MD14G1100900.v1.1

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
malus_domestica
Chr14
Physical Location & Seq
Reverse (-)
15569247 .. 15574627
5381 bp
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UTR
Exon/CDS
Intron
MD14G1100900.v1.1.491

Sequence Viewer

Length: 1833 bp
ATGTCAGTCTTATCAATTTCATCATCGTCGTCGTCGTCCGCAGCCGTTGGATTCTGTCCTTCCCACAAACACGCCCTTCCCAATGCCTCATTTCTCACCCCACTCCATCTCGTTGGGGTCCACCCAGCAAGTGACCAGAAGAATACCAAGAAGCAGAAGAGGAGGGCCGCCGCCGTTGGAGGAGGAGTCATGGCCACCAAGCGCACAGTCCTCAGGACCCACCATACCCTTTTCTGTGATGAATTGTTTAAGGACAGTGGCTTCCAAGCAAAAACTAGAGATCCTCTGTGTTTCCGGGCACAATATATCTTATCCACTACACCGCGTTCAACATCAACAGCAACAACTACAGTGCTTGATATGGAGAAGCTCAGACTACCTTCCTTAGAATTTAATTCCGATTCTTTGGCTTCAAGTAGACCGTGGACATACACAGGGGCAATTGATCCTCCCACTGAGGCGAATTTTGGATCAACTTTAGCTACAGAAACTCTTCTTACGAGTGAAGAGGCTGTAATAGCAGCTGCTGCCGCTGAAGCTGTTACTCTTGCAAAAGCAGCTCTGAAGGTTGCAAAGGATGTGGCTATGCTGCATATAGAAACTGAACAGGTTAGAGTAGGAGCTTCCATGGGAGCTGAAACTGCATTTTTGGAAGACCATTTCATTCAATATGCAGAAAAAGAGTCGGAAGAAGTGGAGCGAACAAATGAAGAATTTGAACTTCTGCAGGAGCAACTTTCCAAGGGTATAACGGCAAAATCGAGTCGTCAAACCGAAAGGAAGGCCAGAAGATCAAAAGCAGCAGAAAAGGCTGCTGCAAGTGTTGTGTCTGTGAAGTCTGGTTCAACCACTAGAAAAAAGCGTTCTTCAGTACAAGAAATAGACCACTCTGATCCCTTGCGTTACTTGAGATCTACTACCCACACATCTCGGCTTCTTACTGCGAACGAAGAAATTGAGCTTTCTGCAGGAATTCAGGAACTACTGAAACTGGAAAAGCTGCAGGAGGAGCTTACGCAAAGATGTGGCAGGCAGCCCACCATTGCACAATGGGCTGCAGCAGCAGGAGTTGATCAGAAGACTTTGAGGAAGCGTGTAAACTGTGGTATTCTGTGCAAAGACAAAATGATCAAGAGCAACATAAGGCTTGTTATATCAATTGCAAAAAATTATCAGGGATCTGGGATGAATCTTCAAGATCTTGTGCAGCAAGGATGTCGAGGCCTTGTAAGAGGTGCAGAGAAATTTGACGCTTCAAAGGGTTTTAAGTTCTCAACCTATGCACACTGGTGGATTAAACAGGCTGTTCGAAAATCTCTTTCCGACCAGTCCAGAACAATTCGCTTACCCTTTCACATGGTGGAGGCGACGTATAGAGTTAAAGAGGCCAAAAAGCAATTGTATAGTTTAAATGGAAGACATCCTAATGATGAAGAAGTTGCAGAGGCAACAGGGCTATCAATGAAAAGGCTTTCTGCTGTATTACTGACTCCAAAAGCCCCTAGATCTCTGGACCAGAAAATTGGAATTAACCTGAATTTTAAACCTTCGGAAGTAATCTCAGATCCCGACGCAGAAACAGCAGAAGATCTGCTGATGAAAAAGTTTATGAAACAGGATTTGGAGAAGGTACTAGATAGTCTCAATCCTAGAGAGAAGCAGGTTGTCAGATGGAGGTTTGGATTGGAGGATGGAAGGATGAAGACATTGCAAGAGATAGGGGAGCTGATGGGAGTTAGTAGGGAGAGAATTAGACAAATAGAGTCATGTGCGTTTCGAAAACTGAAGAACAAGAAAAGAACTAAACATTTACAGCAATATGCAGTTTCATAG

