Rorug03G0106100
TCP Family

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_rugosa
GWHBQTZ00000003
OG0001571
Physical Location & Seq
Forward (+)
8469630 .. 8482311
12682 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug03G0106100.1

Sequence Viewer

Length: 1413 bp
ATGTGGGAATTCTCTGTTGGTTTATACATGATAAATGTATGGCCAGACTCTCTACTCTTTGCTGCTATATATGGTGTGGTGGAATCAGCTTCTACTGCGCTTTTTGGACCTTTGGTCGGACGGTGGGTGGATAGATTCTCATATGTAAAGATTCTTCGAGTTTGGTTAGTAACACAAAATCTCTCTTTTATGATTGCTGGAGCCACCGTGATGGCGTTACTGATCTACCCAGATCTAAAGCTCACAAGTTTCTATGCATTTGTTTTACTTATCATATTAACCAACATCTCTGGAGCTCTTGGAGTTCTCTCCACTCTTGCTGGTACCATCTTAGTTGAAAGAGACTGGGTTGTGGTGATATCAGAAGGGCATTCTCCAGAAGTACTAACAAACATGAATTCGGTCATTAGGCGTATTGATCTTTTCTCCAAACTTTTTGCTCCGGTGGTAACCGGCTTCATCATCAGCTTTGTATCACTAAAAGCTTCTGCCTTAACTTTAGTACTCTGGAATACCATATCTGTTTGGCTAGAATACTGGCTATTCATTTCTGTGTATAATGGGATTCCGGCTTTAGGCGAAAGCAGCCAAAGGAAGATATCAAGACGTTCTCAGAGTGATCTTGAAGGCACTGGCACATCTACTTCTCAAGAGAGAAGTAGCTTGCTTTCTAAAGATGAAAATGATTCAGAATTTGCTGAGGAAAGCTGGATAACGGGAGTTATTAAAATGGTGTCAAGGATCCCTTATGTTAGAGCTTGGAGCGTGTATTTGCAGCAAGATGTTGTGCTTCCTGGAGTATCTCTGGCTTTGTTATTTTTCACTGTACTCAGCTTTGGAACATTGATGACAGCTACCTTGGAATGGGAAGGCATACCTGCATACACCATTGGGATAGCTCGTGGAATAAGTGCTGCAATTGGAATTTCTGCAACAGTTGTTTATCCCATCTTGCAATCTCATATCTTAACACTTAGAACCGGACTCTGGTCTATCTGGTCTCAGTGGACCTTCCTCATATTATGTGTTGCTTCAATATGGATCCATAACAGCCTTTGGTCAGCTTATATGCTAATGGCAGGAGTGGCTACTTCTCGGCTTGGGTTGTGGATGTTTGATTTGGCTGTCATCCAACAAATGCAGGATCAAGTTCCTGAATCAGATCGTTGTGTAGTGGGAGGTGTTCAAAACTCCCTTCAGTCCAGCATGGATTTGATGGGCTATGTCATGGGAATAATCATATCTAATCCACAGGAATTCTGGAAGTTGATTTTGGTCTCGTTTGCCGTGGCAACATTGGCAGCATTGCTCTATACCCTGCACGTTTACCGCGTACGAAAGCACCTCCTTCACTTTGAGAAATTAGCCTTCTTTCTGAAATGCTTCACCAGTACACAATCTGAAAATTCATAA
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

470

Amino Acids

52.47

Weight (kDa)

6.1

Isoelectric Point (pI)

