Rh1BG397900

RNA polymerase sigma factor sigE, chloroplastic

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr1B
OG0008760
Physical Location & Seq
Forward (+)
52214431 .. 52217647
3217 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1BG397900.1

Sequence Viewer

Length: 1431 bp
ATGGGAGTTGTGACAGTTTCTAGCTCAGTTTCTAGGACTCCGTTAGGATTGAGCCCAAAATTGGCATCAAGTCAGAGATCAACGTTGAGAAAGCCATTGATTGTTGCCTTTAGAACAGATAAATCCAATAAGAAAACGTTGGTTGCGCCTCAGGAGAAAGTACCTTTGCCAATAGAAACACGAAAGAAGGTCCAAAAACTAGGGAAGGCTCGAAAGCTCCCCGAAAGTGTAAAAGCTGCATTGATAGAGGAGGCTCCTACTTGTAATTTGGAACTGGATTACAATGAAGCTGCTGCCAAGCTGGAAAACCTGTACAAGCGCAGCCCAGAGACTGAAGCTTCGGATTTGGAAAATGTAGATGGATTGATGATCAAGAGAAGGCGCAAAAGGAGGAAGAAGATCAGTGAAGTTGATGACAAAGTAGAGAAGAGAAAAAGCGATGACATTGTGGTTGGGAGCAGGACAAAGAAGGCTAAAAGATTGAGTCTTGATAAAAGGGTTGCGTTGAAATGGAATAAGGACGAGAAAGTGGCTGCTCCAGTAGTTCGAAAGAGAAAAGATAGAAAGAGTGAGAATCAGATGATTGAGGAGCTTGTAAGGGAGTATTCGGCTTCAACTGATCTCGTCAGTTTAGACTGGAAAAAGATGAGGATTCCTCCAGTTCTTACTTCTTCTGAGCATACTTGGTTGTTCAAGCTAATGCAACCTATGAAGGCTCTTCTTCAAGTGAAAGAGACTCTGCAGAAAGATTTGGGGAGAGAACCAAATAAGGGTGAACTAGCTGAGGCGACAAGTATGAGTGTGGTTCAAGTGAAAAAACACTTGGAGGTTGGTCGAGCTGCAAGAAACAAACTCATCAAGCATAATCTCCGGCTTGTGTTATTTGTCATTAACAAATACTTTCAAGACTTTGCGAATGGTCCAAAATTTCAAGACCTTTGTCAGGCAGGAGTGAAGGGACTTATCACGGCAATTGATCGCTTTGAACCACAAAGAAGATTCCGGCTTTCCACATATGGTCTTTTCTGGATCAGGCATGCCATCATACGTTCCATGACACTATCAAGCTTTACTCGTGTCTCCTTTGGCCTTGAGTCTGTTAGGGCGGAAATCCAGAAAGCCAAGCTTGAAATGTTGGTTCAGCTTAAAAGAATGCCAACAGAGGACGAGATAATTGAAAAGGTTGGAATTTCCCCTGAGAGGTATCATGAAGTAATGAGGGCCTCAAAACCTGTCTTCTCTCTTCATTCAAGGCATTCAGTCACACAGGAGGAATTTATAAACGCTATTACTGATGTTGACGGCGTTGAAGGTGATAACCGGCGGAAACCTGCTCTTCTCAGGCTTGCTATCGATGATGTGGTAATTACTTTTTCCTCTTTGAGGACAATCAATTATTATTGCCCTGCTTGCTCTGTTCAAACCATTTAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0000988 GO:0000990 GO:0003674 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005739 GO:0006091 GO:0006139 GO:0006351 GO:0006352 GO:0006355 GO:0006725 GO:0006807 GO:0006950 GO:0006970 GO:0006996 GO:0007275 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009314 GO:0009416 GO:0009507 GO:0009536 GO:0009553 GO:0009628 GO:0009637 GO:0009639 GO:0009651 GO:0009657 GO:0009658 GO:0009889 GO:0009891 GO:0009893 GO:0009987 GO:0010114 GO:0010207 GO:0010218 GO:0010467 GO:0010468 GO:0010556 GO:0010557 GO:0010604 GO:0010628 GO:0015979 GO:0016043 GO:0016070 GO:0016987 GO:0018130 GO:0019219 GO:0019222 GO:0019438 GO:0019684 GO:0022607 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0032501 GO:0032502 GO:0032774 GO:0033554 GO:0034622 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043254 GO:0043933 GO:0044085 GO:0044087 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044424 GO:0044444 GO:0044464 GO:0045893 GO:0045935 GO:0046483 GO:0048229 GO:0048518 GO:0048522 GO:0048856 GO:0050789 GO:0050794 GO:0050896 GO:0051128 GO:0051171 GO:0051173 GO:0051252 GO:0051254 GO:0051716 GO:0060255 GO:0065003 GO:0065007 GO:0071214 GO:0071470 GO:0071472 GO:0071478 GO:0071482 GO:0071483 GO:0071704 GO:0071840 GO:0080090 GO:0090304 GO:0097659 GO:0104004 GO:0140110 GO:1901360 GO:1901362 GO:1901576 GO:1902680 GO:1903506 GO:1903508 GO:2000112 GO:2000142 GO:2001141
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
Sigma70_r2 Sigma70_r3 Sigma70_r4

