Rh1DG014500

Polygalacturonase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr1D
OG0010715
Physical Location & Seq
Forward (+)
2379758 .. 2383396
3639 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1DG014500.1

Sequence Viewer

Length: 966 bp
ATGCAATATTCTTCATCTCAAATCCATTTTCTGTCACTATTCCTCCTTCTCATCATTGTACCTTCATATTTTTCCTTCCCTCTTGGCCATAACCATAACCCAGAGGAGCCACCTGTACTTGATCATCATCAAAAAACCTATACTGGTCATAATTTTTTGAGACCCTACCCTACAATATTAAGGACAAGCAGGAGGGAGCTTATTACAGCCAGTGCTTCATCCAAGGTTGTTTTTAATGTGCATGATTTTGGAGCTCAAGCAAATGGAGGAGATGATACCAAGGCATTTAGGAACGCATGGAAGAAGGCATGCTCAAATTCTGAAGGAATAACTGTTGAGCTCGTGGTCCCTAAGAACAGAAACTATCACATCAAACCAATTACATTCTCTGGTCCTTGCAAATCTCAGGTCACCTTTAAGATTTATGGAACGATCAAAGCATCACCATTTCTATCGGATTACGAAAGGGACAGTAGCCATTGGATTATGTTCGAGAATTTGCAGAACTTTAAAGTTGAAGGTGCTGGCACTGGCATCATCAATGGCAATGGAAGGAAATGGTGGGAGAATTCTTGCAAAGTTAACGAGTCCCTTCCTTGCACGAGCGCACCAACTGCTGTGACTTTCTATCAGTGCAATAATTTGGAGGTAGCAAATCTGAGGTTCCAGAATGCACAGAGAATGCATCTGACGTTTCAGAAATGTGCGCTTGTAAAAGTTTTGAATCTCATTATAACAGCACCAGGGAACAGTCCTAACACCGATGGAATCCATGTCACTGAAACACAAGATATTCGCATAAACAGCTGCCGCATTAGGACAGGTGACGACTGTATTTCGATAGTAAGTGGGTCAAGGAATGTTCAAGCTAGCGATATAACCTGCGGACCAGGTCATGGAATCAGGTATTGCATTAGATATGGGGATACGATACCTATATTTATGACAATGTTTCCTAAGTTTTAA

Protein Analysis

321

Amino Acids

36.03

Weight (kDa)

8.97

Isoelectric Point (pI)

34.68

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Glyco_hydro_28 PF00295 109 - 301 5.6e-53 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: OG0010715)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G07970
fragaria_vesca FvH4_7g01140 FvH4_7g01140
malus_domestica MD02G1309400.v1.1 MD07G1011600.v1.1
prunus_persica Prupe.2G014800_v2.0.a1
pyrus_communis pycom02g26060 pycom07g00970
rosa_chinensis RchiOBHm_Chr1g0316321
rosa_laevigata RLG00000030679
rosa_multiflora Rmu_sc0002531.1_g000005 Rmu_sc0004511.1_g000005
rosa_roxburghii Rroxscaffold_4G00331050
rosa_rugosa Rorug01G0009700 Rorug01G0009700
rosa_samantha Rh1AG019500 Rh1BG014600 Rh1CG017100 Rh1DG014500
rosa_wichuraiana Rw1G001310

