FvH4_3g12830

Polygalacturonase QRT3

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0016157
Physical Location & Seq
Reverse (-)
7669222 .. 7672820
3599 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g12830.t1

Sequence Viewer

Length: 1467 bp
ATGAGAATGAGACCCATCTCAGCATTGTGTAGTCTCCTGCTACTAATGCTGTTGGTAGAAGAAGCTACATCTATTTCCAGAAGAAATGAAATGCTCTCATCATTTCAGGCAAAGCTTCATGAAAAATCACTCTCCGGTCCAACCAAACCGCCTCTCTCATCATTGTTCGAAGCTTCAAATGTCACTAAGGATGGGAGAGTGTTTTACCCGATCGGGTACGGGGCAGACCCGACCGGAGCAAATGACAGCACAGAAGCCATAGCAAAAGCTTTAGAGGAAGCTTTTCAGTTGGAAAGCAGCCTTGAAATGCTGCCTGGAATCACTGACTTGGGTGGCGTTGTCATTGATCTGCAAGGTGGAAATTACAAGATTGCCCAGCCTTTGAGGTTCCCTCCAAACAGAGGCAACATTGTGATACAAGGAGGAACGCTGCGAGCCTCTGAAACATTTCCCGGCGACCGCCACCTAGTCGAATTATGGTCTCCAAATTCCCAAAAGCTTAGGGGAAAAACCTCCATCACCAATCAATTCTTCTTTGATCAGAAAGTCCAAGACGGTGAAGGAATCTACTACGAAGACATCATCTTTATAGATATTCTATTCGATTCAAGCTTCAGAGGAGGAGGCATTTACATAGTCAATTCGGCTCGAATTCGCATAACCAATTGCTTCTTCCTACACTTCACAACACAAGGAATTCTAGTCGAAAAGGGCCACGAAACCTACATATCAAACACATTCTTGGGACAACACTCCACAGTTGGCGGCGACCATGGCGAGAGAGGATTTACCGGCACCGGCATCGATCTTGCTAGCAATGATAATGCTGTAACGGATGTCGTAATTTTCTCAGCTGAAGTCGGGATCGTGTTAAGGGGTCAGGCTAACATGATCACAGGGGTACATTGTTACAACAAGGCAACTGGCTTTGGGGGTATAGGCATTTTGGTGAAGTTAGCAGGAAACTCACAAACTAGGATTGACAATTGCTACTTGGATTTCAATGCTATAGTCATGGAAGACCCGGTTCAAGTTCATGTGACCAATGGCTTCTTTCTGGGTGATGGTAATGTGGTGTTGAAATCTGTTAATGGTAAGATTCTAGGGTTAAACATTGTGAACAATATGTTCACCGGAAACCCTAGAAGTATGGTTCCCATGGTTCAATTAGACGGGCAATTTGGTGACATTGATCAAGTGGTGATTGACCAGAACAATGTGATCGGGATGAGCTTGAAATCAACTGTAGGGAGACAAAGTGTGGAGGGGAATGGGACGAAATGGGTGGCTGATTTTTCTTCTCAGTTGGTCTTTCCCAACCGGATTAATCATTTTCAGTATTCTTTACATACAAAAGGGGAAACCAAGTTTACAACACATGCTGTGACAAATGTATCGAACAATGTGGTCGTTGTGGAGAGTCAGAATGTGGTTAATGGTGTGGTTTCGATTGTTGTTCACCAGTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
Beta_helix

Protein Analysis

489

Amino Acids

53.1

Weight (kDa)

5.75

Isoelectric Point (pI)

22.09

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pect-lyase_RHGA_epim PF12708 73 - 309 4.9e-06 Rhamnogalacturonase A/epimerase, pectate lyase-like
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: OG0016157)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G20040
fragaria_vesca FvH4_3g12830
malus_domestica MD05G1247600.v1.1
prunus_persica Prupe.4G116400_v2.0.a1
pyrus_communis pycom05g22370
rosa_chinensis RchiOBHm_Chr5g0020771
rosa_laevigata RLG00000032561
rosa_multiflora Rmu_sc0002527.1_g000005
rosa_roxburghii Rroxscaffold_1G00057530
rosa_rugosa Rorug05G0062800
rosa_samantha Rh5AG152700 Rh5BG152400 Rh5CG164000 Rh5DG151900
rosa_wichuraiana Rw5G013540

