Rh3CG170200

Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr3C
OG0004828
Physical Location & Seq
Forward (+)
14839317 .. 14845892
6576 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh3CG170200.1

Sequence Viewer

Length: 1221 bp
ATGGAGGCTGGAAGGCATTTTCTTTCTTCATCTTCAGCATTTCCATCAACAACCCAACTCAGGCATCCTCTTCCTCCTCCTTCTCCTTCTACTACTTCAGTCTTGATGCTTCATGAGCAAGCAGCTCCTGCACTTACTTCTCTGCCGACTACATTTATAACTCGACATTTTCCTACTTCAGTTCTTATACAAGAGCAGCGCGATGAGTTCAAGCCTCTATTGCACATATTTAAGGAAGAGAAACCATCTCAGGCCACATTAGATCGGATGCAGATAGAGAATACCACTGCTGAGGAAGATTTCAACATTGATGACTTTTACAAGTTGGTCAAAGACTTTCGCCAGTTGCATGTTTTACCCTTACAAACAGGTGAAAATTCATCCACCACTTTGGCTTCGAAGTCTAATACCATTGCTAATGAGCATATGGCTGTTAAGCCATGTGATGCATTGTCCCTTGCTAAAAATGCTTTGTCGGCCTCAATAGAAGCAGCCTCTTTAGCTGAAAGCTCCAACTCGATCGGAGCTGCTTTTAATGAGTCTATTTCTATGGGTTTGGGGTGGGAAGAGGAAACTGTAAGGTCAACCCGACTTCTAGAGAGGCGGCGCAAGCGACTTAAGAAAAGGAATTTGCTTAACTCAAAAGTTCCAATTCATGAGACTAGCAGTTATAGAAGTTCAGATGTACGGAGAAAATCTAGTGACGGATTAAATCCTAATGATCCCCTGCGATTATTCTTGTGGGGACCTGAAACGAGACAACTTTTGACACTTAAAGAAGAGACTGAGTTGATTGCCCGAGTTCAGGATGTATTCGAGTTAGAAGCGGTGAAGAGTAGACTTCAATCTCAATATGGCCGTGAACCAACTTTGGTTGAATGGGCTGAAGCTGTTGGTATTAGTTGTCAGATGTTGCAATCACAACTTCGCTCTGGTACGAGCAGCCGTGAAAAGTTGATATATGCCAACTTACGTATGGTGGTGCACATTGCTAAACAATATCAAGGGAGAGGTCTTGGCCTTCAGGATTTACTGCAGGAGGGAAGTATGGGTCTAATGAAAAGTGTTGAGAAATTCAAACCCCAAGCTGGTTGCCGATTTGCTACTTATGCATACTGGTGGGTGAGACAAACAATTAGGAAGGCCATATTTCAACATTCCAGGACTATCCGCTTGCCGGTAATAACCATCTTTATCACCTCTCTGGTCTTCAATTTATAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
Sigma70_r2 Sigma70_r3 Sigma70_r4

Protein Analysis

406

Amino Acids

45.92

Weight (kDa)

9.33

Isoelectric Point (pI)

