AT3G55140

Pectate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
3
OG0008283
Physical Location & Seq
Forward (+)
20438627 .. 20440452
1826 bp
Loading structure...
UTR
Exon/CDS
Intron
AT3G55140.2

Sequence Viewer

Length: 996 bp
ATGACGTCGCTACCGTACGCCGATGCCGATTGTAGCCTCAGGGCTTTAGCTGGCCGTGCAGAGGGATTCGGACGCTTCGCCGTCGGTGGTCTCCACGGCGATCTCTATGTCGTCACTTCTCTTGCAGATGATGGACCTGGGACTCTTCGTGAAGGAGGTAGGAGGAAAGAGCCGTTATGGATTGTTTTTGCAGTTTCTGGAACTATAAATCTCAATTCATACTTGAGTGTATCGTCTTACAAGACGATTGATGGACGAGGACAACGAATTAAGCTCACAGGGAAAGGAATAAGATTGAAGGAATGTGAACATATCATCATTTGCAATTTGGAGTTTGAAGGTGGTAGAGGTCATGATGTTGATGGTATTCAGATTAAACCAAAGTCTAGACACATTTGGATTGATCGGTGTAGTCTCCGCGATTACGATGATGGGCTTATTGATATTACTAGACAAAGCACGGATATTACTGTTTCTAGATGTTATTTTGCACAGCATGACAAGACGATGCTGATTGGAGCAGATCCTTCTCATGTTGAGGATAGATGTATCCGAGTGACCATTCACCATTGTTTCTTTGATGGAACTAGGCAGAGACAACCTCGTCTCAGATTTGGAAAAGTTCATTTGTACAACAACTACACAAGAAACTGGGGAATATATGCTGTTTGTGCTAGTGTAGAAGCGCAGGTGTTCTCTCAATGCAATATATACGAAGCAGGAGTGAAGAAGAAAACTTTTGAATACTACTCAGAAAAGGCTGCTGACAAGGAAGAAGCGAGAACTGGGTTAGTACGATCTGAAAATGACTTGTTCTTGAATGGAGCTCAACCTTCCTTGATGACAGGAGCCAGTGAAGAATGTGTATTCCATCCAAGTGAACACTACCCAACATGGACTGTGGAGCCACCATCAGAAACTCTCAAGCAAATCATGCAAATTTGTACCGGTTGGCAATCTTTGTCCCGTCCTTCTGATCATGGAGTTCCTAAGTAA
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

331

Amino Acids

37.19

Weight (kDa)

7.16

Isoelectric Point (pI)

