RchiOBHm_Chr4g0399401

Polygalacturonase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
4
OG0000579
Physical Location & Seq
Forward (+)
16634347 .. 16637364
3018 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ37153

Sequence Viewer

Length: 1143 bp
ATGGGCTATGTTATGGCCAAAATCGTACTCTTAACGTACTTGATTTTGGTGCCTCTGGCTTTCTTAAATGCATGGAAGACACTTTGCGAGACTGGCCAAACCCTAAACATCCCCGCAGGGAAGACCTTTGTAGTCAAACCTCTTCAACTTGTAGGTCCATGCAAATCCAATAACGTTGGAATTCAGATTGATGGGAATATTGTCGGTCCATCCACTCTTAGCGAATGGGCAGACGCGTGCAAAATCGGACAATGTTGGCTATGCTTTCTAAACGTGAAGGGCCTCGTCATCAAGGGGGAAGGACTTATAAATGGCAATGGTCCAATTTGGTGGAAACAAGAAACCCAATCCATAAATGACACTGACATGACTTGCAAACCACCTACGGCTTTAAACTTCCACAAATGCGACCAACTTCAATTATCTGGATTTACTTCCCGTGATAGTCCGAGAGCCCATATATTTATACATAGCAGCAATGGTGTACGTATCTCAAACATTCACTTGAGTGCACCGGAAAAAAGCCCGAATACTGATGGCATTGACATCTCTTTATCAAGCCAAGTGACCATACAAGACTCTTTCATCGGAACTGGGCAAGATCCAGCTACTACAGATAATGTCGAACAAGTACACTTTCAGAATTGTATCTGCAACAAATCTACAAACTGTGCAAGAATCAAAACATGGATGGGTGGATCTGGATATGCTCGGGCGATTTTCTTCAGACAAATGATCCTTGAACAGTCACAAAATCCTATTATAATTGACCAACACTACTGCAATGGCGGACATAATTGCCCAGCTAAGACGGGAGCAGTGAAAGTTAGCAATGTAACATTCAGTGGCATTACCGGAACTTCAGCAAGTGAGCAAGCAATCACACTGGATTGCTCCGACTTGGGTTGTACCGATATCTTGATGGATCATGTCAACATAACCTCCGCATCCGGATTGCCACTTCGTTCTGTGTGCAACAAGGCCAGTGGGAAAGCTAGTTTTACTTCACCTCCGATTCCATGCCTGTCGTCTAATGGATCTTTGTCATCAGTGATTGCACCAATCTCGGTCAACTTATTAAGGCCAAACCATTCTTATTTGAGTTATTTTGGAATTCATGCCCATAAAACAATCAAAGCTTAA

Protein Analysis

380

Amino Acids

40.87

Weight (kDa)

8.29

Isoelectric Point (pI)

