AT3G24230

Pectate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
3
OG0010648
Physical Location & Seq
Forward (+)
8774541 .. 8777612
3072 bp
Loading structure...
UTR
Exon/CDS
Intron
AT3G24230.1

Sequence Viewer

Length: 1359 bp
ATGGCGACGTCATCTCTGAAACTGACCAGTGCTTGTTTCGTCTTGCTCTTCATCTTCGTTGGCTGCGTTCTCACAGCAACAAATCTCCGAAACAACGAAATCTCTCGATCGAGGAAGCTGAAAACAGAGGATTCAAAGAGCTTTAACAGTTCACCAATGACGACTAGGCTTGATGGTGTAGTAGAGTTGAATGAACACGCAGTTACTGATCCAGACAAAGTTGCCCATGAAGTCTCTAACCTTATTCACATGAGTGAACAGAACATCACTGCAAGGAGGAAGCTTGGCTTCTTTTCATGTGGAAATGGCAATCTAATAGATGATTGTTGGCGTTGCGACCGCAACTGGAACAAGAACCGTAAACACCTAGCGGATTGTGGGATGGGTTTTGGAAGTAAAGCGTTTGGTGGTCGTAATGGAAGTTACTATGTGGTCACTGACCATAGTGATGATGACGTTGTGAATCCAAAGCCAGGAACTTTACGTCATGCCGTGATCCAGGTTGAACCATTATGGATCATCTTTAAAAGAGACATGGTGATAAAGTTGAAACAAGAACTGATCATGAACAGTTTCAAAACCATTGATGCTCGTGGTGCCAATGTCCACATTGCCAATGGTGCTTGCATAACAATCCAAAATATAACCAATGTTATCGTTCATGGCTTGCACATTCACGATTGCAAGAGAACCGGGAATGTAACTGTCAGAAGCTCGCCAAGTCAGGCCGGGTTTAGGGGAACGGCTGATGGTGATGCTATTAATATATTTGGGTCAAGTCATATTTGGATCGACCACAACTCGCTCTCTAACTGTACTGATGGTCTTGTTGATGTTGTAAACGGTTCCACTGCCATTACCATTTCCAATAACCATTTCACTCACCACGATGAGGTGATGTTGCTAGGGCACAATGATTCGTACACACGAGACAAGATGATGCAAGTGACAGTTGCGTATAACCATTTTGGAGAAGGGCTCATACAGAGAATGCCAAGGTGCAGGCATGGTTATTTCCATGTGGTTAACAACGATTACACACATTGGAAAATGTATGCTATTGGAGGAAGTGCAAACCCAACGATAAACAGTCAAGGCAATAGATTTGCTGCTCCCAAAAACCACTCCGCCAAGGAGGTGACAAAAAGATTAGACACAAAAGGTAATGAGTGGATGGAGTGGAATTGGAGATCAGAAAAAGACCTTCTAGTGAATGGAGCGTTTTTTACACCATCAGGTGAAGGAGCATCAGGAGACTCACAAACTTTAAGCTTACCGGCTAAACCAGCTTCAATGGTCGACGCAATCACTGCTAGTGCAGGTGCACTTAGTTGCCGTAGAGGCAAACCTTGCTACTAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0005575 GO:0016020
KEGG Pathways
Metabolic & Signaling
ko00040 ko02024 map00040 map02024
Pfam Domains
Protein Families
Pec_lyase_C

Protein Analysis

452

Amino Acids

49.98

Weight (kDa)

8.65

Isoelectric Point (pI)

36.99

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pectate_lyase_4 PF00544 185 - 387 3.6e-22 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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Orthologous Genes (Group: OG0010648)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G24230 AT4G13710 AT4G13710
fragaria_vesca FvH4_4g05760 FvH4_4g05760 FvH4_4g05760 FvH4_4g05760 FvH4_4g05760
malus_domestica MD13G1231000.v1.1 MD16G1236000.v1.1
prunus_persica Prupe.1G060900_v2.0.a1
pyrus_communis pycom13g20360 pycom16g19790
rosa_chinensis RchiOBHm_Chr4g0396921
rosa_laevigata RLG00000009489
rosa_roxburghii Rroxscaffold_5G00341840
rosa_rugosa Rorug03G0346100
rosa_samantha Rh4AG075300 Rh4DG069100
rosa_wichuraiana Rw4G006040