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 794
AciI CCGC 3 cut(s) 149, 460, 765
AclWI GGATC 1 cut(s) 872
AcsI RAATTY 3 cut(s) 487, 651, 696
AcuI CTGAAG 2 cut(s) 598, 876
AfaI GTAC 2 cut(s) 218, 903
AfiI CCNNNNNNNGG 1 cut(s) 401
AgsI TTSAA 8 cut(s) 177, 305, 609, 1003, 1031, 1081, 1166, 1237
AjnI CCWGG 1 cut(s) 313
AjuI GAANNNNNNNTTGG 4 cut(s) 515, 547, 656, 688
AluBI AGCT 9 cut(s) 65, 115, 173, 269, 281, 499, 612, 854, 1233
AluI AGCT 9 cut(s) 65, 115, 173, 269, 281, 499, 612, 854, 1233
Alw26I GTCTC 4 cut(s) 4, 38, 486, 1246
AlwI GGATC 1 cut(s) 872
AoxI GGCC 1 cut(s) 712
ApeKI GCWGC 3 cut(s) 297, 310, 430
ApoI RAATTY 3 cut(s) 487, 651, 696
ArsI GACNNNNNNTTYG 2 cut(s) 1163, 1195
AseI ATTAAT 1 cut(s) 1326
Asp700I GAANNNNTTC 2 cut(s) 282, 447
AspS9I GGNCC 2 cut(s) 137, 712
AsuC2I CCSGG 2 cut(s) 453, 1025
AsuHPI GGTGA 8 cut(s) 511, 569, 961, 1073, 1123, 1196, 1213, 1451
AsuII TTCGAA 1 cut(s) 168
AsuNHI GCTAGC 1 cut(s) 812
AvaII GGWCC 1 cut(s) 137
BaeI ACNNNNGTAYC 2 cut(s) 1377, 1410
BanI GGYRCC 1 cut(s) 794
BbsI GAAGAC 2 cut(s) 582, 1026
BbvI GCAGC 3 cut(s) 297, 309, 417
BccI CCATC 4 cut(s) 23, 185, 524, 1058
BcgI CGANNNNNNTGC 2 cut(s) 784, 818
BciT130I CCWGG 1 cut(s) 315
BclI TGATCA 3 cut(s) 538, 891, 1192
BcnI CCSGG 2 cut(s) 453, 1025
BcoDI GTCTC 4 cut(s) 4, 38, 486, 1246
BfaI CTAG 6 cut(s) 467, 701, 813, 975, 1103, 1143
BfmI CTRYAG 2 cut(s) 1008, 1245
BisI GCNGC 4 cut(s) 298, 311, 431, 766
BlsI GCNGC 4 cut(s) 299, 312, 432, 767
Bme1390I CCNGG 3 cut(s) 315, 453, 1025
Bme18I GGWCC 1 cut(s) 137
BmgT120I GGNCC 2 cut(s) 137, 712
BmiI GGNNCC 3 cut(s) 389, 796, 1155
BmrFI CCNGG 3 cut(s) 315, 453, 1025
BmsI GCATC 1 cut(s) 810
BmtI GCTAGC 1 cut(s) 816
BpiI GAAGAC 2 cut(s) 582, 1026
BplI GAGNNNNNCTC 2 cut(s) 376, 408
Bpu10I CCTNAGC 1 cut(s) 500
Bpu14I TTCGAA 1 cut(s) 168
BpuMI CCSGG 2 cut(s) 453, 1025
Bsa29I ATCGAT 1 cut(s) 804
BsaI GGTCTC 2 cut(s) 4, 486
BsaJI CCNNGG 2 cut(s) 772, 1158
BsaWI WCCGGW 4 cut(s) 134, 233, 1133, 1320
BsaXI ACNNNNNCTCC 2 cut(s) 1243, 1273
Bsc4I CCNNNNNNNGG 1 cut(s) 401
Bse118I RCCGGY 2 cut(s) 791, 797
Bse1I ACTGG 2 cut(s) 928, 1462
Bse3DI GCAATG 1 cut(s) 823
BseBI CCWGG 1 cut(s) 315
BseCI ATCGAT 1 cut(s) 804
BseDI CCNNGG 2 cut(s) 772, 1158
BseGI GGATG 3 cut(s) 196, 841, 1233
BseLI CCNNNNNNNGG 1 cut(s) 401
BseMI GCAATG 1 cut(s) 823
