Rroxscaffold_5G00344320

Polygalacturonase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000005
OG0000579
Physical Location & Seq
Forward (+)
14323147 .. 14326359
3213 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_5G00344320.1

Sequence Viewer

Length: 1131 bp
ATGGGTCTACTTTCGCTACTTACCTCTGTGTTGTTTTCATGGATTGTTGCTTCACCTAGATTTGGCATCGGGCCATGGTATGGCCAAAACGGTACTCTTAACGTACTTGATTTTGGTGCCTCTGGTGATGGCATAGCAGATGATACTGAAGCTTTCTTAAATGCATGGAAGACACTTTGCGAGACCGGCCAAACCCTAAACATCCCTGCAGGGAAGACCTTTGTAGTGAAACCTCTTCAACTTGTAGGTCCATGCAAATCCAATAACGTTGGAATTCAGGCTTTAAATTTCCACAAATGCGACCAACTTCAATTATCTGGATTTACTTCCCGTGATAGTCCGAGGGCCCATATATTTATACATAGCAGCAATTATGTACGTATCTCAAACATTAATTTGAGTGCACCGGAAAAAAGCCCGAATACCGACGGCATTGACGTATCTTTATCAAGCCAAGTAACCATACAAGACTCTTTCATCGGAACTGGTGATGATTGCATTGCAATTAAGGGAGGCTCCTCTTTTGTAAACATAACTCATGTAACATGCGGACCAGGTCATGGTTTCAGTGTGGGTAGTTTAGGACAAGATCCAGCTACTACAGATAATGTCGAACAAGTATACTTTCAGAATTGTATCTGCAACAAATCTACAAACTGTGCAAGAATCAAGACATGGATGGGTGGATCTGGGTATGCTCGGGCGATTTTCTTCAGACAAATGACCCTTGAACAGTCACAAAATCCTATTATAATTGACCAACACTACTGCAATGGCGAACATAATTGCCCAGCTAAGACGGGAGCAGTGAAAGTTAGCAATGTAACATTCAGTGGCATTACCGGAACTTCAGCAAGTGAGCAAGCAATAACACTGGATTGCTCCGACTTGGGTTGTACCAATATCTTGATGGATCATGTCAACATAACCTCCGCATCCGGACTGCCACTTCGTTCTGTGTGCAACAAGGCCAGTGGGAAAGCTAGTTTTACTTCACCTCCGATTCCTTGCCTGTCGTCGAATGGATCTTTGTCATCAGTGATTGCACCAATCTCGGTCAATTTATTAAAGCCAAACCATTCTTATTTGAGTTATTTCGGAATTCATGCCCATAAAACAATCGAAGCTTAA

Protein Analysis

376

Amino Acids

39.93

Weight (kDa)

6.58

Isoelectric Point (pI)

