RchiOBHm_Chr4g0399471

Polygalacturonase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
4
OG0000579
Physical Location & Seq
Reverse (-)
16716213 .. 16719254
3042 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ37159

Sequence Viewer

Length: 1236 bp
ATGCAGGGTCTTCCTTCACTACTTAGCTCTGTTGTGCTTTTATGGATTGTTGCTTCATCTAGTTTTGGCATTGGGTATGGCCAAACTGGTAATCTTAGTGTACTTGATTTTGGTGCCTCCGGCGATGGCGTAGGAGATGATACCCAAGCTTTCTTGAATGCATGGAAAACAGTTTGTGCGACTGACCAAGCCCTAACTATTCCTGCGGGGAAGACCTTTGTACTCAAACCTCTTCAACTTGTAGGTCCTTGCAAATCCAGTAGTGTTGTAATTCAGATTGATGGGAATATTGTTGGTCCATCCACTCTTAGCGAATGGGCAGACGTGTGCAAAATGGGACAGTGCTGGCTATGCTTCCAAAACGTGAAGGGCCTCGTCATCAAAGGGGGAGGACTTATAGATGGCAAGGGTTCAATTTGGTGGAACCAAAAAACCCAATCCATAAATGCTTTACACTTCCACAAATGCGACCAACTTCAATTATCTGGATTTACTTCCCGTGATAGTCCGAAAGGCCATATATTTATACATAGCAGCAATGATGTACGTATCTCAAACATTCATTTGAATGCACCGAAGAACAGCCCAAATACTGATGGCATCGGCATCTCTTTATCAAGCCGAGTAACTATACAAGACTCTTCCATTGGAACTGGTGATGATTGTATTGCAATTAAGGGAGGGTCTTCTTTTGTAAACGTAACTCATGTGACATGCGGACCAGGTCATGGTTTCAGTGTGGGTAGTTTAGGACAAGCTCCAGCTACTCCAGATAAAGTCGAACAAGTATACTTTCAAAATTGTATCTGTGACAAAACGATGAACTGCGCAAGAATCAAAACATGGATGGGAGGATCTGGGAATGCTAGGGCGATTTTCTTCAAACAAATGACCCTTAAACAGTCAAATAATCCTATTGTGATTGATCAACACTACTGCGATGGTGCAGCTAATTGCGCAGCTAAGACTGGAGCGGTGAAAGTTAGTGACGTAACTTTCAGTGGCTTCACTGGAACTTCAGCAAGTGAGCAAGCAATAACACTGAATTGCTCCGACTTGGGTTGCACCAATATTTTGATGGATCATGTCATCCTAACCTCCGCAATCGGAAAGCCACTTCGTTCTGTATGCAACAAGGCCAGTGGGAAAGCTAGTTTTACTTCACCTCCCGTTCCTTGTCTGTCGTCGAAGCAATCCCTGTCACCAACAATTGCACCAATCTCAATCACAAATTAA

Protein Analysis

411

Amino Acids

43.1

Weight (kDa)

8.4

Isoelectric Point (pI)