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 734
Acc36I ACCTGC 1 cut(s) 890
AccB7I CCANNNNNTGG 1 cut(s) 896
AciI CCGC 2 cut(s) 811, 885
AcoI YGGCCR 1 cut(s) 85
AcsI RAATTY 3 cut(s) 316, 496, 568
AcuI CTGAAG 1 cut(s) 342
AfaI GTAC 2 cut(s) 60, 117
AfiI CCNNNNNNNGG 1 cut(s) 896
AgsI TTSAA 3 cut(s) 518, 724, 866
AjnI CCWGG 2 cut(s) 742, 889
AluBI AGCT 5 cut(s) 199, 254, 340, 807, 869
AluI AGCT 5 cut(s) 199, 254, 340, 807, 869
Alw21I GWGCWC 2 cut(s) 256, 342
Alw26I GTCTC 1 cut(s) 154
AoxI GGCC 1 cut(s) 85
ApeKI GCWGC 1 cut(s) 807
ApoI RAATTY 3 cut(s) 316, 496, 568
ArsI GACNNNNNNTTYG 2 cut(s) 393, 425
AspLEI GCGC 2 cut(s) 608, 709
AspS9I GGNCC 3 cut(s) 346, 392, 887
AsuHPI GGTGA 3 cut(s) 403, 435, 836
AsuNHI GCTAGC 1 cut(s) 869
AvaII GGWCC 3 cut(s) 346, 392, 887
BalI TGGCCA 1 cut(s) 87
BanII GRGCYC 2 cut(s) 256, 342
BauI CACGAG 2 cut(s) 341, 601
Bbv12I GWGCWC 2 cut(s) 256, 342
BbvI GCAGC 1 cut(s) 794
BccI CCATC 1 cut(s) 758
BciT130I CCWGG 2 cut(s) 744, 891
BciVI GTATCC 1 cut(s) 919
BclI TGATCA 1 cut(s) 121
BcoDI GTCTC 1 cut(s) 154
BfaI CTAG 1 cut(s) 870
BfuAI ACCTGC 1 cut(s) 890
BfuI GTATCC 1 cut(s) 919
BisI GCNGC 2 cut(s) 808, 811
BlsI GCNGC 2 cut(s) 809, 812
Bme1390I CCNGG 2 cut(s) 744, 891
Bme18I GGWCC 3 cut(s) 346, 392, 887
BmgT120I GGNCC 3 cut(s) 346, 392, 887
BmiI GGNNCC 3 cut(s) 108, 348, 665
BmrFI CCNGG 2 cut(s) 744, 891
BmsI GCATC 3 cut(s) 449, 543, 694
BmtI GCTAGC 1 cut(s) 873
BpuEI CTTGAG 1 cut(s) 240
BsaBI GATNNNNATC 1 cut(s) 126
BsaI GGTCTC 1 cut(s) 154
BsaJI CCNNGG 3 cut(s) 222, 279, 743
BsaXI ACNNNNNCTCC 2 cut(s) 27, 57
Bsc4I CCNNNNNNNGG 1 cut(s) 896
Bse1I ACTGG 3 cut(s) 148, 210, 535
Bse3DI GCAATG 1 cut(s) 553
Bse8I GATNNNNATC 1 cut(s) 126
BseBI CCWGG 2 cut(s) 744, 891
BseDI CCNNGG 3 cut(s) 222, 279, 743
BseGI GGATG 1 cut(s) 218
BseJI GATNNNNATC 1 cut(s) 126
BseLI CCNNNNNNNGG 1 cut(s) 896
BseMI GCAATG 1 cut(s) 553
BseMII CTCAG 2 cut(s) 419, 650
BseNI ACTGG 3 cut(s) 148, 210, 535
BseRI GAGGAG 2 cut(s) 119, 282
BseXI GCAGC 1 cut(s) 794
BshFI GGCC 1 cut(s) 87
BsiHKAI GWGCWC 2 cut(s) 256, 342
BslFI GGGAC 3 cut(s) 332, 482, 574
BslI CCNNNNNNNGG 1 cut(s) 896
BsmAI GTCTC 1 cut(s) 154
BsmFI GGGAC 3 cut(s) 332, 482, 574
