FvH4_1g29160

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

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb1
Physical Location & Seq
Reverse (-)
21808175 .. 21812691
4517 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_1g29160.t2

Sequence Viewer

Length: 1851 bp
ATGTCAATCTTATCATCTTCTTCATCATTGTTAGTTGGGTTTTGCGACGCCCACAAACACGCCTCTTCCTCTTCTGTAATATGTTGTTCCTTTCTCACCCCACTATCCGTTCCGCACCCCAAACCCAAGAACAAGAACAATAAGAAGAAGAAGAAGCTCACCCAAATATGCACTGATCACATTGCCGTGGGCTTCCAAGCAAAAGCTAGATATCCTATCAGCTTCTGCGCACAATATATGTCGTCTAGCACATCACATTCAACATCAACACCAACAGCTACCTTGCTTGATATGGAGGAGTTCAGTTTACCTTCTTTAACAGTTAATTCTGATTCTTTGATTGTAAATCGACCCTGGACATACACCGGAGCAATCGGCCCTCCCACTGAGGCAAACTATGGAGCAGCGTTAGCTACAGAAACACTTCTTACAAGTGAAGAGGCTGTAATAGCAGCTGCTGCTGCTGAAGCTGTTACTCTTGCAAAAGCAGCTCTGAAGGTTGCAAAGGATGTAGCTTTGCTGGTTAGCAATAATCACTATGCTAAAGTAGAAAATTCATCTCCAGTTTCTTGTGGGACCAGTGCTTTTCATATCAACTGGGCTCAGCATCTGGAAACTGAACCAACTCTGAGAATTGGAGATTCCATGGCATCTGAAACTGCACTGGTGGAGGATCATTTCCTTCAAATTGCCATAAATGAATCTGAAAATGTGGAACCAGCAAATGAAGAATTTGAACTTCTGCAGGAGCAACTTTCTAACGGTATAGCTGCGAGATCAAGTCGCCAAACAGAAAGGAAGGCAAGAAGAACCAGAGCAGCAGAAAAGGCTGCTGCCAGTATTGTGTCCGTGAAATCTGGTTCAACCAGCCGAAAAAAGCGTGCTTCTTTACAAGATGTAGACCATTCCGATCCATTGCGTTACTTGAGAGCAACTACTCATACTTCTAGGCTTCTTACTGCAAATGAAGAAATTGAACTATCAGAAGGAATACAGGAACTTTTAAAACTAGAAAAGCTCCAGGAGGATCTTGCACAAAGATGCGGCACTCAGCCCACCTTTGCACAATGGGCCGCAGCAGCAGGAGTTGACCAGAAGACATTAAGGAAGCGAGTAAACTACGGTATTATGTGCAAGGACAAAATGATTAAGAGCAACATACGCCTTGTTATATCGATTGCAAAGAATTATCAGGGAGCTGGAATGAATCTTCAGGATCTTGTGCAGGAAGGTTGTCGTGGCCTTGTAAGAGGTGCAGAAAAATTTGATGCTTCAAAGGGTTTTAAGTTCTCAACCTATGCTCACTGGTGGATCAAACAGGCTGTCCGAAAGTCTCTTTCTGATCAATCGAGGACAATTCGTTTACCATTTCACATGGTGGAGGCAACTTATAGAGTGAGAGAGGCTAAAAAGCAATTGTATAGTGTAAACGGAAGACATCCTAATGATGAAGAAGTTGCAGAGGCAACAGGGCTATCAATGAAGAGGCTTGCTGCTGTCCTACTGACTCCAAAAGCTCCTAGATCTCTCGAGCAGAAAATTGGAATCAACCAGAATCTTAAACCTTCGGACGTAATTGCAGATCCTGACGCAGAAACAGCTGAAGACCTATTGATGAAAAAGTTTATGAAACAGGATTTGGAGAAGGTACTGGATAGTCTCAATCCAAGAGAGAAGCAGGTGATCAGATGGAGGTTTGGGATGGAGGATGGGAGGATGAAGACATTGCAAGAAATAGGGGAGCTAATGGGTGTTAGTAGAGAGAGAATTAGACAAATTGAATCATGTGCATTCCGAAAGCTGAAGAACAAGAAAAGAACTAAACATTTGCAGCAGTATGTGCTTTCATAG

