Rh4BG092300

Polygalacturonase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr4B
OG0000579
Physical Location & Seq
Reverse (-)
15849421 .. 15852529
3109 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh4BG092300.1

Sequence Viewer

Length: 894 bp
ATGCAGGGTCTTCCTTCACTACTTAGCTCTGTTGTGCTTTTATGGATTGTTGCTTCATCTAGTCTTGGCATTGGGTATGGCCAAAATGGTAATCTTAGTGTACTTGATTTTGGTGCCTCCGGCGACGGCGTAGGAGATGATACCCAAGCTTTCTTGAATGCATGGAAGACACTTTGCGCAACTGGCCAAACCCTAACTATCCCTGCAGGGAAGACTTTTGTACTCAAACCTCTTCAACTTGTAGGTCCTTGCAAATCCAGCAGTGTTGTAATTCAGATTGATGGGAATATTGTTGGTCCATCCACTGTTAGCGAATGGGCAGACGTGTGCAAAATGGGACAGTGCTGGCTATGCTTCCAAAACGTGAAGGGCCTCATCATCAAAGGGGGAGGACTTATAGATGGCAAGGGTTCAATTTGGTGGAACCAAAAAAACCAATCCATAAATGCTTTACACTTCCACAAATGCGACCAACTTCAATTATCTGGATTTACTTCCCGTGATAGTCCGAGAGCCCATATATTTATACATAGCAGCAATGATGTACGTATCTCAAACATTCATTTGAATGCACCGGGGAACAGCCCAAATACTGATGGCATCGGCATCTCTTTATCAAGCCAAACTGGAGCGGTGAAAGTTAGTGACGTAACTTTCAGTGGCTTCACCGGAACTTCAGCAAGCGAGCAAGCAATAACACTGAATTGCTCCGACTTGGGTTGCACCAATATTTTGATGGATCATGTCATCCTAACCTCCGCAATCGGAAAGCCACTTCGTTCTGTATGCAACAAGGCCAGTGGGAAAGCTAGTTTTACTTCACCTCCCGTTCCTTGTCTGTCGTCGAAGCAATCCCTGTCACCAACAATTGCACCAATCTCAATCACACATTAA

Protein Analysis

297

Amino Acids

31.04

Weight (kDa)

8.33

Isoelectric Point (pI)