Protein Analysis

611

Amino Acids

67.88

Weight (kDa)

9.57

Isoelectric Point (pI)

47.74

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Sigma70_r2 PF04542 376 - 446 6.7e-20 Sigma-70 region 2
Sigma70_r3 PF04539 455 - 530 4.2e-16 Sigma-70 region 3
Sigma70_r4 PF04545 544 - 596 1.2e-18 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)
Acc36I ACCTGC 1 cut(s) 1651
AccI GTMKAC 1 cut(s) 418
AccII CGCG 1 cut(s) 325
AciI CCGC 5 cut(s) 39, 168, 171, 323, 531
AclWI GGATC 6 cut(s) 275, 440, 478, 887, 1186, 1559
AcoI YGGCCR 1 cut(s) 192
AcsI RAATTY 6 cut(s) 389, 463, 713, 972, 1244, 1537
AcuI CTGAAG 4 cut(s) 555, 584, 852, 1805
AdeI CACNNNGTG 1 cut(s) 1360
AfaI GTAC 2 cut(s) 873, 1632
AgsI TTSAA 7 cut(s) 330, 414, 668, 719, 846, 1196, 1257
AjuI GAANNNNNNNTTGG 2 cut(s) 1604, 1636
AleI CACNNNNGTG 1 cut(s) 1288
Alw26I GTCTC 1 cut(s) 1646
AlwI GGATC 6 cut(s) 275, 440, 478, 887, 1186, 1559
AlwNI CAGNNNCTG 1 cut(s) 527
AoxI GGCC 5 cut(s) 165, 192, 783, 1222, 1386
ApoI RAATTY 6 cut(s) 389, 463, 713, 972, 1244, 1537
Asp700I GAANNNNTTC 1 cut(s) 492
AspLEI GCGC 1 cut(s) 204
AspS9I GGNCC 4 cut(s) 118, 165, 216, 1513
AsuC2I CCSGG 1 cut(s) 296
AsuHPI GGTGA 1 cut(s) 88
AsuII TTCGAA 2 cut(s) 1309, 1777
AvaII GGWCC 3 cut(s) 118, 216, 1513
AxyI CCTNAGG 1 cut(s) 212
BaeGI GKGCMC 1 cut(s) 301
BalI TGGCCA 1 cut(s) 194
BbsI GAAGAC 4 cut(s) 660, 1085, 1423, 1709
BccI CCATC 4 cut(s) 114, 1665, 1685, 1723
BceAI ACGGC 3 cut(s) 29, 158, 768
BcgI CGANNNNNNTGC 2 cut(s) 1199, 1233
BclI TGATCA 2 cut(s) 1072, 1128
BcnI CCSGG 1 cut(s) 296
BcoDI GTCTC 1 cut(s) 1646
BfaI CTAG 5 cut(s) 276, 852, 1503, 1634, 1650
BfmI CTRYAG 6 cut(s) 348, 483, 725, 966, 1001, 1056
BfuAI ACCTGC 1 cut(s) 1651
BglII AGATCT 4 cut(s) 911, 1198, 1505, 1588
Bme1390I CCNGG 1 cut(s) 296
Bme18I GGWCC 3 cut(s) 118, 216, 1513
BmgT120I GGNCC 4 cut(s) 118, 165, 216, 1513
BmiI GGNNCC 2 cut(s) 119, 218
BmrFI CCNGG 1 cut(s) 296
BpiI GAAGAC 4 cut(s) 660, 1085, 1423, 1709
Bpu14I TTCGAA 2 cut(s) 1309, 1777
BpuEI CTTGAG 1 cut(s) 928
BpuMI CCSGG 1 cut(s) 296
BsaJI CCNNGG 3 cut(s) 422, 627, 741
BsaXI ACNNNNNCTCC 4 cut(s) 171, 201, 1355, 1385
Bse1I ACTGG 3 cut(s) 996, 1292, 1327
Bse21I CCTNAGG 1 cut(s) 212
Bse3DI GCAATG 2 cut(s) 1041, 1706
BseDI CCNNGG 3 cut(s) 422, 627, 741
BseGI GGATG 6 cut(s) 583, 1191, 1220, 1420, 1696, 1704