Protein Analysis

617

Amino Acids

68.35

Weight (kDa)

9.26

Isoelectric Point (pI)

47.59

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Sigma70_r2 PF04542 373 - 443 2.9e-20 Sigma-70 region 2
Sigma70_r3 PF04539 452 - 527 3.2e-17 Sigma-70 region 3
Sigma70_r4 PF04545 541 - 593 5.3e-19 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

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AarI CACCTGC 1 cut(s) 1669
Acc16I TGCGCA 1 cut(s) 229
Acc36I ACCTGC 1 cut(s) 1669
AccI GTMKAC 1 cut(s) 900
AciI CCGC 3 cut(s) 113, 1044, 1074
AclWI GGATC 6 cut(s) 681, 905, 1035, 1224, 1319, 1577
AcsI RAATTY 3 cut(s) 553, 731, 1262
AcuI CTGAAG 5 cut(s) 486, 515, 1196, 1623, 1823
AcyI GRCGYC 1 cut(s) 48
AdeI CACNNNGTG 1 cut(s) 1378
AfaI GTAC 1 cut(s) 1650
AgsI TTSAA 7 cut(s) 261, 686, 737, 864, 977, 1275, 1781
AjnI CCWGG 2 cut(s) 353, 1020
AjuI GAANNNNNNNTTGG 2 cut(s) 1622, 1654
Alw26I GTCTC 2 cut(s) 1338, 1664
AlwI GGATC 6 cut(s) 681, 905, 1035, 1224, 1319, 1577
AlwNI CAGNNNCTG 4 cut(s) 225, 458, 610, 1586
Ama87I CYCGRG 1 cut(s) 1529
AoxI GGCC 3 cut(s) 376, 1071, 1240
ApoI RAATTY 3 cut(s) 553, 731, 1262
ArsI GACNNNNNNTTYG 2 cut(s) 1308, 1340
Asp700I GAANNNNTTC 1 cut(s) 423
AspLEI GCGC 1 cut(s) 230
AspS9I GGNCC 3 cut(s) 377, 576, 1071
AsuHPI GGTGA 3 cut(s) 88, 151, 1693
AvaI CYCGRG 1 cut(s) 1529
AvaII GGWCC 1 cut(s) 576
BanII GRGCYC 1 cut(s) 604
BbsI GAAGAC 4 cut(s) 1103, 1441, 1611, 1727
BccI CCATC 3 cut(s) 1683, 1696, 1703
BceAI ACGGC 1 cut(s) 170
BciT130I CCWGG 2 cut(s) 355, 1022
BclI TGATCA 3 cut(s) 175, 1342, 1683
BcoDI GTCTC 2 cut(s) 1338, 1664
BfaI CTAG 5 cut(s) 207, 246, 948, 1010, 1521
BfmI CTRYAG 2 cut(s) 414, 743
BfuAI ACCTGC 1 cut(s) 1669
BglII AGATCT 1 cut(s) 1523
BlpI GCTNAGC 1 cut(s) 603
Bme1390I CCNGG 2 cut(s) 355, 1022
Bme18I GGWCC 1 cut(s) 576
BmeT110I CYCGRG 1 cut(s) 1529
BmgT120I GGNCC 3 cut(s) 377, 576, 1071
BmiI GGNNCC 2 cut(s) 577, 717
BmrFI CCNGG 2 cut(s) 355, 1022
BmrI ACTGGG 1 cut(s) 607
BmsI GCATC 4 cut(s) 616, 659, 1031, 1258
BmuI ACTGGG 1 cut(s) 607
BpiI GAAGAC 4 cut(s) 1103, 1441, 1611, 1727
BpmI CTGGAG 2 cut(s) 546, 1004
Bpu1102I GCTNAGC 1 cut(s) 603
BpuEI CTTGAG 1 cut(s) 946
Bsa29I ATCGAT 1 cut(s) 1175
BsaHI GRCGYC 1 cut(s) 48
BsaJI CCNNGG 3 cut(s) 186, 353, 645
BsaWI WCCGGW 1 cut(s) 365