Protein Analysis

476

Amino Acids

54.34

Weight (kDa)

9.96

Isoelectric Point (pI)

51.67

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Sigma70_r3 PF04539 240 - 280 9.3e-06 Sigma-70 region 3
Sigma70_r2 PF04542 285 - 351 8e-11 Sigma-70 region 2
Sigma70_r3 PF04539 369 - 434 2e-11 Sigma-70 region 3
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 1280
Acc36I ACCTGC 1 cut(s) 1339
AciI CCGC 2 cut(s) 1106, 1324
AclI AACGTT 2 cut(s) 83, 137
AclWI GGATC 1 cut(s) 1037
AcsI RAATTY 3 cut(s) 926, 1188, 1274
AcuI CTGAAG 1 cut(s) 354
AfaI GTAC 2 cut(s) 162, 314
AfiI CCNNNNNNNGG 5 cut(s) 61, 770, 943, 1200, 1383
AjuI GAANNNNNNNTTGG 2 cut(s) 806, 838
Alw26I GTCTC 3 cut(s) 323, 728, 1084
AlwI GGATC 1 cut(s) 1037
AlwNI CAGNNNCTG 1 cut(s) 332
AoxI GGCC 2 cut(s) 1087, 1221
ApeKI GCWGC 6 cut(s) 236, 290, 293, 321, 533, 839
ApoI RAATTY 3 cut(s) 926, 1188, 1274
ArsI GACNNNNNNTTYG 2 cut(s) 322, 354
AspLEI GCGC 3 cut(s) 148, 321, 384
AspS9I GGNCC 3 cut(s) 190, 920, 1221
AsuHPI GGTGA 2 cut(s) 785, 1325
AsuII TTCGAA 1 cut(s) 547
AvaII GGWCC 2 cut(s) 190, 920
AxyI CCTNAGG 1 cut(s) 150
BanII GRGCYC 1 cut(s) 56
BauI CACGAG 1 cut(s) 1074
BbsI GAAGAC 1 cut(s) 1228
BbvCI CCTCAGC 1 cut(s) 783
BbvI GCAGC 6 cut(s) 223, 277, 280, 333, 520, 826
BccI CCATC 2 cut(s) 353, 1049
BceAI ACGGC 2 cut(s) 984, 1318
BclI TGATCA 1 cut(s) 369
BcoDI GTCTC 3 cut(s) 323, 728, 1084
BfaI CTAG 4 cut(s) 21, 33, 200, 779
BfmI CTRYAG 1 cut(s) 740
BfuAI ACCTGC 1 cut(s) 1339
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
BmgT120I GGNCC 3 cut(s) 190, 920, 1221
BmiI GGNNCC 1 cut(s) 255
BmsI GCATC 1 cut(s) 74
BoxI GACNNNNGTC 1 cut(s) 939
BpiI GAAGAC 1 cut(s) 1228
BplI GAGNNNNNCTC 2 cut(s) 640, 672
BpmI CTGGAG 2 cut(s) 522, 642
Bpu10I CCTNAGC 1 cut(s) 783
Bpu14I TTCGAA 1 cut(s) 547
BpuEI CTTGAG 1 cut(s) 1112
Bsa29I ATCGAT 1 cut(s) 1353
Bsc4I CCNNNNNNNGG 5 cut(s) 61, 770, 943, 1200, 1383
Bse118I RCCGGY 1 cut(s) 1320
Bse1I ACTGG 4 cut(s) 279, 539, 641, 659
Bse21I CCTNAGG 1 cut(s) 150
BseCI ATCGAT 1 cut(s) 1353
BseLI CCNNNNNNNGG 5 cut(s) 61, 770, 943, 1200, 1383
BseMII CTCAG 6 cut(s) 39, 164, 666, 774, 1188, 1354
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
BshFI GGCC 2 cut(s) 1089, 1223
BshVI ATCGAT 1 cut(s) 1353
BsiSI CCGG 3 cut(s) 871, 1003, 1321
