MD16G1106400.v1.1

Pectate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr16
OG0013798
Physical Location & Seq
Reverse (-)
7468946 .. 7471200
2255 bp
Loading structure...
UTR
Exon/CDS
Intron
MD16G1106400.v1.1.491

Sequence Viewer

Length: 1206 bp
ATGGCAATGCCACTCTCTCTTTTGCTCCTCTCCCTTCTCCTAATCCCAACCACCATTTCCTCCTCCCCTGTCAAAGATCCTGAACTGGTGATGCAAGAAGTACAAGAGAGCATCAATGCCTCAAGGAGAAATTTGGGTTATCTTTCATGTGGCACAGGAAACCCCATTGACGACTGCTGGAGGTGTGACCCCAACTGGGAGAAAAACCGCCAACGGCTAGCTGACTGCGCAATTGGATTCGGAAAGCACGCCATTGGAGGCAGGGACGGTAAAATCTACGTGGTGACGGACTCAGGCGACCATCCTGTAAACCCTAAACCCGGAACCCTCCGATACGGCGTGATCCAAAACGAACCACTCTGGATCATCTTCCAGCGTGACATGACGATCAAGTTGAACGAAGAGCTGATGATGAACTCCTTCAAGACAATCGACGGCAGAGGAAGTAGCGTACACATTGCAGGCGGGCCCTGCATTACGATACAGTACGTGACAAACATTATTATCCACGGATTAAACATTCACGACTGTAAGCAAGGCGGGAACGCCTACGTTAGGGACTCGCCGGAGCACTTTGGGTGGCGGACGCTTTCCGACGGCGACGGGGTCTCCATTTTTGGTGGTAGTCATGTTTGGGTGGATCATAACTCACTTTCCAACTGCCGTGACGGGCTAATTGATGCTATCCATGGATCAACCTCCATCACTATTTCAAACAATTACATGACTCACCATAACAAGGTCATGCTCTTGGGGCACAGTGATTCCTACACTCAGGACAAGAATATGCAGGTCACCATTGCATTCAACCACTTTGGAGAAGGGCTTATTCAGAGGATGCCAAGATGTAGACATGGGAATTTTCATGTGGTGAACAATGACTACACCCATTGGGAAATGTATGCAATTGGTGGGAGTGCTTCTCCAACCATCAACAGCCAAGGCAACAGATTTCTGGCACCAAATGATAGATTCAACAAAGAGGTTACCAAGCATGAGGATGCACCACAGAAAGAGTGGAGCAAATGGAACTGGAGGTCCTCAGGAGATTTGCTGCTAAACGGTGCGTTCTTCACAGCATCCGGTGCCGGAGCATCTACTAGTTACTCCAAAGCATCGAGTCTGAGTGCGAGACCGTCGTCGCTCGTGAGTTCGCTCACTGCCGGAGCTGGTTCGCTCAGGTGCAAGAAGGGCTCGCGTTGCTGA
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

402

Amino Acids

44.12

Weight (kDa)

8.03

Isoelectric Point (pI)

35.36

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pectate_lyase_4 PF00544 138 - 362 4.1e-20 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
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0013798)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G67750
fragaria_vesca FvH4_4g25110
malus_domestica MD13G1106200.v1.1 MD16G1106400.v1.1
prunus_persica Prupe.1G239900_v2.0.a1 Prupe.1G239900_v2.0.a1
pyrus_communis pycom13g09220 pycom16g09060
rosa_chinensis RchiOBHm_Chr4g0432291
rosa_laevigata RLG00000006855
rosa_multiflora Rmu_sc0001084.1_g000044
rosa_roxburghii Rroxscaffold_5G00373750
rosa_rugosa Rorug04G0256800
rosa_samantha Rh4BG320700 Rh4CG335900 Rh4DG316200
rosa_wichuraiana Rw4G027220

