Rh1DG428700

RNA polymerase sigma factor sigE, chloroplastic

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr1D
OG0008760
Physical Location & Seq
Forward (+)
64122296 .. 64125740
3445 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1DG428700.1

Sequence Viewer

Length: 1119 bp
ATGGGAGTTGTGACAGTTTCTAGCTCAGTTTCTAGGACTCCGTTAGGATTGAGCCCAAAATTGGCATCAAGTCAGAGATCAACGTTGAGAAAGCCATTGATTGTTGCCTTTAGAACAGATAAATCCAATAAGAAAACGTTGGTTGCGCCTCAGGAGAAAGTACCTTTGCCAATAGAAACACGAAAGAAGGTCCAAAAACTAGGGAAGGCTCGAAAGCTCCCCGAAAGTGTAAAAGCTGCATTGATAGAGGAGGCTCCTACTTGTAATTTGGAACTGGATTACAATGAAGCTGCTGCCAAGCTGGAAAACCTGTACAAGCGCAGCCCAGAGACTGAAGCTTCGGATTTGGAAAATGTAGATGGATTGATGATCAAGAGAAGGCGCAAAAGGAGGAAGAAGATCAGTGAAGTTGATGACAAAGTAGAGAAGAGAAAAAGCGATGACATTGTGGTTGGGAGCAGGACAAAGAAGGCTAAAAGATTGAGTCTTGATAAAAGGGTTGCGTTGAAATGGAATAAGGACGAGAAAGTGGCTGCTCCAGTAGTTCGAAAGAGAAAAGATAGAAAGAGTGAGAATCAGATGATTGAGGAGCTTGTAAGGGAGTATTCGGCTTCAACTGATCTCGTCAGTTTAGACTGGAAAAAGATGAGGATTCCTCCAGTTCTTACTTCTTCTGAGCATACTTGGTTGTTCAAGCTAATGCAACCTATGAAGGCTCTTCTTCAAGTGAAAGAGACTCTGCAGAAAGATTTGGGGAGAGAACCAAATAAGGGTGAACTAGCTGAGGCGACAAGTATGAGTGTGGTTCAAGTGAAAAAACACTTGGAGGTTGGTCGAGCTGCAAGAAACAAACTCATCAAGCATAATCTCCGGCTTGTGTTATTTGTCATTAACAAATACTTTCAAGACTTTGCGAATGGTCCAAAATTTCAAGACCTTTGTCAGGCAGGAGTGAAGGGACTTATCACGGCAATTGATCGCTTTGAACCACAAAGAAGATTCCGGCTTTCCACATATGGTCTTTTCTGGATCAGGCATGCCATCATACGTTCCATGACACTATCAAGCTTTACTCGTGTCTCCTTTGGCCTTGAGTCTGTAAGCTCTCTTGCTCCTTAA
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

372

Amino Acids

42.36

Weight (kDa)

10.2

Isoelectric Point (pI)

