MD03G1260800.v1.1

Polygalacturonase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr03
OG0000579
Physical Location & Seq
Forward (+)
34732639 .. 34733449
811 bp
Loading structure...
UTR
Exon/CDS
Intron
MD03G1260800.v1.1.491

Sequence Viewer

Length: 711 bp
ATGTCACCATTCGTGATTCGTCTATCGGGACAGGCGACGATTGTATTTCCATTGGCGACCGGTGTTCCTTTCTCTCCATCACCAACATTGCTTGCGGACCAGGTCATGGAATTAGGTATTGTTGGAAGCTTGGGAGAAGATGGCGCTAGTGGTAAAGTGGACAATATATATGTGAAAGATTGTAGTTTCACTGGAACTACAAATGGAGCGAGAATAAAGACGTGGCAGGGCGGCTCCGGGTATGCGAGAAACATCACGTTCGAGAGGATCAAACTTGACAGAGCTCAATATCCTATCATTATTGATCAGTACTATTGTAATGGGGAACACGATTGCAAAAGTCAGTCGTCGGCCGTGGTGGTGGCGGATGTGATGTACATCGATTTTGAAGGCACTTCTGCGACGGAGGAGGCGATTAAACTCGATTGCGATCAAGTTTCAGGTGGCTGTCACAATATTGTGATGGATAGGATTAATATAATGCCAGCGGTGAGGGATATGAAGATTTTTGCGACTTGTAAAAACGCCAAAGGGACTTATGTCGGCACTACGGTGCCCAACGTGCCTTGTCTACAGAGTTCAGCGACGGAGCCTACAAGGCCAACAACCATCTACACCGGAAGTGGAGGTTCTGGCAGTGCTAATCTACATATAAACTACTACCTGTTTTGTCCACTGATGACGGTTCTTGTTGCAATAGCTGTTTTTTGA
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

Protein Analysis

237

Amino Acids

25.31

Weight (kDa)

5.34

Isoelectric Point (pI)

42.13

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Glyco_hydro_28 PF00295 41 - 177 2.3e-30 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: OG0000579)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G32370 AT4G32375 AT4G32380 AT4G32380
fragaria_vesca FvH4_2g29242 FvH4_2g29270 FvH4_4g07180 FvH4_4g07190 FvH4_6g32320 FvH4_6g35100
malus_domestica MD03G1260700.v1.1 MD03G1260800.v1.1 MD09G1203400.v1.1 MD15G1065500.v1.1 MD15G1124200.v1.1 MD15G1124300.v1.1
prunus_persica Prupe.1G247300_v2.0.a1 Prupe.1G247300_v2.0.a1 Prupe.1G479600_v2.0.a1 Prupe.1G479700_v2.0.a1 Prupe.3G043600_v2.0.a1 Prupe.4G130600_v2.0.a1 Prupe.7G064200_v2.0.a1
pyrus_communis pycom03g20830 pycom15g06200
rosa_chinensis RchiOBHm_Chr2g0140421 RchiOBHm_Chr2g0146281 RchiOBHm_Chr3g0458021 RchiOBHm_Chr3g0481551 RchiOBHm_Chr4g0399361 RchiOBHm_Chr4g0399381 RchiOBHm_Chr4g0399391 RchiOBHm_Chr4g0399401 RchiOBHm_Chr4g0399411 RchiOBHm_Chr4g0399471
rosa_laevigata RLG00000009265 RLG00000009272 RLG00000011536 RLG00000011537 RLG00000019863 RLG00000020193 RLG00000023386
rosa_multiflora Rmu_sc0000384.1_g000011 Rmu_sc0002800.1_g000011 Rmu_sc0002800.1_g000012 Rmu_sc0017309.1_g000001 Rmu_sc0022824.1_g000003
rosa_roxburghii Rroxscaffold_153G00436780 Rroxscaffold_2G00100180 Rroxscaffold_5G00344320 Rroxscaffold_5G00344370 Rroxscaffold_6G00400330 Rroxscaffold_6G00421350 Rroxscaffold_7G00169940 Rroxscaffold_7G00169950
rosa_rugosa Rorug02G0362600 Rorug02G0394100 Rorug03G0024300 Rorug03G0192500 Rorug04G0016900 Rorug04G0017100 Rorug06G0278700
rosa_samantha Rh2CG399600 Rh2CG437200 Rh3AG084800 Rh3BG087600 Rh3CG088100 Rh3DG088500 Rh3DG270800 Rh4BG091900 Rh4BG092300 Rh5AG287300 Rh6DG389600
rosa_wichuraiana Rw0G012400 Rw2G033880 Rw2G036760 Rw3G007220 Rw3G021790 Rw4G007750 Rw4G007770 Rw4G007810