57.5

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Sigma70_r2 PF04542 320 - 389 2.3e-18 Sigma-70 region 2
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 2 cut(s) 158, 1219
AccI GTMKAC 1 cut(s) 838
AccII CGCG 1 cut(s) 201
AciI CCGC 3 cut(s) 604, 827, 1171
AclWI GGATC 1 cut(s) 716
AcoI YGGCCR 1 cut(s) 856
AcsI RAATTY 3 cut(s) 376, 628, 1073
AcuI CTGAAG 5 cut(s) 18, 81, 162, 906, 1007
AfaI GTAC 2 cut(s) 687, 937
AfiI CCNNNNNNNGG 4 cut(s) 60, 805, 1088, 1177
AflII CTTAAG 1 cut(s) 617
AgsI TTSAA 7 cut(s) 211, 304, 845, 878, 1078, 1154, 1213
AjnI CCWGG 1 cut(s) 1160
AluBI AGCT 6 cut(s) 125, 503, 510, 527, 890, 1088
AluI AGCT 6 cut(s) 125, 503, 510, 527, 890, 1088
Alw21I GWGCWC 1 cut(s) 987
Alw26I GTCTC 4 cut(s) 653, 751, 776, 1120
Alw44I GTGCAC 1 cut(s) 983
AlwI GGATC 1 cut(s) 716
AlwNI CAGNNNCTG 1 cut(s) 128
Ama87I CYCGRG 1 cut(s) 798
AoxI GGCC 5 cut(s) 252, 477, 856, 1018, 1143
ApaLI GTGCAC 1 cut(s) 983
ApeKI GCWGC 5 cut(s) 122, 196, 491, 527, 942
ApoI RAATTY 3 cut(s) 376, 628, 1073
AspLEI GCGC 2 cut(s) 201, 609
AspS9I GGNCC 1 cut(s) 746
AsuHPI GGTGA 4 cut(s) 383, 841, 1135, 1189
AsuII TTCGAA 1 cut(s) 398
AvaI CYCGRG 1 cut(s) 798
AvaII GGWCC 1 cut(s) 746
BaeGI GKGCMC 1 cut(s) 987
BbsI GAAGAC 1 cut(s) 1201
Bbv12I GWGCWC 1 cut(s) 987
BbvCI CCTCAGC 1 cut(s) 291
BbvI GCAGC 5 cut(s) 134, 208, 503, 514, 954
BccI CCATC 3 cut(s) 52, 253, 1196
BceAI ACGGC 2 cut(s) 843, 930
BciT130I CCWGG 1 cut(s) 1162
BcoDI GTCTC 4 cut(s) 653, 751, 776, 1120
BfaI CTAG 3 cut(s) 596, 663, 699
BfmI CTRYAG 1 cut(s) 1034
BfrI CTTAAG 1 cut(s) 617
BisI GCNGC 6 cut(s) 123, 197, 492, 528, 605, 943
BlsI GCNGC 6 cut(s) 124, 198, 493, 529, 606, 944
Bme1390I CCNGG 1 cut(s) 1162
Bme18I GGWCC 1 cut(s) 746
BmeT110I CYCGRG 1 cut(s) 798
BmgT120I GGNCC 1 cut(s) 746
BmiI GGNNCC 1 cut(s) 747
BmrFI CCNGG 1 cut(s) 1162
BmsI GCATC 4 cut(s) 73, 96, 258, 436
BpiI GAAGAC 1 cut(s) 1201
Bpu10I CCTNAGC 1 cut(s) 291
Bpu14I TTCGAA 1 cut(s) 398
BsaAI YACGTR 1 cut(s) 974
Bsc4I CCNNNNNNNGG 4 cut(s) 60, 805, 1088, 1177
Bse118I RCCGGY 1 cut(s) 1177
Bse1I ACTGG 2 cut(s) 343, 1121
Bse3DI GCAATG 2 cut(s) 411, 987
BseBI CCWGG 1 cut(s) 1162
BseGI GGATG 4 cut(s) 64, 273, 380, 814
BseLI CCNNNNNNNGG 4 cut(s) 60, 805, 1088, 1177
BseMI GCAATG 2 cut(s) 411, 987
BseMII CTCAG 4 cut(s) 73, 263, 282, 777
BseNI ACTGG 2 cut(s) 343, 1121
BseRI GAGGAG 1 cut(s) 66
BseSI GKGCMC 1 cut(s) 987
BseXI GCAGC 5 cut(s) 134, 208, 503, 514, 954
