RchiOBHm_Chr4g0399411

Polygalacturonase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
4
OG0000579
Physical Location & Seq
Forward (+)
16650371 .. 16653547
3177 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ37154

Sequence Viewer

Length: 1236 bp
ATGGGTCTACTTTCGCTACTTACCTCTGTGTTGATTTCATGGATTGTTGCTTCACCTAGATTTGGCAATGGGCTATGTTATGGCCAAAATCGTACTCTTAACGTACTTGATTTTGGTGCCTCTGGTGATGGCATAGCAGATGATACTGAAGCTTTCTTAAATGCATGGAAGACACTTTGCGAGACTGGCCAAACCCTAAACATCCCCGCAGGGAAGACCTTTGTAGTCAAACCTCTTCAACTTGTAGGTCCATGCAAATCCAATAACGTTGGAATTCAGATTGATGGGAATATTGTCGGTCCATCCACTCTTAGCGAATGGGCAGACGCGTGCAAAATCGGACAATGTTGGCTATGCTTTCTAAACGTGAAGGGCCTCGTCATCAAGGGGGAAGGACTTATAAATGGCAATGGTCCAATTTGGTGGAAACAAGAAACCCAATCCATAAATGACACTGACATGACTTGCAAACCACCTACGGCTTTAAACTTCCACAAATGCGACCAACTTCAATTATTTGGATTTACTTCCCGTGATAGTCCGAGAGCCCATATATTTATACATAGCAGCAATGGTGTACGTATCTCAAACATTCACTTGAGTGCACCGGAAAAAAGCCCGAATACTGATGGCATTGACATCTCTTTATCAAGCCAAGTGACCATACAAGACTCTTTCATCGGAACTGGGCAAGATCCAGCTACTACAGATAATGTCGAACAAGTACACTTTCAGAATTGTATCTGCAACAAATCTACAAACTGTGCAAGAATCAAAACATGGATGGGTGGATCTGGATATGCTCGGGCGATTTTCTTCAGACAAATGATCCTTGAACAGTCACAAAATCCTATTATAATTGACCAACACTACTGCAATGGCGGACATAATTGCCCAGCTAAGACGGGAGCAGTGAAAGTTAGCAATGTAACATTCAGTGGCATTACCGGAACTTCAGCAAGTGAGCAAGCAATCACACTGGATTGCTCCGACTTGGGTTGTACCGATATCTTGATGGATCATGTCAACATAACCTCCGCATCCGGATTGCCACTTCGTTCTGTGTGCAACAAGGCCAGTGGGAAAGCTAGTTTTACTTCACCTCCGATTCCATGCCTGTCGTCGAATGGATCTTTGTCATCAGTGATTGCACCGATCTCGGTCAACTTATTAAGGCCAAACCATTCTTATTTGAGTTATTTTGGAATTCATGCCCATAAAACAATCAAAGCTTAA

Protein Analysis

411

Amino Acids

44.04

Weight (kDa)

7.11

Isoelectric Point (pI)

