AT1G64860

RNA polymerase sigma

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
1
Physical Location & Seq
Forward (+)
24097736 .. 24100970
3235 bp
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UTR
Exon/CDS
Intron
AT1G64860.1

Sequence Viewer

Length: 1509 bp
ATGGCTACTGCAGCTGTTATAGGACTCAACACTGGCAAAAGATTGTTGAGTTCATCGTTTTATCACTCAGATGTTACAGAGAAGTTTCTATCTGTAAATGATCATTGTTCATCACAGTATCATATTGCTTCAACGAAAAGCGGGATAACTGCGAAAAAGGCGTCGAACTATAGTCCGAGTTTTCCTTCGTCGAATCGTCACACACAATCTGCTAAAGCTTTGAAAGAGAGTGTAGATGTTGCTTCTACTGAGAAGCCATGGCTACCTAATGGAACTGATAAGGAATTGGAAGAAGAATGTTATGATGATGATGATCTAATTAGTCATTCTGTTGAGGCAATTTTACTGTTACAGAAGTCTATGTTAGAGAAAAGTTGGAATCTTTCATTTGAAAAGGCGGTGTCGAGTGAGTATCCGGGCAAGGGGACTATACGGAAGAAGAAGATTCCGGTTATCACCTGTTCAGGGATTTCAGCTCGTCAAAGAAGGATTGGTGCTAAGAAGAAAACTAATATGACTCATGTTAAAGCAGTTTCTGATGTTTCTAGTGGAAAGCAAGTTAGAGGTTATGTGAAAGGTGTAATAAGTGAAGATGTGCTTAGTCATGTGGAAGTTGTGCGCTTGTCTAAGAAAATCAAATCTGGTCTTCGTCTTGATGATCATAAGTCAAGATTGAAGGATAGATTAGGCTGTGAGCCTTCTGATGAACAGCTTGCAGTATCTTTGAAGATATCTCGGGCCGAGCTTCAGGCGTGGTTGATGGAGTGTCATCTAGCTAGAGAGAAGTTGGCTATGAGTAATGTGCGTTTGGTTATGTCTATTGCTCAGCGTTATGATAATTTGGGAGCAGAAATGTCTGACCTTGTTCAGGGTGGTCTTATCGGACTTTTGCGGGGAATAGAGAAATTTGATTCTTCCAAAGGTTTCAGAATTTCAACTTATGTATATTGGTGGATTCGACAGGGTGTCTCAAGAGCACTAGTGGACAACTCAAGAACCTTGAGGTTACCTACTCACCTACATGAAAGACTCGGTTTAATCCGAAATGCAAAGCTTAGACTTCAAGAGAAAGGAATCACACCCTCCATTGATAGGATTGCAGAGTCTCTAAACATGTCGCAGAAGAAAGTTAGAAATGCAACAGAGGCTGTAAGCAAAGTATTTTCTCTAGACAGAGATGCATTTCCTTCTTTGAATGGTCTCCCTGGAGAAACTCATCACAGTTACATTGCGGATACTCGTTTGGAGAACAATCCGTGGCACGGGTATGATGATTTGGCACTCAAGGAGGAAGTAAGCAAGCTTATAAGTGCAACACTCGGAGAACGGGAAAAAGAGATCATTCGATTATACTATGGTCTAGACAAAGAATGTCTCACATGGGAAGACATTAGTAAACGGATAGGATTATCGAGAGAGAGGGTGAGACAGGTAGGGCTTGTGGCACTGGAGAAACTAAAACACGCAGCGAGGAAGAGAAAAATGGAGGCAATGATCCTTAAGAATTGA

Protein Analysis

502

Amino Acids

56.4

Weight (kDa)

9.51

Isoelectric Point (pI)

41.37

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Sigma70_r2 PF04542 264 - 333 1.4e-17 Sigma-70 region 2
Sigma70_r3 PF04539 342 - 412 1.5e-13 Sigma-70 region 3
Sigma70_r4 PF04545 438 - 488 2.4e-10 Sigma-70, region 4
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready

Orthologous Genes (Group: OG0013559)