36.59

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pect-lyase_RHGA_epim PF12708 33 - 212 3.5e-08 Rhamnogalacturonase A/epimerase, pectate lyase-like
Glyco_hydro_28 PF00295 94 - 325 5.7e-66 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) 752
AccB1I GGYRCC 1 cut(s) 116
AccB7I CCANNNNNTGG 2 cut(s) 80, 560
AccI GTMKAC 2 cut(s) 7, 621
AccIII TCCGGA 1 cut(s) 938
AciI CCGC 2 cut(s) 549, 933
AclI AACGTT 1 cut(s) 267
AclWI GGATC 4 cut(s) 584, 694, 921, 1033
AcoI YGGCCR 2 cut(s) 82, 187
AcsI RAATTY 3 cut(s) 273, 286, 1101
AcuI CTGAAG 3 cut(s) 168, 697, 834
AfaI GTAC 4 cut(s) 94, 105, 378, 898
AfiI CCNNNNNNNGG 3 cut(s) 62, 80, 560
AgsI TTSAA 3 cut(s) 239, 311, 731
AjnI CCWGG 1 cut(s) 553
AluBI AGCT 5 cut(s) 152, 596, 794, 983, 1127
AluI AGCT 5 cut(s) 152, 596, 794, 983, 1127
Alw21I GWGCWC 1 cut(s) 406
Alw26I GTCTC 1 cut(s) 176
Alw44I GTGCAC 1 cut(s) 402
AlwI GGATC 4 cut(s) 584, 694, 921, 1033
Ama87I CYCGRG 1 cut(s) 699
Aor13HI TCCGGA 1 cut(s) 938
AoxI GGCC 5 cut(s) 71, 82, 187, 345, 969
ApaI GGGCCC 1 cut(s) 349
ApaLI GTGCAC 1 cut(s) 402
ApeKI GCWGC 1 cut(s) 366
ApoI RAATTY 3 cut(s) 273, 286, 1101
ArsI GACNNNNNNTTYG 2 cut(s) 933, 965
AseI ATTAAT 1 cut(s) 393
AspS9I GGNCC 5 cut(s) 71, 248, 345, 346, 551
AsuHPI GGTGA 4 cut(s) 45, 137, 500, 987
AvaI CYCGRG 1 cut(s) 699
AvaII GGWCC 2 cut(s) 248, 551
BaeGI GKGCMC 2 cut(s) 349, 406
BalI TGGCCA 1 cut(s) 84
BanI GGYRCC 1 cut(s) 116
BanII GRGCYC 1 cut(s) 349
BbsI GAAGAC 2 cut(s) 176, 221
Bbv12I GWGCWC 1 cut(s) 406
BbvI GCAGC 1 cut(s) 378
BccI CCATC 3 cut(s) 122, 673, 904
BceAI ACGGC 1 cut(s) 445
BcgI CGANNNNNNTGC 2 cut(s) 1035, 1069
BciT130I CCWGG 1 cut(s) 555
BcoDI GTCTC 1 cut(s) 176
BfaI CTAG 2 cut(s) 57, 984
BfmI CTRYAG 2 cut(s) 207, 600
BisI GCNGC 1 cut(s) 367
BlsI GCNGC 1 cut(s) 368
Bme1390I CCNGG 1 cut(s) 555
Bme18I GGWCC 2 cut(s) 248, 551
BmeT110I CYCGRG 1 cut(s) 699
BmgT120I GGNCC 5 cut(s) 71, 248, 345, 346, 551
BmiI GGNNCC 3 cut(s) 118, 347, 517
BmrFI CCNGG 1 cut(s) 555
BmsI GCATC 2 cut(s) 75, 944
BpiI GAAGAC 2 cut(s) 176, 221
BsaAI YACGTR 1 cut(s) 380
BsaI GGTCTC 1 cut(s) 176
BsaJI CCNNGG 2 cut(s) 74, 341
BsaWI WCCGGW 3 cut(s) 406, 842, 938
BsaXI ACNNNNNCTCC 4 cut(s) 914, 944, 982, 1012
Bsc4I CCNNNNNNNGG 3 cut(s) 62, 80, 560
Bse118I RCCGGY 1 cut(s) 185
Bse1I ACTGG 3 cut(s) 490, 879, 972
Bse3DI GCAATG 3 cut(s) 498, 778, 826
BseAI TCCGGA 1 cut(s) 938
BseBI CCWGG 1 cut(s) 555
