MD03G1260700.v1.1

Polygalacturonase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr03
OG0000579
Physical Location & Seq
Forward (+)
34731966 .. 34732487
522 bp
Loading structure...
UTR
Exon/CDS
Intron
MD03G1260700.v1.1.491

Sequence Viewer

Length: 522 bp
ATGTCAATCATCAACACACTCATTCACATTTTAATTTTCTTCTTCCTCCCTTTGCCGTTGTTTATTAGCATTGCACATAGCCAAAAAATACTGGACATAACCAAGTACGGTGCTGTGGGAGACGGGCAAACGGATGATTCCCCAGCTTTTGTGAATGCATGGAAATATTTATGTCAAGGAATTAATGAAGCTATTAATGGCATACCAACACTTAATGTGCCGGAGGGGAAAACATTCTTGTTGCAACGTTTAAAATTTGAAGGTCCATGCAATACAAAGAACGTTCACCTTCAAGTTCTAGGAAATTTGTTGGCACCTGCACGTGGTGCATGGAAAGAATGCGATTCGGAGGACTGGCTAAGTTTTTCAAACGTCGAAAACCTAATGCTCGACGGCTCAGGCAAAATCGACGGCCAGGGGGCTGCATGGTGGAGCACTAGCCAATACGACGGGAGATCGCGCAAGCTCTTGGGGGATAACGACTGCAAACCACAGAAGGCACTGCAATTCCAGAACTGCTAA
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

174

Amino Acids

19.2

Weight (kDa)

5.87

Isoelectric Point (pI)

