Rh3BG312600

Polygalacturonase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr3B
OG0012763
Physical Location & Seq
Reverse (-)
31762450 .. 31765007
2558 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh3BG312600.1

Sequence Viewer

Length: 891 bp
ATGAAGAAGCTTTCCAAATTATCACTAATGTGCGTTTTATTCTTTGGCTTCTTTCTTCTGTCAACCCAAGCCAGATGGCATAACCATACCAAACACAGCAAGCACAACCACCCTCACAAGATTTCTTACATTTCACAGCCTCCTTCCACTTCACCTGGACCTACTGCTAGCTATAGTCCTCCTCCCGAAGAGCCTAAGAATCCATACAACTCCACACCTGGTGTTTTTGATGTTCGATCATATGGGGCTGTTGGGGATGGCCAAACAGATGACACACAGGCATTTAAGATGGCTTGGGACACAGCCTGCCAAAGTGAATCACCAGCAAAGTTACTTGTTCCGAACCATTTCACATTCATGATTCAGTCCACAATATTTACCGGTCCCTGCCTTTCAGGCCTGGTGTTACAGGTTGATGGGACTATAGTACCACCTGATGGACCAGAGTCCTGGCCAAAAAACAACAGCAGGCGCCAATGGCTCGTCTTTTATCGAATCAACGAGCTGTCGCTGCAAGGGGGTGGTGTTATAGATGGGAGAGGAGACAAATGGTGGCATCTTCCCTGCAAACCCCACATGGGGATAAATGGAACCACCTTGCCCGGACCATGTGATAGCCCAGTTGCCATTAGGTTTTTCATGAGCTCTAACTTGACAGTACAAGGTCTTAGGATTAAGAACAGCCCCCAATTCCACTTCAGATTTGATGGTTGCAGGAATGTGCATGTAGAGTCCATTTCTATATCAGCTCCTGCTCGAAGTCCAAATACAGATGGGATTCACATAGAGAATACTAATGATGTCAAAATTTATAATTCAGTCATTTCTAATGGTAGGAGCATTACTAAACCTTCAATACCACTATTTATCCCGGCCCATTGGCTCTCATGA

Protein Analysis

296

Amino Acids

32.85

Weight (kDa)

9.14

Isoelectric Point (pI)

56.02

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Glyco_hydro_28 PF00295 103 - 278 5.1e-32 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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Orthologous Genes (Group: OG0012763)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G02460
fragaria_vesca FvH4_1g26650
malus_domestica MD09G1287300.v1.1 MD17G1279500.v1.1
prunus_persica Prupe.3G005900_v2.0.a1 Prupe.6G307200_v2.0.a1
pyrus_communis pycom09g19460 pycom17g27760
rosa_chinensis RchiOBHm_Chr3g0486841
rosa_laevigata RLG00000023055
rosa_multiflora Rmu_sc0005709.1_g000005
rosa_roxburghii Rroxscaffold_6G00395520
rosa_rugosa Rorug03G0227400.1
rosa_samantha Rh3AG277500 Rh3BG312600 Rh3CG311500 Rh3DG308100
rosa_wichuraiana Rw3G024640