BseDI CCNNGG 2 cut(s) 74, 341
BseGI GGATG 3 cut(s) 201, 684, 935
BseLI CCNNNNNNNGG 3 cut(s) 62, 80, 560
BseMI GCAATG 3 cut(s) 498, 778, 826
BseNI ACTGG 3 cut(s) 490, 879, 972
BseRI GAGGAG 1 cut(s) 508
BseSI GKGCMC 2 cut(s) 349, 406
BseXI GCAGC 1 cut(s) 378
BseYI CCCAGC 1 cut(s) 790
BshFI GGCC 5 cut(s) 73, 84, 189, 347, 971
BshNI GGYRCC 1 cut(s) 116
BsiHKAI GWGCWC 1 cut(s) 406
BsiHKCI CYCGRG 1 cut(s) 699
BsiSI CCGG 4 cut(s) 186, 407, 843, 939
BslI CCNNNNNNNGG 3 cut(s) 62, 80, 560
BsmAI GTCTC 1 cut(s) 176
BsnI GGCC 5 cut(s) 73, 84, 189, 347, 971
Bso31I GGTCTC 1 cut(s) 176
BsoBI CYCGRG 1 cut(s) 699
Bsp120I GGGCCC 1 cut(s) 345
Bsp1286I GDGCHC 2 cut(s) 349, 406
Bsp13I TCCGGA 1 cut(s) 938
Bsp143I GATC 4 cut(s) 589, 686, 913, 1025
Bsp19I CCATGG 1 cut(s) 74
BspACI CCGC 2 cut(s) 549, 933
BspANI GGCC 5 cut(s) 73, 84, 189, 347, 971
BspEI TCCGGA 1 cut(s) 938
BspLI GGNNCC 3 cut(s) 118, 347, 517
BspMAI CTGCAG 1 cut(s) 211
BspPI GGATC 4 cut(s) 584, 694, 921, 1033
BspT107I GGYRCC 1 cut(s) 116
BspTNI GGTCTC 1 cut(s) 176
BsrDI GCAATG 3 cut(s) 498, 778, 826
BsrFI RCCGGY 1 cut(s) 185
BsrI ACTGG 3 cut(s) 490, 879, 972
BssAI RCCGGY 1 cut(s) 185
BssECI CCNNGG 2 cut(s) 74, 341
BssMI GATC 4 cut(s) 589, 686, 913, 1025
BssNAI GTATAC 1 cut(s) 622
BssT1I CCWWGG 1 cut(s) 74
Bst1107I GTATAC 1 cut(s) 622
Bst2UI CCWGG 1 cut(s) 555
Bst4CI ACNGT 3 cut(s) 92, 659, 735
Bst6I CTCTTC 1 cut(s) 240
BstBAI YACGTR 1 cut(s) 380
BstC8I GCNNGC 1 cut(s) 864
BstDEI CTNAG 1 cut(s) 795
BstDSI CCRYGG 1 cut(s) 74
BstF5I GGATG 3 cut(s) 201, 684, 935
BstKTI GATC 4 cut(s) 592, 689, 916, 1028
BstMAI GTCTC 1 cut(s) 176
BstMBI GATC 4 cut(s) 589, 686, 913, 1025
BstMWI GCNNNNNNNGC 1 cut(s) 186
BstNI CCWGG 1 cut(s) 555
BstNSI RCATGY 1 cut(s) 549
BstSCI CCNGG 1 cut(s) 553
BstSFI CTRYAG 2 cut(s) 207, 600
BstSLI GKGCMC 2 cut(s) 349, 406
BstSNI TACGTA 1 cut(s) 380
BstV1I GCAGC 1 cut(s) 378
BstV2I GAAGAC 2 cut(s) 176, 221
BstX2I RGATCY 3 cut(s) 589, 686, 1025
BstYI RGATCY 3 cut(s) 589, 686, 1025
BstZ17I GTATAC 1 cut(s) 622
BsuRI GGCC 5 cut(s) 73, 84, 189, 347, 971
BtgI CCRYGG 1 cut(s) 74
BtsCI GGATG 3 cut(s) 201, 684, 935
BtsI GCAGTG 1 cut(s) 813
BtsIMutI CAGTG 6 cut(s) 574, 813, 838, 872, 979, 1044
Cac8I GCNNGC 1 cut(s) 864
Cfr10I RCCGGY 1 cut(s) 185
Cfr13I GGNCC 5 cut(s) 71, 248, 345, 346, 551
CsiI ACCWGGT 1 cut(s) 553
Csp6I GTAC 4 cut(s) 93, 104, 377, 897
CspCI CAANNNNNGTGG 2 cut(s) 955, 990