39.91

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Glyco_hydro_28 PF00295 33 - 201 1.4e-30 Glycosyl hydrolases family 28
Glyco_hydro_28 PF00295 206 - 329 3.6e-28 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 2 cut(s) 308, 764
AccB1I GGYRCC 1 cut(s) 49
AccII CGCG 1 cut(s) 236
AccIII TCCGGA 1 cut(s) 950
AciI CCGC 3 cut(s) 114, 789, 945
AclI AACGTT 1 cut(s) 174
AclWI GGATC 5 cut(s) 596, 706, 730, 933, 1045
AcoI YGGCCR 2 cut(s) 15, 94
AcsI RAATTY 2 cut(s) 180, 1113
AcuI CTGAAG 2 cut(s) 709, 846
AfaI GTAC 5 cut(s) 27, 38, 486, 633, 910
AflIII ACRYGT 1 cut(s) 234
AgsI TTSAA 3 cut(s) 146, 419, 743
AleI CACNNNNGTG 1 cut(s) 507
AluBI AGCT 4 cut(s) 608, 806, 995, 1139
AluI AGCT 4 cut(s) 608, 806, 995, 1139
Alw21I GWGCWC 1 cut(s) 514
Alw26I GTCTC 1 cut(s) 83
Alw44I GTGCAC 1 cut(s) 510
AlwI GGATC 5 cut(s) 596, 706, 730, 933, 1045
Ama87I CYCGRG 1 cut(s) 711
Aor13HI TCCGGA 1 cut(s) 950
AoxI GGCC 5 cut(s) 15, 94, 280, 981, 1082
ApaLI GTGCAC 1 cut(s) 510
ApeKI GCWGC 1 cut(s) 474
ApoI RAATTY 2 cut(s) 180, 1113
AspS9I GGNCC 4 cut(s) 155, 206, 280, 320
AsuHPI GGTGA 1 cut(s) 999
AvaI CYCGRG 1 cut(s) 711
AvaII GGWCC 3 cut(s) 155, 206, 320
BaeGI GKGCMC 1 cut(s) 514
BalI TGGCCA 2 cut(s) 17, 96
BanI GGYRCC 1 cut(s) 49
BanII GRGCYC 1 cut(s) 457
BbsI GAAGAC 2 cut(s) 83, 128
Bbv12I GWGCWC 1 cut(s) 514
BbvI GCAGC 1 cut(s) 486
BccI CCATC 5 cut(s) 185, 217, 530, 685, 916
BceAI ACGGC 1 cut(s) 402
BcgI CGANNNNNNTGC 2 cut(s) 1047, 1081
BcoDI GTCTC 1 cut(s) 83
BfaI CTAG 1 cut(s) 996
BfmI CTRYAG 1 cut(s) 612
BisI GCNGC 1 cut(s) 475
BlsI GCNGC 1 cut(s) 476
Bme18I GGWCC 3 cut(s) 155, 206, 320
BmeT110I CYCGRG 1 cut(s) 711
BmgT120I GGNCC 4 cut(s) 155, 206, 280, 320
BmiI GGNNCC 1 cut(s) 51
BmrI ACTGGG 1 cut(s) 603
BmsI GCATC 1 cut(s) 956
BmuI ACTGGG 1 cut(s) 603
BpiI GAAGAC 2 cut(s) 83, 128
BpuEI CTTGAG 1 cut(s) 526
BsaAI YACGTR 1 cut(s) 488
BsaWI WCCGGW 3 cut(s) 514, 854, 950
BsaXI ACNNNNNCTCC 4 cut(s) 926, 956, 994, 1024
Bse1I ACTGG 4 cut(s) 97, 598, 891, 984
Bse3DI GCAATG 4 cut(s) 322, 484, 790, 838
BseAI TCCGGA 1 cut(s) 950
BseGI GGATG 4 cut(s) 108, 209, 696, 947
BseMI GCAATG 4 cut(s) 322, 484, 790, 838
BseNI ACTGG 4 cut(s) 97, 598, 891, 984
BseSI GKGCMC 1 cut(s) 514
BseXI GCAGC 1 cut(s) 486
BseYI CCCAGC 1 cut(s) 802
Bsh1236I CGCG 1 cut(s) 236
BshFI GGCC 5 cut(s) 17, 96, 282, 983, 1084
BshNI GGYRCC 1 cut(s) 49
BsiHKAI GWGCWC 1 cut(s) 514
BsiHKCI CYCGRG 1 cut(s) 711
BsiSI CCGG 3 cut(s) 515, 855, 951
BsmAI GTCTC 1 cut(s) 83
BsnI GGCC 5 cut(s) 17, 96, 282, 983, 1084
BsoBI CYCGRG 1 cut(s) 711
Bsp1286I GDGCHC 2 cut(s) 457, 514
Bsp13I TCCGGA 1 cut(s) 950
Bsp143I GATC 5 cut(s) 601, 698, 735, 925, 1037
BspACI CCGC 3 cut(s) 114, 789, 945
BspANI GGCC 5 cut(s) 17, 96, 282, 983, 1084
BspEI TCCGGA 1 cut(s) 950
BspFNI CGCG 1 cut(s) 236
BspLI GGNNCC 1 cut(s) 51
BspPI GGATC 5 cut(s) 596, 706, 730, 933, 1045
BspT107I GGYRCC 1 cut(s) 49
BsrDI GCAATG 4 cut(s) 322, 484, 790, 838