Bse1I ACTGG 7 cut(s) 563, 579, 602, 669, 837, 1310, 1656
Bse3DI GCAATG 3 cut(s) 180, 914, 1724
BseBI CCWGG 2 cut(s) 355, 1022
BseCI ATCGAT 1 cut(s) 1175
BseDI CCNNGG 3 cut(s) 186, 353, 645
BseGI GGATG 5 cut(s) 514, 1438, 1707, 1714, 1722
BseMI GCAATG 3 cut(s) 180, 914, 1724
BseMII CTCAG 4 cut(s) 378, 617, 620, 1064
BseNI ACTGG 7 cut(s) 563, 579, 602, 669, 837, 1310, 1656
BseRI GAGGAG 1 cut(s) 311
BsgI GTGCAG 3 cut(s) 645, 1244, 1275
BshFI GGCC 3 cut(s) 378, 1073, 1242
BshVI ATCGAT 1 cut(s) 1175
BsiHKCI CYCGRG 1 cut(s) 1529
BsiSI CCGG 1 cut(s) 366
BslFI GGGAC 1 cut(s) 589
BsmAI GTCTC 2 cut(s) 1338, 1664
BsmFI GGGAC 1 cut(s) 589
BsmI GAATGC 1 cut(s) 1790
BsnI GGCC 3 cut(s) 378, 1073, 1242
BsoBI CYCGRG 1 cut(s) 1529
Bsp1286I GDGCHC 1 cut(s) 604
Bsp1720I GCTNAGC 1 cut(s) 603
Bsp19I CCATGG 1 cut(s) 645
BspACI CCGC 3 cut(s) 113, 1044, 1074
BspANI GGCC 3 cut(s) 378, 1073, 1242
BspCNI CTCAG 4 cut(s) 379, 616, 621, 1063
BspDI ATCGAT 1 cut(s) 1175
BspLI GGNNCC 2 cut(s) 577, 717
BspMAI CTGCAG 1 cut(s) 747
BspMI ACCTGC 1 cut(s) 1669
BspPI GGATC 6 cut(s) 681, 905, 1035, 1224, 1319, 1577
BsrDI GCAATG 3 cut(s) 180, 914, 1724
BsrI ACTGG 7 cut(s) 563, 579, 602, 669, 837, 1310, 1656
BssECI CCNNGG 3 cut(s) 186, 353, 645
BssNI GRCGYC 1 cut(s) 48
BssT1I CCWWGG 1 cut(s) 645
Bst2UI CCWGG 2 cut(s) 355, 1022
Bst4CI ACNGT 3 cut(s) 322, 764, 1124
Bst6I CTCTTC 4 cut(s) 70, 76, 432, 1478
BstACI GRCGYC 1 cut(s) 48
BstAPI GCANNNNNTGC 2 cut(s) 458, 1840
BstC8I GCNNGC 2 cut(s) 882, 1491
BstDEI CTNAG 4 cut(s) 387, 603, 629, 1050
BstDSI CCRYGG 2 cut(s) 186, 645
BstF5I GGATG 5 cut(s) 514, 1438, 1707, 1714, 1722
BstHHI GCGC 1 cut(s) 230
BstMAI GTCTC 2 cut(s) 1338, 1664
BstNI CCWGG 2 cut(s) 355, 1022
BstSCI CCNGG 2 cut(s) 353, 1020
BstSFI CTRYAG 2 cut(s) 414, 743
BstV2I GAAGAC 4 cut(s) 1103, 1441, 1611, 1727
BstX2I RGATCY 4 cut(s) 1027, 1216, 1523, 1582
BstYI RGATCY 4 cut(s) 1027, 1216, 1523, 1582
Bsu15I ATCGAT 1 cut(s) 1175
BsuRI GGCC 3 cut(s) 378, 1073, 1242
BsuTUI ATCGAT 1 cut(s) 1175
BtgI CCRYGG 2 cut(s) 186, 645
BtsCI GGATG 5 cut(s) 514, 1438, 1707, 1714, 1722
BtsIMutI CAGTG 5 cut(s) 171, 384, 586, 662, 1303
BveI ACCTGC 1 cut(s) 1669
Cac8I GCNNGC 2 cut(s) 882, 1491
CaiI CAGNNNCTG 4 cut(s) 225, 458, 610, 1586
CfoI GCGC 1 cut(s) 230
Cfr13I GGNCC 3 cut(s) 377, 576, 1071