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc16I TGCGCA 1 cut(s) 229
Acc36I ACCTGC 1 cut(s) 781
AccB1I GGYRCC 2 cut(s) 958, 1085
AccI GTMKAC 1 cut(s) 850
AccII CGCG 1 cut(s) 1198
AciI CCGC 4 cut(s) 208, 465, 540, 583
AclWI GGATC 5 cut(s) 71, 337, 371, 648, 700
AcsI RAATTY 2 cut(s) 130, 859
AfaI GTAC 3 cut(s) 102, 453, 488
AfiI CCNNNNNNNGG 4 cut(s) 196, 320, 555, 739
AgsI TTSAA 5 cut(s) 397, 424, 714, 808, 976
AhlI ACTAGT 1 cut(s) 1100
AjuI GAANNNNNNNTTGG 2 cut(s) 40, 72
AloI GAACNNNNNNTCC 2 cut(s) 1022, 1054
AluBI AGCT 3 cut(s) 221, 406, 1169
AluI AGCT 3 cut(s) 221, 406, 1169
Alw21I GWGCWC 1 cut(s) 573
Alw26I GTCTC 2 cut(s) 613, 1126
AlwI GGATC 5 cut(s) 71, 337, 371, 648, 700
AoxI GGCC 1 cut(s) 467
ApaI GGGCCC 1 cut(s) 471
ApeKI GCWGC 1 cut(s) 1054
ApoI RAATTY 2 cut(s) 130, 859
Asp700I GAANNNNTTC 1 cut(s) 419
AspLEI GCGC 1 cut(s) 230
AspS9I GGNCC 3 cut(s) 467, 468, 1038
AsuC2I CCSGG 1 cut(s) 321
AsuHPI GGTGA 5 cut(s) 100, 295, 722, 787, 883
AsuNHI GCTAGC 1 cut(s) 217
AvaII GGWCC 1 cut(s) 1038
AxyI CCTNAGG 1 cut(s) 1042
BaeGI GKGCMC 2 cut(s) 471, 759
BanI GGYRCC 2 cut(s) 958, 1085
BanII GRGCYC 2 cut(s) 471, 1196
BauI CACGAG 1 cut(s) 1145
Bbv12I GWGCWC 1 cut(s) 573
BbvI GCAGC 1 cut(s) 1041
BccI CCATC 3 cut(s) 309, 710, 938
BceAI ACGGC 5 cut(s) 230, 352, 451, 613, 648
BcnI CCSGG 1 cut(s) 321
BcoDI GTCTC 2 cut(s) 613, 1126
BcuI ACTAGT 1 cut(s) 1100
BfaI CTAG 2 cut(s) 218, 1101
BfuAI ACCTGC 1 cut(s) 781
BisI GCNGC 1 cut(s) 1055
BlsI GCNGC 1 cut(s) 1056
Bme1390I CCNGG 1 cut(s) 321
Bme18I GGWCC 1 cut(s) 1038
BmgT120I GGNCC 3 cut(s) 467, 468, 1038
BmiI GGNNCC 4 cut(s) 325, 469, 960, 1087
BmrFI CCNGG 1 cut(s) 321
BmrI ACTGGG 1 cut(s) 205
BmsI GCATC 8 cut(s) 81, 120, 670, 828, 991, 1088, 1103, 1124
BmtI GCTAGC 1 cut(s) 221
BmuI ACTGGG 1 cut(s) 205
BoxI GACNNNNGTC 1 cut(s) 1138
BplI GAGNNNNNCTC 2 cut(s) 907, 939
BpmI CTGGAG 2 cut(s) 199, 1054
Bpu10I CCTNAGC 1 cut(s) 1178
BpuEI CTTGAG 1 cut(s) 106
BpuMI CCSGG 1 cut(s) 321
BsaAI YACGTR 2 cut(s) 280, 490
BsaI GGTCTC 2 cut(s) 613, 1126
BsaJI CCNNGG 3 cut(s) 508, 688, 940
BsaWI WCCGGW 1 cut(s) 1082
BsaXI ACNNNNNCTCC 2 cut(s) 593, 623
Bsc4I CCNNNNNNNGG 4 cut(s) 196, 320, 555, 739
