Rh4DG328300

Polygalacturonase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr4D
OG0015960
Physical Location & Seq
Reverse (-)
55168254 .. 55170483
2230 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh4DG328300.1

Sequence Viewer

Length: 1173 bp
ATGCCAACCAATCAGGCGCTCATAGCGGCATGGAAAGCTGCCTGCAAAGTGAATGGGGCTAGTGTAGAAATCCCTTCAGGATTCAAGTTCCTCATCAAGCCAATAACTCTTCAAGGCCCTTGTATGCCTGACGTTGTTCTTCAGATAGATGGAACTCTAATGGCTCCTCCAAAAGTTAGCTCATGGTCAAAGTCCAGTTTGTTTCAGTGGATAAACTTCAAATGGGTTCATAACTTCACCATCCAGGGCACCGGAGTTGTCGATGGCCAGGGCTCTGACTGGTGGACTGGTAGTTCCTCTTCCTCTTCAATCTATAATTACTTGCAGAAGAAGTCCAACAAGCATATGCCGAATTTCAAACCCACTGCTTTGAGATTCTATTCAAGCTATGATGTGACAGTACGAGATATCAGAATCATAAACAGCCCTCAGTGCCATTTGAAATTTGACAGCTCTGGAGGGATCATAGTTGACAACATTACCATATCTTCACCAGAGAATAGTCCAAATACTGATGGAATTCACTTGCAGAACACCCAAAATGTCGAAATTCATCATTCTACTATTGGTTGTGGAGATGACTGTGTATCCATACAAACTGGCTGCTCCAATGTTCATGTTCATCATATCAATTGTGGCCCTGGCCATGGCATAAGTCTAGGAGGACTTGGAAAAGACAGAAGTGTTGCTTGTGTCTCAAATATAATTGTCAATGACATTACATTTCAAAACACTCTATCTGGAGTTAGGATCAAAACATGGCAGGGAGGCATTGGGTCTGTGAAGAATGTATCTTTTTCCAATATCCAAGTTTCAAATGTGAAGGTTCCGATAATGATAGACCAGTACTACTGTGACAAGAAGTCCTGCAAGAACCAAACAGGAGCTGTAGCAATCTCAGGTGTGAAATATGACCAAATAATTGGGACTTATTCGGTGCAGCCTGTTCATCTTGCTTGCAGCAGCGACATTCCATGCAAAGATGTTGATCTCATTGATATTCAGCTCAAGCCCTCAGCAGGGTACCAGAGATTTCAACACGCTTTGTGTTGGAACTCTTATGGCAAGTCACAAGCTCCTTTGGTCCCTTCAAGCATAGACTACTGCTTGAGAAGAGATGAAAATCCAGTCGAGAGAATAGCAAAGTCACAGGATCGTCAGCATCAGTGCTAG

Protein Analysis

390

Amino Acids

42.72

Weight (kDa)

8.54

Isoelectric Point (pI)

41.79

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Glyco_hydro_28 PF00295 20 - 339 6.1e-81 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: OG0015960)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G26610
fragaria_vesca FvH4_4g26050
malus_domestica MD16G1097700.v1.1
prunus_persica Prupe.1G249200_v2.0.a1
rosa_chinensis RchiOBHm_Chr4g0433511
rosa_laevigata RLG00000006749
rosa_multiflora Rmu_sc0000312.1_g000004
rosa_roxburghii Rroxscaffold_5G00375030
rosa_rugosa Rorug04G0269200
rosa_samantha Rh4AG323800 Rh4BG331800 Rh4CG347100 Rh4DG328300
rosa_wichuraiana Rw0G020120 Rw4G028060