BsgI GTGCAG 1 cut(s) 114
Bsh1236I CGCG 1 cut(s) 201
Bsh1285I CGRYCG 1 cut(s) 522
BshFI GGCC 5 cut(s) 254, 479, 858, 1020, 1145
BsiEI CGRYCG 1 cut(s) 522
BsiHKAI GWGCWC 1 cut(s) 987
BsiHKCI CYCGRG 1 cut(s) 798
BsiSI CCGG 1 cut(s) 1178
BslFI GGGAC 2 cut(s) 439, 759
BslI CCNNNNNNNGG 4 cut(s) 60, 805, 1088, 1177
BsmAI GTCTC 4 cut(s) 653, 751, 776, 1120
BsmFI GGGAC 2 cut(s) 439, 759
BsnI GGCC 5 cut(s) 254, 479, 858, 1020, 1145
BsoBI CYCGRG 1 cut(s) 798
Bsp119I TTCGAA 1 cut(s) 398
Bsp1286I GDGCHC 1 cut(s) 987
Bsp143I GATC 3 cut(s) 262, 519, 721
BspACI CCGC 3 cut(s) 604, 827, 1171
BspANI GGCC 5 cut(s) 254, 479, 858, 1020, 1145
BspCNI CTCAG 4 cut(s) 72, 262, 283, 778
BspFNI CGCG 1 cut(s) 201
BspHI TCATGA 2 cut(s) 112, 655
BspLI GGNNCC 1 cut(s) 747
BspMAI CTGCAG 1 cut(s) 1038
BspPI GGATC 1 cut(s) 716
BspT104I TTCGAA 1 cut(s) 398
BspTI CTTAAG 1 cut(s) 617
BsrDI GCAATG 2 cut(s) 411, 987
BsrFI RCCGGY 1 cut(s) 1177
BsrI ACTGG 2 cut(s) 343, 1121
BssAI RCCGGY 1 cut(s) 1177
BssMI GATC 3 cut(s) 262, 519, 721
Bst2UI CCWGG 1 cut(s) 1162
Bst4CI ACNGT 1 cut(s) 577
Bst6I CTCTTC 5 cut(s) 75, 231, 561, 774, 827
BstAFI CTTAAG 1 cut(s) 617
BstAPI GCANNNNNTGC 1 cut(s) 128
BstBAI YACGTR 1 cut(s) 974
BstBI TTCGAA 1 cut(s) 398
BstC8I GCNNGC 3 cut(s) 120, 611, 1175
BstDEI CTNAG 4 cut(s) 59, 249, 291, 786
BstF5I GGATG 4 cut(s) 64, 273, 380, 814
BstFNI CGCG 1 cut(s) 201
BstHHI GCGC 2 cut(s) 201, 609
BstKTI GATC 3 cut(s) 265, 522, 724
BstMAI GTCTC 4 cut(s) 653, 751, 776, 1120
BstMBI GATC 3 cut(s) 262, 519, 721
BstMCI CGRYCG 1 cut(s) 522
BstMWI GCNNNNNNNGC 8 cut(s) 115, 128, 220, 467, 476, 500, 610, 1109
BstNI CCWGG 1 cut(s) 1162
BstNSI RCATGY 1 cut(s) 353
BstSCI CCNGG 1 cut(s) 1160
BstSFI CTRYAG 1 cut(s) 1034
BstSLI GKGCMC 1 cut(s) 987
BstSNI TACGTA 1 cut(s) 974
BstUI CGCG 1 cut(s) 201
BstV1I GCAGC 5 cut(s) 134, 208, 503, 514, 954
BstV2I GAAGAC 1 cut(s) 1201
BstXI CCANNNNNNTGG 1 cut(s) 391
BsuRI GGCC 5 cut(s) 254, 479, 858, 1020, 1145
BtgZI GCGATG 1 cut(s) 216
BtsCI GGATG 4 cut(s) 64, 273, 380, 814
BtsI GCAGTG 1 cut(s) 285
BtsIMutI CAGTG 1 cut(s) 285
Cac8I GCNNGC 3 cut(s) 120, 611, 1175
CaiI CAGNNNCTG 1 cut(s) 128
CciI TCATGA 2 cut(s) 112, 655
CfoI GCGC 2 cut(s) 201, 609
Cfr10I RCCGGY 1 cut(s) 1177
Cfr13I GGNCC 1 cut(s) 746
Csp6I GTAC 2 cut(s) 686, 936
CviAII CATG 4 cut(s) 113, 350, 441, 656
CviQI GTAC 2 cut(s) 686, 936
DdeI CTNAG 4 cut(s) 59, 249, 291, 786