BsmI GAATGC 2 cut(s) 676, 687
BsnI GGCC 1 cut(s) 87
Bso31I GGTCTC 1 cut(s) 154
Bsp1286I GDGCHC 2 cut(s) 256, 342
Bsp143I GATC 2 cut(s) 121, 432
BspACI CCGC 2 cut(s) 811, 885
BspANI GGCC 1 cut(s) 87
BspCNI CTCAG 2 cut(s) 418, 651
BspLI GGNNCC 3 cut(s) 108, 348, 665
BspMI ACCTGC 1 cut(s) 890
BspOI GCTAGC 1 cut(s) 873
BspTNI GGTCTC 1 cut(s) 154
BsrDI GCAATG 1 cut(s) 553
BsrI ACTGG 3 cut(s) 148, 210, 535
BssECI CCNNGG 3 cut(s) 222, 279, 743
BssMI GATC 2 cut(s) 121, 432
BssSI CACGAG 2 cut(s) 341, 601
BssT1I CCWWGG 2 cut(s) 222, 279
Bst2BI CACGAG 2 cut(s) 341, 601
Bst2UI CCWGG 2 cut(s) 744, 891
Bst4CI ACNGT 4 cut(s) 334, 473, 752, 833
BstAPI GCANNNNNTGC 1 cut(s) 614
BstC8I GCNNGC 3 cut(s) 310, 526, 871
BstDEI CTNAG 4 cut(s) 351, 405, 659, 957
BstEII GGTNACC 1 cut(s) 409
BstF5I GGATG 1 cut(s) 218
BstHHI GCGC 2 cut(s) 608, 709
BstKTI GATC 2 cut(s) 124, 435
BstMAI GTCTC 1 cut(s) 154
BstMBI GATC 2 cut(s) 121, 432
BstMWI GCNNNNNNNGC 2 cut(s) 614, 804
BstNI CCWGG 2 cut(s) 744, 891
BstNSI RCATGY 1 cut(s) 312
BstPI GGTNACC 1 cut(s) 409
BstSCI CCNGG 2 cut(s) 742, 889
BstV1I GCAGC 1 cut(s) 794
BsuI GTATCC 1 cut(s) 919
BsuRI GGCC 1 cut(s) 87
BtsCI GGATG 1 cut(s) 218
BtsIMutI CAGTG 4 cut(s) 217, 528, 638, 777
BveI ACCTGC 1 cut(s) 890
Cac8I GCNNGC 3 cut(s) 310, 526, 871
CfoI GCGC 2 cut(s) 608, 709
Cfr13I GGNCC 3 cut(s) 346, 392, 887
CsiI ACCWGGT 1 cut(s) 889
Csp6I GTAC 2 cut(s) 59, 116
CviAII CATG 5 cut(s) 242, 297, 309, 773, 896
CviJI RGCY 9 cut(s) 87, 109, 199, 209, 254, 340, 477, 807, 869
CviKI_1 RGCY 9 cut(s) 87, 109, 199, 209, 254, 340, 477, 807, 869
CviQI GTAC 2 cut(s) 59, 116
DdeI CTNAG 4 cut(s) 351, 405, 659, 957
DpnI GATC 2 cut(s) 123, 434
DpnII GATC 2 cut(s) 121, 432
DraI TTTAAA 1 cut(s) 511
EaeI YGGCCR 1 cut(s) 85
Ecl136II GAGCTC 2 cut(s) 254, 340
Eco130I CCWWGG 2 cut(s) 222, 279
Eco24I GRGCYC 2 cut(s) 256, 342
Eco31I GGTCTC 1 cut(s) 154
Eco47I GGWCC 3 cut(s) 346, 392, 887
Eco53kI GAGCTC 2 cut(s) 254, 340
Eco57I CTGAAG 1 cut(s) 342
Eco91I GGTNACC 1 cut(s) 409
EcoICRI GAGCTC 2 cut(s) 254, 340
EcoO65I GGTNACC 1 cut(s) 409
EcoRI GAATTC 1 cut(s) 568
EcoRII CCWGG 2 cut(s) 742, 889
EcoT14I CCWWGG 2 cut(s) 222, 279