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 813
AccB1I GGYRCC 1 cut(s) 471
AccB7I CCANNNNNTGG 1 cut(s) 437
AcoI YGGCCR 2 cut(s) 259, 452
AcsI RAATTY 1 cut(s) 807
AcuI CTGAAG 1 cut(s) 682
AcyI GRCGYC 1 cut(s) 472
AdeI CACNNNGTG 1 cut(s) 221
AfaI GTAC 2 cut(s) 429, 660
AfiI CCNNNNNNNGG 3 cut(s) 437, 578, 579
AgeI ACCGGT 1 cut(s) 380
AgsI TTSAA 1 cut(s) 855
AjnI CCWGG 4 cut(s) 154, 217, 399, 449
AleI CACNNNNGTG 1 cut(s) 28
AluBI AGCT 5 cut(s) 10, 171, 505, 645, 749
AluI AGCT 5 cut(s) 10, 171, 505, 645, 749
Alw21I GWGCWC 1 cut(s) 647
Alw26I GTCTC 1 cut(s) 537
AlwNI CAGNNNCTG 1 cut(s) 752
AoxI GGCC 4 cut(s) 259, 397, 452, 873
ApeKI GCWGC 1 cut(s) 511
ApoI RAATTY 1 cut(s) 807
AsiGI ACCGGT 1 cut(s) 380
Asp700I GAANNNNTTC 1 cut(s) 347
AspLEI GCGC 1 cut(s) 474
AspS9I GGNCC 5 cut(s) 158, 383, 440, 605, 874
AsuC2I CCSGG 2 cut(s) 603, 872
AsuHPI GGTGA 2 cut(s) 144, 312
AsuNHI GCTAGC 1 cut(s) 167
AvaII GGWCC 4 cut(s) 158, 383, 440, 605
BaeI ACNNNNGTAYC 2 cut(s) 411, 444
BalI TGGCCA 2 cut(s) 261, 454
BanI GGYRCC 1 cut(s) 471
BanII GRGCYC 1 cut(s) 647
BarI GAAGNNNNNNTAC 2 cut(s) 751, 783
Bbv12I GWGCWC 1 cut(s) 647
BbvI GCAGC 1 cut(s) 498
BccI CCATC 8 cut(s) 69, 251, 283, 410, 431, 527, 701, 767
BciT130I CCWGG 4 cut(s) 156, 219, 401, 451
BcnI CCSGG 2 cut(s) 603, 872
BcoDI GTCTC 1 cut(s) 537
BfaI CTAG 1 cut(s) 168
BfmI CTRYAG 2 cut(s) 172, 423
BfoI RGCGCY 1 cut(s) 475
BglI GCCNNNNNGGC 1 cut(s) 396
BisI GCNGC 1 cut(s) 512
BlsI GCNGC 1 cut(s) 513
Bme1390I CCNGG 6 cut(s) 156, 219, 401, 451, 603, 872
Bme18I GGWCC 4 cut(s) 158, 383, 440, 605
BmgT120I GGNCC 5 cut(s) 158, 383, 440, 605, 874
BmiI GGNNCC 3 cut(s) 385, 473, 592
BmrFI CCNGG 6 cut(s) 156, 219, 401, 451, 603, 872
BmrI ACTGGG 1 cut(s) 614
BmsI GCATC 1 cut(s) 565
BmtI GCTAGC 1 cut(s) 171
BmuI ACTGGG 1 cut(s) 614
BoxI GACNNNNGTC 1 cut(s) 445
BpuMI CCSGG 2 cut(s) 603, 872
BsaHI GRCGYC 1 cut(s) 472
BsaWI WCCGGW 1 cut(s) 380
Bsc4I CCNNNNNNNGG 3 cut(s) 437, 578, 579
Bse118I RCCGGY 1 cut(s) 380
Bse1I ACTGG 1 cut(s) 620
BseBI CCWGG 4 cut(s) 156, 219, 401, 451
BseGI GGATG 1 cut(s) 262
BseLI CCNNNNNNNGG 3 cut(s) 437, 578, 579
BseNI ACTGG 1 cut(s) 620
BseRI GAGGAG 2 cut(s) 171, 555
BseXI GCAGC 1 cut(s) 498