39.76

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
FPN1 PF06963 1 - 429 1.2e-153 Ferroportin1 (FPN1)
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 886
Acc65I GGTACC 1 cut(s) 323
AccB1I GGYRCC 1 cut(s) 323
AccII CGCG 1 cut(s) 1332
AciI CCGC 1 cut(s) 1330
AclWI GGATC 5 cut(s) 736, 749, 1036, 1049, 1152
AcoI YGGCCR 1 cut(s) 41
AcsI RAATTY 6 cut(s) 8, 397, 692, 924, 1256, 1405
AcuI CTGAAG 1 cut(s) 1181
AfaI GTAC 6 cut(s) 325, 384, 504, 828, 1335, 1393
AfiI CCNNNNNNNGG 4 cut(s) 116, 575, 864, 987
AgsI TTSAA 4 cut(s) 338, 626, 1035, 1187
AhdI GACNNNNNGTC 1 cut(s) 113
AjnI CCWGG 1 cut(s) 793
AjuI GAANNNNNNNTTGG 3 cut(s) 32, 1256, 1288
Alw21I GWGCWC 1 cut(s) 298
Alw26I GTCTC 3 cut(s) 336, 1005, 1282
AlwI GGATC 5 cut(s) 736, 749, 1036, 1049, 1152
AoxI GGCC 1 cut(s) 41
ApeKI GCWGC 5 cut(s) 62, 585, 775, 914, 1301
ApoI RAATTY 6 cut(s) 8, 397, 692, 924, 1256, 1405
Asp700I GAANNNNTTC 1 cut(s) 1382
Asp718I GGTACC 1 cut(s) 323
AspLEI GCGC 1 cut(s) 100
AspS9I GGNCC 2 cut(s) 107, 1008
AsuHPI GGTGA 2 cut(s) 367, 1378
AvaII GGWCC 2 cut(s) 107, 1008
BalI TGGCCA 1 cut(s) 43
BamHI GGATCC 2 cut(s) 741, 1041
BanI GGYRCC 1 cut(s) 323
BanII GRGCYC 1 cut(s) 298
BarI GAAGNNNNNNTAC 2 cut(s) 138, 170
BauI CACGAG 1 cut(s) 900
Bbv12I GWGCWC 1 cut(s) 298
BbvCI CCTCAGC 1 cut(s) 699
BbvI GCAGC 5 cut(s) 49, 597, 787, 901, 1313
BccI CCATC 4 cut(s) 205, 335, 956, 1210
BceAI ACGGC 1 cut(s) 1271
BciT130I CCWGG 1 cut(s) 795
BcoDI GTCTC 3 cut(s) 336, 1005, 1282
BfaI CTAG 1 cut(s) 530
BfuAI ACCTGC 1 cut(s) 886
BglII AGATCT 1 cut(s) 232
BisI GCNGC 5 cut(s) 63, 586, 776, 915, 1302
BlsI GCNGC 5 cut(s) 64, 587, 777, 916, 1303
BmcAI AGTACT 2 cut(s) 384, 504
Bme1390I CCNGG 1 cut(s) 795
Bme18I GGWCC 2 cut(s) 107, 1008
BmeRI GACNNNNNGTC 1 cut(s) 113
BmgT120I GGNCC 2 cut(s) 107, 1008
BmiI GGNNCC 4 cut(s) 202, 325, 743, 1043
BmrFI CCNGG 1 cut(s) 795
BmrI ACTGGG 1 cut(s) 355
BmuI ACTGGG 1 cut(s) 355
BoxI GACNNNNGTC 1 cut(s) 988
BpmI CTGGAG 4 cut(s) 219, 312, 360, 816
Bpu10I CCTNAGC 1 cut(s) 699
BpuEI CTTGAG 1 cut(s) 633
BsaI GGTCTC 2 cut(s) 1005, 1282
BsaJI CCNNGG 2 cut(s) 858, 1287