BseMII CTCAG 3 cut(s) 33, 864, 1316
BseNI ACTGG 2 cut(s) 928, 1462
BseRI GAGGAG 2 cut(s) 633, 636
BseXI GCAGC 3 cut(s) 297, 309, 417
BseYI CCCAGC 1 cut(s) 375
Bsh1285I CGRYCG 3 cut(s) 213, 234, 460
BshFI GGCC 1 cut(s) 714
BshNI GGYRCC 1 cut(s) 794
BshVI ATCGAT 1 cut(s) 804
BsiEI CGRYCG 3 cut(s) 213, 234, 460
BsiSI CCGG 8 cut(s) 135, 234, 453, 792, 798, 1025, 1134, 1321
BslFI GGGAC 2 cut(s) 759, 1288
BslI CCNNNNNNNGG 1 cut(s) 401
BsmAI GTCTC 4 cut(s) 4, 38, 486, 1246
BsmFI GGGAC 2 cut(s) 759, 1288
BsnI GGCC 1 cut(s) 714
Bso31I GGTCTC 2 cut(s) 4, 486
Bsp119I TTCGAA 1 cut(s) 168
Bsp143I GATC 8 cut(s) 210, 346, 538, 805, 864, 891, 1192, 1221
Bsp19I CCATGG 2 cut(s) 772, 1158
BspACI CCGC 3 cut(s) 149, 460, 765
BspANI GGCC 1 cut(s) 714
BspCNI CTCAG 3 cut(s) 32, 863, 1315
BspDI ATCGAT 1 cut(s) 804
BspHI TCATGA 1 cut(s) 118
BspLI GGNNCC 3 cut(s) 389, 796, 1155
BspOI GCTAGC 1 cut(s) 816
BspPI GGATC 1 cut(s) 872
BspT104I TTCGAA 1 cut(s) 168
BspT107I GGYRCC 1 cut(s) 794
BspTNI GGTCTC 2 cut(s) 4, 486
BsrDI GCAATG 1 cut(s) 823
BsrFI RCCGGY 2 cut(s) 791, 797
BsrI ACTGG 2 cut(s) 928, 1462
BssAI RCCGGY 2 cut(s) 791, 797
BssECI CCNNGG 2 cut(s) 772, 1158
BssMI GATC 8 cut(s) 210, 346, 538, 805, 864, 891, 1192, 1221
BssT1I CCWWGG 2 cut(s) 772, 1158
Bst2UI CCWGG 1 cut(s) 315
Bst4CI ACNGT 3 cut(s) 557, 760, 1246
BstBI TTCGAA 1 cut(s) 168
BstC8I GCNNGC 2 cut(s) 435, 814
BstDEI CTNAG 5 cut(s) 19, 186, 500, 850, 1302
BstDSI CCRYGG 2 cut(s) 772, 1158
BstF5I GGATG 3 cut(s) 196, 841, 1233
BstKTI GATC 8 cut(s) 213, 349, 541, 808, 867, 894, 1195, 1224
BstMAI GTCTC 4 cut(s) 4, 38, 486, 1246
BstMBI GATC 8 cut(s) 210, 346, 538, 805, 864, 891, 1192, 1221
BstMCI CGRYCG 3 cut(s) 213, 234, 460
BstMWI GCNNNNNNNGC 2 cut(s) 46, 774
BstNI CCWGG 1 cut(s) 315
BstNSI RCATGY 1 cut(s) 1382
BstSCI CCNGG 3 cut(s) 313, 451, 1023
BstSFI CTRYAG 2 cut(s) 1008, 1245
BstV1I GCAGC 3 cut(s) 297, 309, 417
BstV2I GAAGAC 2 cut(s) 582, 1026
Bsu15I ATCGAT 1 cut(s) 804
BsuRI GGCC 1 cut(s) 714
BsuTUI ATCGAT 1 cut(s) 804
BtgI CCRYGG 2 cut(s) 772, 1158
BtsCI GGATG 3 cut(s) 196, 841, 1233
BtsIMutI CAGTG 1 cut(s) 321
Cac8I GCNNGC 2 cut(s) 435, 814
CciI TCATGA 1 cut(s) 118
Cfr10I RCCGGY 2 cut(s) 791, 797
Cfr13I GGNCC 2 cut(s) 137, 712
ClaI ATCGAT 1 cut(s) 804
Csp6I GTAC 2 cut(s) 217, 902
CviAII CATG 7 cut(s) 119, 773, 889, 1015, 1037, 1159, 1379
CviQI GTAC 2 cut(s) 217, 902
