AT3G09540

Pectate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
3
OG0009024
Physical Location & Seq
Reverse (-)
2928752 .. 2931362
2611 bp
Loading structure...
UTR
Exon/CDS
Intron
AT3G09540.1

Sequence Viewer

Length: 1137 bp
ATGGGAAACTTACATGGCATTCACAGATCCCATCACGGCGGTTCTAATTTTCCCGGCGAAGCTCCCAATTCACCTTTCCCACCACCATATACAGCCGCTCCAGCTCCAGCTCCAGCTCCGTCATCGCCATCCGATCACCACATGACAGTGGGACCTTATTGCCACGTAGACTCCAGCCTCCGCTCTCTCGCCGGAAAGGCCGAAGGTTTCGGCCGCGCCGCCGTTGGTGGTCTAAATGGTCCGATTTGCCACGTCACTTCTTTAGCTGACGAGGGTCCAGGATCGTTGCGAGAGGCTTGCAAGAGGCCAGAACCTTTATGGATCGTGTTCGATGTATCGGGAACGATCAATCTGTCTTCGTTTGTCAACGTATCATCGCACACAACGGTGGACGGGAGAGGACAAAAAGTGAAGATAACGGGAAAAGGGTTAAGGCTAAAAGAGTGTGAAAACGTTATAATCTGCAATCTTGAATTTGAAGGCGGTGTGGGACCAGACGCAGACGCTATTCAGATCAAACCAAAATCGCACAATATTTGGATTGATCGGTGTAGTCTCAAGAATTACTATGATGGTTTGATTGATATCACACGAGAAAGCACTGACATCACTGTCTCAAGATGCCATTTCATGAACCACAACAAAACTATGTTAATAGGAGCGGACACAAGTCACGTTACGGACCGATGCATAAGAGTTACGATACATCACTGCTTCTTCGACGGTACACGTCAGCGACACCCTCGCGTTCGCTTCGCAAAAGTCCATCTCTTCAACAACTACACTCGTCATTGGGCCATTTACGCTGTTGGTGCTGGTGTCGAATCTCAGATACATTCTCAGTGCAACATATATGAAGCTGGTGAAAAGAAAACTGTCTTTAAGTACATCACTGAGAAGGCCGCTGATAAAGAGAAACCCGGAGCTGGATTCGTAAGATCAGAAGGGGATTTGTTGTTGAACGGAGCCAAATCGTGTCTTAGTCAGGGCGGAGAGCGCTATGTGTTCTCTCCAATCCAACACTATTCTGAATGGACCGTCGAATCTCCAACCGATATACTCAAGAACTATCTGAAACACTCGACCGGCTGGCAGAACCTTCCCCTCCCACTAGACCGGCCTCCGACCACCGCATAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00040 ko02024 map00040 map02024
Pfam Domains
Protein Families
Pec_lyase_C

Protein Analysis

378

Amino Acids

41.47

Weight (kDa)

8.24

Isoelectric Point (pI)

