Rh5CG165700

Polygalacturonase-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5C
OG0000702
Physical Location & Seq
Forward (+)
15442800 .. 15444949
2150 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5CG165700.1

Sequence Viewer

Length: 1092 bp
ATGGAAAATCCCATAAGCCTCATTTTTCTCTCACTTTTTATCGTCTTCATAAACTCAGCCGTATCAACTGCAGTCACTTACAATGTGGCTAATTTAGGAGCCAAACCAGATGGCAAAACTGACTCAACCAAGGCCTTCCTTTCTGGATGGGCCGAAGCTTGTGCCTCGGCCAAGCCCTCGGTCATTTATGTCCCAGCCGGAAGGTTCTTGCTTCGCAATGCGATTTTCAACGGGCCATGCAAGAACAGGGCCATCACTTTTCGCATTGCTGGCACACTCGTCGTCCCTTCATATTACCAGGTCATAGGAAATGCTGGTAACTGGCTTTTCTTTAGGCATGTGAATGGGGTTACCATCTCCCGTGGAATTCTTGACGGACAAGGCACTGGTTTGTGGGATTGCAAGGCCTCCGGCAAGGTTTGCGCCAGCGGAGCAACTACACTGGAGTTTTCCAACTCGAACAACATTATCGTGAGTGGAGTGACATCCCTAAACGCCCAAATGTTCCACATAGTCATCAACGGCTGCAACAATGTGAAAGTGCAAGGTGTTAGGGTTTCTGCCTCTGGTCACAGCCCAAACACCGATGGAATCCACGTCCAAAAGTCCTCGGGCGTCACTATTCTCAACTCTAAGATTGCAATCATTGGGAGTTTAGGCAAGGACCTGGAGGAGGATGGAGTGCAAAATGTAACCGTCAAAACTGTTACATTTACAGGTACTCAAAATGGTCTGAGAATCAAATCATGGGGAAGACCCAGTACTGGGTTTGCTAAGAACATTCTTTTCCAACATGCCGTCATGTTCAATGTCCAAAATCCGATCGTTATTGATCAAAATTATTGCCCAGGCGAAAAAGGGTGCCCTGGTCAGGTTTCGGGAGTTCAAATTAGTGACGTGACATATCAAAACATCCACGGCACATCAGCAACACAAGTTGCTGTGAAATTCGACTGTTGTTCTAGGTACCCTTGTAGCAAGATCACACTGGATGATGTGAAGCTCAGTTACAAGAACCAAGCAGCCGAAGCTTCATGTAGCCATGCCGGTGGAACAGCTGTGGGTATGGTTCAGCCGACAAGTTGTTTGTAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0005575 GO:0005576 GO:0005618 GO:0005623 GO:0030312 GO:0044464 GO:0071944
KEGG Pathways
Metabolic & Signaling
ko00040 ko01100 map00040 map01100
Pfam Domains
Protein Families
Glyco_hydro_28

Protein Analysis

363

Amino Acids

38.42

Weight (kDa)

9.04

Isoelectric Point (pI)

21.0

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pect-lyase_RHGA_epim PF12708 28 - 251 1.1e-15 Rhamnogalacturonase A/epimerase, pectate lyase-like
Glyco_hydro_28 PF00295 54 - 214 1.4e-27 Glycosyl hydrolases family 28
Glyco_hydro_28 PF00295 216 - 347 1.9e-34 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: OG0000702)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G43870 AT3G59850 AT3G59850
fragaria_vesca FvH4_1g00290 FvH4_1g00290 FvH4_1g21842 FvH4_1g21850 FvH4_1g21851
malus_domestica MD00G1070500.v1.1 MD00G1087900.v1.1
prunus_persica Prupe.4G261700_v2.0.a1 Prupe.4G261800_v2.0.a1 Prupe.4G261900_v2.0.a1 Prupe.4G262200_v2.0.a1 Prupe.4G262200_v2.0.a1 Prupe.7G269200_v2.0.a1
pyrus_communis pycom02g00030 pycom03g19680
rosa_chinensis RchiOBHm_Chr2g0084591 RchiOBHm_Chr2g0085391 RchiOBHm_Chr2g0115741 RchiOBHm_Chr2g0115771 RchiOBHm_Chr2g0115801 RchiOBHm_Chr2g0115811 RchiOBHm_Chr2g0115821 RchiOBHm_Chr5g0021021 RchiOBHm_Chr5g0021031
rosa_laevigata RLG00000015683 RLG00000018208 RLG00000018211 RLG00000018212
rosa_multiflora Rmu_co8137638.1_g000001 Rmu_sc0000742.1_g000006 Rmu_sc0004926.1_g000013 Rmu_sc0008355.1_g000010 Rmu_sc0011452.1_g000015 Rmu_ssc0000197.1_g000031 Rmu_ssc0000197.1_g000032 Rmu_ssc0000197.1_g000056
rosa_roxburghii Rroxscaffold_2G00127770 Rroxscaffold_2G00127780 Rroxscaffold_2G00127790 Rroxscaffold_2G00127830 Rroxscaffold_2G00127850 Rroxscaffold_2G00128630 Rroxscaffold_2G00128640 Rroxscaffold_2G00128680 Rroxscaffold_2G00128730 Rroxscaffold_2G00128740
rosa_rugosa Rorug01G0455200 Rorug01G0460100 Rorug02G0199800 Rorug02G0199900
rosa_samantha Rh2BG003000 Rh2BG267500 Rh2BG267700 Rh2BG267800 Rh2BG267900 Rh2CG003400 Rh2CG010000 Rh2CG262800 Rh2CG263200 Rh2CG263300 Rh2CG263400 Rh5CG165700 Rh5CG165800
rosa_wichuraiana Rw0G014320 Rw0G014330 Rw1G010220 Rw2G000800 Rw2G020110 Rw2G020130 Rw2G020150 Rw2G020160