36.24

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pect-lyase_RHGA_epim PF12708 33 - 255 8.3e-09 Rhamnogalacturonase A/epimerase, pectate lyase-like
Glyco_hydro_28 PF00295 64 - 232 6.6e-30 Glycosyl hydrolases family 28
Glyco_hydro_28 PF00295 237 - 360 4.2e-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) 401, 857
AccB1I GGYRCC 1 cut(s) 116
AccI GTMKAC 1 cut(s) 7
AccII CGCG 1 cut(s) 329
AccIII TCCGGA 1 cut(s) 1043
AciI CCGC 3 cut(s) 207, 882, 1038
AclI AACGTT 1 cut(s) 267
AclWI GGATC 5 cut(s) 689, 799, 823, 1026, 1138
AcoI YGGCCR 2 cut(s) 82, 187
AcsI RAATTY 2 cut(s) 273, 1206
AcuI CTGAAG 3 cut(s) 168, 802, 939
AfaI GTAC 5 cut(s) 94, 105, 579, 726, 1003
AfiI CCNNNNNNNGG 1 cut(s) 62
AflIII ACRYGT 1 cut(s) 327
AgsI TTSAA 3 cut(s) 239, 512, 836
AleI CACNNNNGTG 1 cut(s) 600
AluBI AGCT 5 cut(s) 152, 701, 899, 1088, 1232
AluI AGCT 5 cut(s) 152, 701, 899, 1088, 1232
Alw21I GWGCWC 1 cut(s) 607
Alw26I GTCTC 1 cut(s) 176
Alw44I GTGCAC 1 cut(s) 603
AlwI GGATC 5 cut(s) 689, 799, 823, 1026, 1138
Ama87I CYCGRG 1 cut(s) 804
Aor13HI TCCGGA 1 cut(s) 1043
AoxI GGCC 5 cut(s) 82, 187, 373, 1074, 1175
ApaLI GTGCAC 1 cut(s) 603
ApeKI GCWGC 1 cut(s) 567
ApoI RAATTY 2 cut(s) 273, 1206
AspS9I GGNCC 4 cut(s) 248, 299, 373, 413
AsuHPI GGTGA 3 cut(s) 45, 137, 1092
AvaI CYCGRG 1 cut(s) 804
AvaII GGWCC 3 cut(s) 248, 299, 413
BaeGI GKGCMC 1 cut(s) 607
BalI TGGCCA 2 cut(s) 84, 189
BanI GGYRCC 1 cut(s) 116
BanII GRGCYC 1 cut(s) 550
BbsI GAAGAC 2 cut(s) 176, 221
Bbv12I GWGCWC 1 cut(s) 607
BbvI GCAGC 1 cut(s) 579
BccI CCATC 6 cut(s) 122, 278, 310, 623, 778, 1009
BceAI ACGGC 1 cut(s) 495
BcgI CGANNNNNNTGC 2 cut(s) 1140, 1174
BcoDI GTCTC 1 cut(s) 176
BfaI CTAG 2 cut(s) 57, 1089
BfmI CTRYAG 1 cut(s) 705
BisI GCNGC 1 cut(s) 568
BlsI GCNGC 1 cut(s) 569
Bme18I GGWCC 3 cut(s) 248, 299, 413
BmeT110I CYCGRG 1 cut(s) 804
BmgT120I GGNCC 4 cut(s) 248, 299, 373, 413
BmiI GGNNCC 1 cut(s) 118
BmrI ACTGGG 1 cut(s) 696
BmsI GCATC 1 cut(s) 1049
BmuI ACTGGG 1 cut(s) 696
BpiI GAAGAC 2 cut(s) 176, 221
BpuEI CTTGAG 1 cut(s) 619
BsaAI YACGTR 1 cut(s) 581
BsaWI WCCGGW 3 cut(s) 607, 947, 1043
BsaXI ACNNNNNCTCC 4 cut(s) 1019, 1049, 1087, 1117
Bsc4I CCNNNNNNNGG 1 cut(s) 62
Bse1I ACTGG 4 cut(s) 190, 691, 984, 1077
Bse3DI GCAATG 5 cut(s) 73, 415, 577, 883, 931
BseAI TCCGGA 1 cut(s) 1043
BseGI GGATG 4 cut(s) 201, 302, 789, 1040