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AarI CACCTGC 1 cut(s) 1310
AatII GACGTC 1 cut(s) 11
Acc36I ACCTGC 1 cut(s) 1310
AccB1I GGYRCC 1 cut(s) 596
AccI GTMKAC 1 cut(s) 1299
AciI CCGC 3 cut(s) 340, 371, 1128
AclWI GGATC 4 cut(s) 203, 490, 524, 797
AcyI GRCGYC 1 cut(s) 8
AfaI GTAC 2 cut(s) 817, 923
AfiI CCNNNNNNNGG 3 cut(s) 473, 735, 892
AgsI TTSAA 6 cut(s) 135, 190, 506, 550, 577, 1293
AjnI CCWGG 2 cut(s) 472, 498
AjuI GAANNNNNNNTTGG 2 cut(s) 860, 892
AleI CACNNNNGTG 1 cut(s) 252
AluBI AGCT 6 cut(s) 118, 141, 283, 714, 1272, 1289
AluI AGCT 6 cut(s) 118, 141, 283, 714, 1272, 1289
Alw21I GWGCWC 1 cut(s) 1327
Alw26I GTCTC 4 cut(s) 238, 525, 924, 1248
Alw44I GTGCAC 1 cut(s) 1323
AlwI GGATC 4 cut(s) 203, 490, 524, 797
AlwNI CAGNNNCTG 1 cut(s) 206
AoxI GGCC 1 cut(s) 726
ApaLI GTGCAC 1 cut(s) 1323
ApeKI GCWGC 2 cut(s) 63, 1109
AseI ATTAAT 1 cut(s) 762
Asp700I GAANNNNTTC 1 cut(s) 572
AsuC2I CCSGG 2 cut(s) 694, 730
AsuHPI GGTGA 7 cut(s) 144, 550, 764, 875, 907, 1150, 1250
BaeGI GKGCMC 2 cut(s) 912, 1327
BanI GGYRCC 1 cut(s) 596
BanII GRGCYC 1 cut(s) 981
BarI GAAGNNNNNNTAC 2 cut(s) 966, 998
BauI CACGAG 2 cut(s) 591, 927
Bbv12I GWGCWC 1 cut(s) 1327
BbvI GCAGC 2 cut(s) 50, 1096
BccI CCATC 6 cut(s) 167, 376, 743, 815, 1168, 1240
BceAI ACGGC 3 cut(s) 476, 759, 1320
BciT130I CCWGG 2 cut(s) 474, 500
BclI TGATCA 1 cut(s) 561
BcnI CCSGG 2 cut(s) 694, 730
BcoDI GTCTC 4 cut(s) 238, 525, 924, 1248
BfaI CTAG 6 cut(s) 165, 368, 905, 1208, 1314, 1357
BfuAI ACCTGC 1 cut(s) 1310
BglI GCCNNNNNGGC 1 cut(s) 1341
BisI GCNGC 2 cut(s) 64, 1110
BlsI GCNGC 2 cut(s) 65, 1111
Bme1390I CCNGG 4 cut(s) 474, 500, 694, 730
BmiI GGNNCC 2 cut(s) 598, 847
BmrFI CCNGG 4 cut(s) 474, 500, 694, 730
BmsI GCATC 4 cut(s) 577, 745, 930, 1256
BplI GAGNNNNNCTC 2 cut(s) 963, 995
BpuMI CCSGG 2 cut(s) 694, 730
BsaHI GRCGYC 1 cut(s) 8
BsaJI CCNNGG 2 cut(s) 995, 1131
Bsc4I CCNNNNNNNGG 3 cut(s) 473, 735, 892
Bse118I RCCGGY 1 cut(s) 1276
Bse1I ACTGG 2 cut(s) 27, 350
Bse3DI GCAATG 1 cut(s) 609
BseBI CCWGG 2 cut(s) 474, 500
BseDI CCNNGG 2 cut(s) 995, 1131
BseGI GGATG 2 cut(s) 387, 1179
BseLI CCNNNNNNNGG 3 cut(s) 473, 735, 892
BseMI GCAATG 1 cut(s) 609
BseNI ACTGG 2 cut(s) 27, 350
BseSI GKGCMC 2 cut(s) 912, 1327
BseXI GCAGC 2 cut(s) 50, 1096
BsgI GTGCAG 2 cut(s) 1021, 1338
Bsh1285I CGRYCG 2 cut(s) 110, 340
BshFI GGCC 1 cut(s) 728
BshNI GGYRCC 1 cut(s) 596