40.6

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pect-lyase_RHGA_epim PF12708 33 - 234 2.1e-09 Rhamnogalacturonase A/epimerase, pectate lyase-like
Glyco_hydro_28 PF00295 63 - 207 2.3e-23 Glycosyl hydrolases family 28
Glyco_hydro_28 PF00295 207 - 266 2.3e-07 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)
Acc16I TGCGCA 1 cut(s) 178
AccB1I GGYRCC 1 cut(s) 113
AccBSI CCGCTC 1 cut(s) 632
AciI CCGC 2 cut(s) 632, 759
AclWI GGATC 1 cut(s) 747
AcoI YGGCCR 2 cut(s) 79, 184
AcuI CTGAAG 1 cut(s) 660
AfaI GTAC 3 cut(s) 102, 222, 546
AflIII ACRYGT 1 cut(s) 324
AgsI TTSAA 5 cut(s) 157, 236, 414, 479, 568
AjiI CACGTC 1 cut(s) 325
AluBI AGCT 3 cut(s) 27, 149, 809
AluI AGCT 3 cut(s) 27, 149, 809
AlwI GGATC 1 cut(s) 747
AoxI GGCC 4 cut(s) 79, 184, 370, 795
ApeKI GCWGC 1 cut(s) 534
AspLEI GCGC 1 cut(s) 179
AspS9I GGNCC 3 cut(s) 245, 296, 370
AsuC2I CCSGG 1 cut(s) 576
AsuHPI GGTGA 4 cut(s) 646, 658, 813, 852
AvaII GGWCC 2 cut(s) 245, 296
BalI TGGCCA 2 cut(s) 81, 186
BanI GGYRCC 1 cut(s) 113
BanII GRGCYC 1 cut(s) 517
BbsI GAAGAC 3 cut(s) 2, 173, 218
BbvI GCAGC 1 cut(s) 546
BccI CCATC 5 cut(s) 275, 307, 395, 590, 730
BceAI ACGGC 1 cut(s) 142
BcnI CCSGG 1 cut(s) 576
BfaI CTAG 2 cut(s) 60, 810
BfmI CTRYAG 1 cut(s) 204
BisI GCNGC 1 cut(s) 535
BlsI GCNGC 1 cut(s) 536
Bme1390I CCNGG 1 cut(s) 576
Bme18I GGWCC 2 cut(s) 245, 296
BmgBI CACGTC 1 cut(s) 325
BmgT120I GGNCC 3 cut(s) 245, 296, 370
BmiI GGNNCC 2 cut(s) 115, 425
BmrFI CCNGG 1 cut(s) 576
BmsI GCATC 2 cut(s) 609, 615
BpiI GAAGAC 3 cut(s) 2, 173, 218
BpmI CTGGAG 1 cut(s) 648
BpuMI CCSGG 1 cut(s) 576
BsaAI YACGTR 1 cut(s) 548
BsaJI CCNNGG 1 cut(s) 575
BsaWI WCCGGW 1 cut(s) 668
BsaXI ACNNNNNCTCC 2 cut(s) 808, 838
Bse1I ACTGG 3 cut(s) 187, 631, 798
Bse3DI GCAATG 1 cut(s) 544
BseDI CCNNGG 1 cut(s) 575
BseGI GGATG 2 cut(s) 299, 747
BseMI GCAATG 1 cut(s) 544
BseNI ACTGG 3 cut(s) 187, 631, 798
BseXI GCAGC 1 cut(s) 546
BshFI GGCC 4 cut(s) 81, 186, 372, 797
BshNI GGYRCC 1 cut(s) 113
BsiSI CCGG 3 cut(s) 120, 575, 669
BslFI GGGAC 1 cut(s) 351
BsmFI GGGAC 1 cut(s) 351
BsmI GAATGC 2 cut(s) 163, 574
BsnI GGCC 4 cut(s) 81, 186, 372, 797
Bsp1286I GDGCHC 1 cut(s) 517
Bsp143I GATC 1 cut(s) 739
BspACI CCGC 2 cut(s) 632, 759
BspANI GGCC 4 cut(s) 81, 186, 372, 797
BspLI GGNNCC 2 cut(s) 115, 425
BspMAI CTGCAG 1 cut(s) 208
BspPI GGATC 1 cut(s) 747
BspT107I GGYRCC 1 cut(s) 113
BsrBI CCGCTC 1 cut(s) 632
BsrDI GCAATG 1 cut(s) 544
BsrI ACTGG 3 cut(s) 187, 631, 798
BssECI CCNNGG 1 cut(s) 575