BslFI GGGAC 1 cut(s) 972
BslI CCNNNNNNNGG 5 cut(s) 61, 770, 943, 1200, 1383
BsmAI GTCTC 3 cut(s) 323, 728, 1084
BsmFI GGGAC 1 cut(s) 972
BsmI GAATGC 2 cut(s) 1158, 1255
BsnI GGCC 2 cut(s) 1089, 1223
Bsp119I TTCGAA 1 cut(s) 547
Bsp1286I GDGCHC 1 cut(s) 56
Bsp1407I TGTACA 1 cut(s) 312
Bsp143I GATC 6 cut(s) 77, 369, 399, 619, 976, 1029
BspACI CCGC 2 cut(s) 1106, 1324
BspANI GGCC 2 cut(s) 1089, 1223
BspCNI CTCAG 6 cut(s) 38, 163, 667, 775, 1189, 1353
BspDI ATCGAT 1 cut(s) 1353
BspHI TCATGA 1 cut(s) 1207
BspLI GGNNCC 1 cut(s) 255
BspMAI CTGCAG 1 cut(s) 744
BspMI ACCTGC 1 cut(s) 1339
BspPI GGATC 1 cut(s) 1037
BspQI GCTCTTC 2 cut(s) 723, 1341
BspT104I TTCGAA 1 cut(s) 547
BsrFI RCCGGY 1 cut(s) 1320
BsrGI TGTACA 1 cut(s) 312
BsrI ACTGG 4 cut(s) 279, 539, 641, 659
BssAI RCCGGY 1 cut(s) 1320
BssMI GATC 6 cut(s) 77, 369, 399, 619, 976, 1029
BssSI CACGAG 1 cut(s) 1074
Bst2BI CACGAG 1 cut(s) 1074
Bst4CI ACNGT 1 cut(s) 16
Bst6I CTCTTC 4 cut(s) 422, 723, 1248, 1341
BstAUI TGTACA 1 cut(s) 312
BstBI TTCGAA 1 cut(s) 547
BstC8I GCNNGC 3 cut(s) 1038, 1347, 1411
BstDEI CTNAG 6 cut(s) 25, 150, 675, 783, 1197, 1340
BstENI CCTNNNNNAGG 2 cut(s) 941, 1381
BstHHI GCGC 3 cut(s) 148, 321, 384
BstKTI GATC 6 cut(s) 80, 372, 402, 622, 979, 1032
BstMAI GTCTC 3 cut(s) 323, 728, 1084
BstMBI GATC 6 cut(s) 77, 369, 399, 619, 976, 1029
BstMWI GCNNNNNNNGC 1 cut(s) 1410
BstNSI RCATGY 1 cut(s) 1040
BstPAI GACNNNNGTC 1 cut(s) 939
BstSFI CTRYAG 1 cut(s) 740
BstV1I GCAGC 6 cut(s) 223, 277, 280, 333, 520, 826
BstV2I GAAGAC 1 cut(s) 1228
Bsu15I ATCGAT 1 cut(s) 1353
Bsu36I CCTNAGG 1 cut(s) 150
BsuRI GGCC 2 cut(s) 1089, 1223
BsuTUI ATCGAT 1 cut(s) 1353
BtgZI GCGATG 1 cut(s) 453
BtsIMutI CAGTG 1 cut(s) 409
BveI ACCTGC 1 cut(s) 1339
Cac8I GCNNGC 3 cut(s) 1038, 1347, 1411
CaiI CAGNNNCTG 1 cut(s) 332
CciI TCATGA 1 cut(s) 1207
CfoI GCGC 3 cut(s) 148, 321, 384
Cfr10I RCCGGY 1 cut(s) 1320
Cfr13I GGNCC 3 cut(s) 190, 920, 1221
ClaI ATCGAT 1 cut(s) 1353
Csp6I GTAC 2 cut(s) 161, 313
CviAII CATG 3 cut(s) 1037, 1054, 1208
CviQI GTAC 2 cut(s) 161, 313
DdeI CTNAG 6 cut(s) 25, 150, 675, 783, 1197, 1340
DpnI GATC 6 cut(s) 79, 371, 401, 621, 978, 1031
DpnII GATC 6 cut(s) 77, 369, 399, 619, 976, 1029
Eam1104I CTCTTC 4 cut(s) 422, 723, 1248, 1341
