RchiOBHm_Chr4g0399361

Polygalacturonase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
4
OG0000579
Physical Location & Seq
Forward (+)
16584289 .. 16587592
3304 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ37149

Sequence Viewer

Length: 1005 bp
ATGTCATTCGTTGTTAATCCCAGCAAAGTTGATTGTATACATGCATTGCCAACTCGAGTGAGATTATCAGAAGGCTACGAGGAACTAAGTGGTCTATTTTCGCTACTTACCTCTGTGTTGTTTTCATGGATTGTTGCTTCACCTAGATTTGGCATTGGGCCATGTTATGGCCAAAATCGTACTCTTAACATACTTGATTTTAGTGCCTCTGGTGATGGCATATCAGATGCTACTGAGGCTTTCTTAAATGCATGGAAGACACTTTGCGAGACTGGCCAAACCCTAAACATCCCCGCAGGGAAGACCTTTGTAGTCAAACCTCTTCAACTTGTAGGTCCATGCAAATCTAATAATGTTGGAATTCAGGCTTTAAACTTCCACAAATGCGACCAACTTCAATTATCTGGATTTACTTCCCGTGATAGTGCGAGAGCCCATATATTTATACATAGCAGCAGTGGTGTACGTATCTCAAACATTCACTTGAGTGCACCGGAAAAAAGCCCGAATACTGATGGCATTGACATCTCTTTATCAAGCCAAGTGACCATACAAGACTCTTTCATCGGAACTGGACAAGATCCAGCTACTACAGATAATGTCGAACAAGTACACTTTCAAAATTGTATCTGCAACAAATCTACAAACTGTGCAAGAATCAAAACATGGATGACGGGAGCAGTGAAAGTTAGCAATGTAACATTCAGTGGCATTACCGGAACTTCATCAAGTGAGCAAGCAATAACACTGGATTGCTCCGACTTGGGTTGTACCGATATCTTGATGGATCATGTCAACATAACCTCCGCATCCGGACTGCCACTTCACTCTGTGTGCAACAAGGCCAGTGGGAAAGCTAGTTTTACTTCACCTCCAATTCCTTGCCTATCGTCGAATGGATCTTTGTCATCAGTGATTGCACCGATCTCGGTCAACTTATTAAAGCCAAACCATTCTTATTTGAGTTATATCGGAATTCATGCCCATAAAACAATCGAAGCTTAA

Protein Analysis

334

Amino Acids

35.55

Weight (kDa)

6.58

Isoelectric Point (pI)