39.08

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Glyco_hydro_28 PF00295 70 - 148 4.1e-10 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)
AarI CACCTGC 1 cut(s) 325
Acc36I ACCTGC 1 cut(s) 325
AccB1I GGYRCC 1 cut(s) 313
AccII CGCG 1 cut(s) 460
AclI AACGTT 2 cut(s) 247, 282
AcoI YGGCCR 1 cut(s) 412
AcsI RAATTY 2 cut(s) 254, 304
AcvI CACGTG 1 cut(s) 323
AdeI CACNNNGTG 1 cut(s) 326
AfaI GTAC 1 cut(s) 107
AfiI CCNNNNNNNGG 1 cut(s) 323
AgsI TTSAA 3 cut(s) 260, 293, 369
AjnI CCWGG 1 cut(s) 414
AluBI AGCT 3 cut(s) 146, 191, 466
AluI AGCT 3 cut(s) 146, 191, 466
Alw21I GWGCWC 1 cut(s) 437
Alw26I GTCTC 1 cut(s) 114
AoxI GGCC 1 cut(s) 412
ApeKI GCWGC 1 cut(s) 422
ApoI RAATTY 2 cut(s) 254, 304
AseI ATTAAT 2 cut(s) 183, 195
Asp700I GAANNNNTTC 1 cut(s) 233
AspLEI GCGC 1 cut(s) 462
AspS9I GGNCC 1 cut(s) 263
AsuHPI GGTGA 1 cut(s) 278
AvaII GGWCC 1 cut(s) 263
BanI GGYRCC 1 cut(s) 313
BbrPI CACGTG 1 cut(s) 323
Bbv12I GWGCWC 1 cut(s) 437
BbvI GCAGC 1 cut(s) 409
BceAI ACGGC 3 cut(s) 40, 409, 427
BciT130I CCWGG 1 cut(s) 416
BcoDI GTCTC 1 cut(s) 114
BfaI CTAG 2 cut(s) 299, 438
BfuAI ACCTGC 1 cut(s) 325
BisI GCNGC 1 cut(s) 423
BlsI GCNGC 1 cut(s) 424
Bme1390I CCNGG 1 cut(s) 416
Bme18I GGWCC 1 cut(s) 263
BmgT120I GGNCC 1 cut(s) 263
BmiI GGNNCC 1 cut(s) 315
BmrFI CCNGG 1 cut(s) 416
Bpu10I CCTNAGC 1 cut(s) 397
BsaAI YACGTR 1 cut(s) 323
BsaJI CCNNGG 1 cut(s) 415
Bsc4I CCNNNNNNNGG 1 cut(s) 323
Bse1I ACTGG 2 cut(s) 96, 359
Bse3DI GCAATG 1 cut(s) 69
BseBI CCWGG 1 cut(s) 416
BseDI CCNNGG 1 cut(s) 415
BseGI GGATG 1 cut(s) 139
BseLI CCNNNNNNNGG 1 cut(s) 323
BseMI GCAATG 1 cut(s) 69
BseMII CTCAG 1 cut(s) 411
BseNI ACTGG 2 cut(s) 96, 359
BseXI GCAGC 1 cut(s) 409
BseYI CCCAGC 1 cut(s) 142
BsgI GTGCAG 1 cut(s) 303
Bsh1236I CGCG 1 cut(s) 460
BshFI GGCC 1 cut(s) 414
BshNI GGYRCC 1 cut(s) 313
BsiHKAI GWGCWC 1 cut(s) 437
BsiSI CCGG 1 cut(s) 221
BslI CCNNNNNNNGG 1 cut(s) 323
BsmAI GTCTC 1 cut(s) 114
BsmBI CGTCTC 1 cut(s) 114
BsmI GAATGC 2 cut(s) 160, 344
BsnI GGCC 1 cut(s) 414
Bsp1286I GDGCHC 1 cut(s) 437
Bsp143I GATC 1 cut(s) 455
BspANI GGCC 1 cut(s) 414
BspCNI CTCAG 1 cut(s) 410
BspFNI CGCG 1 cut(s) 460
BspLI GGNNCC 1 cut(s) 315
BspMI ACCTGC 1 cut(s) 325
BspT107I GGYRCC 1 cut(s) 313
BsrDI GCAATG 1 cut(s) 69
BsrI ACTGG 2 cut(s) 96, 359
BssECI CCNNGG 1 cut(s) 415
BssMI GATC 1 cut(s) 455
Bst2UI CCWGG 1 cut(s) 416
Bst4CI ACNGT 1 cut(s) 110
BstAPI GCANNNNNTGC 1 cut(s) 326
BstBAI YACGTR 1 cut(s) 323
BstC8I GCNNGC 1 cut(s) 464
BstDEI CTNAG 2 cut(s) 359, 397
BstF5I GGATG 1 cut(s) 139
BstFNI CGCG 1 cut(s) 460
BstHHI GCGC 1 cut(s) 462
BstKTI GATC 1 cut(s) 458
BstMAI GTCTC 1 cut(s) 114
BstMBI GATC 1 cut(s) 455
BstMWI GCNNNNNNNGC 1 cut(s) 326
BstNI CCWGG 1 cut(s) 416
BstSCI CCNGG 1 cut(s) 414
BstUI CGCG 1 cut(s) 460
BstV1I GCAGC 1 cut(s) 409
BsuRI GGCC 1 cut(s) 414
BtsCI GGATG 1 cut(s) 139
BtsI GCAGTG 1 cut(s) 500
BtsIMutI CAGTG 1 cut(s) 500
BveI ACCTGC 1 cut(s) 325
Cac8I GCNNGC 1 cut(s) 464
CfoI GCGC 1 cut(s) 462
Cfr13I GGNCC 1 cut(s) 263
Csp6I GTAC 1 cut(s) 106
CviAII CATG 4 cut(s) 159, 267, 330, 426
CviJI RGCY 9 cut(s) 81, 146, 191, 358, 396, 414, 422, 441, 466
CviKI_1 RGCY 9 cut(s) 81, 146, 191, 358, 396, 414, 422, 441, 466
CviQI GTAC 1 cut(s) 106
DdeI CTNAG 2 cut(s) 359, 397
DpnI GATC 1 cut(s) 457
DpnII GATC 1 cut(s) 455
DraI TTTAAA 1 cut(s) 252
DraIII CACNNNGTG 1 cut(s) 326
EaeI YGGCCR 1 cut(s) 412