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 553
AccB7I CCANNNNNTGG 1 cut(s) 106
AccI GTMKAC 1 cut(s) 571
AciI CCGC 4 cut(s) 95, 231, 365, 488
AclWI GGATC 1 cut(s) 275
AcoI YGGCCR 1 cut(s) 351
AfaI GTAC 2 cut(s) 311, 377
AfiI CCNNNNNNNGG 1 cut(s) 106
AgeI ACCGGT 1 cut(s) 59
AgsI TTSAA 1 cut(s) 389
AjiI CACGTC 1 cut(s) 222
AjnI CCWGG 1 cut(s) 99
AleI CACNNNNGTG 1 cut(s) 551
AluBI AGCT 3 cut(s) 129, 284, 701
AluI AGCT 3 cut(s) 129, 284, 701
Alw21I GWGCWC 1 cut(s) 286
AlwI GGATC 1 cut(s) 275
AoxI GGCC 2 cut(s) 351, 599
AseI ATTAAT 1 cut(s) 474
AsiGI ACCGGT 1 cut(s) 59
AspLEI GCGC 1 cut(s) 146
AspS9I GGNCC 1 cut(s) 97
AsuC2I CCSGG 1 cut(s) 238
AsuHPI GGTGA 2 cut(s) 72, 502
AvaII GGWCC 1 cut(s) 97
BaeGI GKGCMC 1 cut(s) 558
BanI GGYRCC 1 cut(s) 553
BanII GRGCYC 1 cut(s) 286
Bbv12I GWGCWC 1 cut(s) 286
BccI CCATC 4 cut(s) 85, 134, 457, 617
BceAI ACGGC 1 cut(s) 338
BciT130I CCWGG 1 cut(s) 101
BclI TGATCA 1 cut(s) 304
BcnI CCSGG 1 cut(s) 238
BfaI CTAG 1 cut(s) 147
BfmI CTRYAG 1 cut(s) 572
BfoI RGCGCY 1 cut(s) 147
BglI GCCNNNNNGGC 1 cut(s) 598
BisI GCNGC 1 cut(s) 232
BlsI GCNGC 1 cut(s) 233
BmcAI AGTACT 1 cut(s) 311
Bme1390I CCNGG 2 cut(s) 101, 238
Bme18I GGWCC 1 cut(s) 97
BmgBI CACGTC 1 cut(s) 222
BmgT120I GGNCC 1 cut(s) 97
BmiI GGNNCC 3 cut(s) 235, 555, 591
BmrFI CCNGG 2 cut(s) 101, 238
BoxI GACNNNNGTC 1 cut(s) 539
BpuMI CCSGG 1 cut(s) 238
Bsa29I ATCGAT 1 cut(s) 381
BsaBI GATNNNNATC 2 cut(s) 377, 429
BsaJI CCNNGG 1 cut(s) 354
BsaWI WCCGGW 2 cut(s) 59, 617
Bsc4I CCNNNNNNNGG 1 cut(s) 106
Bse118I RCCGGY 1 cut(s) 59
Bse1I ACTGG 1 cut(s) 196
Bse3DI GCAATG 1 cut(s) 86
Bse8I GATNNNNATC 2 cut(s) 377, 429
BseBI CCWGG 1 cut(s) 101
BseCI ATCGAT 1 cut(s) 381
BseDI CCNNGG 1 cut(s) 354
BseGI GGATG 1 cut(s) 373
BseJI GATNNNNATC 2 cut(s) 377, 429
BseLI CCNNNNNNNGG 1 cut(s) 106
BseMI GCAATG 1 cut(s) 86
BseNI ACTGG 1 cut(s) 196
BseRI GAGGAG 1 cut(s) 422
BseSI GKGCMC 1 cut(s) 558
BseX3I CGGCCG 1 cut(s) 351
