Rh3AG138400

Pectate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr3A
OG0009024
Physical Location & Seq
Reverse (-)
12137489 .. 12140026
2538 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh3AG138400.1

Sequence Viewer

Length: 1128 bp
ATGGGCAACTCCCACGGCCACCGCAAACACCGTAACGGCGCAAACCGCCCCGTAACGCCCAATCCACCCTTTAAATATGGCCCGTCCGATCCGCAAGCACATATCCCCAGCTCAGCTAAACCCATCATGGCGGTGTCCTTGCCTTACTCTCATGTTGACTCCACCCTTCGCGCCCTCGCTGCCCAAGCTGAAGGCTTTGGCCGCTTAGCAATCGGCGGCCTCCATGGTCCTCTTTACCACGTTACTACTCTAGCCGATGATGGTCCAGGGTCACTTAGGGAAGCCTGTCGAAAGAAAGAGCCACTTTGGATTGTCTTTGATATTTCGGGCACTATCCATCTCTCGTCTTACTTGAATGTGTCGTCACATAAGACAATTGATGGCCGGGGTCAGAGGATTAAGTTTACTGGGAAGGGGTTGAGGCTGAAGGAATGTGAGCATGTGATTATATGCAATCTAGAGTTTGAAGGTGGTAGAGGACCAGATGTTGATGGTATTCAGATAAAACCAAACTCTAAGCACATATGGATAGACCGGTGCAGCCTTCGTGATTATGAAGACGGACTTATAGATATCACCAGATGCAGCACGGATATTACAATTTCGAGGTGTCATTTCTCGCAGCATGATAAGACAATGCTAATCGGAGCAGACCCCTCTCATGTAGATGACAGATGCATCCGGGTTACAATTCACCACTGTTTCTTTGATGGGACCCGACAGCGGCATCCTCGTGTTAGATTCGCCAAAGTACATCTATACAACAATTACACCCGAAACTGGGGCATATATGCTGTTTGTGCCAGTGTAGAATCACAGATATACTCTCAATGCAATATATATGAAGCAGGACAGAAGAAAATAGCGTTTAAATACCTTACAGAGAAGGCAGTGGACAGGGAGGCGGCAACGACTGGCTTCATTAGGTCGGAAGGGGACTTATTCATAACTGGAACTCAAGCAGGATTAGCCACCGAGGGTGGTGAAAATTGCATGTTTCATCCTAGCCAACACTACCAGACATGGACAGTAGGACCTCCAGTGGATGATCTGAAACATGTTCTCCAACATTGCACCGGATGGCAGTCCATTCCCCGGCCAGCTGATCAGGCAAGTGTAGCACAGTAA
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

375

Amino Acids

41.76

Weight (kDa)

8.54

Isoelectric Point (pI)