42.26

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pectate_lyase_4 PF00544 121 - 302 2e-28 Pectate lyase
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 458
AasI GACNNNNNNGTC 1 cut(s) 611
AccBSI CCGCTC 3 cut(s) 98, 183, 662
AccI GTMKAC 1 cut(s) 168
AccII CGCG 2 cut(s) 216, 747
AclI AACGTT 1 cut(s) 453
AclWI GGATC 3 cut(s) 21, 289, 329
AcoI YGGCCR 1 cut(s) 211
AcsI RAATTY 1 cut(s) 473
AfaI GTAC 2 cut(s) 727, 887
AfeI AGCGCT 1 cut(s) 998
AfiI CCNNNNNNNGG 1 cut(s) 926
AflIII ACRYGT 1 cut(s) 728
AgsI TTSAA 4 cut(s) 473, 479, 775, 961
AjiI CACGTC 2 cut(s) 253, 731
AjnI CCWGG 1 cut(s) 277
AjuI GAANNNNNNNTTGG 2 cut(s) 59, 91
AleI CACNNNNGTG 1 cut(s) 386
AluBI AGCT 7 cut(s) 62, 104, 110, 116, 266, 860, 926
AluI AGCT 7 cut(s) 62, 104, 110, 116, 266, 860, 926
Alw26I GTCTC 2 cut(s) 560, 619
AlwI GGATC 3 cut(s) 21, 289, 329
Aor51HI AGCGCT 1 cut(s) 998
AoxI GGCC 6 cut(s) 198, 211, 305, 795, 900, 1118
ApoI RAATTY 1 cut(s) 473
AspLEI GCGC 2 cut(s) 218, 999
AspS9I GGNCC 7 cut(s) 152, 239, 275, 491, 682, 795, 1035
AsuC2I CCSGG 2 cut(s) 54, 921
AsuHPI GGTGA 3 cut(s) 63, 128, 875
AvaII GGWCC 6 cut(s) 152, 239, 275, 491, 682, 1035
BauI CACGAG 1 cut(s) 591
BbsI GAAGAC 1 cut(s) 348
BccI CCATC 4 cut(s) 39, 136, 566, 774
BceAI ACGGC 2 cut(s) 52, 206
BcgI CGANNNNNNTGC 2 cut(s) 279, 313
BciT130I CCWGG 1 cut(s) 279
BcnI CCSGG 2 cut(s) 54, 921
BcoDI GTCTC 2 cut(s) 560, 619
BfaI CTAG 1 cut(s) 1112
BfoI RGCGCY 1 cut(s) 1000
BglI GCCNNNNNGGC 1 cut(s) 197
BisI GCNGC 4 cut(s) 96, 214, 219, 903
BlsI GCNGC 4 cut(s) 97, 215, 220, 904
Bme1390I CCNGG 3 cut(s) 54, 279, 921
Bme18I GGWCC 6 cut(s) 152, 239, 275, 491, 682, 1035
BmgBI CACGTC 2 cut(s) 253, 731
BmgT120I GGNCC 7 cut(s) 152, 239, 275, 491, 682, 795, 1035
BmiI GGNNCC 4 cut(s) 153, 276, 492, 967
BmrFI CCNGG 3 cut(s) 54, 279, 921
BmsI GCATC 2 cut(s) 611, 677
BoxI GACNNNNGTC 2 cut(s) 273, 669
BpiI GAAGAC 1 cut(s) 348
BpmI CTGGAG 4 cut(s) 84, 90, 96, 157
BpuEI CTTGAG 3 cut(s) 542, 601, 1046
BpuMI CCSGG 2 cut(s) 54, 921
BsaAI YACGTR 1 cut(s) 166
BsaBI GATNNNNATC 1 cut(s) 584
BsaXI ACNNNNNCTCC 4 cut(s) 82, 112, 155, 185
Bsc4I CCNNNNNNNGG 1 cut(s) 926
Bse118I RCCGGY 2 cut(s) 1085, 1116
Bse8I GATNNNNATC 1 cut(s) 584
BseBI CCWGG 1 cut(s) 279
BseGI GGATG 1 cut(s) 128
BseJI GATNNNNATC 1 cut(s) 584
BseLI CCNNNNNNNGG 1 cut(s) 926
BseMII CTCAG 3 cut(s) 842, 854, 885
BseX3I CGGCCG 1 cut(s) 211
Bsh1236I CGCG 2 cut(s) 216, 747
Bsh1285I CGRYCG 2 cut(s) 214, 1086
BshFI GGCC 6 cut(s) 200, 213, 307, 797, 902, 1120