Bse1I ACTGG 3 cut(s) 90, 200, 1037
Bse21I CCTNAGG 1 cut(s) 1042
Bse3DI GCAATG 3 cut(s) 12, 456, 798
BseDI CCNNGG 3 cut(s) 508, 688, 940
BseGI GGATG 4 cut(s) 301, 843, 1006, 1079
BseLI CCNNNNNNNGG 4 cut(s) 196, 320, 555, 739
BseMI GCAATG 3 cut(s) 12, 456, 798
BseMII CTCAG 5 cut(s) 306, 788, 1056, 1115, 1192
BseNI ACTGG 3 cut(s) 90, 200, 1037
BseRI GAGGAG 2 cut(s) 17, 52
BseSI GKGCMC 2 cut(s) 471, 759
BseXI GCAGC 1 cut(s) 1041
Bsh1236I CGCG 1 cut(s) 1198
BshFI GGCC 1 cut(s) 469
BshNI GGYRCC 2 cut(s) 958, 1085
BsiHKAI GWGCWC 1 cut(s) 573
BsiSI CCGG 5 cut(s) 321, 566, 1083, 1089, 1164
BslFI GGGAC 2 cut(s) 278, 572
BslI CCNNNNNNNGG 4 cut(s) 196, 320, 555, 739
BsmAI GTCTC 2 cut(s) 613, 1126
BsmFI GGGAC 2 cut(s) 278, 572
BsmI GAATGC 1 cut(s) 803
BsnI GGCC 1 cut(s) 469
Bso31I GGTCTC 2 cut(s) 613, 1126
Bsp120I GGGCCC 1 cut(s) 467
Bsp1286I GDGCHC 4 cut(s) 471, 573, 759, 1196
Bsp143I GATC 6 cut(s) 76, 342, 363, 387, 640, 692
Bsp19I CCATGG 1 cut(s) 688
BspACI CCGC 4 cut(s) 208, 465, 540, 583
BspANI GGCC 1 cut(s) 469
BspCNI CTCAG 5 cut(s) 305, 787, 1055, 1116, 1191
BspFNI CGCG 1 cut(s) 1198
BspLI GGNNCC 4 cut(s) 325, 469, 960, 1087
BspMI ACCTGC 1 cut(s) 781
BspOI GCTAGC 1 cut(s) 221
BspPI GGATC 5 cut(s) 71, 337, 371, 648, 700
BspQI GCTCTTC 1 cut(s) 396
BspT107I GGYRCC 2 cut(s) 958, 1085
BspTNI GGTCTC 2 cut(s) 613, 1126
BsrDI GCAATG 3 cut(s) 12, 456, 798
BsrI ACTGG 3 cut(s) 90, 200, 1037
BssECI CCNNGG 3 cut(s) 508, 688, 940
BssMI GATC 6 cut(s) 76, 342, 363, 387, 640, 692
BssSI CACGAG 1 cut(s) 1145
BssT1I CCWWGG 2 cut(s) 688, 940
Bst2BI CACGAG 1 cut(s) 1145
Bst4CI ACNGT 6 cut(s) 269, 486, 530, 761, 1064, 1137
Bst6I CTCTTC 1 cut(s) 396
BstAPI GCANNNNNTGC 1 cut(s) 1085
BstBAI YACGTR 2 cut(s) 280, 490
BstC8I GCNNGC 5 cut(s) 219, 249, 463, 467, 1196
BstDEI CTNAG 5 cut(s) 292, 774, 1042, 1124, 1178
BstDSI CCRYGG 2 cut(s) 508, 688
BstEII GGTNACC 2 cut(s) 793, 985
BstENI CCTNNNNNAGG 1 cut(s) 553
BstF5I GGATG 4 cut(s) 301, 843, 1006, 1079
BstFNI CGCG 1 cut(s) 1198
BstHHI GCGC 1 cut(s) 230
BstKTI GATC 6 cut(s) 79, 345, 366, 390, 643, 695
BstMAI GTCTC 2 cut(s) 613, 1126
BstMBI GATC 6 cut(s) 76, 342, 363, 387, 640, 692
