MD09G1287300.v1.1

Polygalacturonase At1g48100-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr09
OG0012763
Physical Location & Seq
Forward (+)
36643320 .. 36645154
1835 bp
Loading structure...
UTR
Exon/CDS
Intron
MD09G1287300.v1.1.491

Sequence Viewer

Length: 1377 bp
ATGAAGAATTGCAAGTTTTCACTGCTTGTTTTCTGCATTTCATTCTTTTGCTTCTTATTAGTGCCCAACCAAGCCTGCAGATGGCATAACCATACAAAACAGAAGTACTCTCACAAGCAATCCCACATTTCACCACCTCCTTGCTCTCTGCCTGATCCCACTACTCCTCCCGAAGAGCCGCCTACCAAGCCGTATCATTCCTCCGGTATTTTTGATGTAAGATCATTTGGTGCTGTTGGAGATGGCCAAACTGATGACACCGTGGCGTTTAAGATGGCATGGGACACAGCCTGCCAAAGTGATGAATCTACTGCAAGGATTCTTGTTCCCCAAGGTTTCTCATTCATGATACAATCTACAATATTCACTGGTCCCTGCCTTGGGGGCCTGGTGTTACAGGTTGATGGAACTCTAGTGCCACCTGATGGACCAGGATCCTGGCCAAAGCACATCAGCAGGCACCAATGGCTGGTCTTTAACCGAATCAACGAGATGTCGCTGCAAGGCGGTGGTGTAATTGACGGGAGAGGAGAGAAATGGTGGAATCTTCCCTGCAAACCCCATAGGGGGATAAATGGAACCACATTGCCAGGACCATGTGATAGCCCAATTGCTATTAGGTTCTTTATGAGCTCCAACTTGACAGTTCAAGGACTTACAATTAAGAATAGCCCCCAATTCCACTTCAGGTTTGATAGTTGCAGGAATGTGCATATAGAATCCATTTCTATATCATCACCTGCTAAAAGTCCGAATACAGATGGGATTCATATAGAGAAAACATATGATGTCCAAATTTATAACTCAGTCATTTCTAATGGCTGTTATGATGTAAACATAAGGAACCTTACTTGTGGACCTGGTCATGGAATCAGCATTGGGAGTCTCGGAAATCACAACTCACGAGCATGCGTCTCTAACATTACTGTTAGGGACTCGATAATGAAAGGGACGGATAATGGAGTTAGGATCAAGACATGGCAGGGCGGGTCTGGTTCGGTGTCTGGAGTAACATTCAGTAACATTCACATGGATAATGTTAAGAACCCTATTATGATTGACCAATACTACTGCCCTACCAAACGGTGCACCAACCAAACTTCAGCTGTGTTTGTATCGGACATACTCTATTCGAACATAAAGGGGACTTATGACGTTTGGAGTTCACCAATGCATTTTGCCTGTAGTGATGCTCTCCCATGCACTAACTTGACACTCTCAGAAGTTGAGCTCCTTCCTGCAGTAAGATATAAGGTATCTGATCCGTATTGTTGGAATGCTTATGGAGAGCTGCTAACAGGAACAATTCCACCAATCTCTTGCTTGTTGGATGGCGTTCCTCGATCCCTACTGGGCCATGAAATTGAGCGTTGCTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00040 ko01100 map00040 map01100
Pfam Domains
Protein Families
Glyco_hydro_28 Pectate_lyase_3

Protein Analysis

459

Amino Acids

50.41

Weight (kDa)

7.51

Isoelectric Point (pI)

60.23

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Glyco_hydro_28 PF00295 101 - 411 1.2e-82 Glycosyl hydrolases family 28
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: OG0012763)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G02460
fragaria_vesca FvH4_1g26650
malus_domestica MD09G1287300.v1.1 MD17G1279500.v1.1
prunus_persica Prupe.3G005900_v2.0.a1 Prupe.6G307200_v2.0.a1
pyrus_communis pycom09g19460 pycom17g27760
rosa_chinensis RchiOBHm_Chr3g0486841
rosa_laevigata RLG00000023055
rosa_multiflora Rmu_sc0005709.1_g000005
rosa_roxburghii Rroxscaffold_6G00395520
rosa_rugosa Rorug03G0227400.1
rosa_samantha Rh3AG277500 Rh3BG312600 Rh3CG311500 Rh3DG308100
rosa_wichuraiana Rw3G024640