36.0

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pect-lyase_RHGA_epim PF12708 33 - 236 1e-08 Rhamnogalacturonase A/epimerase, pectate lyase-like
Glyco_hydro_28 PF00295 62 - 380 3.5e-77 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)
Acc16I TGCGCA 2 cut(s) 829, 958
AccB1I GGYRCC 1 cut(s) 113
AccB7I CCANNNNNTGG 1 cut(s) 728
AccBSI CCGCTC 1 cut(s) 974
AccI GTMKAC 1 cut(s) 789
AciI CCGC 4 cut(s) 206, 717, 974, 1101
AclWI GGATC 2 cut(s) 862, 1089
AcoI YGGCCR 1 cut(s) 79
AcuI CTGAAG 1 cut(s) 1002
AfaI GTAC 3 cut(s) 102, 222, 546
AfiI CCNNNNNNNGG 1 cut(s) 728
AflIII ACRYGT 1 cut(s) 324
AgsI TTSAA 7 cut(s) 157, 236, 414, 479, 568, 797, 883
AjiI CACGTC 1 cut(s) 325
AjnI CCWGG 1 cut(s) 721
AluBI AGCT 7 cut(s) 27, 149, 758, 764, 950, 962, 1151
AluI AGCT 7 cut(s) 27, 149, 758, 764, 950, 962, 1151
AlwI GGATC 2 cut(s) 862, 1089
AoxI GGCC 4 cut(s) 79, 370, 514, 1137
ApeKI GCWGC 3 cut(s) 534, 947, 959
AspLEI GCGC 2 cut(s) 830, 959
AspS9I GGNCC 4 cut(s) 245, 296, 370, 719
AsuHPI GGTGA 4 cut(s) 668, 988, 1155, 1194
AvaII GGWCC 3 cut(s) 245, 296, 719
BalI TGGCCA 1 cut(s) 81
BanI GGYRCC 1 cut(s) 113
BbsI GAAGAC 3 cut(s) 2, 218, 678
BbvI GCAGC 3 cut(s) 546, 959, 971
BccI CCATC 8 cut(s) 119, 275, 307, 395, 590, 841, 935, 1072
BciT130I CCWGG 1 cut(s) 723
BclI TGATCA 1 cut(s) 925
BfaI CTAG 3 cut(s) 60, 867, 1152
BisI GCNGC 3 cut(s) 535, 948, 960
BlsI GCNGC 3 cut(s) 536, 949, 961
Bme1390I CCNGG 1 cut(s) 723
Bme18I GGWCC 3 cut(s) 245, 296, 719
BmgBI CACGTC 1 cut(s) 325
BmgT120I GGNCC 4 cut(s) 245, 296, 370, 719
BmiI GGNNCC 2 cut(s) 115, 425
BmrFI CCNGG 1 cut(s) 723
BmsI GCATC 2 cut(s) 609, 615
BpiI GAAGAC 3 cut(s) 2, 218, 678
BpmI CTGGAG 3 cut(s) 744, 753, 990
BsaAI YACGTR 1 cut(s) 548
BsaXI ACNNNNNCTCC 2 cut(s) 1150, 1180
Bsc4I CCNNNNNNNGG 1 cut(s) 728
Bse1I ACTGG 6 cut(s) 91, 258, 658, 973, 1015, 1140
Bse3DI GCAATG 1 cut(s) 544
BseBI CCWGG 1 cut(s) 723
BseGI GGATG 3 cut(s) 299, 852, 1089
BseLI CCNNNNNNNGG 1 cut(s) 728
BseMI GCAATG 1 cut(s) 544
BseNI ACTGG 6 cut(s) 91, 258, 658, 973, 1015, 1140
BseXI GCAGC 3 cut(s) 546, 959, 971
BsgI GTGCAG 1 cut(s) 966
BshFI GGCC 4 cut(s) 81, 372, 516, 1139
BshNI GGYRCC 1 cut(s) 113
BsiSI CCGG 1 cut(s) 120
BslFI GGGAC 1 cut(s) 351