Eco47I GGWCC 1 cut(s) 263
Eco72I CACGTG 1 cut(s) 323
EcoRII CCWGG 1 cut(s) 414
EcoT22I ATGCAT 1 cut(s) 160
Esp3I CGTCTC 1 cut(s) 114
FaeI CATG 4 cut(s) 162, 270, 333, 429
FaiI YATR 8 cut(s) 78, 98, 160, 172, 203, 268, 331, 427
FatI CATG 4 cut(s) 158, 266, 329, 425
Fnu4HI GCNGC 1 cut(s) 423
FokI GGATG 1 cut(s) 146
Fsp4HI GCNGC 1 cut(s) 423
FspBI CTAG 2 cut(s) 299, 438
GlaI GCGC 1 cut(s) 461
GluI GCNGC 1 cut(s) 423
GsaI CCCAGC 1 cut(s) 146
HaeIII GGCC 1 cut(s) 414
HapII CCGG 1 cut(s) 221
HhaI GCGC 1 cut(s) 462
Hin1II CATG 4 cut(s) 162, 270, 333, 429
Hin6I GCGC 1 cut(s) 460
HinP1I GCGC 1 cut(s) 460
HinfI GANTC 2 cut(s) 137, 344
HpaII CCGG 1 cut(s) 221
HphI GGTGA 1 cut(s) 278
Hpy166II GTNNAC 1 cut(s) 286
Hpy188I TCNGA 1 cut(s) 349
Hpy188III TCNNGA 1 cut(s) 511
Hpy8I GTNNAC 1 cut(s) 286
Hpy99I CGWCG 4 cut(s) 377, 395, 413, 452
HpyAV CCTTC 3 cut(s) 254, 299, 490
HpyCH4III ACNGT 1 cut(s) 110
HpyCH4IV ACGT 4 cut(s) 247, 282, 322, 372
HpyCH4V TGCA 9 cut(s) 74, 158, 244, 270, 320, 329, 425, 486, 505
HpyF10VI GCNNNNNNNGC 1 cut(s) 326
HpyF3I CTNAG 2 cut(s) 359, 397
HpySE526I ACGT 4 cut(s) 247, 282, 322, 372
Hsp92II CATG 4 cut(s) 162, 270, 333, 429
HspAI GCGC 1 cut(s) 460
Kzo9I GATC 1 cut(s) 455
LmnI GCTCC 1 cut(s) 432
LpnPI CCDG 8 cut(s) 77, 156, 234, 330, 340, 384, 401, 428
Lsp1109I GCAGC 1 cut(s) 409
MaeI CTAG 2 cut(s) 299, 438
MaeII ACGT 4 cut(s) 247, 282, 322, 372
MalI GATC 1 cut(s) 457
MboI GATC 1 cut(s) 455
MboII GAAGA 2 cut(s) 31, 34
MhlI GDGCHC 1 cut(s) 437
MluCI AATT 5 cut(s) 33, 180, 254, 304, 506
MnlI CCTC 3 cut(s) 56, 217, 343
Mph1103I ATGCAT 1 cut(s) 160
MroXI GAANNNNTTC 1 cut(s) 233
MseI TTAA 5 cut(s) 32, 183, 195, 213, 251
MspI CCGG 1 cut(s) 221
MspR9I CCNGG 1 cut(s) 416
Mva1269I GAATGC 2 cut(s) 160, 344
MvaI CCWGG 1 cut(s) 416
MvnI CGCG 1 cut(s) 460
MwoI GCNNNNNNNGC 1 cut(s) 326
NdeII GATC 1 cut(s) 455
NlaIII CATG 4 cut(s) 162, 270, 333, 429
NlaIV GGNNCC 1 cut(s) 315
NsiI ATGCAT 1 cut(s) 160
PaqCI CACCTGC 1 cut(s) 325
PctI GAATGC 2 cut(s) 160, 344
PdmI GAANNNNTTC 1 cut(s) 233
PfeI GAWTC 2 cut(s) 137, 344
PkrI GCNGC 1 cut(s) 424
PmaCI CACGTG 1 cut(s) 323
PmlI CACGTG 1 cut(s) 323
Ppu21I YACGTR 1 cut(s) 323
PshBI ATTAAT 2 cut(s) 183, 195
Psp1406I AACGTT 2 cut(s) 247, 282
Psp6I CCWGG 1 cut(s) 414
PspCI CACGTG 1 cut(s) 323
PspFI CCCAGC 1 cut(s) 142
PspGI CCWGG 1 cut(s) 414
PspN4I GGNNCC 1 cut(s) 315
PspPI GGNCC 1 cut(s) 263
RsaI GTAC 1 cut(s) 107
RsaNI GTAC 1 cut(s) 106
SaqAI TTAA 5 cut(s) 32, 183, 195, 213, 251
SatI GCNGC 1 cut(s) 423
Sau3AI GATC 1 cut(s) 455
Sau96I GGNCC 1 cut(s) 263
ScrFI CCNGG 1 cut(s) 416
SduI GDGCHC 1 cut(s) 437
SinI GGWCC 1 cut(s) 263
Sse9I AATT 5 cut(s) 33, 180, 254, 304, 506
SspI AATATT 1 cut(s) 167
SspMI CTAG 2 cut(s) 299, 438
StyD4I CCNGG 1 cut(s) 414
TaaI ACNGT 1 cut(s) 110
TaiI ACGT 4 cut(s) 250, 285, 325, 375
TaqI TCGA 3 cut(s) 375, 390, 408
TasI AATT 5 cut(s) 33, 180, 254, 304, 506
TfiI GAWTC 2 cut(s) 137, 344
Tru1I TTAA 5 cut(s) 32, 183, 195, 213, 251
Tru9I TTAA 5 cut(s) 32, 183, 195, 213, 251
TscAI CASTG 1 cut(s) 507
TseI GCWGC 1 cut(s) 422
TspDTI ATGAA 1 cut(s) 201
TspGWI ACGGA 1 cut(s) 146
TspRI CASTG 1 cut(s) 507
VpaK11BI GGWCC 1 cut(s) 263
VspI ATTAAT 2 cut(s) 183, 195
XapI RAATTY 2 cut(s) 254, 304
XmnI GAANNNNTTC 1 cut(s) 233
XspI CTAG 2 cut(s) 299, 438
Zsp2I ATGCAT 1 cut(s) 160
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.