EcoT22I ATGCAT 1 cut(s) 687
EcoT38I GRGCYC 2 cut(s) 256, 342
ErhI CCWWGG 2 cut(s) 222, 279
FaeI CATG 5 cut(s) 245, 300, 312, 776, 899
FaqI GGGAC 3 cut(s) 332, 482, 574
FatI CATG 5 cut(s) 241, 296, 308, 772, 895
FbaI TGATCA 1 cut(s) 121
Fnu4HI GCNGC 2 cut(s) 808, 811
FokI GGATG 1 cut(s) 205
FriOI GRGCYC 2 cut(s) 256, 342
Fsp4HI GCNGC 2 cut(s) 808, 811
FspBI CTAG 1 cut(s) 870
GlaI GCGC 2 cut(s) 607, 708
GluI GCNGC 2 cut(s) 808, 811
HaeIII GGCC 1 cut(s) 87
HhaI GCGC 2 cut(s) 608, 709
Hin1II CATG 5 cut(s) 245, 300, 312, 776, 899
Hin6I GCGC 2 cut(s) 606, 707
HinP1I GCGC 2 cut(s) 606, 707
HincII GTYRAC 1 cut(s) 583
HindII GTYRAC 1 cut(s) 583
HinfI GANTC 4 cut(s) 587, 724, 768, 900
HpaI GTTAAC 1 cut(s) 583
HphI GGTGA 3 cut(s) 403, 435, 836
Hpy166II GTNNAC 1 cut(s) 583
Hpy188I TCNGA 5 cut(s) 322, 457, 660, 690, 699
Hpy188III TCNNGA 2 cut(s) 493, 667
Hpy8I GTNNAC 1 cut(s) 583
HpyAV CCTTC 8 cut(s) 56, 72, 85, 298, 317, 512, 546, 602
HpyCH4III ACNGT 4 cut(s) 334, 473, 752, 833
HpyCH4IV ACGT 1 cut(s) 692
HpyF10VI GCNNNNNNNGC 2 cut(s) 614, 804
HpyF3I CTNAG 4 cut(s) 351, 405, 659, 957
HpySE526I ACGT 1 cut(s) 692
Hsp92II CATG 5 cut(s) 245, 300, 312, 776, 899
HspAI GCGC 2 cut(s) 606, 707
Ksp22I TGATCA 1 cut(s) 121
KspAI GTTAAC 1 cut(s) 583
Kzo9I GATC 2 cut(s) 121, 432
LmnI GCTCC 3 cut(s) 106, 196, 251
Lsp1109I GCAGC 1 cut(s) 794
LweI GCATC 3 cut(s) 449, 543, 694
MabI ACCWGGT 1 cut(s) 889
MaeI CTAG 1 cut(s) 870
MaeII ACGT 1 cut(s) 692
MaeIII GTNAC 5 cut(s) 33, 409, 619, 775, 824
MalI GATC 2 cut(s) 123, 434
MboI GATC 2 cut(s) 121, 432
MboII GAAGA 2 cut(s) 3, 313
MhlI GDGCHC 2 cut(s) 256, 342
MlsI TGGCCA 1 cut(s) 87
MluCI AATT 6 cut(s) 151, 316, 378, 496, 568, 640
MluNI TGGCCA 1 cut(s) 87
MlyI GAGTC 1 cut(s) 596
MnlI CCTC 7 cut(s) 53, 90, 97, 186, 260, 640, 654
Mox20I TGGCCA 1 cut(s) 87
Mph1103I ATGCAT 1 cut(s) 687
MscI TGGCCA 1 cut(s) 87
MseI TTAA 6 cut(s) 179, 234, 417, 510, 582, 964
Msp20I TGGCCA 1 cut(s) 87
MspA1I CMGCKG 1 cut(s) 807
MspR9I CCNGG 2 cut(s) 744, 891
Mva1269I GAATGC 2 cut(s) 676, 687
MvaI CCWGG 2 cut(s) 744, 891
MwoI GCNNNNNNNGC 2 cut(s) 614, 804
NdeII GATC 2 cut(s) 121, 432
NheI GCTAGC 1 cut(s) 869
NlaIII CATG 5 cut(s) 245, 300, 312, 776, 899