Bsh1285I CGRYCG 2 cut(s) 60, 354
BshFI GGCC 2 cut(s) 353, 601
BshNI GGYRCC 1 cut(s) 553
BshTI ACCGGT 1 cut(s) 59
BshVI ATCGAT 1 cut(s) 381
BsiEI CGRYCG 2 cut(s) 60, 354
BsiHKAI GWGCWC 1 cut(s) 286
BsiSI CCGG 3 cut(s) 60, 237, 618
BslFI GGGAC 2 cut(s) 42, 547
BslI CCNNNNNNNGG 1 cut(s) 106
BsmFI GGGAC 2 cut(s) 42, 547
BsnI GGCC 2 cut(s) 353, 601
Bsp1286I GDGCHC 2 cut(s) 286, 558
Bsp1407I TGTACA 1 cut(s) 375
Bsp143I GATC 3 cut(s) 267, 304, 430
BspACI CCGC 4 cut(s) 95, 231, 365, 488
BspANI GGCC 2 cut(s) 353, 601
BspDI ATCGAT 1 cut(s) 381
BspLI GGNNCC 3 cut(s) 235, 555, 591
BspPI GGATC 1 cut(s) 275
BspT107I GGYRCC 1 cut(s) 553
BsrDI GCAATG 1 cut(s) 86
BsrFI RCCGGY 1 cut(s) 59
BsrGI TGTACA 1 cut(s) 375
BsrI ACTGG 1 cut(s) 196
BssAI RCCGGY 1 cut(s) 59
BssECI CCNNGG 1 cut(s) 354
BssMI GATC 3 cut(s) 267, 304, 430
Bst2UI CCWGG 1 cut(s) 101
Bst4CI ACNGT 2 cut(s) 553, 685
BstAUI TGTACA 1 cut(s) 375
BstC8I GCNNGC 2 cut(s) 93, 486
BstDSI CCRYGG 1 cut(s) 354
BstF5I GGATG 1 cut(s) 373
BstH2I RGCGCY 1 cut(s) 147
BstHHI GCGC 1 cut(s) 146
BstKTI GATC 3 cut(s) 270, 307, 433
BstMBI GATC 3 cut(s) 267, 304, 430
BstMCI CGRYCG 2 cut(s) 60, 354
BstMWI GCNNNNNNNGC 2 cut(s) 562, 598
BstNI CCWGG 1 cut(s) 101
BstPAI GACNNNNGTC 1 cut(s) 539
BstSCI CCNGG 2 cut(s) 99, 236
BstSFI CTRYAG 1 cut(s) 572
BstSLI GKGCMC 1 cut(s) 558
BstZI CGGCCG 1 cut(s) 351
Bsu15I ATCGAT 1 cut(s) 381
BsuRI GGCC 2 cut(s) 353, 601
BsuTUI ATCGAT 1 cut(s) 381
BtgI CCRYGG 1 cut(s) 354
BtrI CACGTC 1 cut(s) 222
BtsCI GGATG 1 cut(s) 373
BtsI GCAGTG 1 cut(s) 643
BtsIMutI CAGTG 3 cut(s) 189, 643, 674
Cac8I GCNNGC 2 cut(s) 93, 486
CfoI GCGC 1 cut(s) 146
Cfr10I RCCGGY 1 cut(s) 59
Cfr13I GGNCC 1 cut(s) 97
ClaI ATCGAT 1 cut(s) 381
CsiI ACCWGGT 1 cut(s) 99
Csp6I GTAC 2 cut(s) 310, 376
CspAI ACCGGT 1 cut(s) 59
CviAII CATG 1 cut(s) 106
CviJI RGCY 8 cut(s) 129, 234, 284, 353, 447, 592, 601, 701
CviKI_1 RGCY 8 cut(s) 129, 234, 284, 353, 447, 592, 601, 701
CviQI GTAC 2 cut(s) 310, 376