37.37

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pectate_lyase_4 PF00544 51 - 221 3.7e-28 Pectate lyase
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)
AarI CACCTGC 1 cut(s) 679
AasI GACNNNNNNGTC 1 cut(s) 603
AatII GACGTC 1 cut(s) 8
Acc36I ACCTGC 1 cut(s) 679
AccII CGCG 1 cut(s) 420
AciI CCGC 1 cut(s) 418
AclWI GGATC 1 cut(s) 518
AcoI YGGCCR 1 cut(s) 52
AcsI RAATTY 1 cut(s) 939
AcyI GRCGYC 1 cut(s) 5
AfaI GTAC 4 cut(s) 17, 632, 795, 946
AfiI CCNNNNNNNGG 1 cut(s) 61
AgeI ACCGGT 1 cut(s) 947
AgsI TTSAA 4 cut(s) 298, 338, 743, 820
AjnI CCWGG 1 cut(s) 136
AluBI AGCT 3 cut(s) 50, 274, 827
AluI AGCT 3 cut(s) 50, 274, 827
Alw21I GWGCWC 1 cut(s) 829
Alw26I GTCTC 4 cut(s) 95, 419, 589, 611
AlwI GGATC 1 cut(s) 518
AlwNI CAGNNNCTG 1 cut(s) 197
AoxI GGCC 1 cut(s) 52
ApeKI GCWGC 1 cut(s) 761
ApoI RAATTY 1 cut(s) 939
AsiGI ACCGGT 1 cut(s) 947
AspLEI GCGC 1 cut(s) 688
AspS9I GGNCC 1 cut(s) 134
AsuHPI GGTGA 1 cut(s) 557
AvaII GGWCC 1 cut(s) 134
AxyI CCTNAGG 1 cut(s) 38
BanII GRGCYC 1 cut(s) 829
Bbv12I GWGCWC 1 cut(s) 829
BbvI GCAGC 1 cut(s) 748
BccI CCATC 7 cut(s) 125, 245, 356, 425, 575, 879, 919
BceAI ACGGC 4 cut(s) 39, 65, 112, 157
BciT130I CCWGG 1 cut(s) 138
BciVI GTATCC 1 cut(s) 560
BclI TGATCA 1 cut(s) 976
BcoDI GTCTC 4 cut(s) 95, 419, 589, 611
BfaI CTAG 5 cut(s) 387, 450, 477, 588, 675
BfuAI ACCTGC 1 cut(s) 679
BfuI GTATCC 1 cut(s) 560
BisI GCNGC 1 cut(s) 762
BlsI GCNGC 1 cut(s) 763
Bme1390I CCNGG 1 cut(s) 138
Bme18I GGWCC 1 cut(s) 134
BmgT120I GGNCC 1 cut(s) 134
BmiI GGNNCC 2 cut(s) 850, 906
BmrFI CCNGG 1 cut(s) 138
BmrI ACTGGG 2 cut(s) 661, 795
BmsI GCATC 2 cut(s) 13, 498
BmuI ACTGGG 2 cut(s) 661, 795
BplI GAGNNNNNCTC 2 cut(s) 586, 618
BpuEI CTTGAG 2 cut(s) 244, 908
BsaHI GRCGYC 1 cut(s) 5
BsaI GGTCTC 1 cut(s) 95
BsaJI CCNNGG 2 cut(s) 94, 137
BsaWI WCCGGW 1 cut(s) 947
Bsc4I CCNNNNNNNGG 1 cut(s) 61
Bse118I RCCGGY 1 cut(s) 947
Bse1I ACTGG 3 cut(s) 656, 790, 852
Bse21I CCTNAGG 1 cut(s) 38
BseBI CCWGG 1 cut(s) 138
BseDI CCNNGG 2 cut(s) 94, 137
BseGI GGATG 1 cut(s) 871
BseLI CCNNNNNNNGG 1 cut(s) 61
BseMII CTCAG 3 cut(s) 52, 622, 765
BseNI ACTGG 3 cut(s) 656, 790, 852
BseXI GCAGC 1 cut(s) 748
BsgI GTGCAG 1 cut(s) 78
Bsh1236I CGCG 1 cut(s) 420
BshFI GGCC 1 cut(s) 54
BshTI ACCGGT 1 cut(s) 947
BsiHKAI GWGCWC 1 cut(s) 829
BsiSI CCGG 1 cut(s) 948
BsiWI CGTACG 1 cut(s) 15
BslFI GGGAC 2 cut(s) 154, 949
BslI CCNNNNNNNGG 1 cut(s) 61
BsmAI GTCTC 4 cut(s) 95, 419, 589, 611
BsmBI CGTCTC 1 cut(s) 611
BsmFI GGGAC 2 cut(s) 154, 949
BsnI GGCC 1 cut(s) 54
Bso31I GGTCTC 1 cut(s) 95
Bsp1286I GDGCHC 1 cut(s) 829
Bsp1407I TGTACA 1 cut(s) 630
Bsp143I GATC 5 cut(s) 100, 403, 523, 797, 976
BspACI CCGC 1 cut(s) 418
BspANI GGCC 1 cut(s) 54
BspCNI CTCAG 3 cut(s) 51, 621, 764
BspFNI CGCG 1 cut(s) 420
BspHI TCATGA 1 cut(s) 352
BspLI GGNNCC 2 cut(s) 850, 906
BspMI ACCTGC 1 cut(s) 679
BspPI GGATC 1 cut(s) 518
BspTNI GGTCTC 1 cut(s) 95