BssMI GATC 1 cut(s) 739
Bst4CI ACNGT 2 cut(s) 307, 342
Bst6I CTCTTC 1 cut(s) 237
BstBAI YACGTR 1 cut(s) 548
BstC8I GCNNGC 4 cut(s) 347, 682, 686, 690
BstDEI CTNAG 2 cut(s) 23, 95
BstF5I GGATG 2 cut(s) 299, 747
BstHHI GCGC 1 cut(s) 179
BstKTI GATC 1 cut(s) 742
BstMBI GATC 1 cut(s) 739
BstMWI GCNNNNNNNGC 3 cut(s) 183, 258, 351
BstSCI CCNGG 1 cut(s) 574
BstSFI CTRYAG 1 cut(s) 204
BstSNI TACGTA 1 cut(s) 548
BstV1I GCAGC 1 cut(s) 546
BstV2I GAAGAC 3 cut(s) 2, 173, 218
BsuRI GGCC 4 cut(s) 81, 186, 372, 797
BtrI CACGTC 1 cut(s) 325
BtsCI GGATG 2 cut(s) 299, 747
BtsI GCAGTG 1 cut(s) 268
BtsIMutI CAGTG 6 cut(s) 268, 303, 347, 664, 698, 805
Cac8I GCNNGC 4 cut(s) 347, 682, 686, 690
CfoI GCGC 1 cut(s) 179
Cfr13I GGNCC 3 cut(s) 245, 296, 370
Csp6I GTAC 3 cut(s) 101, 221, 545
CspCI CAANNNNNGTGG 2 cut(s) 781, 816
CviAII CATG 2 cut(s) 162, 743
CviQI GTAC 3 cut(s) 101, 221, 545
DdeI CTNAG 2 cut(s) 23, 95
DpnI GATC 1 cut(s) 741
DpnII GATC 1 cut(s) 739
EaeI YGGCCR 2 cut(s) 79, 184
Eam1104I CTCTTC 1 cut(s) 237
EarI CTCTTC 1 cut(s) 237
Eco105I TACGTA 1 cut(s) 548
Eco24I GRGCYC 1 cut(s) 517
Eco47I GGWCC 2 cut(s) 245, 296
Eco57I CTGAAG 1 cut(s) 660
EcoO109I RGGNCCY 2 cut(s) 245, 370
EcoT22I ATGCAT 1 cut(s) 163
EcoT38I GRGCYC 1 cut(s) 517
FaeI CATG 2 cut(s) 165, 746
FaqI GGGAC 1 cut(s) 351
FatI CATG 2 cut(s) 161, 742
Fnu4HI GCNGC 1 cut(s) 535
FokI GGATG 2 cut(s) 286, 734
FriOI GRGCYC 1 cut(s) 517
Fsp4HI GCNGC 1 cut(s) 535
FspBI CTAG 2 cut(s) 60, 810
FspI TGCGCA 1 cut(s) 178
GlaI GCGC 1 cut(s) 178
GluI GCNGC 1 cut(s) 535
GsuI CTGGAG 1 cut(s) 648
HaeIII GGCC 4 cut(s) 81, 186, 372, 797
HapII CCGG 3 cut(s) 120, 575, 669
HhaI GCGC 1 cut(s) 179
Hin1II CATG 2 cut(s) 165, 746
Hin6I GCGC 1 cut(s) 177
HinP1I GCGC 1 cut(s) 177
HindIII AAGCTT 1 cut(s) 147
HpaII CCGG 3 cut(s) 120, 575, 669
HphI GGTGA 4 cut(s) 646, 658, 813, 852
Hpy166II GTNNAC 1 cut(s) 101
Hpy188I TCNGA 4 cut(s) 276, 510, 712, 767
Hpy188III TCNNGA 2 cut(s) 154, 486
Hpy8I GTNNAC 1 cut(s) 101
Hpy99I CGWCG 2 cut(s) 128, 847
HpyAV CCTTC 2 cut(s) 24, 361
HpyCH4III ACNGT 2 cut(s) 307, 342
HpyCH4IV ACGT 4 cut(s) 324, 363, 547, 648
HpyCH4V TGCA 9 cut(s) 4, 161, 206, 252, 330, 572, 723, 789, 872
HpyF10VI GCNNNNNNNGC 3 cut(s) 183, 258, 351
HpyF3I CTNAG 2 cut(s) 23, 95
HpySE526I ACGT 4 cut(s) 324, 363, 547, 648
Hsp92II CATG 2 cut(s) 165, 746
HspAI GCGC 1 cut(s) 177
Kzo9I GATC 1 cut(s) 739
LmnI GCTCC 2 cut(s) 629, 713
Lsp1109I GCAGC 1 cut(s) 546
LweI GCATC 2 cut(s) 609, 615