DdeI CTNAG 5 cut(s) 19, 186, 500, 850, 1302
DpnI GATC 8 cut(s) 212, 348, 540, 807, 866, 893, 1194, 1223
DpnII GATC 8 cut(s) 210, 346, 538, 805, 864, 891, 1192, 1221
Eco130I CCWWGG 2 cut(s) 772, 1158
Eco31I GGTCTC 2 cut(s) 4, 486
Eco47I GGWCC 1 cut(s) 137
Eco57I CTGAAG 2 cut(s) 598, 876
EcoRI GAATTC 2 cut(s) 651, 696
EcoRII CCWGG 1 cut(s) 313
EcoT14I CCWWGG 2 cut(s) 772, 1158
ErhI CCWWGG 2 cut(s) 772, 1158
FaeI CATG 7 cut(s) 122, 776, 892, 1018, 1040, 1162, 1382
FaqI GGGAC 2 cut(s) 759, 1288
FatI CATG 7 cut(s) 118, 772, 888, 1014, 1036, 1158, 1378
FbaI TGATCA 3 cut(s) 538, 891, 1192
Fnu4HI GCNGC 4 cut(s) 298, 311, 431, 766
FokI GGATG 3 cut(s) 203, 848, 1240
Fsp4HI GCNGC 4 cut(s) 298, 311, 431, 766
FspBI CTAG 6 cut(s) 467, 701, 813, 975, 1103, 1143
GluI GCNGC 4 cut(s) 298, 311, 431, 766
GsaI CCCAGC 1 cut(s) 379
HaeIII GGCC 1 cut(s) 714
HapII CCGG 8 cut(s) 135, 234, 453, 792, 798, 1025, 1134, 1321
Hin1II CATG 7 cut(s) 122, 776, 892, 1018, 1040, 1162, 1382
HindIII AAGCTT 6 cut(s) 113, 171, 267, 279, 497, 610
HinfI GANTC 5 cut(s) 318, 564, 605, 1099, 1420
HpaII CCGG 8 cut(s) 135, 234, 453, 792, 798, 1025, 1134, 1321
HphI GGTGA 8 cut(s) 511, 569, 961, 1073, 1123, 1196, 1213, 1451
Hpy166II GTNNAC 4 cut(s) 1120, 1131, 1371, 1459
Hpy188I TCNGA 4 cut(s) 442, 543, 617, 1425
Hpy188III TCNNGA 4 cut(s) 78, 119, 862, 1225
Hpy8I GTNNAC 4 cut(s) 1120, 1131, 1371, 1459
HpyAV CCTTC 1 cut(s) 554
HpyCH4III ACNGT 3 cut(s) 557, 760, 1246
HpyCH4V TGCA 1 cut(s) 352
HpyF10VI GCNNNNNNNGC 2 cut(s) 46, 774
HpyF3I CTNAG 5 cut(s) 19, 186, 500, 850, 1302
Hsp92II CATG 7 cut(s) 122, 776, 892, 1018, 1040, 1162, 1382
Ksp22I TGATCA 3 cut(s) 538, 891, 1192
Kzo9I GATC 8 cut(s) 210, 346, 538, 805, 864, 891, 1192, 1221
LmnI GCTCC 1 cut(s) 236
Lsp1109I GCAGC 3 cut(s) 297, 309, 417
LweI GCATC 1 cut(s) 810
MaeI CTAG 6 cut(s) 467, 701, 813, 975, 1103, 1143
MaeIII GTNAC 6 cut(s) 181, 829, 908, 1039, 1184, 1384
MalI GATC 8 cut(s) 212, 348, 540, 807, 866, 893, 1194, 1223
MboI GATC 8 cut(s) 210, 346, 538, 805, 864, 891, 1192, 1221
MboII GAAGA 7 cut(s) 71, 93, 523, 587, 664, 1031, 1290
MfeI CAATTG 2 cut(s) 664, 985
MlyI GAGTC 1 cut(s) 1429
MmeI TCCRAC 2 cut(s) 164, 270
MroXI GAANNNNTTC 2 cut(s) 282, 447
MseI TTAA 5 cut(s) 872, 1089, 1109, 1326, 1434
MslI CAYNNNNRTG 1 cut(s) 947
MspA1I CMGCKG 1 cut(s) 854
