GCGC 2 cut(s) 148, 321
Hin1II CATG 5 cut(s) 1010, 1027, 1181, 1427, 1444
Hin6I GCGC 2 cut(s) 146, 319
HinP1I GCGC 2 cut(s) 146, 319
HincII GTYRAC 1 cut(s) 1234
HindII GTYRAC 1 cut(s) 1234
HindIII AAGCTT 4 cut(s) 336, 1036, 1094, 1321
HinfI GANTC 7 cut(s) 37, 484, 574, 652, 969, 1064, 1301
HpaII CCGG 3 cut(s) 871, 973, 1255
HphI GGTGA 4 cut(s) 785, 1259, 1339, 1373
Hpy166II GTNNAC 3 cut(s) 776, 1234, 1468
Hpy188I TCNGA 4 cut(s) 75, 343, 579, 676
Hpy8I GTNNAC 3 cut(s) 776, 1234, 1468
HpyAV CCTTC 6 cut(s) 181, 199, 463, 706, 949, 1238
HpyCH4III ACNGT 1 cut(s) 16
HpyCH4IV ACGT 2 cut(s) 83, 1018
HpyCH4V TGCA 4 cut(s) 239, 703, 742, 842
HpyF10VI GCNNNNNNNGC 2 cut(s) 143, 1353
HpyF3I CTNAG 7 cut(s) 25, 150, 675, 783, 1167, 1203, 1274
HpySE526I ACGT 2 cut(s) 83, 1018
Hsp92II CATG 5 cut(s) 1010, 1027, 1181, 1427, 1444
HspAI GCGC 2 cut(s) 146, 319
Ksp22I TGATCA 2 cut(s) 369, 1329
Kzo9I GATC 6 cut(s) 77, 369, 399, 619, 999, 1329
LguI GCTCTTC 2 cut(s) 723, 1275
LmnI GCTCC 5 cut(s) 222, 259, 456, 541, 589
Lsp1109I GCAGC 6 cut(s) 223, 277, 280, 333, 520, 826
LweI GCATC 2 cut(s) 74, 1462
MaeI CTAG 4 cut(s) 21, 33, 200, 779
MaeII ACGT 2 cut(s) 83, 1018
MaeIII GTNAC 2 cut(s) 10, 1361
MalI GATC 6 cut(s) 79, 371, 401, 621, 1001, 1331
MboI GATC 6 cut(s) 77, 369, 399, 619, 999, 1329
MboII GAAGA 8 cut(s) 406, 409, 439, 663, 710, 713, 1262, 1466
MhlI GDGCHC 1 cut(s) 56
MluCI AATT 6 cut(s) 59, 265, 926, 1143, 1158, 1208
MluI ACGCGT 1 cut(s) 135
MlyI GAGTC 3 cut(s) 31, 493, 1073
MmeI TCCRAC 1 cut(s) 1135
MroXI GAANNNNTTC 1 cut(s) 1413
MseI TTAA 3 cut(s) 891, 1116, 1431
MspI CCGG 3 cut(s) 871, 973, 1255
Mva1269I GAATGC 1 cut(s) 1128
MvnI CGCG 1 cut(s) 137
MwoI GCNNNNNNNGC 2 cut(s) 143, 1353
NdeI CATATG 1 cut(s) 985
NdeII GATC 6 cut(s) 77, 369, 399, 619, 999, 1329
NlaIII CATG 5 cut(s) 1010, 1027, 1181, 1427, 1444
NlaIV GGNNCC 1 cut(s) 255
NmuCI GTSAC 2 cut(s) 10, 1361
NspI RCATGY 1 cut(s) 1010
NspV TTCGAA 2 cut(s) 547, 1417
PaeI GCATGC 1 cut(s) 1010
PaeR7I CTCGAG 1 cut(s) 1461
PagI TCATGA 2 cut(s) 1177, 1440
PciSI GCTCTTC 2 cut(s) 723, 1275
PctI GAATGC 1 cut(s) 1128
PdmI GAANNNNTTC 1 cut(s) 1413
PfeI GAWTC 4 cut(s) 574, 652, 969, 1301
PkrI GCNGC 6 cut(s) 238, 292, 295, 323, 535, 841
PleI GAGTC 3 cut(s) 31, 492, 1072
PpsI GAGTC 3 cut(s) 31, 492, 1072
PshAI GACNNNNGTC 1 cut(s) 939
PsiI TTATAA 1 cut(s) 1214
Psp1406I AACGTT 1 cut(s) 83
PspN4I GGNNCC 1 cut(s) 255
PspPI GGNCC 4 cut(s) 190, 920, 1191, 1435
PspXI VCTCGAGB 1 cut(s) 1461
PstI CTGCAG 1 cut(s) 744
RsaI GTAC 2 cut(s) 162, 314
RsaNI GTAC 2 cut(s) 161, 313
SapI GCTCTTC 2 cut(s) 723, 1275
SaqAI TTAA 3 cut(s) 891, 1116, 1431
SatI GCNGC 6 cut(s) 237, 291, 294, 322, 534, 840
Sau3AI GATC 6 cut(s) 77, 369, 399, 619, 999, 1329
Sau96I GGNCC 4 cut(s) 190, 920, 1191, 1435
SchI GAGTC 3 cut(s) 31, 493, 1073
SduI GDGCHC 1 cut(s) 56
SfaNI GCATC 2 cut(s) 74, 1462
SfcI CTRYAG 1 cut(s) 740
Sfr274I CTCGAG 1 cut(s) 1461
SfuI TTCGAA 2 cut(s) 547, 1417
SinI GGWCC 2 cut(s) 190, 920
SlaI CTCGAG 1 cut(s) 1461
SmlI CTYRAG 3 cut(s) 1061, 1448, 1461
SmoI CTYRAG 3 cut(s) 1061, 1448, 1461
SphI GCATGC 1 cut(s) 1010
Sse9I AATT 6 cut(s) 59, 265, 926, 1143, 1158, 1208
SsiI CCGC 2 cut(s) 1076, 1258
SspI AATATT 1 cut(s) 1399
SspMI CTAG 4 cut(s) 21, 33, 200, 779
TaaI ACNGT 1 cut(s) 16
TaiI ACGT 2 cut(s) 86, 1021
TaqI TCGA 6 cut(s) 211, 547, 835, 1287, 1417, 1462
TasI AATT 6 cut(s) 59, 265, 926, 1143, 1158, 1208
TatI WGTACW 1 cut(s) 312
TfiI GAWTC 4 cut(s) 574, 652, 969, 1301
Tru1I TTAA 3 cut(s) 891, 1116, 1431
Tru9I TTAA 3 cut(s) 891, 1116, 1431
TscAI CASTG 1 cut(s) 409
TseFI GTSAC 2 cut(s) 10, 1361
TseI GCWGC 6 cut(s) 236, 290, 293, 321, 533, 839
Tsp45I GTSAC 2 cut(s) 10, 1361
TspDTI ATGAA 5 cut(s) 300, 725, 1194, 1440, 1457
TspGWI ACGGA 1 cut(s) 30
TspRI CASTG 1 cut(s) 409
VpaK11BI GGWCC 2 cut(s) 190, 920
XagI CCTNNNNNAGG 1 cut(s) 941
XapI RAATTY 3 cut(s) 926, 1158, 1208
XceI RCATGY 1 cut(s) 1010
XhoI CTCGAG 1 cut(s) 1461
XmiI GTMKAC 1 cut(s) 1467
XmnI GAANNNNTTC 1 cut(s) 1413
XspI CTAG 4 cut(s) 21, 33, 200, 779
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.