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 801
AarI CACCTGC 1 cut(s) 748
Acc36I ACCTGC 1 cut(s) 748
AccB1I GGYRCC 1 cut(s) 459
AccB7I CCANNNNNTGG 2 cut(s) 425, 469
AciI CCGC 3 cut(s) 179, 507, 987
AclWI GGATC 6 cut(s) 149, 429, 442, 977, 1256, 1338
AcoI YGGCCR 2 cut(s) 244, 440
AcsI RAATTY 1 cut(s) 795
AcuI CTGAAG 2 cut(s) 670, 1086
AfaI GTAC 1 cut(s) 107
AfiI CCNNNNNNNGG 8 cut(s) 81, 380, 381, 425, 469, 566, 567, 866
AgsI TTSAA 1 cut(s) 650
AjnI CCWGG 5 cut(s) 387, 430, 437, 589, 859
AluBI AGCT 4 cut(s) 633, 1106, 1231, 1291
AluI AGCT 4 cut(s) 633, 1106, 1231, 1291
Alw21I GWGCWC 3 cut(s) 635, 1091, 1233
Alw26I GTCTC 2 cut(s) 890, 919
Alw44I GTGCAC 1 cut(s) 1087
AlwI GGATC 6 cut(s) 149, 429, 442, 977, 1256, 1338
AoxI GGCC 4 cut(s) 244, 385, 440, 1354
ApaLI GTGCAC 1 cut(s) 1087
ApeKI GCWGC 2 cut(s) 499, 1291
ApoI RAATTY 1 cut(s) 795
AspS9I GGNCC 6 cut(s) 371, 385, 428, 593, 857, 1354
AsuHPI GGTGA 3 cut(s) 123, 729, 1158
AsuII TTCGAA 1 cut(s) 1133
AvaII GGWCC 4 cut(s) 371, 428, 593, 857
BaeGI GKGCMC 2 cut(s) 66, 1091
BalI TGGCCA 2 cut(s) 246, 442
BamHI GGATCC 1 cut(s) 434
BanI GGYRCC 1 cut(s) 459
BanII GRGCYC 2 cut(s) 635, 1233
BauI CACGAG 1 cut(s) 903
Bbv12I GWGCWC 3 cut(s) 635, 1091, 1233
BbvI GCAGC 2 cut(s) 486, 1278
BccI CCATC 7 cut(s) 75, 236, 268, 398, 419, 755, 1325
BceAI ACGGC 1 cut(s) 175
BciT130I CCWGG 5 cut(s) 389, 432, 439, 591, 861
BcoDI GTCTC 2 cut(s) 890, 919
BfaI CTAG 1 cut(s) 413
BfmI CTRYAG 3 cut(s) 76, 1183, 1239
BfuAI ACCTGC 1 cut(s) 748
BglI GCCNNNNNGGC 1 cut(s) 384
BisI GCNGC 3 cut(s) 179, 500, 1292
BlsI GCNGC 3 cut(s) 180, 501, 1293
BmcAI AGTACT 1 cut(s) 107
Bme1390I CCNGG 5 cut(s) 389, 432, 439, 591, 861
Bme18I GGWCC 4 cut(s) 371, 428, 593, 857
BmgT120I GGNCC 6 cut(s) 371, 385, 428, 593, 857, 1354
BmiI GGNNCC 6 cut(s) 373, 386, 436, 461, 580, 845
BmrFI CCNGG 5 cut(s) 389, 432, 439, 591, 861
BmrI ACTGGG 1 cut(s) 1361
BmsI GCATC 1 cut(s) 1180
BmuI ACTGGG 1 cut(s) 1361
BpmI CTGGAG 1 cut(s) 1026
Bpu14I TTCGAA 1 cut(s) 1133
BsaJI CCNNGG 3 cut(s) 261, 331, 379
BsaWI WCCGGW 1 cut(s) 203
BsaXI ACNNNNNCTCC 2 cut(s) 151, 181
Bsc4I CCNNNNNNNGG 8 cut(s) 81, 380, 381, 425, 469, 566, 567, 866