BsrFI RCCGGY 1 cut(s) 947
BsrGI TGTACA 1 cut(s) 630
BsrI ACTGG 3 cut(s) 656, 790, 852
BssAI RCCGGY 1 cut(s) 947
BssECI CCNNGG 2 cut(s) 94, 137
BssMI GATC 5 cut(s) 100, 403, 523, 797, 976
BssNI GRCGYC 1 cut(s) 5
Bst2UI CCWGG 1 cut(s) 138
Bst4CI ACNGT 3 cut(s) 15, 472, 901
Bst6I CTCTTC 1 cut(s) 150
BstACI GRCGYC 1 cut(s) 5
BstAPI GCANNNNNTGC 1 cut(s) 934
BstAUI TGTACA 1 cut(s) 630
BstC8I GCNNGC 1 cut(s) 52
BstDEI CTNAG 4 cut(s) 38, 608, 751, 990
BstDSI CCRYGG 1 cut(s) 94
BstF5I GGATG 1 cut(s) 871
BstFNI CGCG 1 cut(s) 420
BstHHI GCGC 1 cut(s) 688
BstKTI GATC 5 cut(s) 103, 406, 526, 800, 979
BstMAI GTCTC 4 cut(s) 95, 419, 589, 611
BstMBI GATC 5 cut(s) 100, 403, 523, 797, 976
BstMWI GCNNNNNNNGC 3 cut(s) 56, 671, 934
BstNI CCWGG 1 cut(s) 138
BstSCI CCNGG 1 cut(s) 136
BstUI CGCG 1 cut(s) 420
BstV1I GCAGC 1 cut(s) 748
BstX2I RGATCY 1 cut(s) 523
BstYI RGATCY 1 cut(s) 523
Bsu36I CCTNAGG 1 cut(s) 38
BsuI GTATCC 1 cut(s) 560
BsuRI GGCC 1 cut(s) 54
BtgI CCRYGG 1 cut(s) 94
BtsCI GGATG 1 cut(s) 871
BtsIMutI CAGTG 1 cut(s) 859
BveI ACCTGC 1 cut(s) 679
Cac8I GCNNGC 1 cut(s) 52
CaiI CAGNNNCTG 1 cut(s) 197
CciI TCATGA 1 cut(s) 352
CfoI GCGC 1 cut(s) 688
Cfr10I RCCGGY 1 cut(s) 947
Cfr13I GGNCC 1 cut(s) 134
CseI GACGC 1 cut(s) 81
Csp6I GTAC 4 cut(s) 16, 631, 794, 945
CspAI ACCGGT 1 cut(s) 947
CviAII CATG 6 cut(s) 353, 497, 533, 894, 934, 980
CviQI GTAC 4 cut(s) 16, 631, 794, 945
DdeI CTNAG 4 cut(s) 38, 608, 751, 990
DpnI GATC 5 cut(s) 102, 405, 525, 799, 978
DpnII GATC 5 cut(s) 100, 403, 523, 797, 976
DrdI GACNNNNNNGTC 1 cut(s) 603
DseDI GACNNNNNNGTC 1 cut(s) 603
EaeI YGGCCR 1 cut(s) 52
Eam1104I CTCTTC 1 cut(s) 150
EarI CTCTTC 1 cut(s) 150
Ecl136II GAGCTC 1 cut(s) 827
Eco24I GRGCYC 1 cut(s) 829
Eco31I GGTCTC 1 cut(s) 95
Eco47I GGWCC 1 cut(s) 134
Eco53kI GAGCTC 1 cut(s) 827
Eco81I CCTNAGG 1 cut(s) 38
EcoICRI GAGCTC 1 cut(s) 827
EcoRII CCWGG 1 cut(s) 136
EcoT38I GRGCYC 1 cut(s) 829
Esp3I CGTCTC 1 cut(s) 611
FaeI CATG 6 cut(s) 356, 500, 536, 897, 937, 983
FaqI GGGAC 2 cut(s) 154, 949
FatI CATG 6 cut(s) 352, 496, 532, 893, 933, 979
FbaI TGATCA 1 cut(s) 976
Fnu4HI GCNGC 1 cut(s) 762
FokI GGATG 1 cut(s) 858
FriOI GRGCYC 1 cut(s) 829
Fsp4HI GCNGC 1 cut(s) 762
FspBI CTAG 5 cut(s) 387, 450, 477, 588, 675
GlaI GCGC 1 cut(s) 687
GluI GCNGC 1 cut(s) 762
HaeIII GGCC 1 cut(s) 54
HapII CCGG 1 cut(s) 948
HgaI GACGC 1 cut(s) 81
HhaI GCGC 1 cut(s) 688
Hin1I GRCGYC 1 cut(s) 5
Hin1II CATG 6 cut(s) 356, 500, 536, 897, 937, 983
Hin6I GCGC 1 cut(s) 686
HinP1I GCGC 1 cut(s) 686
HinfI GANTC 2 cut(s) 66, 142
HpaII CCGG 1 cut(s) 948
HphI GGTGA 1 cut(s) 557
Hpy166II GTNNAC 2 cut(s) 308, 881
Hpy188I TCNGA 8 cut(s) 71, 372, 554, 611, 754, 802, 916, 976
Hpy188III TCNNGA 6 cut(s) 149, 198, 353, 387, 477, 817
Hpy8I GTNNAC 2 cut(s) 308, 881
Hpy99I CGWCG 2 cut(s) 10, 86
HpyAV CCTTC 6 cut(s) 146, 292, 332, 537, 843, 981
HpyCH4III ACNGT 3 cut(s) 15, 472, 901