BseLI CCNNNNNNNGG 1 cut(s) 62
BseMI GCAATG 5 cut(s) 73, 415, 577, 883, 931
BseNI ACTGG 4 cut(s) 190, 691, 984, 1077
BseSI GKGCMC 1 cut(s) 607
BseXI GCAGC 1 cut(s) 579
BseYI CCCAGC 1 cut(s) 895
Bsh1236I CGCG 1 cut(s) 329
BshFI GGCC 5 cut(s) 84, 189, 375, 1076, 1177
BshNI GGYRCC 1 cut(s) 116
BsiHKAI GWGCWC 1 cut(s) 607
BsiHKCI CYCGRG 1 cut(s) 804
BsiSI CCGG 3 cut(s) 608, 948, 1044
BslI CCNNNNNNNGG 1 cut(s) 62
BsmAI GTCTC 1 cut(s) 176
BsnI GGCC 5 cut(s) 84, 189, 375, 1076, 1177
BsoBI CYCGRG 1 cut(s) 804
Bsp1286I GDGCHC 2 cut(s) 550, 607
Bsp13I TCCGGA 1 cut(s) 1043
Bsp143I GATC 6 cut(s) 694, 791, 828, 1018, 1130, 1155
BspACI CCGC 3 cut(s) 207, 882, 1038
BspANI GGCC 5 cut(s) 84, 189, 375, 1076, 1177
BspEI TCCGGA 1 cut(s) 1043
BspFNI CGCG 1 cut(s) 329
BspLI GGNNCC 1 cut(s) 118
BspPI GGATC 5 cut(s) 689, 799, 823, 1026, 1138
BspT107I GGYRCC 1 cut(s) 116
BsrDI GCAATG 5 cut(s) 73, 415, 577, 883, 931
BsrI ACTGG 4 cut(s) 190, 691, 984, 1077
BssMI GATC 6 cut(s) 694, 791, 828, 1018, 1130, 1155
Bst4CI ACNGT 2 cut(s) 764, 840
Bst6I CTCTTC 1 cut(s) 240
BstBAI YACGTR 1 cut(s) 581
BstC8I GCNNGC 2 cut(s) 331, 969
BstDEI CTNAG 2 cut(s) 311, 900
BstF5I GGATG 4 cut(s) 201, 302, 789, 1040
BstFNI CGCG 1 cut(s) 329
BstKTI GATC 6 cut(s) 697, 794, 831, 1021, 1133, 1158
BstMAI GTCTC 1 cut(s) 176
BstMBI GATC 6 cut(s) 694, 791, 828, 1018, 1130, 1155
BstMWI GCNNNNNNNGC 1 cut(s) 186
BstSFI CTRYAG 1 cut(s) 705
BstSLI GKGCMC 1 cut(s) 607
BstSNI TACGTA 1 cut(s) 581
BstUI CGCG 1 cut(s) 329
BstV1I GCAGC 1 cut(s) 579
BstV2I GAAGAC 2 cut(s) 176, 221
BstX2I RGATCY 3 cut(s) 694, 791, 1130
BstXI CCANNNNNNTGG 1 cut(s) 423
BstYI RGATCY 3 cut(s) 694, 791, 1130
BsuRI GGCC 5 cut(s) 84, 189, 375, 1076, 1177
BtsCI GGATG 4 cut(s) 201, 302, 789, 1040
BtsI GCAGTG 1 cut(s) 918
BtsIMutI CAGTG 6 cut(s) 453, 918, 943, 977, 1084, 1149
Cac8I GCNNGC 2 cut(s) 331, 969
Cfr13I GGNCC 4 cut(s) 248, 299, 373, 413
CseI GACGC 1 cut(s) 335
Csp6I GTAC 5 cut(s) 93, 104, 578, 725, 1002
CspCI CAANNNNNGTGG 2 cut(s) 1060, 1095
CviAII CATG 8 cut(s) 39, 165, 252, 460, 780, 1022, 1113, 1211
CviQI GTAC 5 cut(s) 93, 104, 578, 725, 1002
DdeI CTNAG 2 cut(s) 311, 900
DpnI GATC 6 cut(s) 696, 793, 830, 1020, 1132, 1157
DpnII GATC 6 cut(s) 694, 791, 828, 1018, 1130, 1155
DraI TTTAAA 1 cut(s) 486
EaeI YGGCCR 2 cut(s) 82, 187
Eam1104I CTCTTC 1 cut(s) 240