DpnI GATC 3 cut(s) 269, 306, 432
DpnII GATC 3 cut(s) 267, 304, 430
EaeI YGGCCR 1 cut(s) 351
EagI CGGCCG 1 cut(s) 351
EciI GGCGGA 1 cut(s) 380
Ecl136II GAGCTC 1 cut(s) 284
EclXI CGGCCG 1 cut(s) 351
Eco24I GRGCYC 1 cut(s) 286
Eco47I GGWCC 1 cut(s) 97
Eco52I CGGCCG 1 cut(s) 351
Eco53kI GAGCTC 1 cut(s) 284
EcoICRI GAGCTC 1 cut(s) 284
EcoRII CCWGG 1 cut(s) 99
EcoT38I GRGCYC 1 cut(s) 286
FaeI CATG 1 cut(s) 109
FaqI GGGAC 2 cut(s) 42, 547
FatI CATG 1 cut(s) 105
FbaI TGATCA 1 cut(s) 304
FblI GTMKAC 1 cut(s) 571
Fnu4HI GCNGC 1 cut(s) 232
FokI GGATG 1 cut(s) 380
FriOI GRGCYC 1 cut(s) 286
Fsp4HI GCNGC 1 cut(s) 232
FspBI CTAG 1 cut(s) 147
GlaI GCGC 1 cut(s) 145
GluI GCNGC 1 cut(s) 232
HaeII RGCGCY 1 cut(s) 147
HaeIII GGCC 2 cut(s) 353, 601
HapII CCGG 3 cut(s) 60, 237, 618
HhaI GCGC 1 cut(s) 146
Hin1II CATG 1 cut(s) 109
Hin6I GCGC 1 cut(s) 144
HinP1I GCGC 1 cut(s) 144
HindIII AAGCTT 1 cut(s) 127
HinfI GANTC 1 cut(s) 16
HpaII CCGG 3 cut(s) 60, 237, 618
HphI GGTGA 2 cut(s) 72, 502
Hpy166II GTNNAC 3 cut(s) 160, 572, 674
Hpy188III TCNNGA 3 cut(s) 13, 27, 262
Hpy8I GTNNAC 3 cut(s) 160, 572, 674
Hpy99I CGWCG 4 cut(s) 40, 352, 406, 589
HpyAV CCTTC 1 cut(s) 383
HpyCH4III ACNGT 2 cut(s) 553, 685
HpyCH4IV ACGT 3 cut(s) 221, 257, 561
HpyCH4V TGCA 2 cut(s) 336, 695
HpyF10VI GCNNNNNNNGC 2 cut(s) 562, 598
HpySE526I ACGT 3 cut(s) 221, 257, 561
Hsp92II CATG 1 cut(s) 109
HspAI GCGC 1 cut(s) 144
Ksp22I TGATCA 1 cut(s) 304
Kzo9I GATC 3 cut(s) 267, 304, 430
LmnI GCTCC 3 cut(s) 206, 239, 589
MabI ACCWGGT 1 cut(s) 99
MaeI CTAG 1 cut(s) 147
MaeII ACGT 3 cut(s) 221, 257, 561
MaeIII GTNAC 2 cut(s) 3, 449
MalI GATC 3 cut(s) 269, 306, 432
MboI GATC 3 cut(s) 267, 304, 430
MboII GAAGA 2 cut(s) 149, 514
MhlI GDGCHC 2 cut(s) 286, 558
MluCI AATT 1 cut(s) 110
MmeI TCCRAC 1 cut(s) 103
MnlI CCTC 5 cut(s) 258, 400, 403, 486, 620
MseI TTAA 2 cut(s) 417, 474
MslI CAYNNNNRTG 1 cut(s) 551
MspA1I CMGCKG 1 cut(s) 488
MspI CCGG 3 cut(s) 60, 237, 618