CviQI GTAC 4 cut(s) 93, 104, 377, 897
DdeI CTNAG 1 cut(s) 795
DpnI GATC 4 cut(s) 591, 688, 915, 1027
DpnII GATC 4 cut(s) 589, 686, 913, 1025
DraI TTTAAA 1 cut(s) 285
EaeI YGGCCR 2 cut(s) 82, 187
Eam1104I CTCTTC 1 cut(s) 240
EarI CTCTTC 1 cut(s) 240
Eco105I TACGTA 1 cut(s) 380
Eco130I CCWWGG 1 cut(s) 74
Eco24I GRGCYC 1 cut(s) 349
Eco31I GGTCTC 1 cut(s) 176
Eco47I GGWCC 2 cut(s) 248, 551
Eco57I CTGAAG 3 cut(s) 168, 697, 834
Eco88I CYCGRG 1 cut(s) 699
EcoO109I RGGNCCY 1 cut(s) 345
EcoRI GAATTC 2 cut(s) 273, 1101
EcoRII CCWGG 1 cut(s) 553
EcoT14I CCWWGG 1 cut(s) 74
EcoT22I ATGCAT 1 cut(s) 166
EcoT38I GRGCYC 1 cut(s) 349
ErhI CCWWGG 1 cut(s) 74
FblI GTMKAC 2 cut(s) 7, 621
Fnu4HI GCNGC 1 cut(s) 367
FokI GGATG 3 cut(s) 188, 691, 922
FriOI GRGCYC 1 cut(s) 349
Fsp4HI GCNGC 1 cut(s) 367
FspBI CTAG 2 cut(s) 57, 984
GluI GCNGC 1 cut(s) 367
GsaI CCCAGC 1 cut(s) 794
HaeIII GGCC 5 cut(s) 73, 84, 189, 347, 971
HapII CCGG 4 cut(s) 186, 407, 843, 939
HincII GTYRAC 1 cut(s) 922
HindII GTYRAC 1 cut(s) 922
HindIII AAGCTT 2 cut(s) 150, 1125
HinfI GANTC 3 cut(s) 470, 666, 1003
HpaII CCGG 4 cut(s) 186, 407, 843, 939
HphI GGTGA 4 cut(s) 45, 137, 500, 987
Hpy166II GTNNAC 5 cut(s) 8, 404, 529, 622, 922
Hpy188I TCNGA 7 cut(s) 342, 482, 630, 716, 886, 1002, 1100
Hpy188III TCNNGA 4 cut(s) 318, 670, 907, 939
Hpy8I GTNNAC 5 cut(s) 8, 404, 529, 622, 922
Hpy99I CGWCG 2 cut(s) 431, 1021
HpyCH4III ACNGT 3 cut(s) 92, 659, 735
HpyCH4IV ACGT 4 cut(s) 102, 267, 379, 438
HpyF10VI GCNNNNNNNGC 1 cut(s) 186
HpyF3I CTNAG 1 cut(s) 795
HpySE526I ACGT 4 cut(s) 102, 267, 379, 438
Kpn2I TCCGGA 1 cut(s) 938
Kzo9I GATC 4 cut(s) 589, 686, 913, 1025
LmnI GCTCC 3 cut(s) 521, 803, 887
Lsp1109I GCAGC 1 cut(s) 378
LweI GCATC 2 cut(s) 75, 944
MabI ACCWGGT 1 cut(s) 553
MaeI CTAG 2 cut(s) 57, 984
MaeII ACGT 4 cut(s) 102, 267, 379, 438
MaeIII GTNAC 4 cut(s) 457, 541, 735, 823
MalI GATC 4 cut(s) 591, 688, 915, 1027
MboI GATC 4 cut(s) 589, 686, 913, 1025
MboII GAAGA 4 cut(s) 181, 226, 227, 703
MflI RGATCY 3 cut(s) 589, 686, 1025
MhlI GDGCHC 2 cut(s) 349, 406
MlsI TGGCCA 1 cut(s) 84
MluNI TGGCCA 1 cut(s) 84
MlyI GAGTC 1 cut(s) 464
MmeI TCCRAC 2 cut(s) 250, 909
MnlI CCTC 8 cut(s) 34, 130, 243, 336, 506, 529, 940, 1008
Mox20I TGGCCA 1 cut(s) 84
Mph1103I ATGCAT 1 cut(s) 166
MroI TCCGGA 1 cut(s) 938
MscI TGGCCA 1 cut(s) 84
MseI TTAA 7 cut(s) 99, 158, 284, 393, 507, 1067, 1129
Msp20I TGGCCA 1 cut(s) 84