Bse1I ACTGG 2 cut(s) 373, 1356
Bse3DI GCAATG 1 cut(s) 584
BseBI CCWGG 5 cut(s) 389, 432, 439, 591, 861
BseDI CCNNGG 3 cut(s) 261, 331, 379
BseGI GGATG 1 cut(s) 1336
BseLI CCNNNNNNNGG 8 cut(s) 81, 380, 381, 425, 469, 566, 567, 866
BseMI GCAATG 1 cut(s) 584
BseMII CTCAG 2 cut(s) 819, 1233
BseNI ACTGG 2 cut(s) 373, 1356
BseRI GAGGAG 2 cut(s) 156, 543
BseSI GKGCMC 2 cut(s) 66, 1091
BseXI GCAGC 2 cut(s) 486, 1278
BshFI GGCC 4 cut(s) 246, 387, 442, 1356
BshNI GGYRCC 1 cut(s) 459
BsiHKAI GWGCWC 3 cut(s) 635, 1091, 1233
BsiSI CCGG 1 cut(s) 204
BslFI GGGAC 5 cut(s) 296, 357, 947, 964, 1159
BslI CCNNNNNNNGG 8 cut(s) 81, 380, 381, 425, 469, 566, 567, 866
BsmAI GTCTC 2 cut(s) 890, 919
BsmBI CGTCTC 1 cut(s) 919
BsmFI GGGAC 5 cut(s) 296, 357, 947, 964, 1159
BsmI GAATGC 1 cut(s) 1282
BsnI GGCC 4 cut(s) 246, 387, 442, 1356
Bsp119I TTCGAA 1 cut(s) 1133
Bsp1286I GDGCHC 4 cut(s) 66, 635, 1091, 1233
Bsp143I GATC 6 cut(s) 154, 221, 434, 969, 1261, 1343
BspACI CCGC 3 cut(s) 179, 507, 987
BspANI GGCC 4 cut(s) 246, 387, 442, 1356
BspCNI CTCAG 2 cut(s) 818, 1232
BspHI TCATGA 1 cut(s) 345
BspLI GGNNCC 6 cut(s) 373, 386, 436, 461, 580, 845
BspMAI CTGCAG 2 cut(s) 80, 1243
BspMI ACCTGC 1 cut(s) 748
BspPI GGATC 6 cut(s) 149, 429, 442, 977, 1256, 1338
BspQI GCTCTTC 1 cut(s) 168
BspT104I TTCGAA 1 cut(s) 1133
BspT107I GGYRCC 1 cut(s) 459
BsrDI GCAATG 1 cut(s) 584
BsrI ACTGG 2 cut(s) 373, 1356
BssECI CCNNGG 3 cut(s) 261, 331, 379
BssMI GATC 6 cut(s) 154, 221, 434, 969, 1261, 1343
BssSI CACGAG 1 cut(s) 903
BssT1I CCWWGG 2 cut(s) 331, 379
Bst2BI CACGAG 1 cut(s) 903
Bst2UI CCWGG 5 cut(s) 389, 432, 439, 591, 861
Bst4CI ACNGT 4 cut(s) 262, 646, 928, 1086
Bst6I CTCTTC 1 cut(s) 168
BstBI TTCGAA 1 cut(s) 1133
BstC8I GCNNGC 4 cut(s) 76, 292, 458, 910
BstDEI CTNAG 2 cut(s) 805, 1219
BstDSI CCRYGG 1 cut(s) 261
BstF5I GGATG 1 cut(s) 1336
BstKTI GATC 6 cut(s) 157, 224, 437, 972, 1264, 1346
BstMAI GTCTC 2 cut(s) 890, 919
BstMBI GATC 6 cut(s) 154, 221, 434, 969, 1261, 1343
BstMWI GCNNNNNNNGC 3 cut(s) 187, 384, 466
BstNI CCWGG 5 cut(s) 389, 432, 439, 591, 861
BstNSI RCATGY 1 cut(s) 912
BstSCI CCNGG 5 cut(s) 387, 430, 437, 589, 859
