Rh4BG091900

Polygalacturonase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr4B
OG0000579
Physical Location & Seq
Forward (+)
15804746 .. 15810125
5380 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh4BG091900.1

Sequence Viewer

Length: 1059 bp
ATGGGATCTGATCACACAGTTGCTTGGTTTGTGGAGGGCTGCTGCGCGGCTGTTGGGGAAGCATGGTTTGGTCCATGCAAATCCAATAACGTTGGAATTCAGATTGATGGGAATATTGTCGGTCCATCCACTCTTAGCGAATGGGCAGACGCGTGCAAAATCGGACAATGTTGGCTATGCTTTCTAAACGTGAAGGGCCTCGTCATCAAAGGGGAAGGACTTATAAATGGCAATGGTCCAATTTGGTGGAAACAAGAAACCCAATCCATAAATGAGACTGACATGACTTGCAAACCACCTACGACTTTAAACTTCCACAAATGCGACCAACTTCAATTATCTGGATTTACTTCTCGTGATAGTCCGAGAGCCCATATATTTATACATAGCAGCAATAATGTACGTATCTCAAACATTCACTTGAGTGCACCGGAAAAAAGCCCGAATACTGATGGCATTGACATCTCTTTATCAAGCCAAGTAACCGTACAAGACTCTTTCATCGGAACTGGACAAGATCCAGCTACTACAGATAATGTCGAACAAGTATACTTTCAGAATTGTATCTGCAACAAATCTACAAACTGTGCAAGAATCAAAACATGGATGGGTGGATCTGGATATGCTCGAGCGATTTTCTTCAGACAAATGACCCTTGAACAGTCACAAAATCCTATTATAATTGACCAACACTACTGCAATGGCGGACATAATTGCCCAGCTAAGACGGGAGCAGTGAAAGTTAGCAATGTAACATTCAGTGGCATTACCGGAACTTCAGCAAGTGAGCAAGCAATAACACTGGATTGCTCCGACTTGGGTTGTACCGATATCTTGATGGATCATGTCAACATAACCTCCGCATCCGGACTGCCACTTCGTTCTGTGTGCAACAAGGCCAGTGGGAAAGCTAGTTTTACTTCACCTCCGATTCCTTGCCTGTCGTCGAATGGATCTTCGTCATCAGTGATTGCACCAATCTCGGTCAACTTATTAAAGCCAAACCATTCTTATTTGAGTTATTTCGGAATTCATGCCCATAAAACAATCGAAGCTTAA

Protein Analysis

352

Amino Acids

37.76

Weight (kDa)

6.24

Isoelectric Point (pI)