BsiEI CGRYCG 2 cut(s) 214, 1086
BsiSI CCGG 5 cut(s) 54, 192, 921, 1086, 1117
BslFI GGGAC 2 cut(s) 165, 504
BslI CCNNNNNNNGG 1 cut(s) 926
BsmAI GTCTC 2 cut(s) 560, 619
BsmFI GGGAC 2 cut(s) 165, 504
BsmI GAATGC 1 cut(s) 18
BsnI GGCC 6 cut(s) 200, 213, 307, 797, 902, 1120
Bsp143I GATC 8 cut(s) 26, 133, 281, 321, 345, 513, 544, 938
BspANI GGCC 6 cut(s) 200, 213, 307, 797, 902, 1120
BspCNI CTCAG 3 cut(s) 841, 853, 886
BspFNI CGCG 2 cut(s) 216, 747
BspHI TCATGA 1 cut(s) 630
BspLI GGNNCC 4 cut(s) 153, 276, 492, 967
BspPI GGATC 3 cut(s) 21, 289, 329
BsrBI CCGCTC 3 cut(s) 98, 183, 662
BsrFI RCCGGY 2 cut(s) 1085, 1116
BssAI RCCGGY 2 cut(s) 1085, 1116
BssMI GATC 8 cut(s) 26, 133, 281, 321, 345, 513, 544, 938
BssSI CACGAG 1 cut(s) 591
Bst2BI CACGAG 1 cut(s) 591
Bst2UI CCWGG 1 cut(s) 279
Bst4CI ACNGT 6 cut(s) 148, 388, 613, 725, 877, 1039
Bst6I CTCTTC 1 cut(s) 776
BstBAI YACGTR 1 cut(s) 166
BstC8I GCNNGC 2 cut(s) 298, 1091
BstDEI CTNAG 4 cut(s) 828, 840, 894, 980
BstF5I GGATG 1 cut(s) 128
BstFNI CGCG 2 cut(s) 216, 747
BstH2I RGCGCY 1 cut(s) 1000
BstHHI GCGC 2 cut(s) 218, 999
BstKTI GATC 8 cut(s) 29, 136, 284, 324, 348, 516, 547, 941
BstMAI GTCTC 2 cut(s) 560, 619
BstMBI GATC 8 cut(s) 26, 133, 281, 321, 345, 513, 544, 938
BstMCI CGRYCG 2 cut(s) 214, 1086
BstMWI GCNNNNNNNGC 5 cut(s) 101, 197, 803, 812, 996
BstNI CCWGG 1 cut(s) 279
BstPAI GACNNNNGTC 2 cut(s) 273, 669
BstSCI CCNGG 3 cut(s) 52, 277, 919
BstUI CGCG 2 cut(s) 216, 747
BstV2I GAAGAC 1 cut(s) 348
BstX2I RGATCY 1 cut(s) 26
BstYI RGATCY 1 cut(s) 26
BstZI CGGCCG 1 cut(s) 211
BsuRI GGCC 6 cut(s) 200, 213, 307, 797, 902, 1120
BtgZI GCGATG 2 cut(s) 108, 360
BtrI CACGTC 2 cut(s) 253, 731
BtsCI GGATG 1 cut(s) 128
BtsI GCAGTG 1 cut(s) 709
BtsIMutI CAGTG 6 cut(s) 153, 600, 609, 709, 848, 891
Cac8I GCNNGC 2 cut(s) 298, 1091
CciI TCATGA 1 cut(s) 630
CfoI GCGC 2 cut(s) 218, 999
Cfr10I RCCGGY 2 cut(s) 1085, 1116
Cfr13I GGNCC 7 cut(s) 152, 239, 275, 491, 682, 795, 1035
CpoI CGGWCCG 1 cut(s) 682
CseI GACGC 2 cut(s) 506, 512
Csp6I GTAC 2 cut(s) 726, 886
CspI CGGWCCG 1 cut(s) 682
CviAII CATG 3 cut(s) 14, 142, 631
CviQI GTAC 2 cut(s) 726, 886
DdeI CTNAG 4 cut(s) 828, 840, 894, 980
DpnI GATC 8 cut(s) 28, 135, 283, 323, 347, 515, 546, 940
DpnII GATC 8 cut(s) 26, 133, 281, 321, 345, 513, 544, 938
DrdI GACNNNNNNGTC 1 cut(s) 611
DseDI GACNNNNNNGTC 1 cut(s) 611
EaeI YGGCCR 1 cut(s) 211
EagI CGGCCG 1 cut(s) 211
Eam1104I CTCTTC 1 cut(s) 776
EarI CTCTTC 1 cut(s) 776
EciI GGCGGA 1 cut(s) 1005
EclXI CGGCCG 1 cut(s) 211
Eco32I GATATC 1 cut(s) 586