BstSFI CTRYAG 3 cut(s) 76, 1183, 1239
BstSLI GKGCMC 2 cut(s) 66, 1091
BstV1I GCAGC 2 cut(s) 486, 1278
BstX2I RGATCY 1 cut(s) 434
BstXI CCANNNNNNTGG 1 cut(s) 438
BstYI RGATCY 1 cut(s) 434
BsuRI GGCC 4 cut(s) 246, 387, 442, 1356
BtgI CCRYGG 1 cut(s) 261
BtsCI GGATG 1 cut(s) 1336
BtsI GCAGTG 1 cut(s) 20
BtsIMutI CAGTG 2 cut(s) 20, 366
BveI ACCTGC 1 cut(s) 748
Cac8I GCNNGC 4 cut(s) 76, 292, 458, 910
CciI TCATGA 1 cut(s) 345
Cfr13I GGNCC 6 cut(s) 371, 385, 428, 593, 857, 1354
CseI GACGC 1 cut(s) 901
CsiI ACCWGGT 1 cut(s) 859
Csp6I GTAC 1 cut(s) 106
CviAII CATG 9 cut(s) 279, 346, 597, 866, 909, 978, 1030, 1200, 1358
CviQI GTAC 1 cut(s) 106
DdeI CTNAG 2 cut(s) 805, 1219
DpnI GATC 6 cut(s) 156, 223, 436, 971, 1263, 1345
DpnII GATC 6 cut(s) 154, 221, 434, 969, 1261, 1343
EaeI YGGCCR 2 cut(s) 244, 440
Eam1104I CTCTTC 1 cut(s) 168
EarI CTCTTC 1 cut(s) 168
Ecl136II GAGCTC 2 cut(s) 633, 1231
Eco130I CCWWGG 2 cut(s) 331, 379
Eco24I GRGCYC 2 cut(s) 635, 1233
Eco47I GGWCC 4 cut(s) 371, 428, 593, 857
Eco53kI GAGCTC 2 cut(s) 633, 1231
Eco57I CTGAAG 2 cut(s) 670, 1086
EcoICRI GAGCTC 2 cut(s) 633, 1231
EcoO109I RGGNCCY 1 cut(s) 385
EcoRII CCWGG 5 cut(s) 387, 430, 437, 589, 859
EcoT14I CCWWGG 2 cut(s) 331, 379
EcoT22I ATGCAT 1 cut(s) 1176
EcoT38I GRGCYC 2 cut(s) 635, 1233
ErhI CCWWGG 2 cut(s) 331, 379
Esp3I CGTCTC 1 cut(s) 919
FaeI CATG 9 cut(s) 282, 349, 600, 869, 912, 981, 1033, 1203, 1361
FaqI GGGAC 5 cut(s) 296, 357, 947, 964, 1159
FatI CATG 9 cut(s) 278, 345, 596, 865, 908, 977, 1029, 1199, 1357
FauI CCCGC 1 cut(s) 980
FauNDI CATATG 1 cut(s) 784
Fnu4HI GCNGC 3 cut(s) 179, 500, 1292
FokI GGATG 1 cut(s) 1343
FriOI GRGCYC 2 cut(s) 635, 1233
Fsp4HI GCNGC 3 cut(s) 179, 500, 1292
FspBI CTAG 1 cut(s) 413
GluI GCNGC 3 cut(s) 179, 500, 1292
GsuI CTGGAG 1 cut(s) 1026
HaeIII GGCC 4 cut(s) 246, 387, 442, 1356
HapII CCGG 1 cut(s) 204
HgaI GACGC 1 cut(s) 901
Hin1II CATG 9 cut(s) 282, 349, 600, 869, 912, 981, 1033, 1203, 1361
HinfI GANTC 9 cut(s) 305, 319, 483, 544, 719, 766, 870, 883, 935
HpaII CCGG 1 cut(s) 204
HphI GGTGA 3 cut(s) 123, 729, 1158
Hpy166II GTNNAC 4 cut(s) 835, 857, 1089, 1166
Hpy188I TCNGA 5 cut(s) 753, 890, 1120, 1222, 1261