NlaIV GGNNCC 3 cut(s) 108, 348, 665
NmuCI GTSAC 5 cut(s) 33, 409, 619, 775, 824
NsiI ATGCAT 1 cut(s) 687
NspI RCATGY 1 cut(s) 312
PaeI GCATGC 1 cut(s) 312
PctI GAATGC 2 cut(s) 676, 687
PfeI GAWTC 3 cut(s) 724, 768, 900
PflFI GACNNNGTC 1 cut(s) 891
PflMI CCANNNNNTGG 1 cut(s) 896
PkrI GCNGC 2 cut(s) 809, 812
PleI GAGTC 1 cut(s) 595
PpsI GAGTC 1 cut(s) 595
PsiI TTATAA 1 cut(s) 734
Psp124BI GAGCTC 2 cut(s) 256, 342
Psp6I CCWGG 2 cut(s) 742, 889
PspEI GGTNACC 1 cut(s) 409
PspGI CCWGG 2 cut(s) 742, 889
PspN4I GGNNCC 3 cut(s) 108, 348, 665
PspPI GGNCC 3 cut(s) 346, 392, 887
PsyI GACNNNGTC 1 cut(s) 891
PvuII CAGCTG 1 cut(s) 807
RsaI GTAC 2 cut(s) 60, 117
RsaNI GTAC 2 cut(s) 59, 116
SacI GAGCTC 2 cut(s) 256, 342
SaqAI TTAA 6 cut(s) 179, 234, 417, 510, 582, 964
SatI GCNGC 2 cut(s) 808, 811
Sau3AI GATC 2 cut(s) 121, 432
Sau96I GGNCC 3 cut(s) 346, 392, 887
SchI GAGTC 1 cut(s) 596
ScrFI CCNGG 2 cut(s) 744, 891
SduI GDGCHC 2 cut(s) 256, 342
SexAI ACCWGGT 1 cut(s) 889
SfaNI GCATC 3 cut(s) 449, 543, 694
SinI GGWCC 3 cut(s) 346, 392, 887
SmlI CTYRAG 1 cut(s) 255
SmoI CTYRAG 1 cut(s) 255
SphI GCATGC 1 cut(s) 312
Sse9I AATT 6 cut(s) 151, 316, 378, 496, 568, 640
SsiI CCGC 2 cut(s) 811, 885
SspI AATATT 2 cut(s) 8, 177
SspMI CTAG 1 cut(s) 870
SstI GAGCTC 2 cut(s) 256, 342
StyD4I CCNGG 2 cut(s) 742, 889
StyI CCWWGG 2 cut(s) 222, 279
TaaI ACNGT 4 cut(s) 334, 473, 752, 833
TaiI ACGT 1 cut(s) 695
TaqI TCGA 2 cut(s) 492, 839
TasI AATT 6 cut(s) 151, 316, 378, 496, 568, 640
TatI WGTACW 1 cut(s) 115
TauI GCSGC 1 cut(s) 813
TfiI GAWTC 3 cut(s) 724, 768, 900
Tru1I TTAA 6 cut(s) 179, 234, 417, 510, 582, 964
Tru9I TTAA 6 cut(s) 179, 234, 417, 510, 582, 964
TscAI CASTG 4 cut(s) 217, 535, 638, 784
TseFI GTSAC 5 cut(s) 33, 409, 619, 775, 824
TseI GCWGC 1 cut(s) 807
Tsp45I GTSAC 5 cut(s) 33, 409, 619, 775, 824
TspDTI ATGAA 2 cut(s) 54, 207
TspRI CASTG 4 cut(s) 217, 535, 638, 784
Tth111I GACNNNGTC 1 cut(s) 891
Van91I CCANNNNNTGG 1 cut(s) 896
VpaK11BI GGWCC 3 cut(s) 346, 392, 887
XapI RAATTY 3 cut(s) 316, 496, 568
XceI RCATGY 1 cut(s) 312
XspI CTAG 1 cut(s) 870
Zsp2I ATGCAT 1 cut(s) 687
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.