BsiEI CGRYCG 2 cut(s) 110, 340
BsiHKAI GWGCWC 1 cut(s) 1327
BsiSI CCGG 3 cut(s) 693, 729, 1277
BslI CCNNNNNNNGG 3 cut(s) 473, 735, 892
BsmAI GTCTC 4 cut(s) 238, 525, 924, 1248
BsmI GAATGC 1 cut(s) 996
BsnI GGCC 1 cut(s) 728
Bsp1286I GDGCHC 3 cut(s) 912, 981, 1327
Bsp143I GATC 7 cut(s) 107, 208, 495, 516, 561, 789, 1190
BspACI CCGC 3 cut(s) 340, 371, 1128
BspANI GGCC 1 cut(s) 728
BspHI TCATGA 1 cut(s) 564
BspLI GGNNCC 2 cut(s) 598, 847
BspMI ACCTGC 1 cut(s) 1310
BspPI GGATC 4 cut(s) 203, 490, 524, 797
BspQI GCTCTTC 1 cut(s) 53
BspT107I GGYRCC 1 cut(s) 596
BsrDI GCAATG 1 cut(s) 609
BsrFI RCCGGY 1 cut(s) 1276
BsrI ACTGG 2 cut(s) 27, 350
BssAI RCCGGY 1 cut(s) 1276
BssECI CCNNGG 2 cut(s) 995, 1131
BssMI GATC 7 cut(s) 107, 208, 495, 516, 561, 789, 1190
BssNI GRCGYC 1 cut(s) 8
BssSI CACGAG 2 cut(s) 591, 927
BssT1I CCWWGG 2 cut(s) 995, 1131
Bst2BI CACGAG 2 cut(s) 591, 927
Bst2UI CCWGG 2 cut(s) 474, 500
Bst4CI ACNGT 8 cut(s) 149, 359, 572, 706, 815, 845, 952, 1091
Bst6I CTCTTC 1 cut(s) 53
BstACI GRCGYC 1 cut(s) 8
BstAPI GCANNNNNTGC 2 cut(s) 1310, 1350
BstC8I GCNNGC 4 cut(s) 625, 668, 716, 1004
BstDEI CTNAG 1 cut(s) 1328
BstF5I GGATG 2 cut(s) 387, 1179
BstKTI GATC 7 cut(s) 110, 211, 498, 519, 564, 792, 1193
BstMAI GTCTC 4 cut(s) 238, 525, 924, 1248
BstMBI GATC 7 cut(s) 107, 208, 495, 516, 561, 789, 1190
BstMCI CGRYCG 2 cut(s) 110, 340
BstMWI GCNNNNNNNGC 6 cut(s) 596, 620, 1286, 1310, 1341, 1350
BstNI CCWGG 2 cut(s) 474, 500
BstSCI CCNGG 4 cut(s) 472, 498, 692, 728
BstSLI GKGCMC 2 cut(s) 912, 1327
BstV1I GCAGC 2 cut(s) 50, 1096
BsuRI GGCC 1 cut(s) 728
BtsCI GGATG 2 cut(s) 387, 1179
BtsI GCAGTG 3 cut(s) 267, 849, 1308
BtsIMutI CAGTG 5 cut(s) 34, 267, 435, 849, 1308
BveI ACCTGC 1 cut(s) 1310
Cac8I GCNNGC 4 cut(s) 625, 668, 716, 1004
CaiI CAGNNNCTG 1 cut(s) 206
CciI TCATGA 1 cut(s) 564
Cfr10I RCCGGY 1 cut(s) 1276
CseI GACGC 1 cut(s) 1310
Csp6I GTAC 2 cut(s) 816, 922
CviAII CATG 9 cut(s) 227, 250, 297, 488, 535, 565, 662, 1007, 1019
CviQI GTAC 2 cut(s) 816, 922
DdeI CTNAG 1 cut(s) 1328
DpnI GATC 7 cut(s) 109, 210, 497, 518, 563, 791, 1192
DpnII GATC 7 cut(s) 107, 208, 495, 516, 561, 789, 1190
DraI TTTAAA 1 cut(s) 526
Eam1104I CTCTTC 1 cut(s) 53
EarI CTCTTC 1 cut(s) 53
EciI GGCGGA 1 cut(s) 1117
Eco130I CCWWGG 2 cut(s) 995, 1131
Eco24I GRGCYC 1 cut(s) 981
EcoRII CCWGG 2 cut(s) 472, 498
EcoT14I CCWWGG 2 cut(s) 995, 1131
EcoT38I GRGCYC 1 cut(s) 981