37.73

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Glyco_hydro_28 PF00295 123 - 211 2.4e-15 Glycosyl hydrolases family 28
Glyco_hydro_28 PF00295 225 - 283 1.5e-08 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)
AccB7I CCANNNNNTGG 1 cut(s) 167
AccI GTMKAC 1 cut(s) 37
AccIII TCCGGA 1 cut(s) 812
AciI CCGC 2 cut(s) 294, 807
AclWI GGATC 3 cut(s) 575, 795, 907
AcoI YGGCCR 2 cut(s) 169, 274
AcsI RAATTY 2 cut(s) 360, 975
AdeI CACNNNGTG 1 cut(s) 832
AfaI GTAC 4 cut(s) 181, 465, 612, 772
AfiI CCNNNNNNNGG 2 cut(s) 149, 167
AgsI TTSAA 3 cut(s) 326, 398, 620
AleI CACNNNNGTG 1 cut(s) 486
AluBI AGCT 3 cut(s) 587, 857, 1001
AluI AGCT 3 cut(s) 587, 857, 1001
Alw21I GWGCWC 1 cut(s) 493
Alw26I GTCTC 1 cut(s) 263
Alw44I GTGCAC 1 cut(s) 489
AlwI GGATC 3 cut(s) 575, 795, 907
Ama87I CYCGRG 1 cut(s) 54
Aor13HI TCCGGA 1 cut(s) 812
AoxI GGCC 4 cut(s) 158, 169, 274, 843
ApaLI GTGCAC 1 cut(s) 489
ApeKI GCWGC 1 cut(s) 453
ApoI RAATTY 2 cut(s) 360, 975
AspS9I GGNCC 2 cut(s) 158, 335
AsuHPI GGTGA 3 cut(s) 132, 224, 861
AvaI CYCGRG 1 cut(s) 54
AvaII GGWCC 1 cut(s) 335
BaeGI GKGCMC 1 cut(s) 493
BalI TGGCCA 2 cut(s) 171, 276
BanII GRGCYC 1 cut(s) 436
BbsI GAAGAC 2 cut(s) 263, 308
Bbv12I GWGCWC 1 cut(s) 493
BbvI GCAGC 1 cut(s) 465
BccI CCATC 3 cut(s) 209, 509, 778
BcgI CGANNNNNNTGC 2 cut(s) 909, 943
BcoDI GTCTC 1 cut(s) 263
BfaI CTAG 2 cut(s) 144, 858
BfmI CTRYAG 1 cut(s) 591
BisI GCNGC 1 cut(s) 454
BlsI GCNGC 1 cut(s) 455
Bme18I GGWCC 1 cut(s) 335
BmeT110I CYCGRG 1 cut(s) 54
BmgT120I GGNCC 2 cut(s) 158, 335
BmsI GCATC 2 cut(s) 217, 818
BpiI GAAGAC 2 cut(s) 263, 308
BpuEI CTTGAG 1 cut(s) 505
BsaAI YACGTR 1 cut(s) 467
BsaWI WCCGGW 3 cut(s) 493, 716, 812
BsaXI ACNNNNNCTCC 4 cut(s) 788, 818, 856, 886
Bsc4I CCNNNNNNNGG 2 cut(s) 149, 167
Bse1I ACTGG 4 cut(s) 277, 577, 753, 846
Bse3DI GCAATG 2 cut(s) 44, 700
BseAI TCCGGA 1 cut(s) 812
BseGI GGATG 3 cut(s) 288, 675, 809
BseLI CCNNNNNNNGG 2 cut(s) 149, 167
BseMI GCAATG 2 cut(s) 44, 700
BseMII CTCAG 1 cut(s) 225
BseNI ACTGG 4 cut(s) 277, 577, 753, 846
BseSI GKGCMC 1 cut(s) 493
BseXI GCAGC 1 cut(s) 465
BseYI CCCAGC 1 cut(s) 20
BshFI GGCC 4 cut(s) 160, 171, 276, 845
BsiHKAI GWGCWC 1 cut(s) 493
BsiHKCI CYCGRG 1 cut(s) 54
BsiSI CCGG 3 cut(s) 494, 717, 813
BslI CCNNNNNNNGG 2 cut(s) 149, 167
BsmAI GTCTC 1 cut(s) 263
BsnI GGCC 4 cut(s) 160, 171, 276, 845
BsoBI CYCGRG 1 cut(s) 54
Bsp1286I GDGCHC 2 cut(s) 436, 493
Bsp13I TCCGGA 1 cut(s) 812
Bsp143I GATC 4 cut(s) 580, 787, 899, 924
BspACI CCGC 2 cut(s) 294, 807
BspANI GGCC 4 cut(s) 160, 171, 276, 845
BspCNI CTCAG 1 cut(s) 226
BspEI TCCGGA 1 cut(s) 812
BspPI GGATC 3 cut(s) 575, 795, 907
BsrDI GCAATG 2 cut(s) 44, 700
BsrI ACTGG 4 cut(s) 277, 577, 753, 846
BssMI GATC 4 cut(s) 580, 787, 899, 924
BssNAI GTATAC 1 cut(s) 38
Bst1107I GTATAC 1 cut(s) 38