BsaWI WCCGGW 2 cut(s) 442, 980
BsaXI ACNNNNNCTCC 2 cut(s) 192, 222
Bsc4I CCNNNNNNNGG 4 cut(s) 116, 575, 864, 987
Bse118I RCCGGY 1 cut(s) 452
Bse1I ACTGG 4 cut(s) 350, 542, 637, 1389
Bse3DI GCAATG 1 cut(s) 1304
BseBI CCWGG 1 cut(s) 795
BseDI CCNNGG 2 cut(s) 858, 1287
BseGI GGATG 2 cut(s) 1116, 1128
BseLI CCNNNNNNNGG 4 cut(s) 116, 575, 864, 987
BseMI GCAATG 1 cut(s) 1304
BseMII CTCAG 4 cut(s) 626, 690, 844, 1016
BseNI ACTGG 4 cut(s) 350, 542, 637, 1389
BseXI GCAGC 5 cut(s) 49, 597, 787, 901, 1313
BsgI GTGCAG 1 cut(s) 1304
Bsh1236I CGCG 1 cut(s) 1332
BshFI GGCC 1 cut(s) 43
BshNI GGYRCC 1 cut(s) 323
BsiHKAI GWGCWC 1 cut(s) 298
BsiSI CCGG 4 cut(s) 443, 453, 569, 981
BsiWI CGTACG 1 cut(s) 1333
BslI CCNNNNNNNGG 4 cut(s) 116, 575, 864, 987
BsmAI GTCTC 3 cut(s) 336, 1005, 1282
BsmI GAATGC 1 cut(s) 370
BsnI GGCC 1 cut(s) 43
Bso31I GGTCTC 2 cut(s) 1005, 1282
Bsp1286I GDGCHC 1 cut(s) 298
Bsp143I GATC 8 cut(s) 222, 232, 418, 619, 741, 1041, 1144, 1162
BspACI CCGC 1 cut(s) 1330
BspANI GGCC 1 cut(s) 43
BspCNI CTCAG 4 cut(s) 625, 691, 843, 1015
BspFNI CGCG 1 cut(s) 1332
BspLI GGNNCC 4 cut(s) 202, 325, 743, 1043
BspMI ACCTGC 1 cut(s) 886
BspPI GGATC 5 cut(s) 736, 749, 1036, 1049, 1152
BspT107I GGYRCC 1 cut(s) 323
BspTNI GGTCTC 2 cut(s) 1005, 1282
BsrDI GCAATG 1 cut(s) 1304
BsrFI RCCGGY 1 cut(s) 452
BsrI ACTGG 4 cut(s) 350, 542, 637, 1389
BssAI RCCGGY 1 cut(s) 452
BssECI CCNNGG 2 cut(s) 858, 1287
BssMI GATC 8 cut(s) 222, 232, 418, 619, 741, 1041, 1144, 1162
BssSI CACGAG 1 cut(s) 900
BssT1I CCWWGG 1 cut(s) 858
Bst2BI CACGAG 1 cut(s) 900
Bst2UI CCWGG 1 cut(s) 795
Bst4CI ACNGT 4 cut(s) 123, 208, 826, 937
BstC8I GCNNGC 1 cut(s) 665
BstDEI CTNAG 6 cut(s) 331, 612, 699, 830, 974, 1002
BstDSI CCRYGG 1 cut(s) 1287
BstEII GGTNACC 1 cut(s) 448
BstF5I GGATG 2 cut(s) 1116, 1128
BstFNI CGCG 1 cut(s) 1332
BstHHI GCGC 1 cut(s) 100
BstKTI GATC 8 cut(s) 225, 235, 421, 622, 744, 1044, 1147, 1165
BstMAI GTCTC 3 cut(s) 336, 1005, 1282
BstMBI GATC 8 cut(s) 222, 232, 418, 619, 741, 1041, 1144, 1162
BstMWI GCNNNNNNNGC 4 cut(s) 95, 585, 1085, 1298
BstNI CCWGG 1 cut(s) 795
