Rroxscaffold_7G00169940

Polygalacturonase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000007
OG0000579
Physical Location & Seq
Reverse (-)
10435066 .. 10443801
8736 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_7G00169940.1

Sequence Viewer

Length: 720 bp
ATGGCTAATTATACAATTGATCGACATAACCTTGAAAATTTTCAGAAAACCTTTAGGATTGTGGCGTTTGAAGTAGTAGCACTCGGTTTGGAGTGTGGGGAAGCGATAGCCTCTTCGAAAATGGACTTACCTTCAGTTTCCTTTCTAATATTGGTCCTTGCTTCCTCTATTTTTCGCATTGGATTTGGCGATTTTAATGTGTTAGATTTTGAAGCAGCTGGAGATGGCAGAACTGATGATTCTCAACTTTCAGGGAATCTTGAGGCACCCTCGAGTCTTCGTGAATGGAGAAACTCGGCATTTTGCTGGATATGCTTTTCAAATGTGAGGGATCTCACTCTCATGGGAACTGGACAGATAAATGGCCGTGGTTCAACTTGGCGGAACAAGGGAGGGTATGGGCACGCTAGAGCGATATCTTTTGAGCAAATCACGCTTGAAAATGCAAAGAATCCCATTATAATTAAGCAAACGTACGTTGATAAAAATGGAGCAGTGAAGGTGAGTGATATAACATTTCGCGGCTTTGAAGGAACATCAGCTTCCGCGCAAGCAATAACATTGGATTGCTCACAGTTGGGCTGCACCAACATTGTAATGGATCAAATCGCCTTAAGCTCGGCCGTGCCCAGAATGTCATTGCATTCTTATTGCAGAAATGCCCAAGGAAGATCAATCCTTACTTCACCTTATGTTCCTTGTCTAGAACAGTCAAAATGA
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

239

Amino Acids

26.16

Weight (kDa)

6.3

Isoelectric Point (pI)