EarI CTCTTC 1 cut(s) 240
EciI GGCGGA 1 cut(s) 897
Eco105I TACGTA 1 cut(s) 581
Eco24I GRGCYC 1 cut(s) 550
Eco32I GATATC 1 cut(s) 1009
Eco47I GGWCC 3 cut(s) 248, 299, 413
Eco57I CTGAAG 3 cut(s) 168, 802, 939
Eco88I CYCGRG 1 cut(s) 804
EcoO109I RGGNCCY 1 cut(s) 373
EcoRI GAATTC 2 cut(s) 273, 1206
EcoRV GATATC 1 cut(s) 1009
EcoT22I ATGCAT 1 cut(s) 166
EcoT38I GRGCYC 1 cut(s) 550
FaeI CATG 8 cut(s) 42, 168, 255, 463, 783, 1025, 1116, 1214
FatI CATG 8 cut(s) 38, 164, 251, 459, 779, 1021, 1112, 1210
FauI CCCGC 1 cut(s) 214
FblI GTMKAC 1 cut(s) 7
Fnu4HI GCNGC 1 cut(s) 568
FokI GGATG 4 cut(s) 188, 289, 796, 1027
FriOI GRGCYC 1 cut(s) 550
Fsp4HI GCNGC 1 cut(s) 568
FspBI CTAG 2 cut(s) 57, 1089
GluI GCNGC 1 cut(s) 568
GsaI CCCAGC 1 cut(s) 899
HaeIII GGCC 5 cut(s) 84, 189, 375, 1076, 1177
HapII CCGG 3 cut(s) 608, 948, 1044
HgaI GACGC 1 cut(s) 335
Hin1II CATG 8 cut(s) 42, 168, 255, 463, 783, 1025, 1116, 1214
HincII GTYRAC 2 cut(s) 1027, 1165
HindII GTYRAC 2 cut(s) 1027, 1165
HindIII AAGCTT 2 cut(s) 150, 1230
HinfI GANTC 3 cut(s) 671, 771, 1108
HpaII CCGG 3 cut(s) 608, 948, 1044
HphI GGTGA 3 cut(s) 45, 137, 1092
Hpy166II GTNNAC 6 cut(s) 8, 578, 605, 727, 1027, 1165
Hpy188I TCNGA 8 cut(s) 279, 341, 543, 683, 735, 821, 991, 1107
Hpy188III TCNNGA 3 cut(s) 795, 1012, 1044
Hpy8I GTNNAC 6 cut(s) 8, 578, 605, 727, 1027, 1165
Hpy99I CGWCG 1 cut(s) 1126
HpyAV CCTTC 2 cut(s) 364, 386
HpyCH4III ACNGT 2 cut(s) 764, 840
HpyCH4IV ACGT 4 cut(s) 102, 267, 366, 580
HpyF10VI GCNNNNNNNGC 1 cut(s) 186
HpyF3I CTNAG 2 cut(s) 311, 900
HpySE526I ACGT 4 cut(s) 102, 267, 366, 580
Hsp92II CATG 8 cut(s) 42, 168, 255, 463, 783, 1025, 1116, 1214
Kpn2I TCCGGA 1 cut(s) 1043
Kzo9I GATC 6 cut(s) 694, 791, 828, 1018, 1130, 1155
LmnI GCTCC 2 cut(s) 908, 992
Lsp1109I GCAGC 1 cut(s) 579
LweI GCATC 1 cut(s) 1049
MaeI CTAG 2 cut(s) 57, 1089
MaeII ACGT 4 cut(s) 102, 267, 366, 580
MaeIII GTNAC 3 cut(s) 658, 840, 928
MalI GATC 6 cut(s) 696, 793, 830, 1020, 1132, 1157
MboI GATC 6 cut(s) 694, 791, 828, 1018, 1130, 1155
MboII GAAGA 4 cut(s) 181, 226, 227, 808
MflI RGATCY 3 cut(s) 694, 791, 1130
MhlI GDGCHC 2 cut(s) 550, 607
MlsI TGGCCA 2 cut(s) 84, 189
MluCI AATT 7 cut(s) 273, 417, 512, 736, 858, 889, 1206
MluI ACGCGT 1 cut(s) 327
MluNI TGGCCA 2 cut(s) 84, 189
MlyI GAGTC 1 cut(s) 665
MmeI TCCRAC 2 cut(s) 250, 1014
MnlI CCTC 6 cut(s) 34, 130, 243, 386, 1045, 1113