BslI CCNNNNNNNGG 1 cut(s) 728
BsmFI GGGAC 1 cut(s) 351
BsmI GAATGC 3 cut(s) 163, 574, 868
BsnI GGCC 4 cut(s) 81, 372, 516, 1139
Bsp143I GATC 3 cut(s) 854, 925, 1081
BspACI CCGC 4 cut(s) 206, 717, 974, 1101
BspANI GGCC 4 cut(s) 81, 372, 516, 1139
BspLI GGNNCC 2 cut(s) 115, 425
BspPI GGATC 2 cut(s) 862, 1089
BspT107I GGYRCC 1 cut(s) 113
BsrBI CCGCTC 1 cut(s) 974
BsrDI GCAATG 1 cut(s) 544
BsrI ACTGG 6 cut(s) 91, 258, 658, 973, 1015, 1140
BssMI GATC 3 cut(s) 854, 925, 1081
BssNAI GTATAC 1 cut(s) 790
Bst1107I GTATAC 1 cut(s) 790
Bst2UI CCWGG 1 cut(s) 723
Bst4CI ACNGT 3 cut(s) 172, 342, 903
Bst6I CTCTTC 2 cut(s) 237, 646
BstBAI YACGTR 1 cut(s) 548
BstC8I GCNNGC 2 cut(s) 347, 1032
BstDEI CTNAG 4 cut(s) 23, 95, 308, 963
BstF5I GGATG 3 cut(s) 299, 852, 1089
BstHHI GCGC 2 cut(s) 830, 959
BstKTI GATC 3 cut(s) 857, 928, 1084
BstMBI GATC 3 cut(s) 854, 925, 1081
BstMWI GCNNNNNNNGC 2 cut(s) 351, 956
BstNI CCWGG 1 cut(s) 723
BstNSI RCATGY 1 cut(s) 717
BstSCI CCNGG 1 cut(s) 721
BstSNI TACGTA 1 cut(s) 548
BstV1I GCAGC 3 cut(s) 546, 959, 971
BstV2I GAAGAC 3 cut(s) 2, 218, 678
BstX2I RGATCY 1 cut(s) 854
BstYI RGATCY 1 cut(s) 854
BstZ17I GTATAC 1 cut(s) 790
BsuRI GGCC 4 cut(s) 81, 372, 516, 1139
BtgZI GCGATG 2 cut(s) 138, 954
BtrI CACGTC 1 cut(s) 325
BtsCI GGATG 3 cut(s) 299, 852, 1089
BtsIMutI CAGTG 6 cut(s) 347, 742, 1006, 1008, 1040, 1147
Cac8I GCNNGC 2 cut(s) 347, 1032
CfoI GCGC 2 cut(s) 830, 959
Cfr13I GGNCC 4 cut(s) 245, 296, 370, 719
CsiI ACCWGGT 1 cut(s) 721
Csp6I GTAC 3 cut(s) 101, 221, 545
CspCI CAANNNNNGTGG 2 cut(s) 1123, 1158
CviAII CATG 6 cut(s) 162, 707, 714, 728, 843, 1085
CviQI GTAC 3 cut(s) 101, 221, 545
DdeI CTNAG 4 cut(s) 23, 95, 308, 963
DpnI GATC 3 cut(s) 856, 927, 1083
DpnII GATC 3 cut(s) 854, 925, 1081
EaeI YGGCCR 1 cut(s) 79
Eam1104I CTCTTC 2 cut(s) 237, 646
EarI CTCTTC 2 cut(s) 237, 646
Eco105I TACGTA 1 cut(s) 548
Eco47I GGWCC 3 cut(s) 245, 296, 719
Eco57I CTGAAG 1 cut(s) 1002
EcoO109I RGGNCCY 2 cut(s) 245, 370
EcoRII CCWGG 1 cut(s) 721
EcoT22I ATGCAT 1 cut(s) 163
FaeI CATG 6 cut(s) 165, 710, 717, 731, 846, 1088
FaqI GGGAC 1 cut(s) 351
FatI CATG 6 cut(s) 161, 706, 713, 727, 842, 1084
FauI CCCGC 1 cut(s) 199
FbaI TGATCA 1 cut(s) 925
FblI GTMKAC 1 cut(s) 789