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 1307
AciI CCGC 4 cut(s) 141, 398, 892, 1232
AclWI GGATC 1 cut(s) 1489
AcsI RAATTY 2 cut(s) 905, 930
AcuI CTGAAG 1 cut(s) 731
AcyI GRCGYC 1 cut(s) 161
AfiI CCNNNNNNNGG 5 cut(s) 422, 465, 868, 1092, 1262
AflII CTTAAG 1 cut(s) 1499
AflIII ACRYGT 1 cut(s) 1113
AgsI TTSAA 8 cut(s) 132, 223, 392, 676, 727, 936, 1064, 1195
AhdI GACNNNNNGTC 1 cut(s) 965
AhlI ACTAGT 1 cut(s) 979
AjnI CCWGG 1 cut(s) 1204
AluBI AGCT 8 cut(s) 14, 218, 476, 712, 745, 776, 1054, 1303
AluI AGCT 8 cut(s) 14, 218, 476, 712, 745, 776, 1054, 1303
Alw21I GWGCWC 1 cut(s) 979
Alw26I GTCTC 5 cut(s) 973, 1110, 1205, 1379, 1420
AlwI GGATC 1 cut(s) 1489
AlwNI CAGNNNCTG 2 cut(s) 536, 1148
Ama87I CYCGRG 1 cut(s) 735
AoxI GGCC 1 cut(s) 738
ApeKI GCWGC 2 cut(s) 11, 1466
ApoI RAATTY 2 cut(s) 905, 930
ArsI GACNNNNNNTTYG 2 cut(s) 146, 178
AspLEI GCGC 1 cut(s) 621
AspS9I GGNCC 1 cut(s) 738
AsuC2I CCSGG 1 cut(s) 417
AsuHPI GGTGA 3 cut(s) 448, 1007, 1435
AvaI CYCGRG 1 cut(s) 735
BbsI GAAGAC 2 cut(s) 638, 1392
Bbv12I GWGCWC 1 cut(s) 979
BbvI GCAGC 2 cut(s) 23, 1478
BccI CCATC 1 cut(s) 754
BciT130I CCWGG 1 cut(s) 1206
BciVI GTATCC 2 cut(s) 423, 1228
BclI TGATCA 2 cut(s) 100, 658
BcnI CCSGG 1 cut(s) 417
BcoDI GTCTC 5 cut(s) 973, 1110, 1205, 1379, 1420
BcuI ACTAGT 1 cut(s) 979
BfaI CTAG 6 cut(s) 546, 773, 777, 980, 1169, 1361
BfmI CTRYAG 2 cut(s) 9, 169
BfrI CTTAAG 1 cut(s) 1499
BfuI GTATCC 2 cut(s) 423, 1228
BisI GCNGC 2 cut(s) 12, 1467
BlpI GCTNAGC 1 cut(s) 825
BlsI GCNGC 2 cut(s) 13, 1468
Bme1390I CCNGG 2 cut(s) 417, 1206
BmeRI GACNNNNNGTC 1 cut(s) 965
BmeT110I CYCGRG 1 cut(s) 735
BmgT120I GGNCC 1 cut(s) 738
BmrFI CCNGG 2 cut(s) 417, 1206
BmsI GCATC 1 cut(s) 1168
BpiI GAAGAC 2 cut(s) 638, 1392
BpmI CTGGAG 2 cut(s) 1227, 1469
Bpu1102I GCTNAGC 1 cut(s) 825
BpuEI CTTGAG 4 cut(s) 955, 976, 1021, 1268
BpuMI CCSGG 1 cut(s) 417
BsaBI GATNNNNATC 1 cut(s) 312
BsaHI GRCGYC 1 cut(s) 161
BsaI GGTCTC 1 cut(s) 1205
BsaJI CCNNGG 3 cut(s) 257, 1204, 1256
BsaWI WCCGGW 1 cut(s) 448
Bsc4I CCNNNNNNNGG 5 cut(s) 422, 465, 868, 1092, 1262
Bse1I ACTGG 2 cut(s) 37, 1452
Bse3DI GCAATG 2 cut(s) 1227, 1497
Bse8I GATNNNNATC 1 cut(s) 312
BseBI CCWGG 1 cut(s) 1206
BseDI CCNNGG 3 cut(s) 257, 1204, 1256
BseJI GATNNNNATC 1 cut(s) 312
BseLI CCNNNNNNNGG 5 cut(s) 422, 465, 868, 1092, 1262
BseMI GCAATG 2 cut(s) 1227, 1497