EarI CTCTTC 4 cut(s) 422, 723, 1248, 1341
EciI GGCGGA 2 cut(s) 1121, 1339
Eco24I GRGCYC 1 cut(s) 56
Eco47I GGWCC 2 cut(s) 190, 920
Eco57I CTGAAG 1 cut(s) 354
Eco81I CCTNAGG 1 cut(s) 150
EcoNI CCTNNNNNAGG 2 cut(s) 941, 1381
EcoO109I RGGNCCY 1 cut(s) 1221
EcoT38I GRGCYC 1 cut(s) 56
FaeI CATG 3 cut(s) 1040, 1057, 1211
FalI AAGNNNNNCTT 2 cut(s) 1110, 1142
FaqI GGGAC 1 cut(s) 972
FatI CATG 3 cut(s) 1036, 1053, 1207
FauNDI CATATG 1 cut(s) 1015
FbaI TGATCA 1 cut(s) 369
Fnu4HI GCNGC 6 cut(s) 237, 291, 294, 322, 534, 840
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 3 cut(s) 147, 320, 383
GluI GCNGC 6 cut(s) 237, 291, 294, 322, 534, 840
GsuI CTGGAG 2 cut(s) 522, 642
HaeIII GGCC 2 cut(s) 1089, 1223
HapII CCGG 3 cut(s) 871, 1003, 1321
HhaI GCGC 3 cut(s) 148, 321, 384
Hin1II CATG 3 cut(s) 1040, 1057, 1211
Hin6I GCGC 3 cut(s) 146, 319, 382
HinP1I GCGC 3 cut(s) 146, 319, 382
HincII GTYRAC 1 cut(s) 1300
HindII GTYRAC 1 cut(s) 1300
HindIII AAGCTT 3 cut(s) 336, 1066, 1124
HinfI GANTC 7 cut(s) 37, 484, 574, 652, 736, 999, 1094
HpaII CCGG 3 cut(s) 871, 1003, 1321
HphI GGTGA 2 cut(s) 785, 1325
Hpy166II GTNNAC 2 cut(s) 776, 1300
Hpy188I TCNGA 4 cut(s) 75, 343, 579, 676
Hpy188III TCNNGA 8 cut(s) 152, 373, 488, 905, 932, 1027, 1114, 1208
Hpy8I GTNNAC 2 cut(s) 776, 1300
HpyAV CCTTC 7 cut(s) 181, 199, 372, 463, 706, 949, 1304
HpyCH4III ACNGT 1 cut(s) 16
HpyCH4IV ACGT 3 cut(s) 83, 137, 1048
HpyCH4V TGCA 4 cut(s) 239, 703, 742, 842
HpyF10VI GCNNNNNNNGC 1 cut(s) 1410
HpyF3I CTNAG 6 cut(s) 25, 150, 675, 783, 1197, 1340
HpySE526I ACGT 3 cut(s) 83, 137, 1048
Hsp92II CATG 3 cut(s) 1040, 1057, 1211
HspAI GCGC 3 cut(s) 146, 319, 382
Ksp22I TGATCA 1 cut(s) 369
Kzo9I GATC 6 cut(s) 77, 369, 399, 619, 976, 1029
LguI GCTCTTC 2 cut(s) 723, 1341
LmnI GCTCC 5 cut(s) 222, 259, 456, 541, 589
Lsp1109I GCAGC 6 cut(s) 223, 277, 280, 333, 520, 826
LweI GCATC 1 cut(s) 74
MaeI CTAG 4 cut(s) 21, 33, 200, 779
MaeII ACGT 3 cut(s) 83, 137, 1048
MaeIII GTNAC 2 cut(s) 10, 1261
MalI GATC 6 cut(s) 79, 371, 401, 621, 978, 1031
MboI GATC 6 cut(s) 77, 369, 399, 619, 976, 1029
MfeI CAATTG 1 cut(s) 972
MhlI GDGCHC 1 cut(s) 56
MluCI AATT 9 cut(s) 59, 265, 926, 972, 1173, 1188, 1274, 1365, 1393
MlyI GAGTC 4 cut(s) 31, 493, 730, 1103
MmeI TCCRAC 1 cut(s) 1165