MspR9I CCNGG 2 cut(s) 101, 238
MvaI CCWGG 1 cut(s) 101
MwoI GCNNNNNNNGC 2 cut(s) 562, 598
NciI CCSGG 1 cut(s) 238
NdeII GATC 3 cut(s) 267, 304, 430
NlaIII CATG 1 cut(s) 109
NlaIV GGNNCC 3 cut(s) 235, 555, 591
NmuCI GTSAC 2 cut(s) 3, 449
OliI CACNNNNGTG 1 cut(s) 551
PcsI WCGNNNNNNNCGW 2 cut(s) 32, 410
PfeI GAWTC 1 cut(s) 16
PflFI GACNNNGTC 1 cut(s) 101
PflMI CCANNNNNTGG 1 cut(s) 106
PinAI ACCGGT 1 cut(s) 59
PkrI GCNGC 1 cut(s) 233
PshAI GACNNNNGTC 1 cut(s) 539
PshBI ATTAAT 1 cut(s) 474
Psp124BI GAGCTC 1 cut(s) 286
Psp6I CCWGG 1 cut(s) 99
PspGI CCWGG 1 cut(s) 99
PspN4I GGNNCC 3 cut(s) 235, 555, 591
PspPI GGNCC 1 cut(s) 97
PsyI GACNNNGTC 1 cut(s) 101
RsaI GTAC 2 cut(s) 311, 377
RsaNI GTAC 2 cut(s) 310, 376
RseI CAYNNNNRTG 1 cut(s) 551
SacI GAGCTC 1 cut(s) 286
SaqAI TTAA 2 cut(s) 417, 474
SatI GCNGC 1 cut(s) 232
Sau3AI GATC 3 cut(s) 267, 304, 430
Sau96I GGNCC 1 cut(s) 97
ScaI AGTACT 1 cut(s) 311
ScrFI CCNGG 2 cut(s) 101, 238
SduI GDGCHC 2 cut(s) 286, 558
SexAI ACCWGGT 1 cut(s) 99
SfcI CTRYAG 1 cut(s) 572
SinI GGWCC 1 cut(s) 97
SmiMI CAYNNNNRTG 1 cut(s) 551
Sse9I AATT 1 cut(s) 110
SsiI CCGC 4 cut(s) 95, 231, 365, 488
SspI AATATT 1 cut(s) 457
SspMI CTAG 1 cut(s) 147
SstI GAGCTC 1 cut(s) 286
StyD4I CCNGG 2 cut(s) 99, 236
TaaI ACNGT 2 cut(s) 553, 685
TaiI ACGT 3 cut(s) 224, 260, 564
TaqI TCGA 3 cut(s) 261, 381, 423
TasI AATT 1 cut(s) 110
TatI WGTACW 2 cut(s) 309, 375
TauI GCSGC 1 cut(s) 234
TfiI GAWTC 1 cut(s) 16
Tru1I TTAA 2 cut(s) 417, 474
Tru9I TTAA 2 cut(s) 417, 474
TscAI CASTG 3 cut(s) 196, 643, 681
TseFI GTSAC 2 cut(s) 3, 449
Tsp45I GTSAC 2 cut(s) 3, 449
TspDTI ATGAA 1 cut(s) 515
TspGWI ACGGA 2 cut(s) 419, 602
TspRI CASTG 3 cut(s) 196, 643, 681
Tth111I GACNNNGTC 1 cut(s) 101
Van91I CCANNNNNTGG 1 cut(s) 106
VpaK11BI GGWCC 1 cut(s) 97
VspI ATTAAT 1 cut(s) 474
XmiI GTMKAC 1 cut(s) 571
XspI CTAG 1 cut(s) 147
ZrmI AGTACT 1 cut(s) 311
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.