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc65I GGTACC 1 cut(s) 1023
AccB1I GGYRCC 2 cut(s) 248, 1023
AciI CCGC 1 cut(s) 26
AclWI GGATC 3 cut(s) 470, 758, 1161
AcoI YGGCCR 2 cut(s) 265, 643
AcsI RAATTY 4 cut(s) 352, 443, 519, 549
AcuI CTGAAG 2 cut(s) 60, 125
AfaI GTAC 3 cut(s) 402, 848, 1025
AfiI CCNNNNNNNGG 3 cut(s) 647, 1019, 1020
AhdI GACNNNNNGTC 1 cut(s) 862
AjnI CCWGG 3 cut(s) 243, 267, 640
AloI GAACNNNNNNTCC 2 cut(s) 277, 309
AluBI AGCT 7 cut(s) 38, 180, 387, 453, 887, 1006, 1076
AluI AGCT 7 cut(s) 38, 180, 387, 453, 887, 1006, 1076
Alw26I GTCTC 1 cut(s) 700
AlwI GGATC 3 cut(s) 470, 758, 1161
AlwNI CAGNNNCTG 1 cut(s) 887
AoxI GGCC 4 cut(s) 115, 265, 637, 643
ApeKI GCWGC 5 cut(s) 38, 603, 940, 960, 963
ApoI RAATTY 4 cut(s) 352, 443, 519, 549
Asp718I GGTACC 1 cut(s) 1023
AspLEI GCGC 1 cut(s) 19
AspS9I GGNCC 3 cut(s) 116, 638, 1084
AsuHPI GGTGA 2 cut(s) 229, 483
AvaII GGWCC 1 cut(s) 1084
BaeGI GKGCMC 1 cut(s) 251
BalI TGGCCA 2 cut(s) 267, 645
BanI GGYRCC 2 cut(s) 248, 1023
BanII GRGCYC 1 cut(s) 275
BarI GAAGNNNNNNTAC 2 cut(s) 283, 315
BbvCI CCTCAGC 1 cut(s) 1015
BbvI GCAGC 5 cut(s) 25, 590, 952, 972, 975
BccI CCATC 4 cut(s) 143, 248, 257, 509
BciT130I CCWGG 3 cut(s) 245, 269, 642
BciVI GTATCC 1 cut(s) 598
BcoDI GTCTC 1 cut(s) 700
BfaI CTAG 3 cut(s) 60, 659, 1171
BfmI CTRYAG 1 cut(s) 888
BfoI RGCGCY 1 cut(s) 20
BfuI GTATCC 1 cut(s) 598
BisI GCNGC 6 cut(s) 27, 39, 604, 941, 961, 964
BlsI GCNGC 6 cut(s) 28, 40, 605, 942, 962, 965
BmcAI AGTACT 1 cut(s) 848
Bme1390I CCNGG 3 cut(s) 245, 269, 642
Bme18I GGWCC 1 cut(s) 1084
BmeRI GACNNNNNGTC 1 cut(s) 862
BmgT120I GGNCC 3 cut(s) 116, 638, 1084
BmiI GGNNCC 5 cut(s) 165, 250, 828, 1025, 1086
BmrFI CCNGG 3 cut(s) 245, 269, 642
BpmI CTGGAG 2 cut(s) 477, 762
Bpu10I CCTNAGC 1 cut(s) 1015
BpuEI CTTGAG 2 cut(s) 992, 1129
BsaBI GATNNNNATC 2 cut(s) 987, 1122
BsaJI CCNNGG 4 cut(s) 244, 268, 640, 646
BsaWI WCCGGW 1 cut(s) 251
Bsc4I CCNNNNNNNGG 3 cut(s) 647, 1019, 1020
Bse1I ACTGG 6 cut(s) 195, 284, 292, 604, 844, 1127
Bse8I GATNNNNATC 2 cut(s) 987, 1122
BseBI CCWGG 3 cut(s) 245, 269, 642
BseDI CCNNGG 4 cut(s) 244, 268, 640, 646
BseGI GGATG 1 cut(s) 240
BseJI GATNNNNATC 2 cut(s) 987, 1122
BseLI CCNNNNNNNGG 3 cut(s) 647, 1019, 1020