Hpy188III TCNNGA 5 cut(s) 170, 346, 903, 973, 1005
Hpy8I GTNNAC 4 cut(s) 835, 857, 1089, 1166
HpyAV CCTTC 1 cut(s) 1244
HpyCH4III ACNGT 4 cut(s) 262, 646, 928, 1086
HpyCH4IV ACGT 1 cut(s) 1155
HpyF10VI GCNNNNNNNGC 3 cut(s) 187, 384, 466
HpyF3I CTNAG 2 cut(s) 805, 1219
HpySE526I ACGT 1 cut(s) 1155
Hsp92II CATG 9 cut(s) 282, 349, 600, 869, 912, 981, 1033, 1203, 1361
Kzo9I GATC 6 cut(s) 154, 221, 434, 969, 1261, 1343
LguI GCTCTTC 1 cut(s) 168
LmnI GCTCC 2 cut(s) 638, 1236
Lsp1109I GCAGC 2 cut(s) 486, 1278
LweI GCATC 1 cut(s) 1180
MabI ACCWGGT 1 cut(s) 859
MaeI CTAG 1 cut(s) 413
MaeII ACGT 1 cut(s) 1155
MaeIII GTNAC 3 cut(s) 393, 1009, 1019
MalI GATC 6 cut(s) 156, 223, 436, 971, 1263, 1345
MboI GATC 6 cut(s) 154, 221, 434, 969, 1261, 1343
MboII GAAGA 3 cut(s) 16, 185, 539
MfeI CAATTG 1 cut(s) 609
MflI RGATCY 1 cut(s) 434
MhlI GDGCHC 4 cut(s) 66, 635, 1091, 1233
MlsI TGGCCA 2 cut(s) 246, 442
MluCI AATT 8 cut(s) 7, 516, 609, 660, 677, 795, 1305, 1362
MluNI TGGCCA 2 cut(s) 246, 442
MlyI GAGTC 2 cut(s) 892, 929
MmeI TCCRAC 4 cut(s) 217, 660, 1253, 1308
MnlI CCTC 5 cut(s) 147, 177, 211, 521, 1350
Mox20I TGGCCA 2 cut(s) 246, 442
Mph1103I ATGCAT 1 cut(s) 1176
MscI TGGCCA 2 cut(s) 246, 442
MseI TTAA 4 cut(s) 270, 477, 663, 1041
MslI CAYNNNNRTG 2 cut(s) 907, 1028
Msp20I TGGCCA 2 cut(s) 246, 442
MspA1I CMGCKG 1 cut(s) 1106
MspI CCGG 1 cut(s) 204
MspR9I CCNGG 5 cut(s) 389, 432, 439, 591, 861
MunI CAATTG 1 cut(s) 609
Mva1269I GAATGC 1 cut(s) 1282
MvaI CCWGG 5 cut(s) 389, 432, 439, 591, 861
MwoI GCNNNNNNNGC 3 cut(s) 187, 384, 466
NdeI CATATG 1 cut(s) 784
NdeII GATC 6 cut(s) 154, 221, 434, 969, 1261, 1343
NlaIII CATG 9 cut(s) 282, 349, 600, 869, 912, 981, 1033, 1203, 1361
NlaIV GGNNCC 6 cut(s) 373, 386, 436, 461, 580, 845
NsiI ATGCAT 1 cut(s) 1176
NspI RCATGY 1 cut(s) 912
NspV TTCGAA 1 cut(s) 1133
PaeI GCATGC 1 cut(s) 912
PagI TCATGA 1 cut(s) 345
PaqCI CACCTGC 1 cut(s) 748
PciSI GCTCTTC 1 cut(s) 168
PctI GAATGC 1 cut(s) 1282
PfeI GAWTC 7 cut(s) 305, 319, 483, 544, 719, 766, 870
PflFI GACNNNGTC 1 cut(s) 861
PflMI CCANNNNNTGG 2 cut(s) 425, 469
PkrI GCNGC 3 cut(s) 180, 501, 1293
PleI GAGTC 2 cut(s) 891, 929