35.19

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Glyco_hydro_28 PF00295 130 - 221 1.7e-14 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)
AanI TTATAA 1 cut(s) 461
AccB1I GGYRCC 1 cut(s) 265
AccII CGCG 2 cut(s) 522, 548
AciI CCGC 3 cut(s) 382, 522, 546
AclWI GGATC 2 cut(s) 339, 609
AcoI YGGCCR 2 cut(s) 364, 621
AcsI RAATTY 1 cut(s) 37
AcuI CTGAAG 1 cut(s) 117
AfaI GTAC 1 cut(s) 476
AflII CTTAAG 1 cut(s) 613
AgsI TTSAA 7 cut(s) 35, 71, 212, 321, 375, 440, 530
AluBI AGCT 3 cut(s) 218, 542, 618
AluI AGCT 3 cut(s) 218, 542, 618
AlwI GGATC 2 cut(s) 339, 609
Ama87I CYCGRG 1 cut(s) 271
AoxI GGCC 2 cut(s) 364, 621
ApeKI GCWGC 2 cut(s) 215, 582
ApoI RAATTY 1 cut(s) 37
Asp700I GAANNNNTTC 1 cut(s) 39
AspLEI GCGC 1 cut(s) 550
AspS9I GGNCC 1 cut(s) 154
AsuHPI GGTGA 2 cut(s) 514, 678
AsuII TTCGAA 1 cut(s) 116
AvaI CYCGRG 1 cut(s) 271
AvaII GGWCC 1 cut(s) 154
BaeGI GKGCMC 2 cut(s) 405, 630
BanI GGYRCC 1 cut(s) 265
BbsI GAAGAC 1 cut(s) 269
BbvI GCAGC 2 cut(s) 227, 569
BccI CCATC 1 cut(s) 218
BceAI ACGGC 2 cut(s) 351, 608
BfaI CTAG 2 cut(s) 408, 704
BfrI CTTAAG 1 cut(s) 613
BisI GCNGC 3 cut(s) 216, 523, 583
BlsI GCNGC 3 cut(s) 217, 524, 584
Bme18I GGWCC 1 cut(s) 154
BmeT110I CYCGRG 1 cut(s) 271
BmgT120I GGNCC 1 cut(s) 154
BmiI GGNNCC 1 cut(s) 267
BpiI GAAGAC 1 cut(s) 269
BplI GAGNNNNNCTC 2 cut(s) 254, 286
BpmI CTGGAG 1 cut(s) 240
Bpu14I TTCGAA 1 cut(s) 116
BpuEI CTTGAG 1 cut(s) 281
BsaJI CCNNGG 2 cut(s) 367, 664
Bse1I ACTGG 1 cut(s) 355
Bse3DI GCAATG 1 cut(s) 638
BseDI CCNNGG 2 cut(s) 367, 664
BseMI GCAATG 1 cut(s) 638
BseNI ACTGG 1 cut(s) 355
BseSI GKGCMC 2 cut(s) 405, 630
BseX3I CGGCCG 1 cut(s) 621
BseXI GCAGC 2 cut(s) 227, 569
BsgI GTGCAG 1 cut(s) 568
Bsh1236I CGCG 2 cut(s) 522, 548
Bsh1285I CGRYCG 1 cut(s) 624
BshFI GGCC 2 cut(s) 366, 623
BshNI GGYRCC 1 cut(s) 265
BsiEI CGRYCG 1 cut(s) 624
BsiHKCI CYCGRG 1 cut(s) 271
BsiWI CGTACG 1 cut(s) 474
BsmI GAATGC 1 cut(s) 643
BsnI GGCC 2 cut(s) 366, 623
BsoBI CYCGRG 1 cut(s) 271
Bsp119I TTCGAA 1 cut(s) 116
Bsp1286I GDGCHC 2 cut(s) 405, 630
Bsp143I GATC 4 cut(s) 19, 331, 601, 671
BspACI CCGC 3 cut(s) 382, 522, 546
BspANI GGCC 2 cut(s) 366, 623
BspFNI CGCG 2 cut(s) 522, 548
BspLI GGNNCC 1 cut(s) 267
BspPI GGATC 2 cut(s) 339, 609
BspT104I TTCGAA 1 cut(s) 116
BspT107I GGYRCC 1 cut(s) 265
BspTI CTTAAG 1 cut(s) 613
BsrDI GCAATG 1 cut(s) 638
BsrI ACTGG 1 cut(s) 355
BssECI CCNNGG 2 cut(s) 367, 664
BssMI GATC 4 cut(s) 19, 331, 601, 671