BstMWI GCNNNNNNNGC 6 cut(s) 227, 471, 754, 1085, 1191, 1200
BstPAI GACNNNNGTC 1 cut(s) 1138
BstPI GGTNACC 2 cut(s) 793, 985
BstSCI CCNGG 1 cut(s) 319
BstSLI GKGCMC 2 cut(s) 471, 759
BstUI CGCG 1 cut(s) 1198
BstV1I GCAGC 1 cut(s) 1041
BstX2I RGATCY 1 cut(s) 76
BstYI RGATCY 1 cut(s) 76
Bsu36I CCTNAGG 1 cut(s) 1042
BsuRI GGCC 1 cut(s) 469
BtgI CCRYGG 2 cut(s) 508, 688
BtsCI GGATG 4 cut(s) 301, 843, 1006, 1079
BtsI GCAGTG 1 cut(s) 1158
BtsIMutI CAGTG 2 cut(s) 766, 1158
BveI ACCTGC 1 cut(s) 781
Cac8I GCNNGC 5 cut(s) 219, 249, 463, 467, 1196
CfoI GCGC 1 cut(s) 230
Cfr13I GGNCC 3 cut(s) 467, 468, 1038
CseI GACGC 1 cut(s) 595
Csp6I GTAC 3 cut(s) 101, 452, 487
CviAII CATG 9 cut(s) 147, 382, 629, 689, 724, 745, 854, 866, 995
CviJI RGCY 9 cut(s) 217, 221, 406, 469, 673, 826, 939, 1169, 1194
CviKI_1 RGCY 9 cut(s) 217, 221, 406, 469, 673, 826, 939, 1169, 1194
CviQI GTAC 3 cut(s) 101, 452, 487
DdeI CTNAG 5 cut(s) 292, 774, 1042, 1124, 1178
DpnI GATC 6 cut(s) 78, 344, 365, 389, 642, 694
DpnII GATC 6 cut(s) 76, 342, 363, 387, 640, 692
Eam1104I CTCTTC 1 cut(s) 396
EarI CTCTTC 1 cut(s) 396
EciI GGCGGA 1 cut(s) 598
Eco130I CCWWGG 2 cut(s) 688, 940
Eco24I GRGCYC 2 cut(s) 471, 1196
Eco31I GGTCTC 2 cut(s) 613, 1126
Eco47I GGWCC 1 cut(s) 1038
Eco81I CCTNAGG 1 cut(s) 1042
Eco91I GGTNACC 2 cut(s) 793, 985
EcoNI CCTNNNNNAGG 1 cut(s) 553
EcoO109I RGGNCCY 2 cut(s) 468, 1038
EcoO65I GGTNACC 2 cut(s) 793, 985
EcoT14I CCWWGG 2 cut(s) 688, 940
EcoT38I GRGCYC 2 cut(s) 471, 1196
ErhI CCWWGG 2 cut(s) 688, 940
FaeI CATG 9 cut(s) 150, 385, 632, 692, 727, 748, 857, 869, 998
FaqI GGGAC 2 cut(s) 278, 572
FatI CATG 9 cut(s) 146, 381, 628, 688, 723, 744, 853, 865, 994
FauI CCCGC 2 cut(s) 458, 533
FblI GTMKAC 1 cut(s) 850
Fnu4HI GCNGC 1 cut(s) 1055
FokI GGATG 4 cut(s) 288, 850, 1013, 1066
FriOI GRGCYC 2 cut(s) 471, 1196
Fsp4HI GCNGC 1 cut(s) 1055
FspBI CTAG 2 cut(s) 218, 1101
FspI TGCGCA 1 cut(s) 229
GlaI GCGC 1 cut(s) 229
GluI GCNGC 1 cut(s) 1055
GsuI CTGGAG 2 cut(s) 199, 1054
HaeIII GGCC 1 cut(s) 469
HapII CCGG 5 cut(s) 321, 566, 1083, 1089, 1164
HgaI GACGC 1 cut(s) 595
HhaI GCGC 1 cut(s) 230
Hin1II CATG 9 cut(s) 150, 385, 632, 692, 727, 748, 857, 869, 998
Hin6I GCGC 1 cut(s) 228