BshFI GGCC 4 cut(s) 261, 399, 454, 875
BshNI GGYRCC 1 cut(s) 471
BshTI ACCGGT 1 cut(s) 380
BsiHKAI GWGCWC 1 cut(s) 647
BsiSI CCGG 3 cut(s) 381, 603, 872
BslFI GGGAC 3 cut(s) 311, 369, 433
BslI CCNNNNNNNGG 3 cut(s) 437, 578, 579
BsmAI GTCTC 1 cut(s) 537
BsmFI GGGAC 3 cut(s) 311, 369, 433
BsnI GGCC 4 cut(s) 261, 399, 454, 875
Bsp1286I GDGCHC 1 cut(s) 647
Bsp143I GATC 1 cut(s) 236
BspANI GGCC 4 cut(s) 261, 399, 454, 875
BspHI TCATGA 3 cut(s) 357, 639, 887
BspLI GGNNCC 3 cut(s) 385, 473, 592
BspOI GCTAGC 1 cut(s) 171
BspQI GCTCTTC 1 cut(s) 183
BspT107I GGYRCC 1 cut(s) 471
BsrFI RCCGGY 1 cut(s) 380
BsrI ACTGG 1 cut(s) 620
BssAI RCCGGY 1 cut(s) 380
BssMI GATC 1 cut(s) 236
BssNI GRCGYC 1 cut(s) 472
Bst2UI CCWGG 4 cut(s) 156, 219, 401, 451
Bst4CI ACNGT 1 cut(s) 658
Bst6I CTCTTC 1 cut(s) 183
BstACI GRCGYC 1 cut(s) 472
BstC8I GCNNGC 4 cut(s) 101, 169, 307, 470
BstDEI CTNAG 2 cut(s) 195, 668
BstF5I GGATG 1 cut(s) 262
BstH2I RGCGCY 1 cut(s) 475
BstHHI GCGC 1 cut(s) 474
BstKTI GATC 1 cut(s) 239
BstMAI GTCTC 1 cut(s) 537
BstMBI GATC 1 cut(s) 236
BstMWI GCNNNNNNNGC 3 cut(s) 396, 478, 511
BstNI CCWGG 4 cut(s) 156, 219, 401, 451
BstNSI RCATGY 1 cut(s) 728
BstPAI GACNNNNGTC 1 cut(s) 445
BstSCI CCNGG 6 cut(s) 154, 217, 399, 449, 601, 870
BstSFI CTRYAG 2 cut(s) 172, 423
BstV1I GCAGC 1 cut(s) 498
BstXI CCANNNNNNTGG 1 cut(s) 450
BsuRI GGCC 4 cut(s) 261, 399, 454, 875
BtsCI GGATG 1 cut(s) 262
Cac8I GCNNGC 4 cut(s) 101, 169, 307, 470
CaiI CAGNNNCTG 1 cut(s) 752
CciI TCATGA 3 cut(s) 357, 639, 887
CfoI GCGC 1 cut(s) 474
Cfr10I RCCGGY 1 cut(s) 380
Cfr13I GGNCC 5 cut(s) 158, 383, 440, 605, 874
CsiI ACCWGGT 1 cut(s) 217
Csp6I GTAC 2 cut(s) 428, 659
CspAI ACCGGT 1 cut(s) 380
CviAII CATG 6 cut(s) 358, 577, 609, 640, 725, 888
CviQI GTAC 2 cut(s) 428, 659
DdeI CTNAG 2 cut(s) 195, 668
DinI GGCGCC 1 cut(s) 473
DpnI GATC 1 cut(s) 238
DpnII GATC 1 cut(s) 236
DraIII CACNNNGTG 1 cut(s) 221
EaeI YGGCCR 2 cut(s) 259, 452
Eam1104I CTCTTC 1 cut(s) 183
EarI CTCTTC 1 cut(s) 183
Ecl136II GAGCTC 1 cut(s) 645
Eco147I AGGCCT 1 cut(s) 399
Eco24I GRGCYC 1 cut(s) 647
Eco47I GGWCC 4 cut(s) 158, 383, 440, 605
Eco53kI GAGCTC 1 cut(s) 645
Eco57I CTGAAG 1 cut(s) 682
EcoICRI GAGCTC 1 cut(s) 645