HpyCH4IV ACGT 1 cut(s) 5
HpyCH4V TGCA 7 cut(s) 59, 125, 191, 324, 491, 705, 937
HpyF10VI GCNNNNNNNGC 3 cut(s) 56, 671, 934
HpyF3I CTNAG 4 cut(s) 38, 608, 751, 990
HpySE526I ACGT 1 cut(s) 5
Hsp92I GRCGYC 1 cut(s) 5
Hsp92II CATG 6 cut(s) 356, 500, 536, 897, 937, 983
HspAI GCGC 1 cut(s) 686
Ksp22I TGATCA 1 cut(s) 976
Kzo9I GATC 5 cut(s) 100, 403, 523, 797, 976
LmnI GCTCC 4 cut(s) 518, 824, 848, 904
Lsp1109I GCAGC 1 cut(s) 748
LweI GCATC 2 cut(s) 13, 498
MaeI CTAG 5 cut(s) 387, 450, 477, 588, 675
MaeII ACGT 1 cut(s) 5
MaeIII GTNAC 2 cut(s) 112, 556
MalI GATC 5 cut(s) 102, 405, 525, 799, 978
MboI GATC 5 cut(s) 100, 403, 523, 797, 976
MboII GAAGA 5 cut(s) 137, 739, 742, 785, 869
MflI RGATCY 1 cut(s) 523
MhlI GDGCHC 1 cut(s) 829
MluCI AATT 4 cut(s) 214, 267, 325, 939
MlyI GAGTC 1 cut(s) 136
MnlI CCTC 8 cut(s) 47, 55, 149, 156, 251, 341, 532, 612
MseI TTAA 2 cut(s) 270, 375
MslI CAYNNNNRTG 1 cut(s) 876
MspI CCGG 1 cut(s) 948
MspR9I CCNGG 1 cut(s) 138
MvaI CCWGG 1 cut(s) 138
MvnI CGCG 1 cut(s) 420
MwoI GCNNNNNNNGC 3 cut(s) 56, 671, 934
NdeII GATC 5 cut(s) 100, 403, 523, 797, 976
NlaIII CATG 6 cut(s) 356, 500, 536, 897, 937, 983
NlaIV GGNNCC 2 cut(s) 850, 906
NmuCI GTSAC 2 cut(s) 112, 556
PagI TCATGA 1 cut(s) 352
PaqCI CACCTGC 1 cut(s) 679
PcsI WCGNNNNNNNCGW 3 cut(s) 11, 24, 262
PfeI GAWTC 1 cut(s) 66
Pfl23II CGTACG 1 cut(s) 15
PinAI ACCGGT 1 cut(s) 947
PkrI GCNGC 1 cut(s) 763
PleI GAGTC 1 cut(s) 136
PpsI GAGTC 1 cut(s) 136
Psp124BI GAGCTC 1 cut(s) 829
Psp6I CCWGG 1 cut(s) 136
PspGI CCWGG 1 cut(s) 136
PspLI CGTACG 1 cut(s) 15
PspN4I GGNNCC 2 cut(s) 850, 906
PspPI GGNCC 1 cut(s) 134
PstNI CAGNNNCTG 1 cut(s) 197
PsuI RGATCY 1 cut(s) 523
RsaI GTAC 4 cut(s) 17, 632, 795, 946
RsaNI GTAC 4 cut(s) 16, 631, 794, 945
RseI CAYNNNNRTG 1 cut(s) 876
SacI GAGCTC 1 cut(s) 829
SaqAI TTAA 2 cut(s) 270, 375
SatI GCNGC 1 cut(s) 762
Sau3AI GATC 5 cut(s) 100, 403, 523, 797, 976
Sau96I GGNCC 1 cut(s) 134
SchI GAGTC 1 cut(s) 136
ScrFI CCNGG 1 cut(s) 138
SduI GDGCHC 1 cut(s) 829
SfaNI GCATC 2 cut(s) 13, 498
SinI GGWCC 1 cut(s) 134
SmiMI CAYNNNNRTG 1 cut(s) 876
SmlI CTYRAG 2 cut(s) 223, 923
SmoI CTYRAG 2 cut(s) 223, 923
Sse9I AATT 4 cut(s) 214, 267, 325, 939
SsiI CCGC 1 cut(s) 418
SspMI CTAG 5 cut(s) 387, 450, 477, 588, 675
SstI GAGCTC 1 cut(s) 829
StyD4I CCNGG 1 cut(s) 136
TaaI ACNGT 3 cut(s) 15, 472, 901
TaiI ACGT 1 cut(s) 8
TasI AATT 4 cut(s) 214, 267, 325, 939
TatI WGTACW 1 cut(s) 630
TfiI GAWTC 1 cut(s) 66
Tru1I TTAA 2 cut(s) 270, 375
Tru9I TTAA 2 cut(s) 270, 375
TscAI CASTG 1 cut(s) 859
TseFI GTSAC 2 cut(s) 112, 556
TseI GCWGC 1 cut(s) 761
Tsp45I GTSAC 2 cut(s) 112, 556
TspDTI ATGAA 2 cut(s) 207, 614
TspGWI ACGGA 1 cut(s) 476
TspRI CASTG 1 cut(s) 859
VpaK11BI GGWCC 1 cut(s) 134
XapI RAATTY 1 cut(s) 939
XbaI TCTAGA 2 cut(s) 386, 476
XspI CTAG 5 cut(s) 387, 450, 477, 588, 675
ZraI GACGTC 1 cut(s) 6
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.