40.27

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Glyco_hydro_28 PF00295 24 - 190 2.2e-27 Glycosyl hydrolases family 28
Glyco_hydro_28 PF00295 178 - 301 3.7e-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) 224, 680
AccI GTMKAC 1 cut(s) 549
AccII CGCG 2 cut(s) 47, 152
AccIII TCCGGA 1 cut(s) 866
AciI CCGC 3 cut(s) 47, 705, 861
AclI AACGTT 1 cut(s) 90
AclWI GGATC 5 cut(s) 13, 512, 622, 849, 961
AcsI RAATTY 2 cut(s) 96, 1029
AcuI CTGAAG 2 cut(s) 625, 762
AfaI GTAC 3 cut(s) 402, 489, 826
AflIII ACRYGT 1 cut(s) 150
AgsI TTSAA 2 cut(s) 335, 659
AjuI GAANNNNNNNTTGG 2 cut(s) 51, 83
AleI CACNNNNGTG 1 cut(s) 423
AluBI AGCT 4 cut(s) 524, 722, 911, 1055
AluI AGCT 4 cut(s) 524, 722, 911, 1055
Alw21I GWGCWC 1 cut(s) 430
Alw26I GTCTC 1 cut(s) 269
Alw44I GTGCAC 1 cut(s) 426
AlwI GGATC 5 cut(s) 13, 512, 622, 849, 961
Ama87I CYCGRG 1 cut(s) 627
Aor13HI TCCGGA 1 cut(s) 866
AoxI GGCC 2 cut(s) 196, 897
ApaLI GTGCAC 1 cut(s) 426
ApeKI GCWGC 3 cut(s) 39, 42, 390
ApoI RAATTY 2 cut(s) 96, 1029
ArsI GACNNNNNNTTYG 2 cut(s) 861, 893
AspLEI GCGC 1 cut(s) 47
AspS9I GGNCC 4 cut(s) 71, 122, 196, 236
AsuHPI GGTGA 1 cut(s) 915
AvaI CYCGRG 1 cut(s) 627
AvaII GGWCC 3 cut(s) 71, 122, 236
BaeGI GKGCMC 1 cut(s) 430
BanII GRGCYC 1 cut(s) 373
BauI CACGAG 1 cut(s) 354
Bbv12I GWGCWC 1 cut(s) 430
BbvI GCAGC 3 cut(s) 26, 29, 402
BccI CCATC 5 cut(s) 101, 133, 446, 601, 832
BcgI CGANNNNNNTGC 2 cut(s) 963, 997
BclI TGATCA 1 cut(s) 10
BcoDI GTCTC 1 cut(s) 269
BfaI CTAG 1 cut(s) 912
BfmI CTRYAG 1 cut(s) 528
BisI GCNGC 4 cut(s) 40, 43, 48, 391
BlsI GCNGC 4 cut(s) 41, 44, 49, 392
Bme18I GGWCC 3 cut(s) 71, 122, 236
BmeT110I CYCGRG 1 cut(s) 627
BmgT120I GGNCC 4 cut(s) 71, 122, 196, 236
BmsI GCATC 1 cut(s) 872
BpuEI CTTGAG 1 cut(s) 442
BsaAI YACGTR 1 cut(s) 404
BsaWI WCCGGW 3 cut(s) 430, 770, 866
BsaXI ACNNNNNCTCC 4 cut(s) 842, 872, 910, 940
Bse1I ACTGG 3 cut(s) 514, 807, 900
Bse3DI GCAATG 3 cut(s) 238, 706, 754
BseAI TCCGGA 1 cut(s) 866
BseGI GGATG 3 cut(s) 125, 612, 863
BseMI GCAATG 3 cut(s) 238, 706, 754
BseNI ACTGG 3 cut(s) 514, 807, 900
BseSI GKGCMC 1 cut(s) 430
BseXI GCAGC 3 cut(s) 26, 29, 402
BseYI CCCAGC 1 cut(s) 718
Bsh1236I CGCG 2 cut(s) 47, 152
BshFI GGCC 2 cut(s) 198, 899
BsiHKAI GWGCWC 1 cut(s) 430
BsiHKCI CYCGRG 1 cut(s) 627
BsiSI CCGG 3 cut(s) 431, 771, 867
BsmAI GTCTC 1 cut(s) 269
BsnI GGCC 2 cut(s) 198, 899
BsoBI CYCGRG 1 cut(s) 627
Bsp1286I GDGCHC 2 cut(s) 373, 430
Bsp13I TCCGGA 1 cut(s) 866
Bsp143I GATC 6 cut(s) 5, 10, 517, 614, 841, 953
BspACI CCGC 3 cut(s) 47, 705, 861
BspANI GGCC 2 cut(s) 198, 899
BspEI TCCGGA 1 cut(s) 866
BspFNI CGCG 2 cut(s) 47, 152
BspPI GGATC 5 cut(s) 13, 512, 622, 849, 961
BsrDI GCAATG 3 cut(s) 238, 706, 754
BsrI ACTGG 3 cut(s) 514, 807, 900
BssMI GATC 6 cut(s) 5, 10, 517, 614, 841, 953
BssNAI GTATAC 1 cut(s) 550