BseMII CTCAG 3 cut(s) 81, 240, 839
BseNI ACTGG 2 cut(s) 37, 1452
BseXI GCAGC 2 cut(s) 23, 1478
BshFI GGCC 1 cut(s) 740
BsiHKAI GWGCWC 1 cut(s) 979
BsiHKCI CYCGRG 1 cut(s) 735
BsiSI CCGG 2 cut(s) 416, 449
BslFI GGGAC 1 cut(s) 439
BslI CCNNNNNNNGG 5 cut(s) 422, 465, 868, 1092, 1262
BsmAI GTCTC 5 cut(s) 973, 1110, 1205, 1379, 1420
BsmFI GGGAC 1 cut(s) 439
BsnI GGCC 1 cut(s) 740
Bso31I GGTCTC 1 cut(s) 1205
BsoBI CYCGRG 1 cut(s) 735
Bsp1286I GDGCHC 1 cut(s) 979
Bsp143I GATC 5 cut(s) 100, 313, 658, 1338, 1494
Bsp1720I GCTNAGC 1 cut(s) 825
Bsp19I CCATGG 1 cut(s) 257
BspACI CCGC 4 cut(s) 141, 398, 892, 1232
BspANI GGCC 1 cut(s) 740
BspCNI CTCAG 3 cut(s) 80, 241, 838
BspMAI CTGCAG 1 cut(s) 13
BspPI GGATC 1 cut(s) 1489
BspTI CTTAAG 1 cut(s) 1499
BspTNI GGTCTC 1 cut(s) 1205
BsrDI GCAATG 2 cut(s) 1227, 1497
BsrI ACTGG 2 cut(s) 37, 1452
BssECI CCNNGG 3 cut(s) 257, 1204, 1256
BssMI GATC 5 cut(s) 100, 313, 658, 1338, 1494
BssNI GRCGYC 1 cut(s) 161
BssT1I CCWWGG 1 cut(s) 257
Bst2UI CCWGG 1 cut(s) 1206
Bst4CI ACNGT 3 cut(s) 117, 348, 1223
Bst6I CTCTTC 1 cut(s) 1469
BstACI GRCGYC 1 cut(s) 161
BstAFI CTTAAG 1 cut(s) 1499
BstC8I GCNNGC 2 cut(s) 714, 1301
BstDEI CTNAG 7 cut(s) 67, 249, 498, 599, 627, 825, 1055
BstDSI CCRYGG 2 cut(s) 257, 1256
BstEII GGTNACC 1 cut(s) 1005
BstENI CCTNNNNNAGG 1 cut(s) 866
BstHHI GCGC 1 cut(s) 621
BstKTI GATC 5 cut(s) 103, 316, 661, 1341, 1497
BstMAI GTCTC 5 cut(s) 973, 1110, 1205, 1379, 1420
BstMBI GATC 5 cut(s) 100, 313, 658, 1338, 1494
BstMWI GCNNNNNNNGC 3 cut(s) 11, 158, 1145
BstNI CCWGG 1 cut(s) 1206
BstNSI RCATGY 1 cut(s) 1117
BstPI GGTNACC 1 cut(s) 1005
BstSCI CCNGG 2 cut(s) 415, 1204
BstSFI CTRYAG 2 cut(s) 9, 169
BstV1I GCAGC 2 cut(s) 23, 1478
BstV2I GAAGAC 2 cut(s) 638, 1392
BsuI GTATCC 2 cut(s) 423, 1228
BsuRI GGCC 1 cut(s) 740
BtgI CCRYGG 2 cut(s) 257, 1256
BtsIMutI CAGTG 2 cut(s) 30, 1445
Cac8I GCNNGC 2 cut(s) 714, 1301
CaiI CAGNNNCTG 2 cut(s) 536, 1148
CfoI GCGC 1 cut(s) 621
Cfr13I GGNCC 1 cut(s) 738
CseI GACGC 1 cut(s) 150
CviAII CATG 6 cut(s) 258, 521, 605, 1022, 1114, 1380
DdeI CTNAG 7 cut(s) 67, 249, 498, 599, 627, 825, 1055
DpnI GATC 5 cut(s) 102, 315, 660, 1340, 1496
DpnII GATC 5 cut(s) 100, 313, 658, 1338, 1494
DriI GACNNNNNGTC 1 cut(s) 965
Eam1104I CTCTTC 1 cut(s) 1469
Eam1105I GACNNNNNGTC 1 cut(s) 965
EarI CTCTTC 1 cut(s) 1469
Eco130I CCWWGG 1 cut(s) 257