ClaI ATCGAT 1 cut(s) 1175
CseI GACGC 2 cut(s) 56, 1598
Csp6I GTAC 1 cut(s) 1649
CviAII CATG 3 cut(s) 646, 1375, 1785
CviQI GTAC 1 cut(s) 1649
DdeI CTNAG 4 cut(s) 387, 603, 629, 1050
DraI TTTAAA 1 cut(s) 1005
DraIII CACNNNGTG 1 cut(s) 1378
Eam1104I CTCTTC 4 cut(s) 70, 76, 432, 1478
EarI CTCTTC 4 cut(s) 70, 76, 432, 1478
Eco130I CCWWGG 1 cut(s) 645
Eco24I GRGCYC 1 cut(s) 604
Eco32I GATATC 1 cut(s) 212
Eco47I GGWCC 1 cut(s) 576
Eco57I CTGAAG 5 cut(s) 486, 515, 1196, 1623, 1823
Eco88I CYCGRG 1 cut(s) 1529
EcoRII CCWGG 2 cut(s) 353, 1020
EcoRV GATATC 1 cut(s) 212
EcoT14I CCWWGG 1 cut(s) 645
EcoT38I GRGCYC 1 cut(s) 604
ErhI CCWWGG 1 cut(s) 645
FaeI CATG 3 cut(s) 649, 1378, 1788
FaqI GGGAC 1 cut(s) 589
FatI CATG 3 cut(s) 645, 1374, 1784
FbaI TGATCA 3 cut(s) 175, 1342, 1683
FblI GTMKAC 1 cut(s) 900
FokI GGATG 5 cut(s) 521, 1425, 1714, 1721, 1729
FriOI GRGCYC 1 cut(s) 604
FspBI CTAG 5 cut(s) 207, 246, 948, 1010, 1521
FspI TGCGCA 1 cut(s) 229
GlaI GCGC 1 cut(s) 229
GsuI CTGGAG 2 cut(s) 546, 1004
HaeIII GGCC 3 cut(s) 378, 1073, 1242
HapII CCGG 1 cut(s) 366
HgaI GACGC 2 cut(s) 56, 1598
HhaI GCGC 1 cut(s) 230
Hin1I GRCGYC 1 cut(s) 48
Hin1II CATG 3 cut(s) 649, 1378, 1788
Hin6I GCGC 1 cut(s) 228
HinP1I GCGC 1 cut(s) 228
HincII GTYRAC 1 cut(s) 1090
HindII GTYRAC 1 cut(s) 1090
HinfI GANTC 8 cut(s) 332, 641, 701, 1207, 1507, 1545, 1555, 1781
HpaII CCGG 1 cut(s) 366
HphI GGTGA 3 cut(s) 88, 151, 1693
Hpy166II GTNNAC 6 cut(s) 308, 901, 1090, 1117, 1364, 1429
Hpy188III TCNNGA 4 cut(s) 611, 1214, 1529, 1586
Hpy8I GTNNAC 6 cut(s) 308, 901, 1090, 1117, 1364, 1429
Hpy99I CGWCG 1 cut(s) 50
HpyAV CCTTC 8 cut(s) 321, 490, 692, 793, 980, 1223, 1575, 1639
HpyCH4III ACNGT 3 cut(s) 322, 764, 1124
HpyCH4IV ACGT 1 cut(s) 1572
HpyF3I CTNAG 4 cut(s) 387, 603, 629, 1050
HpySE526I ACGT 1 cut(s) 1572
Hsp92I GRCGYC 1 cut(s) 48
Hsp92II CATG 3 cut(s) 649, 1378, 1788
HspAI GCGC 1 cut(s) 228
Ksp22I TGATCA 3 cut(s) 175, 1342, 1683
LmnI GCTCC 7 cut(s) 368, 401, 748, 1023, 1196, 1522, 1741
LweI GCATC 4 cut(s) 616, 659, 1031, 1258
MaeI CTAG 5 cut(s) 207, 246, 948, 1010, 1521
MaeII ACGT 1 cut(s) 1572
MaeIII GTNAC 2 cut(s) 472, 920
MfeI CAATTG 1 cut(s) 1415
MflI RGATCY 4 cut(s) 1027, 1216, 1523, 1582
MhlI GDGCHC 1 cut(s) 604
MlyI GAGTC 1 cut(s) 1501
MroXI GAANNNNTTC 1 cut(s) 423