BstPAI GACNNNNGTC 1 cut(s) 988
BstPI GGTNACC 1 cut(s) 448
BstSCI CCNGG 1 cut(s) 793
BstUI CGCG 1 cut(s) 1332
BstV1I GCAGC 5 cut(s) 49, 597, 787, 901, 1313
BstX2I RGATCY 3 cut(s) 232, 741, 1041
BstXI CCANNNNNNTGG 1 cut(s) 211
BstYI RGATCY 3 cut(s) 232, 741, 1041
BsuRI GGCC 1 cut(s) 43
BtgI CCRYGG 1 cut(s) 1287
BtsCI GGATG 2 cut(s) 1116, 1128
BtsIMutI CAGTG 3 cut(s) 630, 822, 1010
BveI ACCTGC 1 cut(s) 886
Cac8I GCNNGC 1 cut(s) 665
CfoI GCGC 1 cut(s) 100
Cfr10I RCCGGY 1 cut(s) 452
Cfr13I GGNCC 2 cut(s) 107, 1008
Csp6I GTAC 6 cut(s) 324, 383, 503, 827, 1334, 1392
CviAII CATG 4 cut(s) 28, 394, 1207, 1228
CviQI GTAC 6 cut(s) 324, 383, 503, 827, 1334, 1392
DdeI CTNAG 6 cut(s) 331, 612, 699, 830, 974, 1002
DpnI GATC 8 cut(s) 224, 234, 420, 621, 743, 1043, 1146, 1164
DpnII GATC 8 cut(s) 222, 232, 418, 619, 741, 1041, 1144, 1162
DriI GACNNNNNGTC 1 cut(s) 113
EaeI YGGCCR 1 cut(s) 41
Eam1105I GACNNNNNGTC 1 cut(s) 113
Ecl136II GAGCTC 1 cut(s) 296
Eco130I CCWWGG 1 cut(s) 858
Eco24I GRGCYC 1 cut(s) 298
Eco31I GGTCTC 2 cut(s) 1005, 1282
Eco32I GATATC 2 cut(s) 360, 600
Eco47I GGWCC 2 cut(s) 107, 1008
Eco53kI GAGCTC 1 cut(s) 296
Eco57I CTGAAG 1 cut(s) 1181
Eco91I GGTNACC 1 cut(s) 448
EcoICRI GAGCTC 1 cut(s) 296
EcoO65I GGTNACC 1 cut(s) 448
EcoRI GAATTC 3 cut(s) 8, 397, 1256
EcoRII CCWGG 1 cut(s) 793
EcoRV GATATC 2 cut(s) 360, 600
EcoT14I CCWWGG 1 cut(s) 858
EcoT22I ATGCAT 1 cut(s) 259
EcoT38I GRGCYC 1 cut(s) 298
ErhI CCWWGG 1 cut(s) 858
FaeI CATG 4 cut(s) 31, 397, 1210, 1231
FalI AAGNNNNNCTT 2 cut(s) 730, 762
FatI CATG 4 cut(s) 27, 393, 1206, 1227
FauNDI CATATG 1 cut(s) 142
Fnu4HI GCNGC 5 cut(s) 63, 586, 776, 915, 1302
FokI GGATG 2 cut(s) 1115, 1123
FriOI GRGCYC 1 cut(s) 298
Fsp4HI GCNGC 5 cut(s) 63, 586, 776, 915, 1302
FspBI CTAG 1 cut(s) 530
GlaI GCGC 1 cut(s) 99
GluI GCNGC 5 cut(s) 63, 586, 776, 915, 1302
GsuI CTGGAG 4 cut(s) 219, 312, 360, 816
HaeIII GGCC 1 cut(s) 43
HapII CCGG 4 cut(s) 443, 453, 569, 981
HhaI GCGC 1 cut(s) 100
Hin1II CATG 4 cut(s) 31, 397, 1210, 1231
Hin6I GCGC 1 cut(s) 98
HinP1I GCGC 1 cut(s) 98
HindIII AAGCTT 1 cut(s) 483