MaeI CTAG 2 cut(s) 60, 810
MaeII ACGT 4 cut(s) 324, 363, 547, 648
MaeIII GTNAC 3 cut(s) 644, 649, 858
MalI GATC 1 cut(s) 741
MbiI CCGCTC 1 cut(s) 632
MboI GATC 1 cut(s) 739
MboII GAAGA 3 cut(s) 178, 223, 224
MfeI CAATTG 1 cut(s) 867
MhlI GDGCHC 1 cut(s) 517
MlsI TGGCCA 2 cut(s) 81, 186
MluCI AATT 5 cut(s) 270, 414, 479, 703, 867
MluNI TGGCCA 2 cut(s) 81, 186
MmeI TCCRAC 1 cut(s) 735
MnlI CCTC 6 cut(s) 127, 240, 383, 383, 766, 834
Mox20I TGGCCA 2 cut(s) 81, 186
Mph1103I ATGCAT 1 cut(s) 163
MscI TGGCCA 2 cut(s) 81, 186
MseI TTAA 1 cut(s) 892
MslI CAYNNNNRTG 1 cut(s) 567
Msp20I TGGCCA 2 cut(s) 81, 186
MspI CCGG 3 cut(s) 120, 575, 669
MspR9I CCNGG 1 cut(s) 576
MunI CAATTG 1 cut(s) 867
Mva1269I GAATGC 2 cut(s) 163, 574
MwoI GCNNNNNNNGC 3 cut(s) 183, 258, 351
NciI CCSGG 1 cut(s) 576
NdeII GATC 1 cut(s) 739
NlaIII CATG 2 cut(s) 165, 746
NlaIV GGNNCC 2 cut(s) 115, 425
NmuCI GTSAC 2 cut(s) 644, 858
NsbI TGCGCA 1 cut(s) 178
NsiI ATGCAT 1 cut(s) 163
PctI GAATGC 2 cut(s) 163, 574
PkrI GCNGC 1 cut(s) 536
Ppu21I YACGTR 1 cut(s) 548
PpuMI RGGWCCY 1 cut(s) 245
Psp5II RGGWCCY 1 cut(s) 245
PspN4I GGNNCC 2 cut(s) 115, 425
PspPI GGNCC 3 cut(s) 245, 296, 370
PspPPI RGGWCCY 1 cut(s) 245
PstI CTGCAG 1 cut(s) 208
RsaI GTAC 3 cut(s) 102, 222, 546
RsaNI GTAC 3 cut(s) 101, 221, 545
RseI CAYNNNNRTG 1 cut(s) 567
SaqAI TTAA 1 cut(s) 892
SatI GCNGC 1 cut(s) 535
Sau3AI GATC 1 cut(s) 739
Sau96I GGNCC 3 cut(s) 245, 296, 370
SbfI CCTGCAGG 1 cut(s) 208
ScrFI CCNGG 1 cut(s) 576
SdaI CCTGCAGG 1 cut(s) 208
SduI GDGCHC 1 cut(s) 517
SfaNI GCATC 2 cut(s) 609, 615
SfcI CTRYAG 1 cut(s) 204
SinI GGWCC 2 cut(s) 245, 296
SmiMI CAYNNNNRTG 1 cut(s) 567
SnaBI TACGTA 1 cut(s) 548
Sse8387I CCTGCAGG 1 cut(s) 208
Sse9I AATT 5 cut(s) 270, 414, 479, 703, 867
SsiI CCGC 2 cut(s) 632, 759
SspI AATATT 2 cut(s) 289, 730
SspMI CTAG 2 cut(s) 60, 810
StyD4I CCNGG 1 cut(s) 574
TaaI ACNGT 2 cut(s) 307, 342
TaiI ACGT 4 cut(s) 327, 366, 550, 651
TaqI TCGA 1 cut(s) 845
TasI AATT 5 cut(s) 270, 414, 479, 703, 867
TatI WGTACW 2 cut(s) 100, 220
Tru1I TTAA 1 cut(s) 892
Tru9I TTAA 1 cut(s) 892
TscAI CASTG 6 cut(s) 268, 310, 347, 664, 705, 805
TseFI GTSAC 2 cut(s) 644, 858
TseI GCWGC 1 cut(s) 534
Tsp45I GTSAC 2 cut(s) 644, 858
TspDTI ATGAA 2 cut(s) 45, 551
TspRI CASTG 6 cut(s) 268, 310, 347, 664, 705, 805
VpaK11BI GGWCC 2 cut(s) 245, 296
XcmI CCANNNNNNNNNTGG 1 cut(s) 733
XspI CTAG 2 cut(s) 60, 810
Zsp2I ATGCAT 1 cut(s) 163
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.