BssT1I CCWWGG 1 cut(s) 664
Bst4CI ACNGT 2 cut(s) 576, 711
Bst6I CTCTTC 1 cut(s) 118
BstAFI CTTAAG 1 cut(s) 613
BstBI TTCGAA 1 cut(s) 116
BstC8I GCNNGC 2 cut(s) 405, 552
BstDSI CCRYGG 1 cut(s) 367
BstFNI CGCG 2 cut(s) 522, 548
BstHHI GCGC 1 cut(s) 550
BstKTI GATC 4 cut(s) 22, 334, 604, 674
BstMBI GATC 4 cut(s) 19, 331, 601, 671
BstMCI CGRYCG 1 cut(s) 624
BstMWI GCNNNNNNNGC 2 cut(s) 312, 433
BstSLI GKGCMC 2 cut(s) 405, 630
BstUI CGCG 2 cut(s) 522, 548
BstV1I GCAGC 2 cut(s) 227, 569
BstV2I GAAGAC 1 cut(s) 269
BstX2I RGATCY 1 cut(s) 331
BstYI RGATCY 1 cut(s) 331
BstZI CGGCCG 1 cut(s) 621
BsuRI GGCC 2 cut(s) 366, 623
BtgI CCRYGG 1 cut(s) 367
BtsI GCAGTG 1 cut(s) 501
BtsIMutI CAGTG 1 cut(s) 501
Cac8I GCNNGC 2 cut(s) 405, 552
CfoI GCGC 1 cut(s) 550
Cfr13I GGNCC 1 cut(s) 154
Csp6I GTAC 1 cut(s) 475
CviAII CATG 1 cut(s) 343
CviJI RGCY 9 cut(s) 5, 110, 218, 366, 525, 542, 582, 618, 623
CviKI_1 RGCY 9 cut(s) 5, 110, 218, 366, 525, 542, 582, 618, 623
CviQI GTAC 1 cut(s) 475
DpnI GATC 4 cut(s) 21, 333, 603, 673
DpnII GATC 4 cut(s) 19, 331, 601, 671
EaeI YGGCCR 2 cut(s) 364, 621
EagI CGGCCG 1 cut(s) 621
Eam1104I CTCTTC 1 cut(s) 118
EarI CTCTTC 1 cut(s) 118
EciI GGCGGA 1 cut(s) 397
EclXI CGGCCG 1 cut(s) 621
Eco130I CCWWGG 1 cut(s) 664
Eco32I GATATC 1 cut(s) 417
Eco47I GGWCC 1 cut(s) 154
Eco52I CGGCCG 1 cut(s) 621
Eco57I CTGAAG 1 cut(s) 117
Eco88I CYCGRG 1 cut(s) 271
EcoRV GATATC 1 cut(s) 417
EcoT14I CCWWGG 1 cut(s) 664
ErhI CCWWGG 1 cut(s) 664
FaeI CATG 1 cut(s) 346
FaiI YATR 8 cut(s) 12, 27, 313, 344, 399, 461, 512, 693
FatI CATG 1 cut(s) 342
Fnu4HI GCNGC 3 cut(s) 216, 523, 583
Fsp4HI GCNGC 3 cut(s) 216, 523, 583
FspBI CTAG 2 cut(s) 408, 704
GlaI GCGC 1 cut(s) 549
GluI GCNGC 3 cut(s) 216, 523, 583
GsuI CTGGAG 1 cut(s) 240
HaeIII GGCC 2 cut(s) 366, 623
HhaI GCGC 1 cut(s) 550
Hin1II CATG 1 cut(s) 346
Hin6I GCGC 1 cut(s) 548
HinP1I GCGC 1 cut(s) 548
HinfI GANTC 4 cut(s) 239, 256, 274, 451
HphI GGTGA 2 cut(s) 514, 678
Hpy188I TCNGA 1 cut(s) 45
Hpy188III TCNNGA 3 cut(s) 260, 281, 704
HpyAV CCTTC 3 cut(s) 141, 493, 524
HpyCH4III ACNGT 2 cut(s) 576, 711
HpyCH4IV ACGT 2 cut(s) 473, 477
HpyCH4V TGCA 4 cut(s) 446, 585, 643, 654
HpyF10VI GCNNNNNNNGC 2 cut(s) 312, 433
HpySE526I ACGT 2 cut(s) 473, 477
Hsp92II CATG 1 cut(s) 346
HspAI GCGC 1 cut(s) 548
Kzo9I GATC 4 cut(s) 19, 331, 601, 671
LmnI GCTCC 1 cut(s) 491
LpnPI CCDG 5 cut(s) 204, 237, 292, 336, 643
Lsp1109I GCAGC 2 cut(s) 227, 569