DpnI GATC 3 cut(s) 264, 521, 723
DpnII GATC 3 cut(s) 262, 519, 721
EaeI YGGCCR 1 cut(s) 856
Eam1104I CTCTTC 5 cut(s) 75, 231, 561, 774, 827
EarI CTCTTC 5 cut(s) 75, 231, 561, 774, 827
Eco105I TACGTA 1 cut(s) 974
Eco47I GGWCC 1 cut(s) 746
Eco57I CTGAAG 5 cut(s) 18, 81, 162, 906, 1007
Eco88I CYCGRG 1 cut(s) 798
EcoO109I RGGNCCY 1 cut(s) 746
EcoRII CCWGG 1 cut(s) 1160
EcoT22I ATGCAT 2 cut(s) 451, 1114
FaeI CATG 4 cut(s) 116, 353, 444, 659
FaqI GGGAC 2 cut(s) 439, 759
FatI CATG 4 cut(s) 112, 349, 440, 655
FauNDI CATATG 1 cut(s) 426
FblI GTMKAC 1 cut(s) 838
Fnu4HI GCNGC 6 cut(s) 123, 197, 492, 528, 605, 943
FokI GGATG 4 cut(s) 51, 280, 367, 821
Fsp4HI GCNGC 6 cut(s) 123, 197, 492, 528, 605, 943
FspBI CTAG 3 cut(s) 596, 663, 699
GlaI GCGC 2 cut(s) 200, 608
GluI GCNGC 6 cut(s) 123, 197, 492, 528, 605, 943
HaeIII GGCC 5 cut(s) 254, 479, 858, 1020, 1145
HapII CCGG 1 cut(s) 1178
HhaI GCGC 2 cut(s) 201, 609
Hin1II CATG 4 cut(s) 116, 353, 444, 659
Hin6I GCGC 2 cut(s) 199, 607
HinP1I GCGC 2 cut(s) 199, 607
HincII GTYRAC 1 cut(s) 585
HindII GTYRAC 1 cut(s) 585
HinfI GANTC 1 cut(s) 539
HpaII CCGG 1 cut(s) 1178
HphI GGTGA 4 cut(s) 383, 841, 1135, 1189
Hpy166II GTNNAC 4 cut(s) 585, 839, 863, 985
Hpy188I TCNGA 4 cut(s) 267, 524, 682, 909
Hpy188III TCNNGA 6 cut(s) 103, 113, 596, 656, 806, 1025
Hpy8I GTNNAC 4 cut(s) 585, 839, 863, 985
HpyAV CCTTC 5 cut(s) 6, 90, 96, 1031, 1135
HpyCH4III ACNGT 1 cut(s) 577
HpyCH4IV ACGT 1 cut(s) 973
HpyCH4V TGCA 9 cut(s) 131, 223, 271, 349, 449, 916, 985, 1036, 1112
HpyF10VI GCNNNNNNNGC 8 cut(s) 115, 128, 220, 467, 476, 500, 610, 1109
HpyF3I CTNAG 4 cut(s) 59, 249, 291, 786
HpySE526I ACGT 1 cut(s) 973
Hsp92II CATG 4 cut(s) 116, 353, 444, 659
HspAI GCGC 2 cut(s) 199, 607
Kzo9I GATC 3 cut(s) 262, 519, 721
LmnI GCTCC 3 cut(s) 130, 515, 524
Lsp1109I GCAGC 5 cut(s) 134, 208, 503, 514, 954
LweI GCATC 4 cut(s) 73, 96, 258, 436
MaeI CTAG 3 cut(s) 596, 663, 699
MaeII ACGT 1 cut(s) 973
MaeIII GTNAC 1 cut(s) 701
MalI GATC 3 cut(s) 264, 521, 723
MboI GATC 3 cut(s) 262, 519, 721
MboII GAAGA 9 cut(s) 18, 24, 62, 248, 308, 578, 791, 844, 1201
MhlI GDGCHC 1 cut(s) 987
MluCI AATT 6 cut(s) 376, 628, 651, 1073, 1134, 1213
MlyI GAGTC 1 cut(s) 548
MmeI TCCRAC 1 cut(s) 537
Mph1103I ATGCAT 2 cut(s) 451, 1114
MseI TTAA 7 cut(s) 231, 435, 534, 618, 636, 710, 774
MslI CAYNNNNRTG 1 cut(s) 1117
MspCI CTTAAG 1 cut(s) 617
MspI CCGG 1 cut(s) 1178
MspR9I CCNGG 1 cut(s) 1162