Bst4CI ACNGT 1 cut(s) 650
Bst6I CTCTTC 1 cut(s) 327
BstBAI YACGTR 1 cut(s) 467
BstC8I GCNNGC 1 cut(s) 738
BstDEI CTNAG 2 cut(s) 86, 234
BstF5I GGATG 3 cut(s) 288, 675, 809
BstKTI GATC 4 cut(s) 583, 790, 902, 927
BstMAI GTCTC 1 cut(s) 263
BstMBI GATC 4 cut(s) 580, 787, 899, 924
BstMWI GCNNNNNNNGC 2 cut(s) 236, 273
BstNSI RCATGY 1 cut(s) 44
BstSFI CTRYAG 1 cut(s) 591
BstSLI GKGCMC 1 cut(s) 493
BstSNI TACGTA 1 cut(s) 467
BstV1I GCAGC 1 cut(s) 465
BstV2I GAAGAC 2 cut(s) 263, 308
BstX2I RGATCY 2 cut(s) 580, 899
BstYI RGATCY 2 cut(s) 580, 899
BstZ17I GTATAC 1 cut(s) 38
BsuRI GGCC 4 cut(s) 160, 171, 276, 845
BtsCI GGATG 3 cut(s) 288, 675, 809
BtsI GCAGTG 2 cut(s) 463, 687
BtsIMutI CAGTG 6 cut(s) 463, 687, 712, 746, 853, 918
Cac8I GCNNGC 1 cut(s) 738
Cfr13I GGNCC 2 cut(s) 158, 335
Csp6I GTAC 4 cut(s) 180, 464, 611, 771
CspCI CAANNNNNGTGG 2 cut(s) 829, 864
CviAII CATG 8 cut(s) 41, 126, 162, 252, 339, 666, 791, 980
CviQI GTAC 4 cut(s) 180, 464, 611, 771
DdeI CTNAG 2 cut(s) 86, 234
DpnI GATC 4 cut(s) 582, 789, 901, 926
DpnII GATC 4 cut(s) 580, 787, 899, 924
DraI TTTAAA 1 cut(s) 372
DraIII CACNNNGTG 1 cut(s) 832
EaeI YGGCCR 2 cut(s) 169, 274
Eam1104I CTCTTC 1 cut(s) 327
EarI CTCTTC 1 cut(s) 327
Eco105I TACGTA 1 cut(s) 467
Eco24I GRGCYC 1 cut(s) 436
Eco32I GATATC 1 cut(s) 778
Eco47I GGWCC 1 cut(s) 335
Eco88I CYCGRG 1 cut(s) 54
EcoRI GAATTC 2 cut(s) 360, 975
EcoRV GATATC 1 cut(s) 778
EcoT22I ATGCAT 2 cut(s) 46, 253
EcoT38I GRGCYC 1 cut(s) 436
FaeI CATG 8 cut(s) 44, 129, 165, 255, 342, 669, 794, 983
FatI CATG 8 cut(s) 40, 125, 161, 251, 338, 665, 790, 979
FauI CCCGC 1 cut(s) 301
FblI GTMKAC 1 cut(s) 37
Fnu4HI GCNGC 1 cut(s) 454
FokI GGATG 3 cut(s) 275, 682, 796
FriOI GRGCYC 1 cut(s) 436
Fsp4HI GCNGC 1 cut(s) 454
FspBI CTAG 2 cut(s) 144, 858
GluI GCNGC 1 cut(s) 454
GsaI CCCAGC 1 cut(s) 24
HaeIII GGCC 4 cut(s) 160, 171, 276, 845
HapII CCGG 3 cut(s) 494, 717, 813
Hin1II CATG 8 cut(s) 44, 129, 165, 255, 342, 669, 794, 983
HincII GTYRAC 2 cut(s) 796, 934
HindII GTYRAC 2 cut(s) 796, 934
HindIII AAGCTT 1 cut(s) 999
HinfI GANTC 2 cut(s) 557, 657
HpaII CCGG 3 cut(s) 494, 717, 813
HphI GGTGA 3 cut(s) 132, 224, 861
Hpy166II GTNNAC 6 cut(s) 38, 464, 491, 613, 796, 934
Hpy188I TCNGA 5 cut(s) 70, 226, 569, 760, 974
Hpy188III TCNNGA 3 cut(s) 405, 781, 813
Hpy8I GTNNAC 6 cut(s) 38, 464, 491, 613, 796, 934
Hpy99I CGWCG 1 cut(s) 895
HpyAV CCTTC 1 cut(s) 65
HpyCH4III ACNGT 1 cut(s) 650
HpyCH4IV ACGT 1 cut(s) 466
HpyCH4V TGCA 8 cut(s) 44, 251, 342, 491, 633, 653, 837, 920
HpyF10VI GCNNNNNNNGC 2 cut(s) 236, 273
HpyF3I CTNAG 2 cut(s) 86, 234
HpySE526I ACGT 1 cut(s) 466
Hsp92II CATG 8 cut(s) 44, 129, 165, 255, 342, 669, 794, 983
Kpn2I TCCGGA 1 cut(s) 812
Kzo9I GATC 4 cut(s) 580, 787, 899, 924
LmnI GCTCC 2 cut(s) 677, 761
Lsp1109I GCAGC 1 cut(s) 465