Eco47I GGWCC 6 cut(s) 152, 239, 275, 491, 682, 1035
Eco47III AGCGCT 1 cut(s) 998
Eco52I CGGCCG 1 cut(s) 211
EcoO109I RGGNCCY 1 cut(s) 152
EcoRII CCWGG 1 cut(s) 277
EcoRV GATATC 1 cut(s) 586
EcoT22I ATGCAT 1 cut(s) 692
FaeI CATG 3 cut(s) 17, 145, 634
FaqI GGGAC 2 cut(s) 165, 504
FatI CATG 3 cut(s) 13, 141, 630
FblI GTMKAC 1 cut(s) 168
Fnu4HI GCNGC 4 cut(s) 96, 214, 219, 903
FokI GGATG 1 cut(s) 115
Fsp4HI GCNGC 4 cut(s) 96, 214, 219, 903
FspBI CTAG 1 cut(s) 1112
GlaI GCGC 2 cut(s) 217, 998
GluI GCNGC 4 cut(s) 96, 214, 219, 903
GsuI CTGGAG 4 cut(s) 84, 90, 96, 157
HaeII RGCGCY 1 cut(s) 1000
HaeIII GGCC 6 cut(s) 200, 213, 307, 797, 902, 1120
HapII CCGG 5 cut(s) 54, 192, 921, 1086, 1117
HgaI GACGC 2 cut(s) 506, 512
HhaI GCGC 2 cut(s) 218, 999
Hin1II CATG 3 cut(s) 17, 145, 634
Hin6I GCGC 2 cut(s) 216, 997
HinP1I GCGC 2 cut(s) 216, 997
HincII GTYRAC 1 cut(s) 367
HindII GTYRAC 1 cut(s) 367
HinfI GANTC 4 cut(s) 170, 824, 930, 1043
HpaII CCGG 5 cut(s) 54, 192, 921, 1086, 1117
HphI GGTGA 3 cut(s) 63, 128, 875
Hpy166II GTNNAC 4 cut(s) 169, 367, 391, 728
Hpy188I TCNGA 8 cut(s) 133, 243, 513, 831, 943, 1030, 1074, 1125
Hpy188III TCNNGA 6 cut(s) 339, 470, 559, 618, 631, 1063
Hpy8I GTNNAC 4 cut(s) 169, 367, 391, 728
Hpy99I CGWCG 2 cut(s) 725, 1043
HpyAV CCTTC 5 cut(s) 197, 473, 892, 938, 1109
HpyCH4III ACNGT 6 cut(s) 148, 388, 613, 725, 877, 1039
HpyCH4IV ACGT 6 cut(s) 165, 252, 369, 453, 675, 730
HpyCH4V TGCA 4 cut(s) 300, 465, 690, 846
HpyF10VI GCNNNNNNNGC 5 cut(s) 101, 197, 803, 812, 996
HpyF3I CTNAG 4 cut(s) 828, 840, 894, 980
HpySE526I ACGT 6 cut(s) 165, 252, 369, 453, 675, 730
Hsp92II CATG 3 cut(s) 17, 145, 634
HspAI GCGC 2 cut(s) 216, 997
Kzo9I GATC 8 cut(s) 26, 133, 281, 321, 345, 513, 544, 938
LmnI GCTCC 8 cut(s) 67, 103, 109, 115, 121, 659, 923, 965
LweI GCATC 2 cut(s) 611, 677
MaeI CTAG 1 cut(s) 1112
MaeII ACGT 6 cut(s) 165, 252, 369, 453, 675, 730
MaeIII GTNAC 4 cut(s) 253, 671, 676, 697
MalI GATC 8 cut(s) 28, 135, 283, 323, 347, 515, 546, 940
MbiI CCGCTC 3 cut(s) 98, 183, 662
MboI GATC 8 cut(s) 26, 133, 281, 321, 345, 513, 544, 938
MboII GAAGA 4 cut(s) 348, 424, 709, 763
MflI RGATCY 1 cut(s) 26
MluCI AATT 4 cut(s) 46, 67, 473, 562
MlyI GAGTC 1 cut(s) 164
MmeI TCCRAC 2 cut(s) 1042, 1073
MnlI CCTC 8 cut(s) 188, 265, 286, 297, 392, 753, 1115, 1131
Mph1103I ATGCAT 1 cut(s) 692
MseI TTAA 3 cut(s) 431, 653, 882
MslI CAYNNNNRTG 2 cut(s) 146, 386
MspA1I CMGCKG 1 cut(s) 905
MspI CCGG 5 cut(s) 54, 192, 921, 1086, 1117
MspR9I CCNGG 3 cut(s) 54, 279, 921