30.28

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pectate_lyase_4 PF00544 117 - 288 2.9e-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)
AccII CGCG 1 cut(s) 171
AciI CCGC 8 cut(s) 22, 46, 92, 131, 202, 216, 724, 905
AclWI GGATC 1 cut(s) 83
AcoI YGGCCR 4 cut(s) 16, 199, 382, 1097
AcuI CTGAAG 2 cut(s) 210, 446
AfaI GTAC 1 cut(s) 753
AfiI CCNNNNNNNGG 4 cut(s) 723, 780, 781, 1095
AflIII ACRYGT 1 cut(s) 1057
AgeI ACCGGT 1 cut(s) 534
AgsI TTSAA 2 cut(s) 355, 467
AjnI CCWGG 1 cut(s) 265
AluBI AGCT 4 cut(s) 111, 116, 188, 1103
AluI AGCT 4 cut(s) 111, 116, 188, 1103
AlwI GGATC 1 cut(s) 83
AoxI GGCC 6 cut(s) 16, 79, 199, 217, 382, 1097
ApeKI GCWGC 4 cut(s) 179, 540, 585, 622
AsiGI ACCGGT 1 cut(s) 534
AspLEI GCGC 2 cut(s) 41, 173
AspS9I GGNCC 6 cut(s) 80, 227, 263, 479, 714, 1034
AsuC2I CCSGG 3 cut(s) 386, 683, 1096
AsuHPI GGTGA 3 cut(s) 568, 686, 995
AvaII GGWCC 5 cut(s) 227, 263, 479, 714, 1034
BaeGI GKGCMC 1 cut(s) 332
BauI CACGAG 1 cut(s) 732
BbsI GAAGAC 1 cut(s) 564
BbvI GCAGC 4 cut(s) 166, 552, 597, 634
BccI CCATC 7 cut(s) 131, 254, 345, 374, 485, 704, 1074
BceAI ACGGC 2 cut(s) 31, 52
BciT130I CCWGG 1 cut(s) 267
BclI TGATCA 1 cut(s) 1105
BcnI CCSGG 3 cut(s) 386, 683, 1096
BfaI CTAG 3 cut(s) 251, 458, 1005
BisI GCNGC 8 cut(s) 180, 202, 217, 541, 586, 623, 725, 906
BlpI GCTNAGC 2 cut(s) 112, 205
BlsI GCNGC 8 cut(s) 181, 203, 218, 542, 587, 624, 726, 907
Bme1390I CCNGG 4 cut(s) 267, 386, 683, 1096
Bme18I GGWCC 5 cut(s) 227, 263, 479, 714, 1034
BmgT120I GGNCC 6 cut(s) 80, 227, 263, 479, 714, 1034
BmiI GGNNCC 2 cut(s) 715, 716
BmrFI CCNGG 4 cut(s) 267, 386, 683, 1096
BmrI ACTGGG 2 cut(s) 417, 790
BmsI GCATC 4 cut(s) 572, 665, 687, 736
BmuI ACTGGG 2 cut(s) 417, 790
BpiI GAAGAC 1 cut(s) 564
BpmI CTGGAG 1 cut(s) 1023
Bpu1102I GCTNAGC 2 cut(s) 112, 205
BpuEI CTTGAG 1 cut(s) 942
BpuMI CCSGG 3 cut(s) 386, 683, 1096
BsaJI CCNNGG 6 cut(s) 13, 223, 266, 385, 975, 1094
BsaWI WCCGGW 2 cut(s) 534, 1076
BsaXI ACNNNNNCTCC 2 cut(s) 1047, 1077
Bsc4I CCNNNNNNNGG 4 cut(s) 723, 780, 781, 1095
Bse118I RCCGGY 1 cut(s) 534
Bse1I ACTGG 6 cut(s) 412, 785, 804, 919, 955, 1040
Bse3DI GCAATG 1 cut(s) 1069
BseBI CCWGG 1 cut(s) 267
BseDI CCNNGG 6 cut(s) 13, 223, 266, 385, 975, 1094
BseGI GGATG 5 cut(s) 678, 727, 1000, 1051, 1085
BseLI CCNNNNNNNGG 4 cut(s) 723, 780, 781, 1095
BseMI GCAATG 1 cut(s) 1069
BseMII CTCAG 1 cut(s) 126
BseNI ACTGG 6 cut(s) 412, 785, 804, 919, 955, 1040
BseSI GKGCMC 1 cut(s) 332
BseXI GCAGC 4 cut(s) 166, 552, 597, 634