Fnu4HI GCNGC 3 cut(s) 535, 948, 960
FokI GGATG 3 cut(s) 286, 859, 1076
Fsp4HI GCNGC 3 cut(s) 535, 948, 960
FspBI CTAG 3 cut(s) 60, 867, 1152
FspI TGCGCA 2 cut(s) 829, 958
GlaI GCGC 2 cut(s) 829, 958
GluI GCNGC 3 cut(s) 535, 948, 960
GsuI CTGGAG 3 cut(s) 744, 753, 990
HaeIII GGCC 4 cut(s) 81, 372, 516, 1139
HapII CCGG 1 cut(s) 120
HhaI GCGC 2 cut(s) 830, 959
Hin1II CATG 6 cut(s) 165, 710, 717, 731, 846, 1088
Hin6I GCGC 2 cut(s) 828, 957
HinP1I GCGC 2 cut(s) 828, 957
HindIII AAGCTT 1 cut(s) 147
HinfI GANTC 2 cut(s) 638, 834
HpaII CCGG 1 cut(s) 120
HphI GGTGA 4 cut(s) 668, 988, 1155, 1194
Hpy166II GTNNAC 3 cut(s) 101, 697, 790
Hpy188I TCNGA 4 cut(s) 276, 510, 1054, 1109
Hpy188III TCNNGA 3 cut(s) 154, 486, 770
Hpy8I GTNNAC 3 cut(s) 101, 697, 790
Hpy99I CGWCG 1 cut(s) 1189
HpyAV CCTTC 2 cut(s) 24, 361
HpyCH4III ACNGT 3 cut(s) 172, 342, 903
HpyCH4IV ACGT 5 cut(s) 324, 363, 547, 699, 990
HpyF10VI GCNNNNNNNGC 2 cut(s) 351, 956
HpyF3I CTNAG 4 cut(s) 23, 95, 308, 963
HpySE526I ACGT 5 cut(s) 324, 363, 547, 699, 990
Hsp92II CATG 6 cut(s) 165, 710, 717, 731, 846, 1088
HspAI GCGC 2 cut(s) 828, 957
Ksp22I TGATCA 1 cut(s) 925
Kzo9I GATC 3 cut(s) 854, 925, 1081
LmnI GCTCC 3 cut(s) 763, 971, 1055
Lsp1109I GCAGC 3 cut(s) 546, 959, 971
LweI GCATC 2 cut(s) 609, 615
MabI ACCWGGT 1 cut(s) 721
MaeI CTAG 3 cut(s) 60, 867, 1152
MaeII ACGT 5 cut(s) 324, 363, 547, 699, 990
MaeIII GTNAC 7 cut(s) 625, 700, 709, 809, 986, 991, 1200
MalI GATC 3 cut(s) 856, 927, 1083
MbiI CCGCTC 1 cut(s) 974
MboI GATC 3 cut(s) 854, 925, 1081
MboII GAAGA 6 cut(s) 223, 224, 589, 633, 678, 871
MfeI CAATTG 1 cut(s) 1209
MflI RGATCY 1 cut(s) 854
MlsI TGGCCA 1 cut(s) 81
MluCI AATT 9 cut(s) 270, 414, 479, 672, 799, 952, 1045, 1209, 1231
MluNI TGGCCA 1 cut(s) 81
MlyI GAGTC 1 cut(s) 632
MmeI TCCRAC 1 cut(s) 1077
MnlI CCTC 8 cut(s) 127, 240, 383, 383, 674, 845, 1108, 1176
Mox20I TGGCCA 1 cut(s) 81
Mph1103I ATGCAT 1 cut(s) 163
MscI TGGCCA 1 cut(s) 81
MseI TTAA 3 cut(s) 675, 897, 1234
MslI CAYNNNNRTG 1 cut(s) 567
Msp20I TGGCCA 1 cut(s) 81
MspI CCGG 1 cut(s) 120
MspR9I CCNGG 1 cut(s) 723
MunI CAATTG 1 cut(s) 1209
Mva1269I GAATGC 3 cut(s) 163, 574, 868
MvaI CCWGG 1 cut(s) 723
MwoI GCNNNNNNNGC 2 cut(s) 351, 956
NdeII GATC 3 cut(s) 854, 925, 1081