Mva1269I GAATGC 1 cut(s) 18
MvaI CCWGG 1 cut(s) 279
MvnI CGCG 2 cut(s) 216, 747
MwoI GCNNNNNNNGC 5 cut(s) 101, 197, 803, 812, 996
NciI CCSGG 2 cut(s) 54, 921
NdeII GATC 8 cut(s) 26, 133, 281, 321, 345, 513, 544, 938
NlaIII CATG 3 cut(s) 17, 145, 634
NlaIV GGNNCC 4 cut(s) 153, 276, 492, 967
NmuCI GTSAC 2 cut(s) 253, 671
NsiI ATGCAT 1 cut(s) 692
OliI CACNNNNGTG 1 cut(s) 386
PagI TCATGA 1 cut(s) 630
PctI GAATGC 1 cut(s) 18
PfeI GAWTC 3 cut(s) 824, 930, 1043
PfoI TCCNGGA 1 cut(s) 277
PkrI GCNGC 4 cut(s) 97, 215, 220, 904
PleI GAGTC 1 cut(s) 164
PpsI GAGTC 1 cut(s) 164
Ppu21I YACGTR 1 cut(s) 166
PpuMI RGGWCCY 1 cut(s) 152
PshAI GACNNNNGTC 2 cut(s) 273, 669
PsiI TTATAA 1 cut(s) 458
Psp1406I AACGTT 1 cut(s) 453
Psp5II RGGWCCY 1 cut(s) 152
Psp6I CCWGG 1 cut(s) 277
PspGI CCWGG 1 cut(s) 277
PspN4I GGNNCC 4 cut(s) 153, 276, 492, 967
PspPI GGNCC 7 cut(s) 152, 239, 275, 491, 682, 795, 1035
PspPPI RGGWCCY 1 cut(s) 152
PsuI RGATCY 1 cut(s) 26
RsaI GTAC 2 cut(s) 727, 887
RsaNI GTAC 2 cut(s) 726, 886
RseI CAYNNNNRTG 2 cut(s) 146, 386
Rsr2I CGGWCCG 1 cut(s) 682
RsrII CGGWCCG 1 cut(s) 682
SaqAI TTAA 3 cut(s) 431, 653, 882
SatI GCNGC 4 cut(s) 96, 214, 219, 903
Sau3AI GATC 8 cut(s) 26, 133, 281, 321, 345, 513, 544, 938
Sau96I GGNCC 7 cut(s) 152, 239, 275, 491, 682, 795, 1035
SchI GAGTC 1 cut(s) 164
ScrFI CCNGG 3 cut(s) 54, 279, 921
SfaNI GCATC 2 cut(s) 611, 677
SinI GGWCC 6 cut(s) 152, 239, 275, 491, 682, 1035
SmiMI CAYNNNNRTG 2 cut(s) 146, 386
SmlI CTYRAG 3 cut(s) 557, 616, 1061
SmoI CTYRAG 3 cut(s) 557, 616, 1061
Sse9I AATT 4 cut(s) 46, 67, 473, 562
SspI AATATT 1 cut(s) 535
SspMI CTAG 1 cut(s) 1112
StyD4I CCNGG 3 cut(s) 52, 277, 919
TaaI ACNGT 6 cut(s) 148, 388, 613, 725, 877, 1039
TaiI ACGT 6 cut(s) 168, 255, 372, 456, 678, 733
TaqI TCGA 5 cut(s) 330, 720, 822, 1041, 1082
TaqII GACCGA 1 cut(s) 699
TasI AATT 4 cut(s) 46, 67, 473, 562
TatI WGTACW 1 cut(s) 885
TauI GCSGC 4 cut(s) 98, 216, 221, 905
TfiI GAWTC 3 cut(s) 824, 930, 1043
Tru1I TTAA 3 cut(s) 431, 653, 882
Tru9I TTAA 3 cut(s) 431, 653, 882
TscAI CASTG 6 cut(s) 153, 607, 616, 716, 848, 898
TseFI GTSAC 2 cut(s) 253, 671
Tsp45I GTSAC 2 cut(s) 253, 671
TspDTI ATGAA 3 cut(s) 619, 647, 870
TspGWI ACGGA 3 cut(s) 108, 695, 978
TspRI CASTG 6 cut(s) 153, 607, 616, 716, 848, 898
VpaK11BI GGWCC 6 cut(s) 152, 239, 275, 491, 682, 1035
XapI RAATTY 1 cut(s) 473
XcmI CCANNNNNNNNNTGG 1 cut(s) 315
XmiI GTMKAC 1 cut(s) 168
XspI CTAG 1 cut(s) 1112
Zsp2I ATGCAT 1 cut(s) 692
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.