BseYI CCCAGC 1 cut(s) 107
BsgI GTGCAG 1 cut(s) 559
Bsh1236I CGCG 1 cut(s) 171
BshFI GGCC 6 cut(s) 18, 81, 201, 219, 384, 1099
BshTI ACCGGT 1 cut(s) 534
BsiSI CCGG 5 cut(s) 385, 535, 682, 1077, 1096
BslFI GGGAC 2 cut(s) 727, 950
BslI CCNNNNNNNGG 4 cut(s) 723, 780, 781, 1095
BsmFI GGGAC 2 cut(s) 727, 950
BsnI GGCC 6 cut(s) 18, 81, 201, 219, 384, 1099
Bsp1286I GDGCHC 1 cut(s) 332
Bsp143I GATC 3 cut(s) 88, 1048, 1105
Bsp1720I GCTNAGC 2 cut(s) 112, 205
Bsp19I CCATGG 1 cut(s) 223
BspACI CCGC 8 cut(s) 22, 46, 92, 131, 202, 216, 724, 905
BspANI GGCC 6 cut(s) 18, 81, 201, 219, 384, 1099
BspCNI CTCAG 1 cut(s) 125
BspFNI CGCG 1 cut(s) 171
BspLI GGNNCC 2 cut(s) 715, 716
BspPI GGATC 1 cut(s) 83
BsrDI GCAATG 1 cut(s) 1069
BsrFI RCCGGY 1 cut(s) 534
BsrI ACTGG 6 cut(s) 412, 785, 804, 919, 955, 1040
BssAI RCCGGY 1 cut(s) 534
BssECI CCNNGG 6 cut(s) 13, 223, 266, 385, 975, 1094
BssMI GATC 3 cut(s) 88, 1048, 1105
BssSI CACGAG 1 cut(s) 732
BssT1I CCWWGG 1 cut(s) 223
Bst2BI CACGAG 1 cut(s) 732
Bst2UI CCWGG 1 cut(s) 267
Bst4CI ACNGT 4 cut(s) 32, 701, 1030, 1125
BstC8I GCNNGC 2 cut(s) 96, 1101
BstDEI CTNAG 4 cut(s) 112, 205, 275, 516
BstDSI CCRYGG 2 cut(s) 13, 223
BstF5I GGATG 5 cut(s) 678, 727, 1000, 1051, 1085
BstFNI CGCG 1 cut(s) 171
BstHHI GCGC 2 cut(s) 41, 173
BstKTI GATC 3 cut(s) 91, 1051, 1108
BstMBI GATC 3 cut(s) 88, 1048, 1105
BstMWI GCNNNNNNNGC 8 cut(s) 45, 179, 185, 201, 800, 968, 1109, 1118
BstNI CCWGG 1 cut(s) 267
BstNSI RCATGY 3 cut(s) 443, 997, 1061
BstSCI CCNGG 4 cut(s) 265, 384, 681, 1094
BstSLI GKGCMC 1 cut(s) 332
BstUI CGCG 1 cut(s) 171
BstV1I GCAGC 4 cut(s) 166, 552, 597, 634
BstV2I GAAGAC 1 cut(s) 564
BsuRI GGCC 6 cut(s) 18, 81, 201, 219, 384, 1099
BtgI CCRYGG 2 cut(s) 13, 223
BtsCI GGATG 5 cut(s) 678, 727, 1000, 1051, 1085
BtsI GCAGTG 1 cut(s) 897
BtsIMutI CAGTG 4 cut(s) 697, 811, 897, 1047
Cac8I GCNNGC 2 cut(s) 96, 1101
CfoI GCGC 2 cut(s) 41, 173
Cfr10I RCCGGY 1 cut(s) 534
Cfr13I GGNCC 6 cut(s) 80, 227, 263, 479, 714, 1034
Csp6I GTAC 1 cut(s) 752
CspAI ACCGGT 1 cut(s) 534
CviAII CATG 9 cut(s) 127, 152, 224, 440, 626, 662, 994, 1023, 1058
CviQI GTAC 1 cut(s) 752
DdeI CTNAG 4 cut(s) 112, 205, 275, 516
DpnI GATC 3 cut(s) 90, 1050, 1107
DpnII GATC 3 cut(s) 88, 1048, 1105
DraI TTTAAA 2 cut(s) 73, 871
EaeI YGGCCR 4 cut(s) 16, 199, 382, 1097
Eco130I CCWWGG 1 cut(s) 223
Eco32I GATATC 1 cut(s) 574
Eco47I GGWCC 5 cut(s) 227, 263, 479, 714, 1034
Eco57I CTGAAG 2 cut(s) 210, 446
EcoO109I RGGNCCY 2 cut(s) 714, 1034
EcoRII CCWGG 1 cut(s) 265