Eco31I GGTCTC 1 cut(s) 1205
Eco32I GATATC 1 cut(s) 732
Eco57I CTGAAG 1 cut(s) 731
Eco88I CYCGRG 1 cut(s) 735
Eco91I GGTNACC 1 cut(s) 1005
EcoNI CCTNNNNNAGG 1 cut(s) 866
EcoO65I GGTNACC 1 cut(s) 1005
EcoRII CCWGG 1 cut(s) 1204
EcoRV GATATC 1 cut(s) 732
EcoT14I CCWWGG 1 cut(s) 257
EcoT22I ATGCAT 1 cut(s) 1183
ErhI CCWWGG 1 cut(s) 257
FaeI CATG 6 cut(s) 261, 524, 608, 1025, 1117, 1383
FalI AAGNNNNNCTT 2 cut(s) 582, 614
FaqI GGGAC 1 cut(s) 439
FatI CATG 6 cut(s) 257, 520, 604, 1021, 1113, 1379
FauI CCCGC 2 cut(s) 134, 885
FbaI TGATCA 2 cut(s) 100, 658
Fnu4HI GCNGC 2 cut(s) 12, 1467
Fsp4HI GCNGC 2 cut(s) 12, 1467
FspBI CTAG 6 cut(s) 546, 773, 777, 980, 1169, 1361
GlaI GCGC 1 cut(s) 620
GluI GCNGC 2 cut(s) 12, 1467
GsuI CTGGAG 2 cut(s) 1227, 1469
HaeIII GGCC 1 cut(s) 740
HapII CCGG 2 cut(s) 416, 449
HgaI GACGC 1 cut(s) 150
HhaI GCGC 1 cut(s) 621
Hin1I GRCGYC 1 cut(s) 161
Hin1II CATG 6 cut(s) 261, 524, 608, 1025, 1117, 1383
Hin6I GCGC 1 cut(s) 619
HinP1I GCGC 1 cut(s) 619
HindIII AAGCTT 3 cut(s) 216, 1052, 1301
HpaII CCGG 2 cut(s) 416, 449
HphI GGTGA 3 cut(s) 448, 1007, 1435
Hpy166II GTNNAC 2 cut(s) 985, 1397
Hpy188I TCNGA 9 cut(s) 70, 177, 538, 703, 859, 884, 929, 1043, 1322
Hpy188III TCNNGA 8 cut(s) 653, 669, 972, 993, 1064, 1169, 1361, 1413
Hpy8I GTNNAC 2 cut(s) 985, 1397
Hpy99I CGWCG 2 cut(s) 166, 193
HpyAV CCTTC 5 cut(s) 195, 480, 670, 708, 1197
HpyCH4III ACNGT 3 cut(s) 117, 348, 1223
HpyCH4V TGCA 7 cut(s) 11, 716, 1049, 1100, 1139, 1181, 1313
HpyF10VI GCNNNNNNNGC 3 cut(s) 11, 158, 1145
HpyF3I CTNAG 7 cut(s) 67, 249, 498, 599, 627, 825, 1055
Hsp92I GRCGYC 1 cut(s) 161
Hsp92II CATG 6 cut(s) 261, 524, 608, 1025, 1117, 1383
HspAI GCGC 1 cut(s) 619
Ksp22I TGATCA 2 cut(s) 100, 658
Kzo9I GATC 5 cut(s) 100, 313, 658, 1338, 1494
LmnI GCTCC 1 cut(s) 845
Lsp1109I GCAGC 2 cut(s) 23, 1478
LweI GCATC 1 cut(s) 1168
MaeI CTAG 6 cut(s) 546, 773, 777, 980, 1169, 1361
MaeIII GTNAC 5 cut(s) 73, 197, 348, 1005, 1223
MalI GATC 5 cut(s) 102, 315, 660, 1340, 1496
MboI GATC 5 cut(s) 100, 313, 658, 1338, 1494
MhlI GDGCHC 1 cut(s) 979
MluCI AATT 7 cut(s) 284, 318, 339, 838, 905, 930, 1504
MlyI GAGTC 4 cut(s) 18, 511, 1023, 1112
MmeI TCCRAC 1 cut(s) 356
MnlI CCTC 9 cut(s) 328, 557, 996, 1093, 1138, 1282, 1413, 1464, 1480
Mph1103I ATGCAT 1 cut(s) 1183
MseI TTAA 3 cut(s) 525, 1037, 1500
MslI CAYNNNNRTG 3 cut(s) 69, 1020, 1266