BseMI GCAATG 2 cut(s) 1041, 1706
BseMII CTCAG 4 cut(s) 226, 385, 447, 1575
BseNI ACTGG 3 cut(s) 996, 1292, 1327
BseRI GAGGAG 4 cut(s) 175, 195, 198, 1022
BseSI GKGCMC 1 cut(s) 301
BseYI CCCAGC 1 cut(s) 124
BsgI GTGCAG 2 cut(s) 1226, 1257
Bsh1236I CGCG 1 cut(s) 325
BshFI GGCC 5 cut(s) 167, 194, 785, 1224, 1388
BsiSI CCGG 1 cut(s) 295
BsmAI GTCTC 1 cut(s) 1646
BsnI GGCC 5 cut(s) 167, 194, 785, 1224, 1388
Bsp119I TTCGAA 2 cut(s) 1309, 1777
Bsp1286I GDGCHC 1 cut(s) 301
Bsp19I CCATGG 1 cut(s) 627
BspACI CCGC 5 cut(s) 39, 168, 171, 323, 531
BspANI GGCC 5 cut(s) 167, 194, 785, 1224, 1388
BspCNI CTCAG 4 cut(s) 225, 384, 448, 1574
BspFNI CGCG 1 cut(s) 325
BspLI GGNNCC 2 cut(s) 119, 218
BspMAI CTGCAG 4 cut(s) 729, 970, 1005, 1060
BspMI ACCTGC 1 cut(s) 1651
BspPI GGATC 6 cut(s) 275, 440, 478, 887, 1186, 1559
BspT104I TTCGAA 2 cut(s) 1309, 1777
BsrDI GCAATG 2 cut(s) 1041, 1706
BsrI ACTGG 3 cut(s) 996, 1292, 1327
BssECI CCNNGG 3 cut(s) 422, 627, 741
BssT1I CCWWGG 2 cut(s) 627, 741
Bst4CI ACNGT 5 cut(s) 208, 257, 352, 423, 1103
Bst6I CTCTTC 3 cut(s) 152, 498, 501
BstAPI GCANNNNNTGC 1 cut(s) 527
BstBI TTCGAA 2 cut(s) 1309, 1777
BstC8I GCNNGC 1 cut(s) 1031
BstDEI CTNAG 5 cut(s) 212, 371, 385, 456, 1561
BstDSI CCRYGG 2 cut(s) 422, 627
BstF5I GGATG 6 cut(s) 583, 1191, 1220, 1420, 1696, 1704
BstFNI CGCG 1 cut(s) 325
BstHHI GCGC 1 cut(s) 204
BstMAI GTCTC 1 cut(s) 1646
BstSCI CCNGG 1 cut(s) 294
BstSFI CTRYAG 6 cut(s) 348, 483, 725, 966, 1001, 1056
BstSLI GKGCMC 1 cut(s) 301
BstUI CGCG 1 cut(s) 325
BstV2I GAAGAC 4 cut(s) 660, 1085, 1423, 1709
BstX2I RGATCY 7 cut(s) 280, 911, 1178, 1198, 1505, 1564, 1588
BstXI CCANNNNNNTGG 2 cut(s) 113, 1523
BstYI RGATCY 7 cut(s) 280, 911, 1178, 1198, 1505, 1564, 1588
Bsu36I CCTNAGG 1 cut(s) 212
BsuRI GGCC 5 cut(s) 167, 194, 785, 1224, 1388
BtgI CCRYGG 2 cut(s) 422, 627
BtsCI GGATG 6 cut(s) 583, 1191, 1220, 1420, 1696, 1704
BtsIMutI CAGTG 4 cut(s) 262, 357, 453, 1285
BveI ACCTGC 1 cut(s) 1651
Cac8I GCNNGC 1 cut(s) 1031
CaiI CAGNNNCTG 1 cut(s) 527
CfoI GCGC 1 cut(s) 204
Cfr13I GGNCC 4 cut(s) 118, 165, 216, 1513
CseI GACGC 2 cut(s) 1259, 1580
Csp6I GTAC 2 cut(s) 872, 1631
CspCI CAANNNNNGTGG 2 cut(s) 561, 596
CviAII CATG 4 cut(s) 190, 628, 1357, 1767
CviQI GTAC 2 cut(s) 872, 1631
DdeI CTNAG 5 cut(s) 212, 371, 385, 456, 1561