EcoRII CCWGG 4 cut(s) 154, 217, 399, 449
EcoT38I GRGCYC 1 cut(s) 647
EgeI GGCGCC 1 cut(s) 473
EheI GGCGCC 1 cut(s) 473
FaeI CATG 6 cut(s) 361, 580, 612, 643, 728, 891
FaqI GGGAC 3 cut(s) 311, 369, 433
FatI CATG 6 cut(s) 357, 576, 608, 639, 724, 887
FauNDI CATATG 1 cut(s) 241
Fnu4HI GCNGC 1 cut(s) 512
FokI GGATG 1 cut(s) 269
FriOI GRGCYC 1 cut(s) 647
Fsp4HI GCNGC 1 cut(s) 512
FspBI CTAG 1 cut(s) 168
GlaI GCGC 1 cut(s) 473
GluI GCNGC 1 cut(s) 512
HaeII RGCGCY 1 cut(s) 475
HaeIII GGCC 4 cut(s) 261, 399, 454, 875
HapII CCGG 3 cut(s) 381, 603, 872
HhaI GCGC 1 cut(s) 474
Hin1I GRCGYC 1 cut(s) 472
Hin1II CATG 6 cut(s) 361, 580, 612, 643, 728, 891
Hin6I GCGC 1 cut(s) 472
HinP1I GCGC 1 cut(s) 472
HincII GTYRAC 1 cut(s) 63
HindII GTYRAC 1 cut(s) 63
HindIII AAGCTT 1 cut(s) 8
HinfI GANTC 7 cut(s) 199, 317, 361, 446, 495, 731, 778
HpaII CCGG 3 cut(s) 381, 603, 872
HphI GGTGA 2 cut(s) 144, 312
Hpy166II GTNNAC 2 cut(s) 63, 369
Hpy188I TCNGA 2 cut(s) 342, 701
Hpy188III TCNNGA 4 cut(s) 185, 358, 640, 888
Hpy8I GTNNAC 2 cut(s) 63, 369
HpyAV CCTTC 2 cut(s) 153, 861
HpyCH4III ACNGT 1 cut(s) 658
HpyCH4V TGCA 4 cut(s) 514, 567, 714, 724
HpyF10VI GCNNNNNNNGC 3 cut(s) 396, 478, 511
HpyF3I CTNAG 2 cut(s) 195, 668
Hsp92I GRCGYC 1 cut(s) 472
Hsp92II CATG 6 cut(s) 361, 580, 612, 643, 728, 891
HspAI GCGC 1 cut(s) 472
KasI GGCGCC 1 cut(s) 471
Kzo9I GATC 1 cut(s) 236
LguI GCTCTTC 1 cut(s) 183
LmnI GCTCC 2 cut(s) 754, 837
Lsp1109I GCAGC 1 cut(s) 498
LweI GCATC 1 cut(s) 565
MabI ACCWGGT 1 cut(s) 217
MaeI CTAG 1 cut(s) 168
MaeIII GTNAC 2 cut(s) 330, 405
MalI GATC 1 cut(s) 238
MboI GATC 1 cut(s) 236
MboII GAAGA 4 cut(s) 16, 47, 200, 551
MhlI GDGCHC 1 cut(s) 647
MlsI TGGCCA 2 cut(s) 261, 454
MluCI AATT 4 cut(s) 17, 689, 807, 814
MluNI TGGCCA 2 cut(s) 261, 454
Mly113I GGCGCC 1 cut(s) 472
MlyI GAGTC 2 cut(s) 455, 740
MnlI CCTC 5 cut(s) 123, 150, 189, 192, 533
Mox20I TGGCCA 2 cut(s) 261, 454
MroXI GAANNNNTTC 1 cut(s) 347
MscI TGGCCA 2 cut(s) 261, 454
MseI TTAA 2 cut(s) 285, 675
MslI CAYNNNNRTG 2 cut(s) 28, 356
Msp20I TGGCCA 2 cut(s) 261, 454
MspI CCGG 3 cut(s) 381, 603, 872
MspR9I CCNGG 6 cut(s) 156, 219, 401, 451, 603, 872
MvaI CCWGG 4 cut(s) 156, 219, 401, 451
MwoI GCNNNNNNNGC 3 cut(s) 396, 478, 511