ErhI CCWWGG 2 cut(s) 995, 1131
FaeI CATG 9 cut(s) 230, 253, 300, 491, 538, 568, 665, 1010, 1022
FalI AAGNNNNNCTT 2 cut(s) 272, 304
FatI CATG 9 cut(s) 226, 249, 296, 487, 534, 564, 661, 1006, 1018
FbaI TGATCA 1 cut(s) 561
FblI GTMKAC 1 cut(s) 1299
Fnu4HI GCNGC 2 cut(s) 64, 1110
FokI GGATG 2 cut(s) 394, 1186
FriOI GRGCYC 1 cut(s) 981
Fsp4HI GCNGC 2 cut(s) 64, 1110
FspBI CTAG 6 cut(s) 165, 368, 905, 1208, 1314, 1357
GluI GCNGC 2 cut(s) 64, 1110
HaeIII GGCC 1 cut(s) 728
HapII CCGG 3 cut(s) 693, 729, 1277
HgaI GACGC 1 cut(s) 1310
Hin1I GRCGYC 1 cut(s) 8
Hin1II CATG 9 cut(s) 230, 253, 300, 491, 538, 568, 665, 1010, 1022
HincII GTYRAC 2 cut(s) 1027, 1300
HindII GTYRAC 2 cut(s) 1027, 1300
HindIII AAGCTT 2 cut(s) 281, 1270
HinfI GANTC 4 cut(s) 131, 463, 917, 1256
HpaI GTTAAC 1 cut(s) 1027
HpaII CCGG 3 cut(s) 693, 729, 1277
HphI GGTGA 7 cut(s) 144, 550, 764, 875, 907, 1150, 1250
Hpy166II GTNNAC 9 cut(s) 152, 257, 362, 607, 841, 924, 1027, 1300, 1325
Hpy188I TCNGA 4 cut(s) 18, 89, 710, 1195
Hpy188III TCNNGA 5 cut(s) 105, 212, 565, 677, 1251
Hpy8I GTNNAC 9 cut(s) 152, 257, 362, 607, 841, 924, 1027, 1300, 1325
Hpy99I CGWCG 2 cut(s) 10, 1304
HpyAV CCTTC 3 cut(s) 968, 1214, 1235
HpyCH4III ACNGT 8 cut(s) 149, 359, 572, 706, 815, 845, 952, 1091
HpyCH4IV ACGT 3 cut(s) 8, 456, 484
HpyCH4V TGCA 9 cut(s) 272, 627, 670, 684, 943, 1002, 1073, 1319, 1325
HpyF10VI GCNNNNNNNGC 6 cut(s) 596, 620, 1286, 1310, 1341, 1350
HpyF3I CTNAG 1 cut(s) 1328
HpySE526I ACGT 3 cut(s) 8, 456, 484
Hsp92I GRCGYC 1 cut(s) 8
Hsp92II CATG 9 cut(s) 230, 253, 300, 491, 538, 568, 665, 1010, 1022
Ksp22I TGATCA 1 cut(s) 561
KspAI GTTAAC 1 cut(s) 1027
Kzo9I GATC 7 cut(s) 107, 208, 495, 516, 561, 789, 1190
LguI GCTCTTC 1 cut(s) 53
LmnI GCTCC 3 cut(s) 1117, 1217, 1244
Lsp1109I GCAGC 2 cut(s) 50, 1096
LweI GCATC 4 cut(s) 577, 745, 930, 1256
MaeI CTAG 6 cut(s) 165, 368, 905, 1208, 1314, 1357
MaeII ACGT 3 cut(s) 8, 456, 484
MaeIII GTNAC 6 cut(s) 202, 422, 433, 700, 946, 1138
MalI GATC 7 cut(s) 109, 210, 497, 518, 563, 791, 1192
MboI GATC 7 cut(s) 107, 208, 495, 516, 561, 789, 1190
MboII GAAGA 2 cut(s) 40, 46
MhlI GDGCHC 3 cut(s) 912, 981, 1327
MluCI AATT 1 cut(s) 1183
MlyI GAGTC 1 cut(s) 1250
MnlI CCTC 7 cut(s) 105, 121, 270, 886, 1058, 1129, 1334
MroXI GAANNNNTTC 1 cut(s) 572
MseI TTAA 5 cut(s) 144, 525, 762, 1026, 1268
MslI CAYNNNNRTG 3 cut(s) 252, 447, 888