HinP1I GCGC 1 cut(s) 228
HinfI GANTC 7 cut(s) 237, 290, 560, 727, 764, 972, 1120
HpaII CCGG 5 cut(s) 321, 566, 1083, 1089, 1164
HphI GGTGA 5 cut(s) 100, 295, 722, 787, 883
Hpy166II GTNNAC 4 cut(s) 310, 454, 851, 874
Hpy188I TCNGA 5 cut(s) 242, 332, 595, 834, 1125
Hpy188III TCNNGA 7 cut(s) 80, 361, 424, 524, 776, 1044, 1147
Hpy8I GTNNAC 4 cut(s) 310, 454, 851, 874
Hpy99I CGWCG 5 cut(s) 437, 599, 605, 1141, 1144
HpyAV CCTTC 4 cut(s) 44, 430, 815, 1183
HpyCH4III ACNGT 6 cut(s) 269, 486, 530, 761, 1064, 1137
HpyCH4IV ACGT 3 cut(s) 279, 489, 552
HpyCH4V TGCA 8 cut(s) 94, 461, 474, 790, 803, 905, 1004, 1185
HpyF10VI GCNNNNNNNGC 6 cut(s) 227, 471, 754, 1085, 1191, 1200
HpyF3I CTNAG 5 cut(s) 292, 774, 1042, 1124, 1178
HpySE526I ACGT 3 cut(s) 279, 489, 552
Hsp92II CATG 9 cut(s) 150, 385, 632, 692, 727, 748, 857, 869, 998
HspAI GCGC 1 cut(s) 228
Kzo9I GATC 6 cut(s) 76, 342, 363, 387, 640, 692
LguI GCTCTTC 1 cut(s) 396
LmnI GCTCC 5 cut(s) 30, 568, 1020, 1091, 1166
Lsp1109I GCAGC 1 cut(s) 1041
LweI GCATC 8 cut(s) 81, 120, 670, 828, 991, 1088, 1103, 1124
MaeI CTAG 2 cut(s) 218, 1101
MaeII ACGT 3 cut(s) 279, 489, 552
MaeIII GTNAC 8 cut(s) 185, 283, 377, 490, 665, 793, 985, 1103
MalI GATC 6 cut(s) 78, 344, 365, 389, 642, 694
MboI GATC 6 cut(s) 76, 342, 363, 387, 640, 692
MboII GAAGA 3 cut(s) 361, 413, 1063
MfeI CAATTG 2 cut(s) 231, 906
MflI RGATCY 1 cut(s) 76
MhlI GDGCHC 4 cut(s) 471, 573, 759, 1196
MluCI AATT 6 cut(s) 130, 231, 675, 718, 859, 906
MlyI GAGTC 4 cut(s) 284, 554, 721, 1129
MmeI TCCRAC 3 cut(s) 618, 681, 950
MroXI GAANNNNTTC 1 cut(s) 419
MseI TTAA 1 cut(s) 515
MslI CAYNNNNRTG 1 cut(s) 999
MspI CCGG 5 cut(s) 321, 566, 1083, 1089, 1164
MspR9I CCNGG 1 cut(s) 321
MunI CAATTG 2 cut(s) 231, 906
Mva1269I GAATGC 1 cut(s) 803
MvnI CGCG 1 cut(s) 1198
MwoI GCNNNNNNNGC 6 cut(s) 227, 471, 754, 1085, 1191, 1200
NciI CCSGG 1 cut(s) 321
NcoI CCATGG 1 cut(s) 688
NdeII GATC 6 cut(s) 76, 342, 363, 387, 640, 692
NheI GCTAGC 1 cut(s) 217
NlaIII CATG 9 cut(s) 150, 385, 632, 692, 727, 748, 857, 869, 998
NlaIV GGNNCC 4 cut(s) 325, 469, 960, 1087
NmuCI GTSAC 6 cut(s) 185, 283, 377, 490, 665, 793
NsbI TGCGCA 1 cut(s) 229
PciSI GCTCTTC 1 cut(s) 396