BssSI CACGAG 1 cut(s) 354
Bst1107I GTATAC 1 cut(s) 550
Bst2BI CACGAG 1 cut(s) 354
Bst4CI ACNGT 4 cut(s) 19, 487, 587, 663
BstBAI YACGTR 1 cut(s) 404
BstC8I GCNNGC 2 cut(s) 154, 792
BstDEI CTNAG 2 cut(s) 134, 723
BstF5I GGATG 3 cut(s) 125, 612, 863
BstFNI CGCG 2 cut(s) 47, 152
BstHHI GCGC 1 cut(s) 47
BstKTI GATC 6 cut(s) 8, 13, 520, 617, 844, 956
BstMAI GTCTC 1 cut(s) 269
BstMBI GATC 6 cut(s) 5, 10, 517, 614, 841, 953
BstSFI CTRYAG 1 cut(s) 528
BstSLI GKGCMC 1 cut(s) 430
BstSNI TACGTA 1 cut(s) 404
BstUI CGCG 2 cut(s) 47, 152
BstV1I GCAGC 3 cut(s) 26, 29, 402
BstX2I RGATCY 4 cut(s) 5, 517, 614, 953
BstXI CCANNNNNNTGG 1 cut(s) 246
BstYI RGATCY 4 cut(s) 5, 517, 614, 953
BstZ17I GTATAC 1 cut(s) 550
BsuRI GGCC 2 cut(s) 198, 899
BtsCI GGATG 3 cut(s) 125, 612, 863
BtsI GCAGTG 1 cut(s) 741
BtsIMutI CAGTG 5 cut(s) 741, 766, 800, 907, 972
Cac8I GCNNGC 2 cut(s) 154, 792
CfoI GCGC 1 cut(s) 47
Cfr13I GGNCC 4 cut(s) 71, 122, 196, 236
CseI GACGC 1 cut(s) 158
Csp6I GTAC 3 cut(s) 401, 488, 825
CspCI CAANNNNNGTGG 2 cut(s) 883, 918
CviAII CATG 6 cut(s) 63, 75, 283, 603, 845, 1034
CviQI GTAC 3 cut(s) 401, 488, 825
DdeI CTNAG 2 cut(s) 134, 723
DpnI GATC 6 cut(s) 7, 12, 519, 616, 843, 955
DpnII GATC 6 cut(s) 5, 10, 517, 614, 841, 953
DraI TTTAAA 1 cut(s) 309
EciI GGCGGA 1 cut(s) 720
Eco105I TACGTA 1 cut(s) 404
Eco24I GRGCYC 1 cut(s) 373
Eco32I GATATC 1 cut(s) 832
Eco47I GGWCC 3 cut(s) 71, 122, 236
Eco57I CTGAAG 2 cut(s) 625, 762
Eco88I CYCGRG 1 cut(s) 627
EcoO109I RGGNCCY 1 cut(s) 196
EcoRI GAATTC 2 cut(s) 96, 1029
EcoRV GATATC 1 cut(s) 832
EcoT38I GRGCYC 1 cut(s) 373
FaeI CATG 6 cut(s) 66, 78, 286, 606, 848, 1037
FatI CATG 6 cut(s) 62, 74, 282, 602, 844, 1033
FbaI TGATCA 1 cut(s) 10
FblI GTMKAC 1 cut(s) 549
Fnu4HI GCNGC 4 cut(s) 40, 43, 48, 391
FokI GGATG 3 cut(s) 112, 619, 850
FriOI GRGCYC 1 cut(s) 373
Fsp4HI GCNGC 4 cut(s) 40, 43, 48, 391
FspBI CTAG 1 cut(s) 912
GlaI GCGC 1 cut(s) 46
GluI GCNGC 4 cut(s) 40, 43, 48, 391
GsaI CCCAGC 1 cut(s) 722
HaeIII GGCC 2 cut(s) 198, 899
HapII CCGG 3 cut(s) 431, 771, 867
HgaI GACGC 1 cut(s) 158
HhaI GCGC 1 cut(s) 47
Hin1II CATG 6 cut(s) 66, 78, 286, 606, 848, 1037
Hin6I GCGC 1 cut(s) 45
HinP1I GCGC 1 cut(s) 45
HincII GTYRAC 2 cut(s) 850, 988
HindII GTYRAC 2 cut(s) 850, 988
HindIII AAGCTT 1 cut(s) 1053
HinfI GANTC 3 cut(s) 494, 594, 931
HpaII CCGG 3 cut(s) 431, 771, 867
HphI GGTGA 1 cut(s) 915
Hpy166II GTNNAC 4 cut(s) 428, 550, 850, 988
Hpy188III TCNNGA 5 cut(s) 342, 356, 618, 835, 867
Hpy8I GTNNAC 4 cut(s) 428, 550, 850, 988
Hpy99I CGWCG 1 cut(s) 949
HpyAV CCTTC 2 cut(s) 187, 209
HpyCH4III ACNGT 4 cut(s) 19, 487, 587, 663
HpyCH4IV ACGT 3 cut(s) 90, 189, 403
HpyCH4V TGCA 9 cut(s) 78, 156, 291, 428, 570, 590, 699, 891, 974
HpyF3I CTNAG 2 cut(s) 134, 723
HpySE526I ACGT 3 cut(s) 90, 189, 403