MseI TTAA 7 cut(s) 317, 324, 1004, 1103, 1149, 1284, 1560
MslI CAYNNNNRTG 3 cut(s) 185, 1039, 1443
MspA1I CMGCKG 2 cut(s) 455, 1601
MspI CCGG 1 cut(s) 366
MspR9I CCNGG 2 cut(s) 355, 1022
MunI CAATTG 1 cut(s) 1415
Mva1269I GAATGC 1 cut(s) 1790
MvaI CCWGG 2 cut(s) 355, 1022
NcoI CCATGG 1 cut(s) 645
NlaIII CATG 3 cut(s) 649, 1378, 1788
NlaIV GGNNCC 2 cut(s) 577, 717
NsbI TGCGCA 1 cut(s) 229
PaeR7I CTCGAG 1 cut(s) 1529
PaqCI CACCTGC 1 cut(s) 1669
PctI GAATGC 1 cut(s) 1790
PdmI GAANNNNTTC 1 cut(s) 423
PfeI GAWTC 7 cut(s) 332, 641, 701, 1207, 1545, 1555, 1781
PfoI TCCNGGA 1 cut(s) 1020
PleI GAGTC 1 cut(s) 1501
PpsI GAGTC 1 cut(s) 1501
Psp6I CCWGG 2 cut(s) 353, 1020
PspGI CCWGG 2 cut(s) 353, 1020
PspN4I GGNNCC 2 cut(s) 577, 717
PspPI GGNCC 3 cut(s) 377, 576, 1071
PstI CTGCAG 1 cut(s) 747
PstNI CAGNNNCTG 4 cut(s) 225, 458, 610, 1586
PsuI RGATCY 4 cut(s) 1027, 1216, 1523, 1582
PvuII CAGCTG 2 cut(s) 455, 1601
RsaI GTAC 1 cut(s) 1650
RsaNI GTAC 1 cut(s) 1649
RseI CAYNNNNRTG 3 cut(s) 185, 1039, 1443
SaqAI TTAA 7 cut(s) 317, 324, 1004, 1103, 1149, 1284, 1560
Sau96I GGNCC 3 cut(s) 377, 576, 1071
SchI GAGTC 1 cut(s) 1501
ScrFI CCNGG 2 cut(s) 355, 1022
SduI GDGCHC 1 cut(s) 604
SfaNI GCATC 4 cut(s) 616, 659, 1031, 1258
SfcI CTRYAG 2 cut(s) 414, 743
Sfr274I CTCGAG 1 cut(s) 1529
SinI GGWCC 1 cut(s) 576
SlaI CTCGAG 1 cut(s) 1529
SmiMI CAYNNNNRTG 3 cut(s) 185, 1039, 1443
SmlI CTYRAG 2 cut(s) 925, 1529
SmoI CTYRAG 2 cut(s) 925, 1529
SsiI CCGC 3 cut(s) 113, 1044, 1074
SspMI CTAG 5 cut(s) 207, 246, 948, 1010, 1521
StyD4I CCNGG 2 cut(s) 353, 1020
StyI CCWWGG 1 cut(s) 645
TaaI ACNGT 3 cut(s) 322, 764, 1124
TaiI ACGT 1 cut(s) 1575
TaqI TCGA 4 cut(s) 349, 1175, 1349, 1530
TauI GCSGC 2 cut(s) 1047, 1076
TfiI GAWTC 7 cut(s) 332, 641, 701, 1207, 1545, 1555, 1781
Tru1I TTAA 7 cut(s) 317, 324, 1004, 1103, 1149, 1284, 1560
Tru9I TTAA 7 cut(s) 317, 324, 1004, 1103, 1149, 1284, 1560
TscAI CASTG 5 cut(s) 178, 391, 586, 669, 1310
TspGWI ACGGA 3 cut(s) 97, 838, 1446
TspRI CASTG 5 cut(s) 178, 391, 586, 669, 1310
VpaK11BI GGWCC 1 cut(s) 576
XapI RAATTY 3 cut(s) 553, 731, 1262
XhoI CTCGAG 1 cut(s) 1529
XmiI GTMKAC 1 cut(s) 900
XmnI GAANNNNTTC 1 cut(s) 423
XspI CTAG 5 cut(s) 207, 246, 948, 1010, 1521
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.