50.41

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Sigma70_r3 PF04539 240 - 280 6.6e-06 Sigma-70 region 3
Sigma70_r2 PF04542 285 - 351 5.5e-11 Sigma-70 region 2
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AclI AACGTT 2 cut(s) 83, 137
AclWI GGATC 1 cut(s) 1037
AcsI RAATTY 1 cut(s) 926
AcuI CTGAAG 1 cut(s) 354
AfaI GTAC 2 cut(s) 162, 314
AfiI CCNNNNNNNGG 3 cut(s) 61, 770, 943
AgsI TTSAA 8 cut(s) 508, 615, 694, 725, 809, 905, 932, 986
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 1 cut(s) 1087
ApeKI GCWGC 6 cut(s) 236, 290, 293, 321, 533, 839
ApoI RAATTY 1 cut(s) 926
ArsI GACNNNNNNTTYG 2 cut(s) 322, 354
AspLEI GCGC 3 cut(s) 148, 321, 384
AspS9I GGNCC 2 cut(s) 190, 920
AsuHPI GGTGA 1 cut(s) 785
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
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 1 cut(s) 984
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
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 2 cut(s) 190, 920
BmiI GGNNCC 1 cut(s) 255
BmsI GCATC 1 cut(s) 74
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 1 cut(s) 547
BpuEI CTTGAG 1 cut(s) 1112
Bsc4I CCNNNNNNNGG 3 cut(s) 61, 770, 943
Bse1I ACTGG 4 cut(s) 279, 539, 641, 659
Bse21I CCTNAGG 1 cut(s) 150
BseLI CCNNNNNNNGG 3 cut(s) 61, 770, 943
BseMII CTCAG 4 cut(s) 39, 164, 666, 774
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 1 cut(s) 1089
BsiSI CCGG 2 cut(s) 871, 1003
BslFI GGGAC 1 cut(s) 972
BslI CCNNNNNNNGG 3 cut(s) 61, 770, 943
BsmAI GTCTC 3 cut(s) 323, 728, 1084
BsmFI GGGAC 1 cut(s) 972
BsnI GGCC 1 cut(s) 1089
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
BspANI GGCC 1 cut(s) 1089
BspCNI CTCAG 4 cut(s) 38, 163, 667, 775
BspLI GGNNCC 1 cut(s) 255
BspMAI CTGCAG 1 cut(s) 744
BspPI GGATC 1 cut(s) 1037
BspQI GCTCTTC 1 cut(s) 723
BspT104I TTCGAA 1 cut(s) 547
BsrGI TGTACA 1 cut(s) 312
BsrI ACTGG 4 cut(s) 279, 539, 641, 659
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 2 cut(s) 422, 723
BstAUI TGTACA 1 cut(s) 312
BstBI TTCGAA 1 cut(s) 547
BstC8I GCNNGC 1 cut(s) 1038
BstDEI CTNAG 4 cut(s) 25, 150, 675, 783
BstENI CCTNNNNNAGG 1 cut(s) 941
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
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
Bsu36I CCTNAGG 1 cut(s) 150
BsuRI GGCC 1 cut(s) 1089
BtgZI GCGATG 1 cut(s) 453
BtsIMutI CAGTG 1 cut(s) 409
Cac8I GCNNGC 1 cut(s) 1038
CaiI CAGNNNCTG 1 cut(s) 332
CfoI GCGC 3 cut(s) 148, 321, 384
Cfr13I GGNCC 2 cut(s) 190, 920
Csp6I GTAC 2 cut(s) 161, 313
CviAII CATG 2 cut(s) 1037, 1054
CviQI GTAC 2 cut(s) 161, 313
DdeI CTNAG 4 cut(s) 25, 150, 675, 783
DpnI GATC 6 cut(s) 79, 371, 401, 621, 978, 1031
DpnII GATC 6 cut(s) 77, 369, 399, 619, 976, 1029
Eam1104I CTCTTC 2 cut(s) 422, 723
EarI CTCTTC 2 cut(s) 422, 723
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 1 cut(s) 941
EcoT38I GRGCYC 1 cut(s) 56
FaeI CATG 2 cut(s) 1040, 1057
FaiI YATR 9 cut(s) 681, 710, 797, 864, 1015, 1017, 1038, 1046, 1055
FaqI GGGAC 1 cut(s) 972
FatI CATG 2 cut(s) 1036, 1053
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 1 cut(s) 1089
HapII CCGG 2 cut(s) 871, 1003
HhaI GCGC 3 cut(s) 148, 321, 384
Hin1II CATG 2 cut(s) 1040, 1057
Hin6I GCGC 3 cut(s) 146, 319, 382
HinP1I GCGC 3 cut(s) 146, 319, 382
HindIII AAGCTT 2 cut(s) 336, 1066
HinfI GANTC 7 cut(s) 37, 484, 574, 652, 736, 999, 1094
HpaII CCGG 2 cut(s) 871, 1003
HphI GGTGA 1 cut(s) 785
Hpy166II GTNNAC 1 cut(s) 776
Hpy188I TCNGA 4 cut(s) 75, 343, 579, 676
Hpy188III TCNNGA 6 cut(s) 152, 373, 488, 905, 932, 1027
Hpy8I GTNNAC 1 cut(s) 776
HpyAV CCTTC 6 cut(s) 181, 199, 372, 463, 706, 949
HpyCH4III ACNGT 1 cut(s) 16
HpyCH4IV ACGT 3 cut(s) 83, 137, 1048
HpyCH4V TGCA 4 cut(s) 239, 703, 742, 842
HpyF3I CTNAG 4 cut(s) 25, 150, 675, 783
HpySE526I ACGT 3 cut(s) 83, 137, 1048
Hsp92II CATG 2 cut(s) 1040, 1057
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 1 cut(s) 723
LmnI GCTCC 6 cut(s) 222, 259, 456, 541, 589, 1117
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 1 cut(s) 10
MalI GATC 6 cut(s) 79, 371, 401, 621, 978, 1031
MboI GATC 6 cut(s) 77, 369, 399, 619, 976, 1029
MboII GAAGA 7 cut(s) 406, 409, 439, 663, 710, 713, 1008
MfeI CAATTG 1 cut(s) 972
MhlI GDGCHC 1 cut(s) 56
MluCI AATT 4 cut(s) 59, 265, 926, 972
MlyI GAGTC 4 cut(s) 31, 493, 730, 1103
MnlI CCTC 9 cut(s) 159, 241, 244, 384, 580, 642, 666, 778, 820
MseI TTAA 2 cut(s) 891, 1117
MspI CCGG 2 cut(s) 871, 1003
MunI CAATTG 1 cut(s) 972
NdeI CATATG 1 cut(s) 1015
NdeII GATC 6 cut(s) 77, 369, 399, 619, 976, 1029
NlaIII CATG 2 cut(s) 1040, 1057
NlaIV GGNNCC 1 cut(s) 255
NmuCI GTSAC 1 cut(s) 10
NspI RCATGY 1 cut(s) 1040
NspV TTCGAA 1 cut(s) 547
PaeI GCATGC 1 cut(s) 1040
PciSI GCTCTTC 1 cut(s) 723
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
Psp1406I AACGTT 2 cut(s) 83, 137
PspN4I GGNNCC 1 cut(s) 255
PspPI GGNCC 2 cut(s) 190, 920
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 1 cut(s) 723
SaqAI TTAA 2 cut(s) 891, 1117
SatI GCNGC 6 cut(s) 237, 291, 294, 322, 534, 840
Sau3AI GATC 6 cut(s) 77, 369, 399, 619, 976, 1029
Sau96I GGNCC 2 cut(s) 190, 920
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 4 cut(s) 59, 265, 926, 972
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 3 cut(s) 211, 547, 835
TasI AATT 4 cut(s) 59, 265, 926, 972
TatI WGTACW 1 cut(s) 312
TfiI GAWTC 3 cut(s) 574, 652, 999
Tru1I TTAA 2 cut(s) 891, 1117
Tru9I TTAA 2 cut(s) 891, 1117
TscAI CASTG 1 cut(s) 409
TseFI GTSAC 1 cut(s) 10
TseI GCWGC 6 cut(s) 236, 290, 293, 321, 533, 839
Tsp45I GTSAC 1 cut(s) 10
TspDTI ATGAA 2 cut(s) 300, 725
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 1 cut(s) 926
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.