PctI GAATGC 1 cut(s) 803
PdmI GAANNNNTTC 1 cut(s) 419
PfeI GAWTC 3 cut(s) 237, 764, 972
PflFI GACNNNGTC 1 cut(s) 605
PkrI GCNGC 1 cut(s) 1056
PleI GAGTC 4 cut(s) 284, 554, 721, 1128
PpsI GAGTC 4 cut(s) 284, 554, 721, 1128
Ppu21I YACGTR 2 cut(s) 280, 490
PpuMI RGGWCCY 1 cut(s) 1038
PshAI GACNNNNGTC 1 cut(s) 1138
Psp5II RGGWCCY 1 cut(s) 1038
PspEI GGTNACC 2 cut(s) 793, 985
PspN4I GGNNCC 4 cut(s) 325, 469, 960, 1087
PspOMI GGGCCC 1 cut(s) 467
PspPI GGNCC 3 cut(s) 467, 468, 1038
PspPPI RGGWCCY 1 cut(s) 1038
PsrI GAACNNNNNNTAC 2 cut(s) 866, 898
PsuI RGATCY 1 cut(s) 76
PsyI GACNNNGTC 1 cut(s) 605
RsaI GTAC 3 cut(s) 102, 453, 488
RsaNI GTAC 3 cut(s) 101, 452, 487
RseI CAYNNNNRTG 1 cut(s) 999
SapI GCTCTTC 1 cut(s) 396
SaqAI TTAA 1 cut(s) 515
SatI GCNGC 1 cut(s) 1055
Sau3AI GATC 6 cut(s) 76, 342, 363, 387, 640, 692
Sau96I GGNCC 3 cut(s) 467, 468, 1038
SchI GAGTC 4 cut(s) 284, 554, 721, 1129
ScrFI CCNGG 1 cut(s) 321
SduI GDGCHC 4 cut(s) 471, 573, 759, 1196
SfaNI GCATC 8 cut(s) 81, 120, 670, 828, 991, 1088, 1103, 1124
SinI GGWCC 1 cut(s) 1038
SmiMI CAYNNNNRTG 1 cut(s) 999
SmlI CTYRAG 1 cut(s) 121
SmoI CTYRAG 1 cut(s) 121
SpeI ACTAGT 1 cut(s) 1100
Sse9I AATT 6 cut(s) 130, 231, 675, 718, 859, 906
SsiI CCGC 4 cut(s) 208, 465, 540, 583
SspMI CTAG 2 cut(s) 218, 1101
StyD4I CCNGG 1 cut(s) 319
StyI CCWWGG 2 cut(s) 688, 940
TaaI ACNGT 6 cut(s) 269, 486, 530, 761, 1064, 1137
TaiI ACGT 3 cut(s) 282, 492, 555
TaqI TCGA 2 cut(s) 432, 1118
TasI AATT 6 cut(s) 130, 231, 675, 718, 859, 906
TatI WGTACW 1 cut(s) 100
TfiI GAWTC 3 cut(s) 237, 764, 972
Tru1I TTAA 1 cut(s) 515
Tru9I TTAA 1 cut(s) 515
TscAI CASTG 2 cut(s) 766, 1165
TseFI GTSAC 6 cut(s) 185, 283, 377, 490, 665, 793
TseI GCWGC 1 cut(s) 1054
Tsp45I GTSAC 6 cut(s) 185, 283, 377, 490, 665, 793
TspDTI ATGAA 3 cut(s) 135, 428, 854
TspGWI ACGGA 2 cut(s) 302, 525
TspRI CASTG 2 cut(s) 766, 1165
Tth111I GACNNNGTC 1 cut(s) 605
VpaK11BI GGWCC 1 cut(s) 1038
XagI CCTNNNNNAGG 1 cut(s) 553
XapI RAATTY 2 cut(s) 130, 859
XcmI CCANNNNNNNNNTGG 1 cut(s) 1014
XmiI GTMKAC 1 cut(s) 850
XmnI GAANNNNTTC 1 cut(s) 419
XspI CTAG 2 cut(s) 218, 1101
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.