LweI GCATC 2 cut(s) 217, 818
MaeI CTAG 2 cut(s) 144, 858
MaeII ACGT 1 cut(s) 466
MaeIII GTNAC 2 cut(s) 544, 697
MalI GATC 4 cut(s) 582, 789, 901, 926
MboI GATC 4 cut(s) 580, 787, 899, 924
MboII GAAGA 3 cut(s) 268, 313, 314
MflI RGATCY 2 cut(s) 580, 899
MhlI GDGCHC 2 cut(s) 436, 493
MlsI TGGCCA 2 cut(s) 171, 276
MluCI AATT 5 cut(s) 360, 398, 622, 876, 975
MluNI TGGCCA 2 cut(s) 171, 276
MlyI GAGTC 1 cut(s) 551
MmeI TCCRAC 2 cut(s) 337, 783
MnlI CCTC 7 cut(s) 73, 121, 217, 229, 330, 814, 882
Mox20I TGGCCA 2 cut(s) 171, 276
Mph1103I ATGCAT 2 cut(s) 46, 253
MroI TCCGGA 1 cut(s) 812
MscI TGGCCA 2 cut(s) 171, 276
MseI TTAA 6 cut(s) 15, 186, 245, 371, 941, 1003
MslI CAYNNNNRTG 1 cut(s) 486
Msp20I TGGCCA 2 cut(s) 171, 276
MspI CCGG 3 cut(s) 494, 717, 813
MwoI GCNNNNNNNGC 2 cut(s) 236, 273
NdeII GATC 4 cut(s) 580, 787, 899, 924
NlaIII CATG 8 cut(s) 44, 129, 165, 255, 342, 669, 794, 983
NmuCI GTSAC 1 cut(s) 544
NsiI ATGCAT 2 cut(s) 46, 253
NspI RCATGY 1 cut(s) 44
OliI CACNNNNGTG 1 cut(s) 486
PaeR7I CTCGAG 1 cut(s) 54
PfeI GAWTC 1 cut(s) 657
PflMI CCANNNNNTGG 1 cut(s) 167
PkrI GCNGC 1 cut(s) 455
PleI GAGTC 1 cut(s) 551
PpsI GAGTC 1 cut(s) 551
Ppu21I YACGTR 1 cut(s) 467
PspFI CCCAGC 1 cut(s) 20
PspPI GGNCC 2 cut(s) 158, 335
PspXI VCTCGAGB 1 cut(s) 54
PsuI RGATCY 2 cut(s) 580, 899
RsaI GTAC 4 cut(s) 181, 465, 612, 772
RsaNI GTAC 4 cut(s) 180, 464, 611, 771
RseI CAYNNNNRTG 1 cut(s) 486
SaqAI TTAA 6 cut(s) 15, 186, 245, 371, 941, 1003
SatI GCNGC 1 cut(s) 454
Sau3AI GATC 4 cut(s) 580, 787, 899, 924
Sau96I GGNCC 2 cut(s) 158, 335
SchI GAGTC 1 cut(s) 551
SduI GDGCHC 2 cut(s) 436, 493
SfaNI GCATC 2 cut(s) 217, 818
SfcI CTRYAG 1 cut(s) 591
Sfr274I CTCGAG 1 cut(s) 54
SinI GGWCC 1 cut(s) 335
SlaI CTCGAG 1 cut(s) 54
SmiMI CAYNNNNRTG 1 cut(s) 486
SmlI CTYRAG 2 cut(s) 54, 484
SmoI CTYRAG 2 cut(s) 54, 484
SnaBI TACGTA 1 cut(s) 467
Sse9I AATT 5 cut(s) 360, 398, 622, 876, 975
SsiI CCGC 2 cut(s) 294, 807
SspMI CTAG 2 cut(s) 144, 858
TaaI ACNGT 1 cut(s) 650
TaiI ACGT 1 cut(s) 469
TaqI TCGA 4 cut(s) 55, 603, 893, 996
TaqII GACCGA 1 cut(s) 919
TasI AATT 5 cut(s) 360, 398, 622, 876, 975
TatI WGTACW 1 cut(s) 610
TfiI GAWTC 1 cut(s) 657
Tru1I TTAA 6 cut(s) 15, 186, 245, 371, 941, 1003
Tru9I TTAA 6 cut(s) 15, 186, 245, 371, 941, 1003
TscAI CASTG 6 cut(s) 463, 687, 712, 753, 853, 918
TseFI GTSAC 1 cut(s) 544
TseI GCWGC 1 cut(s) 453
Tsp45I GTSAC 1 cut(s) 544
TspDTI ATGAA 4 cut(s) 114, 553, 714, 968
TspRI CASTG 6 cut(s) 463, 687, 712, 753, 853, 918
Van91I CCANNNNNTGG 1 cut(s) 167
VneI GTGCAC 1 cut(s) 489
VpaK11BI GGWCC 1 cut(s) 335
XapI RAATTY 2 cut(s) 360, 975
XceI RCATGY 1 cut(s) 44
XhoI CTCGAG 1 cut(s) 54
XmiI GTMKAC 1 cut(s) 37
XspI CTAG 2 cut(s) 144, 858
Zsp2I ATGCAT 2 cut(s) 46, 253
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.