MspI CCGG 3 cut(s) 693, 729, 1277
MspR9I CCNGG 4 cut(s) 474, 500, 694, 730
Mva1269I GAATGC 1 cut(s) 996
MvaI CCWGG 2 cut(s) 474, 500
MwoI GCNNNNNNNGC 6 cut(s) 596, 620, 1286, 1310, 1341, 1350
NciI CCSGG 2 cut(s) 694, 730
NdeII GATC 7 cut(s) 107, 208, 495, 516, 561, 789, 1190
NlaIII CATG 9 cut(s) 230, 253, 300, 491, 538, 568, 665, 1010, 1022
NlaIV GGNNCC 2 cut(s) 598, 847
NmuCI GTSAC 3 cut(s) 433, 946, 1138
OliI CACNNNNGTG 1 cut(s) 252
PagI TCATGA 1 cut(s) 564
PaqCI CACCTGC 1 cut(s) 1310
PciSI GCTCTTC 1 cut(s) 53
PcsI WCGNNNNNNNCGW 1 cut(s) 63
PctI GAATGC 1 cut(s) 996
PdmI GAANNNNTTC 1 cut(s) 572
PfeI GAWTC 3 cut(s) 131, 463, 917
PkrI GCNGC 2 cut(s) 65, 1111
Ple19I CGATCG 1 cut(s) 110
PleI GAGTC 1 cut(s) 1250
PpsI GAGTC 1 cut(s) 1250
PshBI ATTAAT 1 cut(s) 762
Psp6I CCWGG 2 cut(s) 472, 498
PspGI CCWGG 2 cut(s) 472, 498
PspN4I GGNNCC 2 cut(s) 598, 847
PstNI CAGNNNCTG 1 cut(s) 206
PvuI CGATCG 1 cut(s) 110
RsaI GTAC 2 cut(s) 817, 923
RsaNI GTAC 2 cut(s) 816, 922
RseI CAYNNNNRTG 3 cut(s) 252, 447, 888
SalI GTCGAC 1 cut(s) 1298
SapI GCTCTTC 1 cut(s) 53
SaqAI TTAA 5 cut(s) 144, 525, 762, 1026, 1268
SatI GCNGC 2 cut(s) 64, 1110
Sau3AI GATC 7 cut(s) 107, 208, 495, 516, 561, 789, 1190
SchI GAGTC 1 cut(s) 1250
ScrFI CCNGG 4 cut(s) 474, 500, 694, 730
SduI GDGCHC 3 cut(s) 912, 981, 1327
SfaNI GCATC 4 cut(s) 577, 745, 930, 1256
SmiMI CAYNNNNRTG 3 cut(s) 252, 447, 888
Sse9I AATT 1 cut(s) 1183
SsiI CCGC 3 cut(s) 340, 371, 1128
SspMI CTAG 6 cut(s) 165, 368, 905, 1208, 1314, 1357
StyD4I CCNGG 4 cut(s) 472, 498, 692, 728
StyI CCWWGG 2 cut(s) 995, 1131
TaaI ACNGT 8 cut(s) 149, 359, 572, 706, 815, 845, 952, 1091
TaiI ACGT 3 cut(s) 11, 459, 487
TaqI TCGA 4 cut(s) 106, 110, 792, 1299
TasI AATT 1 cut(s) 1183
TatI WGTACW 1 cut(s) 815
TfiI GAWTC 3 cut(s) 131, 463, 917
Tru1I TTAA 5 cut(s) 144, 525, 762, 1026, 1268
Tru9I TTAA 5 cut(s) 144, 525, 762, 1026, 1268
TscAI CASTG 5 cut(s) 34, 274, 442, 856, 1315
TseFI GTSAC 3 cut(s) 433, 946, 1138
TseI GCWGC 2 cut(s) 63, 1109
Tsp45I GTSAC 3 cut(s) 433, 946, 1138
TspDTI ATGAA 6 cut(s) 40, 207, 243, 285, 581, 650
TspRI CASTG 5 cut(s) 34, 274, 442, 856, 1315
VneI GTGCAC 1 cut(s) 1323
VspI ATTAAT 1 cut(s) 762
XcmI CCANNNNNNNNNTGG 1 cut(s) 614
XmiI GTMKAC 1 cut(s) 1299
XmnI GAANNNNTTC 1 cut(s) 572
XspI CTAG 6 cut(s) 165, 368, 905, 1208, 1314, 1357
ZraI GACGTC 1 cut(s) 9
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.