MspA1I CMGCKG 1 cut(s) 14
MspCI CTTAAG 1 cut(s) 1499
MspI CCGG 2 cut(s) 416, 449
MspR9I CCNGG 2 cut(s) 417, 1206
MvaI CCWGG 1 cut(s) 1206
MwoI GCNNNNNNNGC 3 cut(s) 11, 158, 1145
NciI CCSGG 1 cut(s) 417
NcoI CCATGG 1 cut(s) 257
NdeII GATC 5 cut(s) 100, 313, 658, 1338, 1494
NlaIII CATG 6 cut(s) 261, 524, 608, 1025, 1117, 1383
NmeAIII GCCGAG 1 cut(s) 766
NmuCI GTSAC 1 cut(s) 197
NsiI ATGCAT 1 cut(s) 1183
NspI RCATGY 1 cut(s) 1117
PciI ACATGT 1 cut(s) 1113
PfeI GAWTC 6 cut(s) 193, 379, 445, 911, 955, 1074
PkrI GCNGC 2 cut(s) 13, 1468
PleI GAGTC 4 cut(s) 18, 511, 1023, 1111
PpsI GAGTC 4 cut(s) 18, 511, 1023, 1111
PscI ACATGT 1 cut(s) 1113
PsiI TTATAA 1 cut(s) 1307
Psp6I CCWGG 1 cut(s) 1204
PspEI GGTNACC 1 cut(s) 1005
PspGI CCWGG 1 cut(s) 1204
PspPI GGNCC 1 cut(s) 738
PstI CTGCAG 1 cut(s) 13
PstNI CAGNNNCTG 2 cut(s) 536, 1148
PvuII CAGCTG 1 cut(s) 14
RseI CAYNNNNRTG 3 cut(s) 69, 1020, 1266
SaqAI TTAA 3 cut(s) 525, 1037, 1500
SatI GCNGC 2 cut(s) 12, 1467
Sau3AI GATC 5 cut(s) 100, 313, 658, 1338, 1494
Sau96I GGNCC 1 cut(s) 738
SchI GAGTC 4 cut(s) 18, 511, 1023, 1112
ScrFI CCNGG 2 cut(s) 417, 1206
SduI GDGCHC 1 cut(s) 979
SfaNI GCATC 1 cut(s) 1168
SfcI CTRYAG 2 cut(s) 9, 169
SmiMI CAYNNNNRTG 3 cut(s) 69, 1020, 1266
SmlI CTYRAG 5 cut(s) 970, 991, 1000, 1283, 1499
SmoI CTYRAG 5 cut(s) 970, 991, 1000, 1283, 1499
SpeI ACTAGT 1 cut(s) 979
Sse9I AATT 7 cut(s) 284, 318, 339, 838, 905, 930, 1504
SsiI CCGC 4 cut(s) 141, 398, 892, 1232
SspMI CTAG 6 cut(s) 546, 773, 777, 980, 1169, 1361
StyD4I CCNGG 2 cut(s) 415, 1204
StyI CCWWGG 1 cut(s) 257
TaaI ACNGT 3 cut(s) 117, 348, 1223
TaqI TCGA 6 cut(s) 164, 191, 404, 958, 1345, 1412
TasI AATT 7 cut(s) 284, 318, 339, 838, 905, 930, 1504
TfiI GAWTC 6 cut(s) 193, 379, 445, 911, 955, 1074
Tru1I TTAA 3 cut(s) 525, 1037, 1500
Tru9I TTAA 3 cut(s) 525, 1037, 1500
TscAI CASTG 2 cut(s) 37, 1452
TseFI GTSAC 1 cut(s) 197
TseI GCWGC 2 cut(s) 11, 1466
Tsp45I GTSAC 1 cut(s) 197
TspDTI ATGAA 5 cut(s) 42, 99, 375, 720, 1038
TspGWI ACGGA 3 cut(s) 448, 1245, 1414
TspRI CASTG 2 cut(s) 37, 1452
Vha464I CTTAAG 1 cut(s) 1499
XagI CCTNNNNNAGG 1 cut(s) 866
XapI RAATTY 2 cut(s) 905, 930
XbaI TCTAGA 2 cut(s) 1168, 1360
XceI RCATGY 1 cut(s) 1117
XspI CTAG 6 cut(s) 546, 773, 777, 980, 1169, 1361
Zsp2I ATGCAT 1 cut(s) 1183
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.