Hsp92II CATG 6 cut(s) 66, 78, 286, 606, 848, 1037
HspAI GCGC 1 cut(s) 45
Kpn2I TCCGGA 1 cut(s) 866
Ksp22I TGATCA 1 cut(s) 10
Kzo9I GATC 6 cut(s) 5, 10, 517, 614, 841, 953
LmnI GCTCC 2 cut(s) 731, 815
Lsp1109I GCAGC 3 cut(s) 26, 29, 402
LweI GCATC 1 cut(s) 872
MaeI CTAG 1 cut(s) 912
MaeII ACGT 3 cut(s) 90, 189, 403
MaeIII GTNAC 3 cut(s) 481, 663, 751
MalI GATC 6 cut(s) 7, 12, 519, 616, 843, 955
MboI GATC 6 cut(s) 5, 10, 517, 614, 841, 953
MboII GAAGA 2 cut(s) 631, 948
MflI RGATCY 4 cut(s) 5, 517, 614, 953
MhlI GDGCHC 2 cut(s) 373, 430
MluCI AATT 7 cut(s) 96, 240, 335, 559, 681, 712, 1029
MluI ACGCGT 1 cut(s) 150
MlyI GAGTC 1 cut(s) 488
MmeI TCCRAC 2 cut(s) 73, 837
MnlI CCTC 4 cut(s) 28, 209, 868, 936
MroI TCCGGA 1 cut(s) 866
MseI TTAA 3 cut(s) 308, 995, 1057
MslI CAYNNNNRTG 1 cut(s) 423
MspI CCGG 3 cut(s) 431, 771, 867
MvnI CGCG 2 cut(s) 47, 152
NdeII GATC 6 cut(s) 5, 10, 517, 614, 841, 953
NlaIII CATG 6 cut(s) 66, 78, 286, 606, 848, 1037
NmuCI GTSAC 1 cut(s) 663
OliI CACNNNNGTG 1 cut(s) 423
PaeR7I CTCGAG 1 cut(s) 627
PfeI GAWTC 2 cut(s) 594, 931
PkrI GCNGC 4 cut(s) 41, 44, 49, 392
PleI GAGTC 1 cut(s) 488
PpsI GAGTC 1 cut(s) 488
Ppu21I YACGTR 1 cut(s) 404
PsiI TTATAA 2 cut(s) 224, 680
Psp1406I AACGTT 1 cut(s) 90
PspFI CCCAGC 1 cut(s) 718
PspPI GGNCC 4 cut(s) 71, 122, 196, 236
PspXI VCTCGAGB 1 cut(s) 627
PsuI RGATCY 4 cut(s) 5, 517, 614, 953
RsaI GTAC 3 cut(s) 402, 489, 826
RsaNI GTAC 3 cut(s) 401, 488, 825
RseI CAYNNNNRTG 1 cut(s) 423
SaqAI TTAA 3 cut(s) 308, 995, 1057
SatI GCNGC 4 cut(s) 40, 43, 48, 391
Sau3AI GATC 6 cut(s) 5, 10, 517, 614, 841, 953
Sau96I GGNCC 4 cut(s) 71, 122, 196, 236
SchI GAGTC 1 cut(s) 488
SduI GDGCHC 2 cut(s) 373, 430
SfaNI GCATC 1 cut(s) 872
SfcI CTRYAG 1 cut(s) 528
Sfr274I CTCGAG 1 cut(s) 627
SinI GGWCC 3 cut(s) 71, 122, 236
SlaI CTCGAG 1 cut(s) 627
SmiMI CAYNNNNRTG 1 cut(s) 423
SmlI CTYRAG 2 cut(s) 421, 627
SmoI CTYRAG 2 cut(s) 421, 627
SnaBI TACGTA 1 cut(s) 404
Sse9I AATT 7 cut(s) 96, 240, 335, 559, 681, 712, 1029
SsiI CCGC 3 cut(s) 47, 705, 861
SspI AATATT 1 cut(s) 115
SspMI CTAG 1 cut(s) 912
TaaI ACNGT 4 cut(s) 19, 487, 587, 663
TaiI ACGT 3 cut(s) 93, 192, 406
TaqI TCGA 4 cut(s) 540, 628, 947, 1050
TaqII GACCGA 2 cut(s) 110, 973
TasI AATT 7 cut(s) 96, 240, 335, 559, 681, 712, 1029
TauI GCSGC 1 cut(s) 50
TfiI GAWTC 2 cut(s) 594, 931
Tru1I TTAA 3 cut(s) 308, 995, 1057
Tru9I TTAA 3 cut(s) 308, 995, 1057
TscAI CASTG 5 cut(s) 741, 766, 807, 907, 972
TseFI GTSAC 1 cut(s) 663
TseI GCWGC 3 cut(s) 39, 42, 390
Tsp45I GTSAC 1 cut(s) 663
TspDTI ATGAA 2 cut(s) 490, 1022
TspRI CASTG 5 cut(s) 741, 766, 807, 907, 972
VneI GTGCAC 1 cut(s) 426
VpaK11BI GGWCC 3 cut(s) 71, 122, 236
XapI RAATTY 2 cut(s) 96, 1029
XhoI CTCGAG 1 cut(s) 627
XmiI GTMKAC 1 cut(s) 549
XspI CTAG 1 cut(s) 912
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.