NarI GGCGCC 1 cut(s) 472
NciI CCSGG 2 cut(s) 603, 872
NdeI CATATG 1 cut(s) 241
NdeII GATC 1 cut(s) 236
NheI GCTAGC 1 cut(s) 167
NlaIII CATG 6 cut(s) 361, 580, 612, 643, 728, 891
NlaIV GGNNCC 3 cut(s) 385, 473, 592
NspI RCATGY 1 cut(s) 728
OliI CACNNNNGTG 1 cut(s) 28
PagI TCATGA 3 cut(s) 357, 639, 887
PceI AGGCCT 1 cut(s) 399
PciSI GCTCTTC 1 cut(s) 183
PdmI GAANNNNTTC 1 cut(s) 347
PfeI GAWTC 5 cut(s) 199, 317, 361, 495, 778
PflMI CCANNNNNTGG 1 cut(s) 437
PinAI ACCGGT 1 cut(s) 380
PkrI GCNGC 1 cut(s) 513
PleI GAGTC 2 cut(s) 454, 739
PluTI GGCGCC 1 cut(s) 475
PpsI GAGTC 2 cut(s) 454, 739
PshAI GACNNNNGTC 1 cut(s) 445
PsiI TTATAA 1 cut(s) 813
Psp124BI GAGCTC 1 cut(s) 647
Psp6I CCWGG 4 cut(s) 154, 217, 399, 449
PspGI CCWGG 4 cut(s) 154, 217, 399, 449
PspN4I GGNNCC 3 cut(s) 385, 473, 592
PspPI GGNCC 5 cut(s) 158, 383, 440, 605, 874
PstNI CAGNNNCTG 1 cut(s) 752
RsaI GTAC 2 cut(s) 429, 660
RsaNI GTAC 2 cut(s) 428, 659
RseI CAYNNNNRTG 2 cut(s) 28, 356
SacI GAGCTC 1 cut(s) 647
SapI GCTCTTC 1 cut(s) 183
SaqAI TTAA 2 cut(s) 285, 675
SatI GCNGC 1 cut(s) 512
Sau3AI GATC 1 cut(s) 236
Sau96I GGNCC 5 cut(s) 158, 383, 440, 605, 874
SchI GAGTC 2 cut(s) 455, 740
ScrFI CCNGG 6 cut(s) 156, 219, 401, 451, 603, 872
SduI GDGCHC 1 cut(s) 647
SexAI ACCWGGT 1 cut(s) 217
SfaNI GCATC 1 cut(s) 565
SfcI CTRYAG 2 cut(s) 172, 423
SfoI GGCGCC 1 cut(s) 473
SinI GGWCC 4 cut(s) 158, 383, 440, 605
SmiMI CAYNNNNRTG 2 cut(s) 28, 356
Sse9I AATT 4 cut(s) 17, 689, 807, 814
SseBI AGGCCT 1 cut(s) 399
SspDI GGCGCC 1 cut(s) 471
SspI AATATT 1 cut(s) 375
SspMI CTAG 1 cut(s) 168
SstI GAGCTC 1 cut(s) 647
StuI AGGCCT 1 cut(s) 399
StyD4I CCNGG 6 cut(s) 154, 217, 399, 449, 601, 870
TaaI ACNGT 1 cut(s) 658
TaqI TCGA 3 cut(s) 235, 493, 757
TasI AATT 4 cut(s) 17, 689, 807, 814
TatI WGTACW 1 cut(s) 658
TfiI GAWTC 5 cut(s) 199, 317, 361, 495, 778
Tru1I TTAA 2 cut(s) 285, 675
Tru9I TTAA 2 cut(s) 285, 675
TseI GCWGC 1 cut(s) 511
TspDTI ATGAA 3 cut(s) 17, 346, 628
Van91I CCANNNNNTGG 1 cut(s) 437
VpaK11BI GGWCC 4 cut(s) 158, 383, 440, 605
XapI RAATTY 1 cut(s) 807
XceI RCATGY 1 cut(s) 728
XmnI GAANNNNTTC 1 cut(s) 347
XspI CTAG 1 cut(s) 168
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.