MspI CCGG 8 cut(s) 135, 234, 453, 792, 798, 1025, 1134, 1321
MspR9I CCNGG 3 cut(s) 315, 453, 1025
MunI CAATTG 2 cut(s) 664, 985
MvaI CCWGG 1 cut(s) 315
MwoI GCNNNNNNNGC 2 cut(s) 46, 774
NciI CCSGG 2 cut(s) 453, 1025
NcoI CCATGG 2 cut(s) 772, 1158
NdeII GATC 8 cut(s) 210, 346, 538, 805, 864, 891, 1192, 1221
NheI GCTAGC 1 cut(s) 812
NlaIII CATG 7 cut(s) 122, 776, 892, 1018, 1040, 1162, 1382
NlaIV GGNNCC 3 cut(s) 389, 796, 1155
NmuCI GTSAC 4 cut(s) 181, 1039, 1184, 1384
NspI RCATGY 1 cut(s) 1382
NspV TTCGAA 1 cut(s) 168
PagI TCATGA 1 cut(s) 118
PdmI GAANNNNTTC 2 cut(s) 282, 447
PfeI GAWTC 4 cut(s) 318, 564, 605, 1099
PkrI GCNGC 4 cut(s) 299, 312, 432, 767
Ple19I CGATCG 1 cut(s) 213
PleI GAGTC 1 cut(s) 1428
PpsI GAGTC 1 cut(s) 1428
PshBI ATTAAT 1 cut(s) 1326
Psp6I CCWGG 1 cut(s) 313
PspFI CCCAGC 1 cut(s) 375
PspGI CCWGG 1 cut(s) 313
PspN4I GGNNCC 3 cut(s) 389, 796, 1155
PspPI GGNCC 2 cut(s) 137, 712
PvuI CGATCG 1 cut(s) 213
PvuII CAGCTG 1 cut(s) 854
RsaI GTAC 2 cut(s) 218, 903
RsaNI GTAC 2 cut(s) 217, 902
RseI CAYNNNNRTG 1 cut(s) 947
SaqAI TTAA 5 cut(s) 872, 1089, 1109, 1326, 1434
SatI GCNGC 4 cut(s) 298, 311, 431, 766
Sau3AI GATC 8 cut(s) 210, 346, 538, 805, 864, 891, 1192, 1221
Sau96I GGNCC 2 cut(s) 137, 712
SchI GAGTC 1 cut(s) 1429
ScrFI CCNGG 3 cut(s) 315, 453, 1025
SfaNI GCATC 1 cut(s) 810
SfcI CTRYAG 2 cut(s) 1008, 1245
SfuI TTCGAA 1 cut(s) 168
SinI GGWCC 1 cut(s) 137
SmiMI CAYNNNNRTG 1 cut(s) 947
SsiI CCGC 3 cut(s) 149, 460, 765
SspMI CTAG 6 cut(s) 467, 701, 813, 975, 1103, 1143
StyD4I CCNGG 3 cut(s) 313, 451, 1023
StyI CCWWGG 2 cut(s) 772, 1158
TaaI ACNGT 3 cut(s) 557, 760, 1246
TaqI TCGA 8 cut(s) 168, 471, 603, 649, 705, 804, 1397, 1448
TauI GCSGC 1 cut(s) 768
TfiI GAWTC 4 cut(s) 318, 564, 605, 1099
Tru1I TTAA 5 cut(s) 872, 1089, 1109, 1326, 1434
Tru9I TTAA 5 cut(s) 872, 1089, 1109, 1326, 1434
TscAI CASTG 1 cut(s) 328
TseFI GTSAC 4 cut(s) 181, 1039, 1184, 1384
TseI GCWGC 3 cut(s) 297, 310, 430
Tsp45I GTSAC 4 cut(s) 181, 1039, 1184, 1384
TspDTI ATGAA 4 cut(s) 102, 107, 135, 1025
TspGWI ACGGA 1 cut(s) 848
TspRI CASTG 1 cut(s) 328
VpaK11BI GGWCC 1 cut(s) 137
VspI ATTAAT 1 cut(s) 1326
XapI RAATTY 3 cut(s) 487, 651, 696
XceI RCATGY 1 cut(s) 1382
XmnI GAANNNNTTC 2 cut(s) 282, 447
XspI CTAG 6 cut(s) 467, 701, 813, 975, 1103, 1143
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.