MaeI CTAG 2 cut(s) 408, 704
MaeII ACGT 2 cut(s) 473, 477
MalI GATC 4 cut(s) 21, 333, 603, 673
MboI GATC 4 cut(s) 19, 331, 601, 671
MboII GAAGA 3 cut(s) 105, 269, 681
MfeI CAATTG 1 cut(s) 15
MflI RGATCY 1 cut(s) 331
MhlI GDGCHC 2 cut(s) 405, 630
MluCI AATT 4 cut(s) 7, 15, 37, 462
MlyI GAGTC 1 cut(s) 283
MnlI CCTC 6 cut(s) 121, 175, 256, 280, 321, 386
MroXI GAANNNNTTC 1 cut(s) 39
MseI TTAA 3 cut(s) 195, 465, 614
MslI CAYNNNNRTG 2 cut(s) 341, 596
MspA1I CMGCKG 1 cut(s) 218
MspCI CTTAAG 1 cut(s) 613
MunI CAATTG 1 cut(s) 15
Mva1269I GAATGC 1 cut(s) 643
MvnI CGCG 2 cut(s) 522, 548
MwoI GCNNNNNNNGC 2 cut(s) 312, 433
NdeII GATC 4 cut(s) 19, 331, 601, 671
NlaIII CATG 1 cut(s) 346
NlaIV GGNNCC 1 cut(s) 267
NmeAIII GCCGAG 2 cut(s) 275, 599
NspV TTCGAA 1 cut(s) 116
PaeR7I CTCGAG 1 cut(s) 271
PctI GAATGC 1 cut(s) 643
PdmI GAANNNNTTC 1 cut(s) 39
PfeI GAWTC 3 cut(s) 239, 256, 451
Pfl23II CGTACG 1 cut(s) 474
PkrI GCNGC 3 cut(s) 217, 524, 584
PleI GAGTC 1 cut(s) 282
PpsI GAGTC 1 cut(s) 282
PsiI TTATAA 1 cut(s) 461
PspLI CGTACG 1 cut(s) 474
PspN4I GGNNCC 1 cut(s) 267
PspPI GGNCC 1 cut(s) 154
PspXI VCTCGAGB 1 cut(s) 271
PsuI RGATCY 1 cut(s) 331
PvuII CAGCTG 1 cut(s) 218
RsaI GTAC 1 cut(s) 476
RsaNI GTAC 1 cut(s) 475
RseI CAYNNNNRTG 2 cut(s) 341, 596
SaqAI TTAA 3 cut(s) 195, 465, 614
SatI GCNGC 3 cut(s) 216, 523, 583
Sau3AI GATC 4 cut(s) 19, 331, 601, 671
Sau96I GGNCC 1 cut(s) 154
SchI GAGTC 1 cut(s) 283
SduI GDGCHC 2 cut(s) 405, 630
Sfr274I CTCGAG 1 cut(s) 271
SfuI TTCGAA 1 cut(s) 116
SinI GGWCC 1 cut(s) 154
SlaI CTCGAG 1 cut(s) 271
SmiMI CAYNNNNRTG 2 cut(s) 341, 596
SmlI CTYRAG 3 cut(s) 260, 271, 613
SmoI CTYRAG 3 cut(s) 260, 271, 613
Sse9I AATT 4 cut(s) 7, 15, 37, 462
SsiI CCGC 3 cut(s) 382, 522, 546
SspI AATATT 1 cut(s) 150
SspMI CTAG 2 cut(s) 408, 704
StyI CCWWGG 1 cut(s) 664
TaaI ACNGT 2 cut(s) 576, 711
TaiI ACGT 2 cut(s) 476, 480
TaqI TCGA 3 cut(s) 22, 116, 272
TasI AATT 4 cut(s) 7, 15, 37, 462
TauI GCSGC 1 cut(s) 525
TfiI GAWTC 3 cut(s) 239, 256, 451
Tru1I TTAA 3 cut(s) 195, 465, 614
Tru9I TTAA 3 cut(s) 195, 465, 614
TscAI CASTG 1 cut(s) 501
TseI GCWGC 2 cut(s) 215, 582
TspRI CASTG 1 cut(s) 501
Vha464I CTTAAG 1 cut(s) 613
VpaK11BI GGWCC 1 cut(s) 154
XapI RAATTY 1 cut(s) 37
XbaI TCTAGA 1 cut(s) 703
XcmI CCANNNNNNNNNTGG 1 cut(s) 595
XhoI CTCGAG 1 cut(s) 271
XmnI GAANNNNTTC 1 cut(s) 39
XspI CTAG 2 cut(s) 408, 704
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.