PpsI GAGTC 2 cut(s) 891, 929
PsiI TTATAA 1 cut(s) 801
Psp124BI GAGCTC 2 cut(s) 635, 1233
Psp6I CCWGG 5 cut(s) 387, 430, 437, 589, 859
PspGI CCWGG 5 cut(s) 387, 430, 437, 589, 859
PspN4I GGNNCC 6 cut(s) 373, 386, 436, 461, 580, 845
PspPI GGNCC 6 cut(s) 371, 385, 428, 593, 857, 1354
PstI CTGCAG 2 cut(s) 80, 1243
PsuI RGATCY 1 cut(s) 434
PsyI GACNNNGTC 1 cut(s) 861
PvuII CAGCTG 1 cut(s) 1106
RsaI GTAC 1 cut(s) 107
RsaNI GTAC 1 cut(s) 106
RseI CAYNNNNRTG 2 cut(s) 907, 1028
SacI GAGCTC 2 cut(s) 635, 1233
SapI GCTCTTC 1 cut(s) 168
SaqAI TTAA 4 cut(s) 270, 477, 663, 1041
SatI GCNGC 3 cut(s) 179, 500, 1292
Sau3AI GATC 6 cut(s) 154, 221, 434, 969, 1261, 1343
Sau96I GGNCC 6 cut(s) 371, 385, 428, 593, 857, 1354
ScaI AGTACT 1 cut(s) 107
SchI GAGTC 2 cut(s) 892, 929
ScrFI CCNGG 5 cut(s) 389, 432, 439, 591, 861
SduI GDGCHC 4 cut(s) 66, 635, 1091, 1233
SexAI ACCWGGT 1 cut(s) 859
SfaNI GCATC 1 cut(s) 1180
SfcI CTRYAG 3 cut(s) 76, 1183, 1239
SfuI TTCGAA 1 cut(s) 1133
SinI GGWCC 4 cut(s) 371, 428, 593, 857
SmiMI CAYNNNNRTG 2 cut(s) 907, 1028
SphI GCATGC 1 cut(s) 912
Sse9I AATT 8 cut(s) 7, 516, 609, 660, 677, 795, 1305, 1362
SsiI CCGC 3 cut(s) 179, 507, 987
SspI AATATT 1 cut(s) 363
SspMI CTAG 1 cut(s) 413
SstI GAGCTC 2 cut(s) 635, 1233
StyD4I CCNGG 5 cut(s) 387, 430, 437, 589, 859
StyI CCWWGG 2 cut(s) 331, 379
TaaI ACNGT 4 cut(s) 262, 646, 928, 1086
TaiI ACGT 1 cut(s) 1158
TaqI TCGA 3 cut(s) 938, 1133, 1342
TasI AATT 8 cut(s) 7, 516, 609, 660, 677, 795, 1305, 1362
TatI WGTACW 1 cut(s) 105
TauI GCSGC 1 cut(s) 181
TfiI GAWTC 7 cut(s) 305, 319, 483, 544, 719, 766, 870
Tru1I TTAA 4 cut(s) 270, 477, 663, 1041
Tru9I TTAA 4 cut(s) 270, 477, 663, 1041
TscAI CASTG 2 cut(s) 27, 373
TseI GCWGC 2 cut(s) 499, 1291
TspDTI ATGAA 7 cut(s) 17, 30, 318, 334, 758, 959, 1374
TspGWI ACGGA 2 cut(s) 968, 1254
TspRI CASTG 2 cut(s) 27, 373
Tth111I GACNNNGTC 1 cut(s) 861
Van91I CCANNNNNTGG 2 cut(s) 425, 469
VneI GTGCAC 1 cut(s) 1087
VpaK11BI GGWCC 4 cut(s) 371, 428, 593, 857
XapI RAATTY 1 cut(s) 795
XceI RCATGY 1 cut(s) 912
XspI CTAG 1 cut(s) 413
ZrmI AGTACT 1 cut(s) 107
Zsp2I ATGCAT 1 cut(s) 1176
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.