HinfI GANTC 8 cut(s) 47, 83, 135, 151, 565, 686, 984, 1157
HpaII CCGG 4 cut(s) 443, 453, 569, 981
HphI GGTGA 2 cut(s) 367, 1378
Hpy166II GTNNAC 3 cut(s) 1008, 1327, 1394
Hpy188I TCNGA 7 cut(s) 119, 364, 615, 691, 1162, 1377, 1402
Hpy188III TCNNGA 8 cut(s) 291, 377, 508, 603, 623, 650, 1154, 1261
Hpy8I GTNNAC 3 cut(s) 1008, 1327, 1394
HpyAV CCTTC 7 cut(s) 359, 620, 863, 1021, 1205, 1358, 1378
HpyCH4III ACNGT 4 cut(s) 123, 208, 826, 937
HpyCH4IV ACGT 2 cut(s) 607, 1323
HpyCH4V TGCA 8 cut(s) 257, 775, 881, 917, 932, 955, 1141, 1321
HpyF10VI GCNNNNNNNGC 4 cut(s) 95, 585, 1085, 1298
HpyF3I CTNAG 6 cut(s) 331, 612, 699, 830, 974, 1002
HpySE526I ACGT 2 cut(s) 607, 1323
Hsp92II CATG 4 cut(s) 31, 397, 1210, 1231
HspAI GCGC 1 cut(s) 98
KpnI GGTACC 1 cut(s) 327
Kzo9I GATC 8 cut(s) 222, 232, 418, 619, 741, 1041, 1144, 1162
LmnI GCTCC 4 cut(s) 200, 293, 445, 762
Lsp1109I GCAGC 5 cut(s) 49, 597, 787, 901, 1313
MaeI CTAG 1 cut(s) 530
MaeII ACGT 2 cut(s) 607, 1323
MaeIII GTNAC 3 cut(s) 169, 216, 448
MalI GATC 8 cut(s) 224, 234, 420, 621, 743, 1043, 1146, 1164
MboI GATC 8 cut(s) 222, 232, 418, 619, 741, 1041, 1144, 1162
MboII GAAGA 2 cut(s) 146, 607
MfeI CAATTG 1 cut(s) 918
MflI RGATCY 3 cut(s) 232, 741, 1041
MhlI GDGCHC 1 cut(s) 298
MlsI TGGCCA 1 cut(s) 43
MluCI AATT 8 cut(s) 8, 397, 692, 918, 924, 1256, 1361, 1405
MluNI TGGCCA 1 cut(s) 43
MlyI GAGTC 2 cut(s) 41, 978
MmeI TCCRAC 2 cut(s) 97, 1156
MnlI CCTC 4 cut(s) 694, 1025, 1172, 1355
Mox20I TGGCCA 1 cut(s) 43
Mph1103I ATGCAT 1 cut(s) 259
MroXI GAANNNNTTC 1 cut(s) 1382
MscI TGGCCA 1 cut(s) 43
MseI TTAA 4 cut(s) 278, 494, 726, 968
MslI CAYNNNNRTG 2 cut(s) 209, 551
Msp20I TGGCCA 1 cut(s) 43
MspI CCGG 4 cut(s) 443, 453, 569, 981
MspR9I CCNGG 1 cut(s) 795
MunI CAATTG 1 cut(s) 918
Mva1269I GAATGC 1 cut(s) 370
MvaI CCWGG 1 cut(s) 795
MvnI CGCG 1 cut(s) 1332
MwoI GCNNNNNNNGC 4 cut(s) 95, 585, 1085, 1298
NdeI CATATG 1 cut(s) 142
NdeII GATC 8 cut(s) 222, 232, 418, 619, 741, 1041, 1144, 1162
NlaIII CATG 4 cut(s) 31, 397, 1210, 1231
NlaIV GGNNCC 4 cut(s) 202, 325, 743, 1043
NmeAIII GCCGAG 1 cut(s) 1075
NsiI ATGCAT 1 cut(s) 259
PcsI WCGNNNNNNNCGW 1 cut(s) 1329