NlaIII CATG 6 cut(s) 165, 710, 717, 731, 846, 1088
NlaIV GGNNCC 2 cut(s) 115, 425
NmeAIII GCCGAG 1 cut(s) 647
NmuCI GTSAC 4 cut(s) 709, 809, 986, 1200
NsbI TGCGCA 2 cut(s) 829, 958
NsiI ATGCAT 1 cut(s) 163
NspI RCATGY 1 cut(s) 717
PctI GAATGC 3 cut(s) 163, 574, 868
PfeI GAWTC 1 cut(s) 834
PflFI GACNNNGTC 1 cut(s) 723
PflMI CCANNNNNTGG 1 cut(s) 728
PkrI GCNGC 3 cut(s) 536, 949, 961
PleI GAGTC 1 cut(s) 632
PpsI GAGTC 1 cut(s) 632
Ppu21I YACGTR 1 cut(s) 548
PpuMI RGGWCCY 1 cut(s) 245
Psp5II RGGWCCY 1 cut(s) 245
Psp6I CCWGG 1 cut(s) 721
PspGI CCWGG 1 cut(s) 721
PspN4I GGNNCC 2 cut(s) 115, 425
PspPI GGNCC 4 cut(s) 245, 296, 370, 719
PspPPI RGGWCCY 1 cut(s) 245
PsuI RGATCY 1 cut(s) 854
PsyI GACNNNGTC 1 cut(s) 723
RsaI GTAC 3 cut(s) 102, 222, 546
RsaNI GTAC 3 cut(s) 101, 221, 545
RseI CAYNNNNRTG 1 cut(s) 567
SaqAI TTAA 3 cut(s) 675, 897, 1234
SatI GCNGC 3 cut(s) 535, 948, 960
Sau3AI GATC 3 cut(s) 854, 925, 1081
Sau96I GGNCC 4 cut(s) 245, 296, 370, 719
SchI GAGTC 1 cut(s) 632
ScrFI CCNGG 1 cut(s) 723
SexAI ACCWGGT 1 cut(s) 721
SfaNI GCATC 2 cut(s) 609, 615
SinI GGWCC 3 cut(s) 245, 296, 719
SmiMI CAYNNNNRTG 1 cut(s) 567
SnaBI TACGTA 1 cut(s) 548
Sse9I AATT 9 cut(s) 270, 414, 479, 672, 799, 952, 1045, 1209, 1231
SsiI CCGC 4 cut(s) 206, 717, 974, 1101
SspI AATATT 2 cut(s) 289, 1072
SspMI CTAG 3 cut(s) 60, 867, 1152
StyD4I CCNGG 1 cut(s) 721
TaaI ACNGT 3 cut(s) 172, 342, 903
TaiI ACGT 5 cut(s) 327, 366, 550, 702, 993
TaqI TCGA 2 cut(s) 780, 1187
TasI AATT 9 cut(s) 270, 414, 479, 672, 799, 952, 1045, 1209, 1231
TatI WGTACW 2 cut(s) 100, 220
TfiI GAWTC 1 cut(s) 834
Tru1I TTAA 3 cut(s) 675, 897, 1234
Tru9I TTAA 3 cut(s) 675, 897, 1234
TscAI CASTG 6 cut(s) 347, 742, 1006, 1015, 1047, 1147
TseFI GTSAC 4 cut(s) 709, 809, 986, 1200
TseI GCWGC 3 cut(s) 534, 947, 959
Tsp45I GTSAC 4 cut(s) 709, 809, 986, 1200
TspDTI ATGAA 3 cut(s) 45, 551, 836
TspRI CASTG 6 cut(s) 347, 742, 1006, 1015, 1047, 1147
Tth111I GACNNNGTC 1 cut(s) 723
Van91I CCANNNNNTGG 1 cut(s) 728
VpaK11BI GGWCC 3 cut(s) 245, 296, 719
XceI RCATGY 1 cut(s) 717
XcmI CCANNNNNNNNNTGG 1 cut(s) 1075
XmiI GTMKAC 1 cut(s) 789
XspI CTAG 3 cut(s) 60, 867, 1152
Zsp2I ATGCAT 1 cut(s) 163
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.