Mox20I TGGCCA 2 cut(s) 84, 189
Mph1103I ATGCAT 1 cut(s) 166
MroI TCCGGA 1 cut(s) 1043
MscI TGGCCA 2 cut(s) 84, 189
MseI TTAA 5 cut(s) 99, 158, 485, 1172, 1234
MslI CAYNNNNRTG 2 cut(s) 458, 600
Msp20I TGGCCA 2 cut(s) 84, 189
MspI CCGG 3 cut(s) 608, 948, 1044
MvnI CGCG 1 cut(s) 329
MwoI GCNNNNNNNGC 1 cut(s) 186
NdeII GATC 6 cut(s) 694, 791, 828, 1018, 1130, 1155
NlaIII CATG 8 cut(s) 42, 168, 255, 463, 783, 1025, 1116, 1214
NlaIV GGNNCC 1 cut(s) 118
NmuCI GTSAC 2 cut(s) 658, 840
NsiI ATGCAT 1 cut(s) 166
OliI CACNNNNGTG 1 cut(s) 600
PfeI GAWTC 2 cut(s) 771, 1108
PkrI GCNGC 1 cut(s) 569
PleI GAGTC 1 cut(s) 665
PpsI GAGTC 1 cut(s) 665
Ppu21I YACGTR 1 cut(s) 581
PsiI TTATAA 2 cut(s) 401, 857
Psp1406I AACGTT 1 cut(s) 267
PspFI CCCAGC 1 cut(s) 895
PspN4I GGNNCC 1 cut(s) 118
PspPI GGNCC 4 cut(s) 248, 299, 373, 413
PsuI RGATCY 3 cut(s) 694, 791, 1130
RsaI GTAC 5 cut(s) 94, 105, 579, 726, 1003
RsaNI GTAC 5 cut(s) 93, 104, 578, 725, 1002
RseI CAYNNNNRTG 2 cut(s) 458, 600
SaqAI TTAA 5 cut(s) 99, 158, 485, 1172, 1234
SatI GCNGC 1 cut(s) 568
Sau3AI GATC 6 cut(s) 694, 791, 828, 1018, 1130, 1155
Sau96I GGNCC 4 cut(s) 248, 299, 373, 413
SchI GAGTC 1 cut(s) 665
SduI GDGCHC 2 cut(s) 550, 607
SfaNI GCATC 1 cut(s) 1049
SfcI CTRYAG 1 cut(s) 705
SinI GGWCC 3 cut(s) 248, 299, 413
SmiMI CAYNNNNRTG 2 cut(s) 458, 600
SmlI CTYRAG 1 cut(s) 598
SmoI CTYRAG 1 cut(s) 598
SnaBI TACGTA 1 cut(s) 581
Sse9I AATT 7 cut(s) 273, 417, 512, 736, 858, 889, 1206
SsiI CCGC 3 cut(s) 207, 882, 1038
SspI AATATT 1 cut(s) 292
SspMI CTAG 2 cut(s) 57, 1089
TaaI ACNGT 2 cut(s) 764, 840
TaiI ACGT 4 cut(s) 105, 270, 369, 583
TaqI TCGA 2 cut(s) 717, 1124
TaqII GACCGA 2 cut(s) 287, 1150
TasI AATT 7 cut(s) 273, 417, 512, 736, 858, 889, 1206
TatI WGTACW 1 cut(s) 724
TfiI GAWTC 2 cut(s) 771, 1108
Tru1I TTAA 5 cut(s) 99, 158, 485, 1172, 1234
Tru9I TTAA 5 cut(s) 99, 158, 485, 1172, 1234
TscAI CASTG 6 cut(s) 460, 918, 943, 984, 1084, 1149
TseFI GTSAC 2 cut(s) 658, 840
TseI GCWGC 1 cut(s) 567
Tsp45I GTSAC 2 cut(s) 658, 840
TspDTI ATGAA 3 cut(s) 27, 667, 1199
TspRI CASTG 6 cut(s) 460, 918, 943, 984, 1084, 1149
VneI GTGCAC 1 cut(s) 603
VpaK11BI GGWCC 3 cut(s) 248, 299, 413
XapI RAATTY 2 cut(s) 273, 1206
XmiI GTMKAC 1 cut(s) 7
XspI CTAG 2 cut(s) 57, 1089
Zsp2I ATGCAT 1 cut(s) 166
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.