PctI GAATGC 1 cut(s) 370
PdmI GAANNNNTTC 1 cut(s) 1382
PfeI GAWTC 6 cut(s) 83, 135, 151, 565, 686, 1157
Pfl23II CGTACG 1 cut(s) 1333
PfoI TCCNGGA 1 cut(s) 793
PkrI GCNGC 5 cut(s) 64, 587, 777, 916, 1303
PleI GAGTC 2 cut(s) 41, 978
PpsI GAGTC 2 cut(s) 41, 978
PshAI GACNNNNGTC 1 cut(s) 988
Psp124BI GAGCTC 1 cut(s) 298
Psp6I CCWGG 1 cut(s) 793
PspEI GGTNACC 1 cut(s) 448
PspGI CCWGG 1 cut(s) 793
PspLI CGTACG 1 cut(s) 1333
PspN4I GGNNCC 4 cut(s) 202, 325, 743, 1043
PspPI GGNCC 2 cut(s) 107, 1008
PsuI RGATCY 3 cut(s) 232, 741, 1041
RsaI GTAC 6 cut(s) 325, 384, 504, 828, 1335, 1393
RsaNI GTAC 6 cut(s) 324, 383, 503, 827, 1334, 1392
RseI CAYNNNNRTG 2 cut(s) 209, 551
SacI GAGCTC 1 cut(s) 298
SaqAI TTAA 4 cut(s) 278, 494, 726, 968
SatI GCNGC 5 cut(s) 63, 586, 776, 915, 1302
Sau3AI GATC 8 cut(s) 222, 232, 418, 619, 741, 1041, 1144, 1162
Sau96I GGNCC 2 cut(s) 107, 1008
ScaI AGTACT 2 cut(s) 384, 504
SchI GAGTC 2 cut(s) 41, 978
ScrFI CCNGG 1 cut(s) 795
SduI GDGCHC 1 cut(s) 298
SinI GGWCC 2 cut(s) 107, 1008
SmiMI CAYNNNNRTG 2 cut(s) 209, 551
SmlI CTYRAG 1 cut(s) 648
SmoI CTYRAG 1 cut(s) 648
Sse9I AATT 8 cut(s) 8, 397, 692, 918, 924, 1256, 1361, 1405
SsiI CCGC 1 cut(s) 1330
SspMI CTAG 1 cut(s) 530
SstI GAGCTC 1 cut(s) 298
StyD4I CCNGG 1 cut(s) 793
StyI CCWWGG 1 cut(s) 858
TaaI ACNGT 4 cut(s) 123, 208, 826, 937
TaiI ACGT 2 cut(s) 610, 1326
TaqI TCGA 1 cut(s) 157
TaqII GACCGA 1 cut(s) 391
TasI AATT 8 cut(s) 8, 397, 692, 918, 924, 1256, 1361, 1405
TatI WGTACW 4 cut(s) 382, 502, 826, 1391
TfiI GAWTC 6 cut(s) 83, 135, 151, 565, 686, 1157
Tru1I TTAA 4 cut(s) 278, 494, 726, 968
Tru9I TTAA 4 cut(s) 278, 494, 726, 968
TscAI CASTG 3 cut(s) 637, 829, 1010
TseI GCWGC 5 cut(s) 62, 585, 775, 914, 1301
TspDTI ATGAA 5 cut(s) 410, 448, 535, 693, 1398
TspRI CASTG 3 cut(s) 637, 829, 1010
VpaK11BI GGWCC 2 cut(s) 107, 1008
XapI RAATTY 6 cut(s) 8, 397, 692, 924, 1256, 1405
XcmI CCANNNNNNNNNTGG 1 cut(s) 1257
XmnI GAANNNNTTC 1 cut(s) 1382
XspI CTAG 1 cut(s) 530
ZrmI AGTACT 2 cut(s) 384, 504
Zsp2I ATGCAT 1 cut(s) 259
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.