DraI TTTAAA 2 cut(s) 1410, 1543
DraIII CACNNNGTG 1 cut(s) 1360
EaeI YGGCCR 1 cut(s) 192
Eam1104I CTCTTC 3 cut(s) 152, 498, 501
EarI CTCTTC 3 cut(s) 152, 498, 501
Eco130I CCWWGG 2 cut(s) 627, 741
Eco147I AGGCCT 1 cut(s) 1224
Eco47I GGWCC 3 cut(s) 118, 216, 1513
Eco57I CTGAAG 4 cut(s) 555, 584, 852, 1805
Eco81I CCTNAGG 1 cut(s) 212
EcoO109I RGGNCCY 1 cut(s) 216
EcoRI GAATTC 1 cut(s) 972
EcoT14I CCWWGG 2 cut(s) 627, 741
ErhI CCWWGG 2 cut(s) 627, 741
FaeI CATG 4 cut(s) 193, 631, 1360, 1770
FatI CATG 4 cut(s) 189, 627, 1356, 1766
FbaI TGATCA 2 cut(s) 1072, 1128
FblI GTMKAC 1 cut(s) 418
FokI GGATG 6 cut(s) 590, 1198, 1227, 1407, 1703, 1711
FspBI CTAG 5 cut(s) 276, 852, 1503, 1634, 1650
GlaI GCGC 1 cut(s) 203
GsaI CCCAGC 1 cut(s) 128
HaeIII GGCC 5 cut(s) 167, 194, 785, 1224, 1388
HapII CCGG 1 cut(s) 295
HgaI GACGC 2 cut(s) 1259, 1580
HhaI GCGC 1 cut(s) 204
Hin1II CATG 4 cut(s) 193, 631, 1360, 1770
Hin6I GCGC 1 cut(s) 202
HinP1I GCGC 1 cut(s) 202
HinfI GANTC 8 cut(s) 51, 186, 401, 683, 763, 1189, 1489, 1763
HpaII CCGG 1 cut(s) 295
HphI GGTGA 1 cut(s) 88
Hpy166II GTNNAC 4 cut(s) 121, 419, 426, 1099
Hpy188III TCNNGA 7 cut(s) 214, 977, 1132, 1196, 1332, 1511, 1568
Hpy8I GTNNAC 4 cut(s) 121, 419, 426, 1099
Hpy99I CGWCG 5 cut(s) 31, 34, 37, 1372, 1574
HpyAV CCTTC 8 cut(s) 69, 86, 390, 559, 775, 1557, 1621, 1689
HpyCH4III ACNGT 5 cut(s) 208, 257, 352, 423, 1103
HpyCH4IV ACGT 1 cut(s) 1370
HpyF3I CTNAG 5 cut(s) 212, 371, 385, 456, 1561
HpySE526I ACGT 1 cut(s) 1370
Hsp92II CATG 4 cut(s) 193, 631, 1360, 1770
HspAI GCGC 1 cut(s) 202
Ksp22I TGATCA 2 cut(s) 1072, 1128
LmnI GCTCC 6 cut(s) 620, 632, 697, 730, 1009, 1723
MaeI CTAG 5 cut(s) 276, 852, 1503, 1634, 1650
MaeII ACGT 1 cut(s) 1370
MaeIII GTNAC 3 cut(s) 131, 541, 902
MfeI CAATTG 3 cut(s) 441, 1158, 1397
MflI RGATCY 7 cut(s) 280, 911, 1178, 1198, 1505, 1564, 1588
MhlI GDGCHC 1 cut(s) 301
MlsI TGGCCA 1 cut(s) 194
MluNI TGGCCA 1 cut(s) 194
MlyI GAGTC 5 cut(s) 195, 692, 772, 1483, 1772
MmeI TCCRAC 4 cut(s) 28, 157, 666, 1347
Mox20I TGGCCA 1 cut(s) 194
MroXI GAANNNNTTC 1 cut(s) 492
MscI TGGCCA 1 cut(s) 194
MseI TTAA 8 cut(s) 249, 393, 1266, 1296, 1380, 1409, 1530, 1542
MslI CAYNNNNRTG 2 cut(s) 1288, 1425
Msp20I TGGCCA 1 cut(s) 194
MspA1I CMGCKG 2 cut(s) 524, 533
MspI CCGG 1 cut(s) 295