MspI CCGG 4 cut(s) 186, 407, 843, 939
MspR9I CCNGG 1 cut(s) 555
MvaI CCWGG 1 cut(s) 555
MwoI GCNNNNNNNGC 1 cut(s) 186
NcoI CCATGG 1 cut(s) 74
NdeII GATC 4 cut(s) 589, 686, 913, 1025
NlaIV GGNNCC 3 cut(s) 118, 347, 517
NmuCI GTSAC 1 cut(s) 735
NsiI ATGCAT 1 cut(s) 166
NspI RCATGY 1 cut(s) 549
PcsI WCGNNNNNNNCGW 1 cut(s) 435
PfeI GAWTC 2 cut(s) 666, 1003
PflFI GACNNNGTC 1 cut(s) 555
PflMI CCANNNNNTGG 2 cut(s) 80, 560
PkrI GCNGC 1 cut(s) 368
PleI GAGTC 1 cut(s) 464
PpsI GAGTC 1 cut(s) 464
Ppu21I YACGTR 1 cut(s) 380
PshBI ATTAAT 1 cut(s) 393
PsiI TTATAA 1 cut(s) 752
Psp1406I AACGTT 1 cut(s) 267
Psp6I CCWGG 1 cut(s) 553
PspFI CCCAGC 1 cut(s) 790
PspGI CCWGG 1 cut(s) 553
PspN4I GGNNCC 3 cut(s) 118, 347, 517
PspOMI GGGCCC 1 cut(s) 345
PspPI GGNCC 5 cut(s) 71, 248, 345, 346, 551
PstI CTGCAG 1 cut(s) 211
PsuI RGATCY 3 cut(s) 589, 686, 1025
PsyI GACNNNGTC 1 cut(s) 555
RsaI GTAC 4 cut(s) 94, 105, 378, 898
RsaNI GTAC 4 cut(s) 93, 104, 377, 897
SaqAI TTAA 7 cut(s) 99, 158, 284, 393, 507, 1067, 1129
SatI GCNGC 1 cut(s) 367
Sau3AI GATC 4 cut(s) 589, 686, 913, 1025
Sau96I GGNCC 5 cut(s) 71, 248, 345, 346, 551
SbfI CCTGCAGG 1 cut(s) 211
SchI GAGTC 1 cut(s) 464
ScrFI CCNGG 1 cut(s) 555
SdaI CCTGCAGG 1 cut(s) 211
SduI GDGCHC 2 cut(s) 349, 406
SexAI ACCWGGT 1 cut(s) 553
SfaNI GCATC 2 cut(s) 75, 944
SfcI CTRYAG 2 cut(s) 207, 600
SinI GGWCC 2 cut(s) 248, 551
SnaBI TACGTA 1 cut(s) 380
Sse8387I CCTGCAGG 1 cut(s) 211
SsiI CCGC 2 cut(s) 549, 933
SspMI CTAG 2 cut(s) 57, 984
StyD4I CCNGG 1 cut(s) 553
StyI CCWWGG 1 cut(s) 74
TaaI ACNGT 3 cut(s) 92, 659, 735
TaiI ACGT 4 cut(s) 105, 270, 382, 441
TaqI TCGA 3 cut(s) 612, 1019, 1122
TaqII GACCGA 1 cut(s) 1045
TfiI GAWTC 2 cut(s) 666, 1003
Tru1I TTAA 7 cut(s) 99, 158, 284, 393, 507, 1067, 1129
Tru9I TTAA 7 cut(s) 99, 158, 284, 393, 507, 1067, 1129
TscAI CASTG 6 cut(s) 574, 813, 838, 879, 979, 1044
TseFI GTSAC 1 cut(s) 735
TseI GCWGC 1 cut(s) 366
Tsp45I GTSAC 1 cut(s) 735
TspDTI ATGAA 3 cut(s) 27, 466, 1094
TspRI CASTG 6 cut(s) 574, 813, 838, 879, 979, 1044
Tth111I GACNNNGTC 1 cut(s) 555
Van91I CCANNNNNTGG 2 cut(s) 80, 560
VneI GTGCAC 1 cut(s) 402
VpaK11BI GGWCC 2 cut(s) 248, 551
VspI ATTAAT 1 cut(s) 393
XapI RAATTY 3 cut(s) 273, 286, 1101
XceI RCATGY 1 cut(s) 549
XcmI CCANNNNNNNNNTGG 1 cut(s) 907
XmiI GTMKAC 2 cut(s) 7, 621
XspI CTAG 2 cut(s) 57, 984
Zsp2I ATGCAT 1 cut(s) 166
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.