BseMII CTCAG 3 cut(s) 443, 912, 1029
BseNI ACTGG 6 cut(s) 195, 284, 292, 604, 844, 1127
BseRI GAGGAG 1 cut(s) 156
BseSI GKGCMC 1 cut(s) 251
BseXI GCAGC 5 cut(s) 25, 590, 952, 972, 975
BsgI GTGCAG 1 cut(s) 959
BshFI GGCC 4 cut(s) 117, 267, 639, 645
BshNI GGYRCC 2 cut(s) 248, 1023
BsiSI CCGG 1 cut(s) 252
BslFI GGGAC 2 cut(s) 940, 1070
BslI CCNNNNNNNGG 3 cut(s) 647, 1019, 1020
BsmAI GTCTC 1 cut(s) 700
BsmFI GGGAC 2 cut(s) 940, 1070
BsnI GGCC 4 cut(s) 117, 267, 639, 645
Bsp1286I GDGCHC 2 cut(s) 251, 275
Bsp143I GATC 4 cut(s) 462, 750, 988, 1153
Bsp19I CCATGG 1 cut(s) 646
BspACI CCGC 1 cut(s) 26
BspANI GGCC 4 cut(s) 117, 267, 639, 645
BspCNI CTCAG 3 cut(s) 442, 911, 1028
BspLI GGNNCC 5 cut(s) 165, 250, 828, 1025, 1086
BspPI GGATC 3 cut(s) 470, 758, 1161
BspT107I GGYRCC 2 cut(s) 248, 1023
BsrI ACTGG 6 cut(s) 195, 284, 292, 604, 844, 1127
BssECI CCNNGG 4 cut(s) 244, 268, 640, 646
BssMI GATC 4 cut(s) 462, 750, 988, 1153
BssT1I CCWWGG 1 cut(s) 646
Bst2UI CCWGG 3 cut(s) 245, 269, 642
Bst4CI ACNGT 3 cut(s) 400, 584, 854
Bst6I CTCTTC 4 cut(s) 114, 304, 310, 1108
BstC8I GCNNGC 2 cut(s) 43, 958
BstDEI CTNAG 3 cut(s) 429, 898, 1015
BstDSI CCRYGG 1 cut(s) 646
BstF5I GGATG 1 cut(s) 240
BstH2I RGCGCY 1 cut(s) 20
BstHHI GCGC 1 cut(s) 19
BstKTI GATC 4 cut(s) 465, 753, 991, 1156
BstMAI GTCTC 1 cut(s) 700
BstMBI GATC 4 cut(s) 462, 750, 988, 1153
BstMWI GCNNNNNNNGC 3 cut(s) 23, 35, 432
BstNI CCWGG 3 cut(s) 245, 269, 642
BstSCI CCNGG 3 cut(s) 243, 267, 640
BstSFI CTRYAG 1 cut(s) 888
BstSLI GKGCMC 1 cut(s) 251
BstV1I GCAGC 5 cut(s) 25, 590, 952, 972, 975
BstXI CCANNNNNNTGG 1 cut(s) 923
BsuI GTATCC 1 cut(s) 598
BsuRI GGCC 4 cut(s) 117, 267, 639, 645
BtgI CCRYGG 1 cut(s) 646
BtsCI GGATG 1 cut(s) 240
BtsI GCAGTG 1 cut(s) 363
BtsIMutI CAGTG 4 cut(s) 212, 363, 437, 1172
Cac8I GCNNGC 2 cut(s) 43, 958
CaiI CAGNNNCTG 1 cut(s) 887
CfoI GCGC 1 cut(s) 19
Cfr13I GGNCC 3 cut(s) 116, 638, 1084
Csp6I GTAC 3 cut(s) 401, 847, 1024
CviAII CATG 6 cut(s) 30, 183, 617, 647, 759, 975
CviQI GTAC 3 cut(s) 401, 847, 1024
DdeI CTNAG 3 cut(s) 429, 898, 1015
DpnI GATC 4 cut(s) 464, 752, 990, 1155
DpnII GATC 4 cut(s) 462, 750, 988, 1153
DriI GACNNNNNGTC 1 cut(s) 862
EaeI YGGCCR 2 cut(s) 265, 643