EcoRV GATATC 1 cut(s) 574
EcoT14I CCWWGG 1 cut(s) 223
EcoT22I ATGCAT 1 cut(s) 680
ErhI CCWWGG 1 cut(s) 223
FaeI CATG 9 cut(s) 130, 155, 227, 443, 629, 665, 997, 1026, 1061
FalI AAGNNNNNCTT 4 cut(s) 288, 320, 549, 581
FaqI GGGAC 2 cut(s) 727, 950
FatI CATG 9 cut(s) 126, 151, 223, 439, 625, 661, 993, 1022, 1057
FauNDI CATATG 1 cut(s) 524
FbaI TGATCA 1 cut(s) 1105
Fnu4HI GCNGC 8 cut(s) 180, 202, 217, 541, 586, 623, 725, 906
FokI GGATG 5 cut(s) 665, 714, 987, 1058, 1092
Fsp4HI GCNGC 8 cut(s) 180, 202, 217, 541, 586, 623, 725, 906
FspBI CTAG 3 cut(s) 251, 458, 1005
GlaI GCGC 2 cut(s) 40, 172
GluI GCNGC 8 cut(s) 180, 202, 217, 541, 586, 623, 725, 906
GsaI CCCAGC 1 cut(s) 111
GsuI CTGGAG 1 cut(s) 1023
HaeIII GGCC 6 cut(s) 18, 81, 201, 219, 384, 1099
HapII CCGG 5 cut(s) 385, 535, 682, 1077, 1096
HhaI GCGC 2 cut(s) 41, 173
Hin1II CATG 9 cut(s) 130, 155, 227, 443, 629, 665, 997, 1026, 1061
Hin6I GCGC 2 cut(s) 39, 171
HinP1I GCGC 2 cut(s) 39, 171
HincII GTYRAC 1 cut(s) 157
HindII GTYRAC 1 cut(s) 157
HinfI GANTC 3 cut(s) 158, 741, 812
HpaII CCGG 5 cut(s) 385, 535, 682, 1077, 1096
HphI GGTGA 3 cut(s) 568, 686, 995
Hpy166II GTNNAC 3 cut(s) 157, 405, 895
Hpy188I TCNGA 6 cut(s) 88, 393, 501, 647, 931, 1053
Hpy188III TCNNGA 2 cut(s) 458, 548
Hpy8I GTNNAC 3 cut(s) 157, 405, 895
HpyAV CCTTC 8 cut(s) 176, 185, 406, 421, 461, 554, 880, 926
HpyCH4III ACNGT 4 cut(s) 32, 701, 1030, 1125
HpyCH4IV ACGT 1 cut(s) 240
HpyCH4V TGCA 7 cut(s) 453, 540, 585, 678, 834, 993, 1074
HpyF10VI GCNNNNNNNGC 8 cut(s) 45, 179, 185, 201, 800, 968, 1109, 1118
HpyF3I CTNAG 4 cut(s) 112, 205, 275, 516
HpySE526I ACGT 1 cut(s) 240
Hsp92II CATG 9 cut(s) 130, 155, 227, 443, 629, 665, 997, 1026, 1061
HspAI GCGC 2 cut(s) 39, 171
KflI GGGWCCC 1 cut(s) 714
Ksp22I TGATCA 1 cut(s) 1105
Kzo9I GATC 3 cut(s) 88, 1048, 1105
LmnI GCTCC 1 cut(s) 647
Lsp1109I GCAGC 4 cut(s) 166, 552, 597, 634
LweI GCATC 4 cut(s) 572, 665, 687, 736
MaeI CTAG 3 cut(s) 251, 458, 1005
MaeII ACGT 1 cut(s) 240
MaeIII GTNAC 6 cut(s) 32, 52, 241, 270, 363, 685
MalI GATC 3 cut(s) 90, 1050, 1107
MboI GATC 3 cut(s) 88, 1048, 1105
MboII GAAGA 2 cut(s) 569, 868
MfeI CAATTG 1 cut(s) 375
MhlI GDGCHC 1 cut(s) 332
MluCI AATT 5 cut(s) 375, 600, 690, 766, 988
MlyI GAGTC 1 cut(s) 152
MmeI TCCRAC 2 cut(s) 909, 1090
Mph1103I ATGCAT 1 cut(s) 680
MseI TTAA 3 cut(s) 72, 399, 870
MslI CAYNNNNRTG 3 cut(s) 131, 666, 732
MspA1I CMGCKG 2 cut(s) 724, 1103
MspI CCGG 5 cut(s) 385, 535, 682, 1077, 1096
MspR9I CCNGG 4 cut(s) 267, 386, 683, 1096