MseI TTAA 2 cut(s) 891, 1146
MspI CCGG 3 cut(s) 871, 1003, 1321
MunI CAATTG 1 cut(s) 972
Mva1269I GAATGC 2 cut(s) 1158, 1255
MwoI GCNNNNNNNGC 1 cut(s) 1410
NdeI CATATG 1 cut(s) 1015
NdeII GATC 6 cut(s) 77, 369, 399, 619, 976, 1029
NlaIII CATG 3 cut(s) 1040, 1057, 1211
NlaIV GGNNCC 1 cut(s) 255
NmuCI GTSAC 2 cut(s) 10, 1261
NspI RCATGY 1 cut(s) 1040
NspV TTCGAA 1 cut(s) 547
PaeI GCATGC 1 cut(s) 1040
PagI TCATGA 1 cut(s) 1207
PciSI GCTCTTC 2 cut(s) 723, 1341
PctI GAATGC 2 cut(s) 1158, 1255
PfeI GAWTC 3 cut(s) 574, 652, 999
PkrI GCNGC 6 cut(s) 238, 292, 295, 323, 535, 841
PleI GAGTC 4 cut(s) 31, 492, 730, 1102
PpsI GAGTC 4 cut(s) 31, 492, 730, 1102
PshAI GACNNNNGTC 1 cut(s) 939
PsiI TTATAA 1 cut(s) 1280
Psp1406I AACGTT 2 cut(s) 83, 137
PspN4I GGNNCC 1 cut(s) 255
PspPI GGNCC 3 cut(s) 190, 920, 1221
PstI CTGCAG 1 cut(s) 744
PstNI CAGNNNCTG 1 cut(s) 332
RsaI GTAC 2 cut(s) 162, 314
RsaNI GTAC 2 cut(s) 161, 313
SapI GCTCTTC 2 cut(s) 723, 1341
SaqAI TTAA 2 cut(s) 891, 1146
SatI GCNGC 6 cut(s) 237, 291, 294, 322, 534, 840
Sau3AI GATC 6 cut(s) 77, 369, 399, 619, 976, 1029
Sau96I GGNCC 3 cut(s) 190, 920, 1221
SchI GAGTC 4 cut(s) 31, 493, 730, 1103
SduI GDGCHC 1 cut(s) 56
SfaNI GCATC 1 cut(s) 74
SfcI CTRYAG 1 cut(s) 740
SfuI TTCGAA 1 cut(s) 547
SinI GGWCC 2 cut(s) 190, 920
SmlI CTYRAG 1 cut(s) 1091
SmoI CTYRAG 1 cut(s) 1091
SphI GCATGC 1 cut(s) 1040
Sse9I AATT 9 cut(s) 59, 265, 926, 972, 1173, 1188, 1274, 1365, 1393
SsiI CCGC 2 cut(s) 1106, 1324
SspMI CTAG 4 cut(s) 21, 33, 200, 779
TaaI ACNGT 1 cut(s) 16
TaiI ACGT 3 cut(s) 86, 140, 1051
TaqI TCGA 4 cut(s) 211, 547, 835, 1353
TasI AATT 9 cut(s) 59, 265, 926, 972, 1173, 1188, 1274, 1365, 1393
TatI WGTACW 1 cut(s) 312
TfiI GAWTC 3 cut(s) 574, 652, 999
Tru1I TTAA 2 cut(s) 891, 1146
Tru9I TTAA 2 cut(s) 891, 1146
TscAI CASTG 1 cut(s) 409
TseFI GTSAC 2 cut(s) 10, 1261
TseI GCWGC 6 cut(s) 236, 290, 293, 321, 533, 839
Tsp45I GTSAC 2 cut(s) 10, 1261
TspDTI ATGAA 4 cut(s) 300, 725, 1224, 1235
TspGWI ACGGA 1 cut(s) 30
TspRI CASTG 1 cut(s) 409
VpaK11BI GGWCC 2 cut(s) 190, 920
XagI CCTNNNNNAGG 2 cut(s) 941, 1381
XapI RAATTY 3 cut(s) 926, 1188, 1274
XceI RCATGY 1 cut(s) 1040
XspI CTAG 4 cut(s) 21, 33, 200, 779
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.