Eam1104I CTCTTC 4 cut(s) 114, 304, 310, 1108
Eam1105I GACNNNNNGTC 1 cut(s) 862
EarI CTCTTC 4 cut(s) 114, 304, 310, 1108
Eco130I CCWWGG 1 cut(s) 646
Eco24I GRGCYC 1 cut(s) 275
Eco32I GATATC 1 cut(s) 409
Eco47I GGWCC 1 cut(s) 1084
Eco57I CTGAAG 2 cut(s) 60, 125
EcoO109I RGGNCCY 1 cut(s) 116
EcoRI GAATTC 1 cut(s) 519
EcoRII CCWGG 3 cut(s) 243, 267, 640
EcoRV GATATC 1 cut(s) 409
EcoT14I CCWWGG 1 cut(s) 646
EcoT38I GRGCYC 1 cut(s) 275
ErhI CCWWGG 1 cut(s) 646
FaeI CATG 6 cut(s) 33, 186, 620, 650, 762, 978
FalI AAGNNNNNCTT 2 cut(s) 673, 705
FaqI GGGAC 2 cut(s) 940, 1070
FatI CATG 6 cut(s) 29, 182, 616, 646, 758, 974
FauNDI CATATG 1 cut(s) 345
Fnu4HI GCNGC 6 cut(s) 27, 39, 604, 941, 961, 964
FokI GGATG 1 cut(s) 227
FriOI GRGCYC 1 cut(s) 275
Fsp4HI GCNGC 6 cut(s) 27, 39, 604, 941, 961, 964
FspBI CTAG 3 cut(s) 60, 659, 1171
GlaI GCGC 1 cut(s) 18
GluI GCNGC 6 cut(s) 27, 39, 604, 941, 961, 964
GsuI CTGGAG 2 cut(s) 477, 762
HaeII RGCGCY 1 cut(s) 20
HaeIII GGCC 4 cut(s) 117, 267, 639, 645
HapII CCGG 1 cut(s) 252
HhaI GCGC 1 cut(s) 19
Hin1II CATG 6 cut(s) 33, 186, 620, 650, 762, 978
Hin6I GCGC 1 cut(s) 17
HinP1I GCGC 1 cut(s) 17
HincII GTYRAC 1 cut(s) 472
HindII GTYRAC 1 cut(s) 472
HinfI GANTC 3 cut(s) 81, 375, 414
HpaII CCGG 1 cut(s) 252
HphI GGTGA 2 cut(s) 229, 483
Hpy166II GTNNAC 2 cut(s) 285, 472
Hpy188I TCNGA 4 cut(s) 144, 277, 413, 831
Hpy188III TCNNGA 4 cut(s) 78, 456, 741, 1132
Hpy8I GTNNAC 2 cut(s) 285, 472
HpyAV CCTTC 3 cut(s) 84, 817, 1098
HpyCH4III ACNGT 3 cut(s) 400, 584, 854
HpyCH4IV ACGT 1 cut(s) 132
HpyCH4V TGCA 7 cut(s) 45, 325, 529, 870, 940, 960, 978
HpyF10VI GCNNNNNNNGC 3 cut(s) 23, 35, 432
HpyF3I CTNAG 3 cut(s) 429, 898, 1015
HpySE526I ACGT 1 cut(s) 132
Hsp92II CATG 6 cut(s) 33, 186, 620, 650, 762, 978
HspAI GCGC 1 cut(s) 17
KpnI GGTACC 1 cut(s) 1027
Kzo9I GATC 4 cut(s) 462, 750, 988, 1153
LmnI GCTCC 4 cut(s) 169, 611, 884, 1081
Lsp1109I GCAGC 5 cut(s) 25, 590, 952, 972, 975
MaeI CTAG 3 cut(s) 60, 659, 1171
MaeII ACGT 1 cut(s) 132
MaeIII GTNAC 4 cut(s) 394, 854, 1068, 1146
MalI GATC 4 cut(s) 464, 752, 990, 1155
MboI GATC 4 cut(s) 462, 750, 988, 1153
MboII GAAGA 8 cut(s) 101, 131, 291, 297, 340, 480, 796, 1125
MfeI CAATTG 1 cut(s) 631
MhlI GDGCHC 2 cut(s) 251, 275