BsrI ACTGG 4 cut(s) 97, 598, 891, 984
BssMI GATC 5 cut(s) 601, 698, 735, 925, 1037
Bst4CI ACNGT 2 cut(s) 671, 747
Bst6I CTCTTC 1 cut(s) 147
BstBAI YACGTR 1 cut(s) 488
BstC8I GCNNGC 2 cut(s) 238, 876
BstDEI CTNAG 2 cut(s) 218, 807
BstF5I GGATG 4 cut(s) 108, 209, 696, 947
BstFNI CGCG 1 cut(s) 236
BstKTI GATC 5 cut(s) 604, 701, 738, 928, 1040
BstMAI GTCTC 1 cut(s) 83
BstMBI GATC 5 cut(s) 601, 698, 735, 925, 1037
BstMWI GCNNNNNNNGC 1 cut(s) 93
BstSFI CTRYAG 1 cut(s) 612
BstSLI GKGCMC 1 cut(s) 514
BstSNI TACGTA 1 cut(s) 488
BstUI CGCG 1 cut(s) 236
BstV1I GCAGC 1 cut(s) 486
BstV2I GAAGAC 2 cut(s) 83, 128
BstX2I RGATCY 3 cut(s) 601, 698, 1037
BstXI CCANNNNNNTGG 1 cut(s) 330
BstYI RGATCY 3 cut(s) 601, 698, 1037
BsuRI GGCC 5 cut(s) 17, 96, 282, 983, 1084
BtsCI GGATG 4 cut(s) 108, 209, 696, 947
BtsI GCAGTG 1 cut(s) 825
BtsIMutI CAGTG 6 cut(s) 360, 825, 850, 884, 991, 1056
Cac8I GCNNGC 2 cut(s) 238, 876
Cfr13I GGNCC 4 cut(s) 155, 206, 280, 320
CseI GACGC 1 cut(s) 242
Csp6I GTAC 5 cut(s) 26, 37, 485, 632, 909
CspCI CAANNNNNGTGG 2 cut(s) 967, 1002
CviAII CATG 7 cut(s) 72, 159, 367, 687, 929, 1020, 1118
CviQI GTAC 5 cut(s) 26, 37, 485, 632, 909
DdeI CTNAG 2 cut(s) 218, 807
DpnI GATC 5 cut(s) 603, 700, 737, 927, 1039
DpnII GATC 5 cut(s) 601, 698, 735, 925, 1037
DraI TTTAAA 1 cut(s) 393
EaeI YGGCCR 2 cut(s) 15, 94
Eam1104I CTCTTC 1 cut(s) 147
EarI CTCTTC 1 cut(s) 147
EciI GGCGGA 1 cut(s) 804
Eco105I TACGTA 1 cut(s) 488
Eco24I GRGCYC 1 cut(s) 457
Eco32I GATATC 1 cut(s) 916
Eco47I GGWCC 3 cut(s) 155, 206, 320
Eco57I CTGAAG 2 cut(s) 709, 846
Eco88I CYCGRG 1 cut(s) 711
EcoO109I RGGNCCY 1 cut(s) 280
EcoRI GAATTC 2 cut(s) 180, 1113
EcoRV GATATC 1 cut(s) 916
EcoT22I ATGCAT 1 cut(s) 73
EcoT38I GRGCYC 1 cut(s) 457
FaeI CATG 7 cut(s) 75, 162, 370, 690, 932, 1023, 1121
FatI CATG 7 cut(s) 71, 158, 366, 686, 928, 1019, 1117
FauI CCCGC 1 cut(s) 121
Fnu4HI GCNGC 1 cut(s) 475
FokI GGATG 4 cut(s) 95, 196, 703, 934
FriOI GRGCYC 1 cut(s) 457
Fsp4HI GCNGC 1 cut(s) 475
FspBI CTAG 1 cut(s) 996
GluI GCNGC 1 cut(s) 475
GsaI CCCAGC 1 cut(s) 806
HaeIII GGCC 5 cut(s) 17, 96, 282, 983, 1084
HapII CCGG 3 cut(s) 515, 855, 951
HgaI GACGC 1 cut(s) 242
Hin1II CATG 7 cut(s) 75, 162, 370, 690, 932, 1023, 1121
HincII GTYRAC 2 cut(s) 934, 1072
HindII GTYRAC 2 cut(s) 934, 1072
HindIII AAGCTT 1 cut(s) 1137
HinfI GANTC 3 cut(s) 578, 678, 1015
HpaII CCGG 3 cut(s) 515, 855, 951
HphI GGTGA 1 cut(s) 999
Hpy166II GTNNAC 5 cut(s) 485, 512, 634, 934, 1072
Hpy188I TCNGA 8 cut(s) 186, 248, 450, 590, 642, 728, 898, 1014
Hpy188III TCNNGA 4 cut(s) 426, 702, 919, 951
Hpy8I GTNNAC 5 cut(s) 485, 512, 634, 934, 1072
HpyAV CCTTC 2 cut(s) 271, 293
HpyCH4III ACNGT 2 cut(s) 671, 747
HpyCH4IV ACGT 4 cut(s) 35, 174, 273, 487
HpyF10VI GCNNNNNNNGC 1 cut(s) 93
HpyF3I CTNAG 2 cut(s) 218, 807
HpySE526I ACGT 4 cut(s) 35, 174, 273, 487
Hsp92II CATG 7 cut(s) 75, 162, 370, 690, 932, 1023, 1121