MspR9I CCNGG 1 cut(s) 296
MunI CAATTG 3 cut(s) 441, 1158, 1397
MvnI CGCG 1 cut(s) 325
NciI CCSGG 1 cut(s) 296
NcoI CCATGG 1 cut(s) 627
NlaIII CATG 4 cut(s) 193, 631, 1360, 1770
NlaIV GGNNCC 2 cut(s) 119, 218
NmeAIII GCCGAG 1 cut(s) 910
NmuCI GTSAC 1 cut(s) 131
NspV TTCGAA 2 cut(s) 1309, 1777
OliI CACNNNNGTG 1 cut(s) 1288
PceI AGGCCT 1 cut(s) 1224
PcsI WCGNNNNNNNCGW 2 cut(s) 32, 758
PdmI GAANNNNTTC 1 cut(s) 492
PfeI GAWTC 3 cut(s) 51, 401, 1189
PleI GAGTC 5 cut(s) 194, 691, 771, 1483, 1771
PpsI GAGTC 5 cut(s) 194, 691, 771, 1483, 1771
PpuMI RGGWCCY 1 cut(s) 216
Psp5II RGGWCCY 1 cut(s) 216
PspFI CCCAGC 1 cut(s) 124
PspN4I GGNNCC 2 cut(s) 119, 218
PspPI GGNCC 4 cut(s) 118, 165, 216, 1513
PspPPI RGGWCCY 1 cut(s) 216
PstI CTGCAG 4 cut(s) 729, 970, 1005, 1060
PstNI CAGNNNCTG 1 cut(s) 527
PsuI RGATCY 7 cut(s) 280, 911, 1178, 1198, 1505, 1564, 1588
PvuII CAGCTG 1 cut(s) 524
RsaI GTAC 2 cut(s) 873, 1632
RsaNI GTAC 2 cut(s) 872, 1631
RseI CAYNNNNRTG 2 cut(s) 1288, 1425
SaqAI TTAA 8 cut(s) 249, 393, 1266, 1296, 1380, 1409, 1530, 1542
Sau96I GGNCC 4 cut(s) 118, 165, 216, 1513
SchI GAGTC 5 cut(s) 195, 692, 772, 1483, 1772
ScrFI CCNGG 1 cut(s) 296
SduI GDGCHC 1 cut(s) 301
SfcI CTRYAG 6 cut(s) 348, 483, 725, 966, 1001, 1056
SfuI TTCGAA 2 cut(s) 1309, 1777
SinI GGWCC 3 cut(s) 118, 216, 1513
SmiMI CAYNNNNRTG 2 cut(s) 1288, 1425
SmlI CTYRAG 1 cut(s) 907
SmoI CTYRAG 1 cut(s) 907
SseBI AGGCCT 1 cut(s) 1224
SsiI CCGC 5 cut(s) 39, 168, 171, 323, 531
SspMI CTAG 5 cut(s) 276, 852, 1503, 1634, 1650
StuI AGGCCT 1 cut(s) 1224
StyD4I CCNGG 1 cut(s) 294
StyI CCWWGG 2 cut(s) 627, 741
TaaI ACNGT 5 cut(s) 208, 257, 352, 423, 1103
TaiI ACGT 1 cut(s) 1373
TaqI TCGA 4 cut(s) 761, 1219, 1309, 1777
TatI WGTACW 1 cut(s) 871
TauI GCSGC 3 cut(s) 170, 173, 533
TfiI GAWTC 3 cut(s) 51, 401, 1189
Tru1I TTAA 8 cut(s) 249, 393, 1266, 1296, 1380, 1409, 1530, 1542
Tru9I TTAA 8 cut(s) 249, 393, 1266, 1296, 1380, 1409, 1530, 1542
TscAI CASTG 4 cut(s) 262, 357, 460, 1292
TseFI GTSAC 1 cut(s) 131
Tsp45I GTSAC 1 cut(s) 131
TspRI CASTG 4 cut(s) 262, 357, 460, 1292
VpaK11BI GGWCC 3 cut(s) 118, 216, 1513
XapI RAATTY 6 cut(s) 389, 463, 713, 972, 1244, 1537
XmiI GTMKAC 1 cut(s) 418
XmnI GAANNNNTTC 1 cut(s) 492
XspI CTAG 5 cut(s) 276, 852, 1503, 1634, 1650
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.