MvaI CCWGG 1 cut(s) 1162
MvnI CGCG 1 cut(s) 201
MwoI GCNNNNNNNGC 8 cut(s) 115, 128, 220, 467, 476, 500, 610, 1109
NdeI CATATG 1 cut(s) 426
NdeII GATC 3 cut(s) 262, 519, 721
NlaIII CATG 4 cut(s) 116, 353, 444, 659
NlaIV GGNNCC 1 cut(s) 747
NmuCI GTSAC 1 cut(s) 701
NsiI ATGCAT 2 cut(s) 451, 1114
NspI RCATGY 1 cut(s) 353
NspV TTCGAA 1 cut(s) 398
PagI TCATGA 2 cut(s) 112, 655
PfoI TCCNGGA 1 cut(s) 1160
PkrI GCNGC 6 cut(s) 124, 198, 493, 529, 606, 944
Ple19I CGATCG 1 cut(s) 522
PleI GAGTC 1 cut(s) 547
PpsI GAGTC 1 cut(s) 547
Ppu21I YACGTR 1 cut(s) 974
PpuMI RGGWCCY 1 cut(s) 746
PsiI TTATAA 2 cut(s) 158, 1219
Psp5II RGGWCCY 1 cut(s) 746
Psp6I CCWGG 1 cut(s) 1160
PspGI CCWGG 1 cut(s) 1160
PspN4I GGNNCC 1 cut(s) 747
PspPI GGNCC 1 cut(s) 746
PspPPI RGGWCCY 1 cut(s) 746
PstI CTGCAG 1 cut(s) 1038
PstNI CAGNNNCTG 1 cut(s) 128
PvuI CGATCG 1 cut(s) 522
RsaI GTAC 2 cut(s) 687, 937
RsaNI GTAC 2 cut(s) 686, 936
RseI CAYNNNNRTG 1 cut(s) 1117
SaqAI TTAA 7 cut(s) 231, 435, 534, 618, 636, 710, 774
SatI GCNGC 6 cut(s) 123, 197, 492, 528, 605, 943
Sau3AI GATC 3 cut(s) 262, 519, 721
Sau96I GGNCC 1 cut(s) 746
SchI GAGTC 1 cut(s) 548
ScrFI CCNGG 1 cut(s) 1162
SduI GDGCHC 1 cut(s) 987
SfaNI GCATC 4 cut(s) 73, 96, 258, 436
SfcI CTRYAG 1 cut(s) 1034
SfuI TTCGAA 1 cut(s) 398
SinI GGWCC 1 cut(s) 746
SmiMI CAYNNNNRTG 1 cut(s) 1117
SmlI CTYRAG 1 cut(s) 617
SmoI CTYRAG 1 cut(s) 617
SnaBI TACGTA 1 cut(s) 974
Sse9I AATT 6 cut(s) 376, 628, 651, 1073, 1134, 1213
SsiI CCGC 3 cut(s) 604, 827, 1171
SspMI CTAG 3 cut(s) 596, 663, 699
StyD4I CCNGG 1 cut(s) 1160
TaaI ACNGT 1 cut(s) 577
TaiI ACGT 1 cut(s) 976
TaqI TCGA 4 cut(s) 163, 398, 518, 816
TasI AATT 6 cut(s) 376, 628, 651, 1073, 1134, 1213
TauI GCSGC 1 cut(s) 607
Tru1I TTAA 7 cut(s) 231, 435, 534, 618, 636, 710, 774
Tru9I TTAA 7 cut(s) 231, 435, 534, 618, 636, 710, 774
TscAI CASTG 1 cut(s) 292
TseFI GTSAC 1 cut(s) 701
TseI GCWGC 5 cut(s) 122, 196, 491, 527, 942
Tsp45I GTSAC 1 cut(s) 701
TspDTI ATGAA 5 cut(s) 18, 101, 369, 644, 1073
TspGWI ACGGA 2 cut(s) 703, 720
TspRI CASTG 1 cut(s) 292
Vha464I CTTAAG 1 cut(s) 617
VneI GTGCAC 1 cut(s) 983
VpaK11BI GGWCC 1 cut(s) 746
XapI RAATTY 3 cut(s) 376, 628, 1073
XbaI TCTAGA 1 cut(s) 595
XceI RCATGY 1 cut(s) 353
XcmI CCANNNNNNNNNTGG 1 cut(s) 973
XmiI GTMKAC 1 cut(s) 838
XspI CTAG 3 cut(s) 596, 663, 699
Zsp2I ATGCAT 2 cut(s) 451, 1114
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.