MunI CAATTG 1 cut(s) 375
MvaI CCWGG 1 cut(s) 267
MvnI CGCG 1 cut(s) 171
MwoI GCNNNNNNNGC 8 cut(s) 45, 179, 185, 201, 800, 968, 1109, 1118
NciI CCSGG 3 cut(s) 386, 683, 1096
NcoI CCATGG 1 cut(s) 223
NdeI CATATG 1 cut(s) 524
NdeII GATC 3 cut(s) 88, 1048, 1105
NlaIII CATG 9 cut(s) 130, 155, 227, 443, 629, 665, 997, 1026, 1061
NlaIV GGNNCC 2 cut(s) 715, 716
NmuCI GTSAC 2 cut(s) 270, 363
NsiI ATGCAT 1 cut(s) 680
NspI RCATGY 3 cut(s) 443, 997, 1061
PciI ACATGT 1 cut(s) 1057
PfeI GAWTC 2 cut(s) 741, 812
PinAI ACCGGT 1 cut(s) 534
PkrI GCNGC 8 cut(s) 181, 203, 218, 542, 587, 624, 726, 907
PleI GAGTC 1 cut(s) 152
PpsI GAGTC 1 cut(s) 152
PpuMI RGGWCCY 2 cut(s) 714, 1034
PscI ACATGT 1 cut(s) 1057
Psp5II RGGWCCY 2 cut(s) 714, 1034
Psp6I CCWGG 1 cut(s) 265
PspFI CCCAGC 1 cut(s) 107
PspGI CCWGG 1 cut(s) 265
PspN4I GGNNCC 2 cut(s) 715, 716
PspPI GGNCC 6 cut(s) 80, 227, 263, 479, 714, 1034
PspPPI RGGWCCY 2 cut(s) 714, 1034
PvuII CAGCTG 1 cut(s) 1103
RsaI GTAC 1 cut(s) 753
RsaNI GTAC 1 cut(s) 752
RseI CAYNNNNRTG 3 cut(s) 131, 666, 732
SaqAI TTAA 3 cut(s) 72, 399, 870
SatI GCNGC 8 cut(s) 180, 202, 217, 541, 586, 623, 725, 906
Sau3AI GATC 3 cut(s) 88, 1048, 1105
Sau96I GGNCC 6 cut(s) 80, 227, 263, 479, 714, 1034
SchI GAGTC 1 cut(s) 152
ScrFI CCNGG 4 cut(s) 267, 386, 683, 1096
SduI GDGCHC 1 cut(s) 332
SfaNI GCATC 4 cut(s) 572, 665, 687, 736
SinI GGWCC 5 cut(s) 227, 263, 479, 714, 1034
SmiMI CAYNNNNRTG 3 cut(s) 131, 666, 732
SmlI CTYRAG 1 cut(s) 957
SmoI CTYRAG 1 cut(s) 957
Sse9I AATT 5 cut(s) 375, 600, 690, 766, 988
SsiI CCGC 8 cut(s) 22, 46, 92, 131, 202, 216, 724, 905
SspMI CTAG 3 cut(s) 251, 458, 1005
StyD4I CCNGG 4 cut(s) 265, 384, 681, 1094
StyI CCWWGG 1 cut(s) 223
TaaI ACNGT 4 cut(s) 32, 701, 1030, 1125
TaiI ACGT 1 cut(s) 243
TaqI TCGA 2 cut(s) 289, 605
TasI AATT 5 cut(s) 375, 600, 690, 766, 988
TatI WGTACW 1 cut(s) 751
TauI GCSGC 4 cut(s) 204, 219, 727, 908
TfiI GAWTC 2 cut(s) 741, 812
Tru1I TTAA 3 cut(s) 72, 399, 870
Tru9I TTAA 3 cut(s) 72, 399, 870
TscAI CASTG 4 cut(s) 704, 811, 897, 1047
TseFI GTSAC 2 cut(s) 270, 363
TseI GCWGC 4 cut(s) 179, 540, 585, 622
Tsp45I GTSAC 2 cut(s) 270, 363
TspDTI ATGAA 5 cut(s) 570, 858, 910, 934, 989
TspGWI ACGGA 2 cut(s) 576, 605
TspRI CASTG 4 cut(s) 704, 811, 897, 1047
VpaK11BI GGWCC 5 cut(s) 227, 263, 479, 714, 1034
XbaI TCTAGA 1 cut(s) 457
XceI RCATGY 3 cut(s) 443, 997, 1061
XspI CTAG 3 cut(s) 251, 458, 1005
Zsp2I ATGCAT 1 cut(s) 680
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.