Kpn2I TCCGGA 1 cut(s) 950
Kzo9I GATC 5 cut(s) 601, 698, 735, 925, 1037
LmnI GCTCC 2 cut(s) 815, 899
Lsp1109I GCAGC 1 cut(s) 486
LweI GCATC 1 cut(s) 956
MaeI CTAG 1 cut(s) 996
MaeII ACGT 4 cut(s) 35, 174, 273, 487
MaeIII GTNAC 3 cut(s) 565, 747, 835
MalI GATC 5 cut(s) 603, 700, 737, 927, 1039
MboI GATC 5 cut(s) 601, 698, 735, 925, 1037
MboII GAAGA 4 cut(s) 88, 133, 134, 715
MflI RGATCY 3 cut(s) 601, 698, 1037
MhlI GDGCHC 2 cut(s) 457, 514
MlsI TGGCCA 2 cut(s) 17, 96
MluCI AATT 7 cut(s) 180, 324, 419, 643, 765, 796, 1113
MluI ACGCGT 1 cut(s) 234
MluNI TGGCCA 2 cut(s) 17, 96
MlyI GAGTC 1 cut(s) 572
MmeI TCCRAC 2 cut(s) 157, 921
MnlI CCTC 5 cut(s) 63, 150, 293, 952, 1020
Mox20I TGGCCA 2 cut(s) 17, 96
Mph1103I ATGCAT 1 cut(s) 73
MroI TCCGGA 1 cut(s) 950
MscI TGGCCA 2 cut(s) 17, 96
MseI TTAA 5 cut(s) 32, 65, 392, 1079, 1141
MslI CAYNNNNRTG 2 cut(s) 365, 507
Msp20I TGGCCA 2 cut(s) 17, 96
MspI CCGG 3 cut(s) 515, 855, 951
MvnI CGCG 1 cut(s) 236
MwoI GCNNNNNNNGC 1 cut(s) 93
NdeII GATC 5 cut(s) 601, 698, 735, 925, 1037
NlaIII CATG 7 cut(s) 75, 162, 370, 690, 932, 1023, 1121
NlaIV GGNNCC 1 cut(s) 51
NmuCI GTSAC 2 cut(s) 565, 747
NsiI ATGCAT 1 cut(s) 73
OliI CACNNNNGTG 1 cut(s) 507
PfeI GAWTC 2 cut(s) 678, 1015
PkrI GCNGC 1 cut(s) 476
PleI GAGTC 1 cut(s) 572
PpsI GAGTC 1 cut(s) 572
Ppu21I YACGTR 1 cut(s) 488
PsiI TTATAA 2 cut(s) 308, 764
Psp1406I AACGTT 1 cut(s) 174
PspFI CCCAGC 1 cut(s) 802
PspN4I GGNNCC 1 cut(s) 51
PspPI GGNCC 4 cut(s) 155, 206, 280, 320
PsuI RGATCY 3 cut(s) 601, 698, 1037
RsaI GTAC 5 cut(s) 27, 38, 486, 633, 910
RsaNI GTAC 5 cut(s) 26, 37, 485, 632, 909
RseI CAYNNNNRTG 2 cut(s) 365, 507
SaqAI TTAA 5 cut(s) 32, 65, 392, 1079, 1141
SatI GCNGC 1 cut(s) 475
Sau3AI GATC 5 cut(s) 601, 698, 735, 925, 1037
Sau96I GGNCC 4 cut(s) 155, 206, 280, 320
SchI GAGTC 1 cut(s) 572
SduI GDGCHC 2 cut(s) 457, 514
SfaNI GCATC 1 cut(s) 956
SfcI CTRYAG 1 cut(s) 612
SinI GGWCC 3 cut(s) 155, 206, 320
SmiMI CAYNNNNRTG 2 cut(s) 365, 507
SmlI CTYRAG 1 cut(s) 505
SmoI CTYRAG 1 cut(s) 505
SnaBI TACGTA 1 cut(s) 488
Sse9I AATT 7 cut(s) 180, 324, 419, 643, 765, 796, 1113
SsiI CCGC 3 cut(s) 114, 789, 945
SspI AATATT 1 cut(s) 199
SspMI CTAG 1 cut(s) 996
TaaI ACNGT 2 cut(s) 671, 747
TaiI ACGT 4 cut(s) 38, 177, 276, 490
TaqI TCGA 1 cut(s) 624
TaqII GACCGA 2 cut(s) 194, 1057
TasI AATT 7 cut(s) 180, 324, 419, 643, 765, 796, 1113
TatI WGTACW 1 cut(s) 631
TfiI GAWTC 2 cut(s) 678, 1015
Tru1I TTAA 5 cut(s) 32, 65, 392, 1079, 1141
Tru9I TTAA 5 cut(s) 32, 65, 392, 1079, 1141
TscAI CASTG 6 cut(s) 367, 825, 850, 891, 991, 1056
TseFI GTSAC 2 cut(s) 565, 747
TseI GCWGC 1 cut(s) 474
Tsp45I GTSAC 2 cut(s) 565, 747
TspDTI ATGAA 2 cut(s) 574, 1106
TspRI CASTG 6 cut(s) 367, 825, 850, 891, 991, 1056
VneI GTGCAC 1 cut(s) 510
VpaK11BI GGWCC 3 cut(s) 155, 206, 320
XapI RAATTY 2 cut(s) 180, 1113
XspI CTAG 1 cut(s) 996
Zsp2I ATGCAT 1 cut(s) 73
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.