MlsI TGGCCA 2 cut(s) 267, 645
MluCI AATT 8 cut(s) 316, 352, 443, 519, 549, 631, 705, 921
MluNI TGGCCA 2 cut(s) 267, 645
MmeI TCCRAC 2 cut(s) 360, 1031
MnlI CCTC 9 cut(s) 101, 177, 307, 313, 438, 452, 656, 761, 1024
Mox20I TGGCCA 2 cut(s) 267, 645
MscI TGGCCA 2 cut(s) 267, 645
Msp20I TGGCCA 2 cut(s) 267, 645
MspI CCGG 1 cut(s) 252
MspR9I CCNGG 3 cut(s) 245, 269, 642
MunI CAATTG 1 cut(s) 631
MvaI CCWGG 3 cut(s) 245, 269, 642
MwoI GCNNNNNNNGC 3 cut(s) 23, 35, 432
NcoI CCATGG 1 cut(s) 646
NdeI CATATG 1 cut(s) 345
NdeII GATC 4 cut(s) 462, 750, 988, 1153
NlaIII CATG 6 cut(s) 33, 186, 620, 650, 762, 978
NlaIV GGNNCC 5 cut(s) 165, 250, 828, 1025, 1086
NmuCI GTSAC 4 cut(s) 394, 854, 1068, 1146
PfeI GAWTC 3 cut(s) 81, 375, 414
PkrI GCNGC 6 cut(s) 28, 40, 605, 942, 962, 965
Psp6I CCWGG 3 cut(s) 243, 267, 640
PspGI CCWGG 3 cut(s) 243, 267, 640
PspN4I GGNNCC 5 cut(s) 165, 250, 828, 1025, 1086
PspPI GGNCC 3 cut(s) 116, 638, 1084
PstNI CAGNNNCTG 1 cut(s) 887
RsaI GTAC 3 cut(s) 402, 848, 1025
RsaNI GTAC 3 cut(s) 401, 847, 1024
SatI GCNGC 6 cut(s) 27, 39, 604, 941, 961, 964
Sau3AI GATC 4 cut(s) 462, 750, 988, 1153
Sau96I GGNCC 3 cut(s) 116, 638, 1084
ScaI AGTACT 1 cut(s) 848
ScrFI CCNGG 3 cut(s) 245, 269, 642
SduI GDGCHC 2 cut(s) 251, 275
SfcI CTRYAG 1 cut(s) 888
SinI GGWCC 1 cut(s) 1084
SmlI CTYRAG 2 cut(s) 1007, 1108
SmoI CTYRAG 2 cut(s) 1007, 1108
Sse9I AATT 8 cut(s) 316, 352, 443, 519, 549, 631, 705, 921
SsiI CCGC 1 cut(s) 26
SspMI CTAG 3 cut(s) 60, 659, 1171
StyD4I CCNGG 3 cut(s) 243, 267, 640
StyI CCWWGG 1 cut(s) 646
TaaI ACNGT 3 cut(s) 400, 584, 854
TaiI ACGT 1 cut(s) 135
TaqI TCGA 3 cut(s) 261, 546, 1131
TasI AATT 8 cut(s) 316, 352, 443, 519, 549, 631, 705, 921
TatI WGTACW 1 cut(s) 846
TauI GCSGC 1 cut(s) 29
TfiI GAWTC 3 cut(s) 81, 375, 414
TscAI CASTG 4 cut(s) 212, 370, 437, 1172
TseFI GTSAC 4 cut(s) 394, 854, 1068, 1146
TseI GCWGC 5 cut(s) 38, 603, 940, 960, 963
Tsp45I GTSAC 4 cut(s) 394, 854, 1068, 1146
TspDTI ATGAA 6 cut(s) 218, 542, 605, 611, 938, 1134
TspRI CASTG 4 cut(s) 212, 370, 437, 1172
VpaK11BI GGWCC 1 cut(s) 1084
XapI RAATTY 4 cut(s) 352, 443, 519, 549
XspI CTAG 3 cut(s) 60, 659, 1171
ZrmI AGTACT 1 cut(s) 848
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.