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc65I GGTACC 1 cut(s) 966
AccB1I GGYRCC 2 cut(s) 861, 966
AciI CCGC 1 cut(s) 429
AcoI YGGCCR 1 cut(s) 168
AcsI RAATTY 2 cut(s) 366, 947
AcyI GRCGYC 1 cut(s) 615
AfaI GTAC 3 cut(s) 721, 763, 968
AfiI CCNNNNNNNGG 4 cut(s) 673, 764, 765, 871
AgsI TTSAA 3 cut(s) 229, 808, 887
AjiI CACGTC 2 cut(s) 598, 898
AjnI CCWGG 4 cut(s) 297, 666, 847, 865
AluBI AGCT 4 cut(s) 158, 1003, 1031, 1058
AluI AGCT 4 cut(s) 158, 1003, 1031, 1058
Ama87I CYCGRG 1 cut(s) 610
AoxI GGCC 6 cut(s) 132, 150, 168, 233, 249, 405
ApeKI GCWGC 2 cut(s) 525, 1022
ApoI RAATTY 2 cut(s) 366, 947
ArsI GACNNNNNNTTYG 1 cut(s) 1069
Asp718I GGTACC 1 cut(s) 966
AspLEI GCGC 1 cut(s) 425
AspS9I GGNCC 4 cut(s) 150, 233, 249, 664
AvaI CYCGRG 1 cut(s) 610
AvaII GGWCC 1 cut(s) 664
BaeGI GKGCMC 1 cut(s) 866
BaeI ACNNNNGTAYC 2 cut(s) 958, 991
BanI GGYRCC 2 cut(s) 861, 966
BarI GAAGNNNNNNTAC 4 cut(s) 745, 777, 992, 1024
BbsI GAAGAC 2 cut(s) 37, 760
BbvI GCAGC 2 cut(s) 512, 1034
BccI CCATC 6 cut(s) 104, 141, 260, 362, 581, 671
BceAI ACGGC 4 cut(s) 44, 538, 782, 934
BcgI CGANNNNNNTGC 4 cut(s) 143, 177, 262, 296
BciT130I CCWGG 4 cut(s) 299, 668, 849, 867
BclI TGATCA 1 cut(s) 832
BfaI CTAG 1 cut(s) 963
BfmI CTRYAG 1 cut(s) 69
BisI GCNGC 2 cut(s) 526, 1023
BlsI GCNGC 2 cut(s) 527, 1024
BmcAI AGTACT 1 cut(s) 763
Bme1390I CCNGG 4 cut(s) 299, 668, 849, 867
Bme18I GGWCC 1 cut(s) 664
BmeT110I CYCGRG 1 cut(s) 610
BmgBI CACGTC 2 cut(s) 598, 898
BmgT120I GGNCC 4 cut(s) 150, 233, 249, 664
BmiI GGNNCC 3 cut(s) 100, 863, 968
BmrFI CCNGG 4 cut(s) 299, 668, 849, 867
BmrI ACTGGG 2 cut(s) 753, 774
BmuI ACTGGG 2 cut(s) 753, 774
BpiI GAAGAC 2 cut(s) 37, 760
BpmI CTGGAG 2 cut(s) 464, 689
BsaBI GATNNNNATC 1 cut(s) 641
BsaHI GRCGYC 1 cut(s) 615
BsaJI CCNNGG 8 cut(s) 129, 165, 177, 361, 609, 847, 865, 916
Bsc4I CCNNNNNNNGG 4 cut(s) 673, 764, 765, 871
Bse118I RCCGGY 1 cut(s) 1046
Bse1I ACTGG 6 cut(s) 326, 391, 447, 759, 769, 993
Bse3DI GCAATG 2 cut(s) 223, 264
Bse8I GATNNNNATC 1 cut(s) 641
BseBI CCWGG 4 cut(s) 299, 668, 849, 867
BseDI CCNNGG 8 cut(s) 129, 165, 177, 361, 609, 847, 865, 916
BseGI GGATG 5 cut(s) 152, 485, 682, 912, 997
BseJI GATNNNNATC 1 cut(s) 641
BseLI CCNNNNNNNGG 4 cut(s) 673, 764, 765, 871
BseMI GCAATG 2 cut(s) 223, 264
BseMII CTCAG 3 cut(s) 69, 725, 1018
BseNI ACTGG 6 cut(s) 326, 391, 447, 759, 769, 993
BseRI GAGGAG 1 cut(s) 686
BseSI GKGCMC 1 cut(s) 866
BseXI GCAGC 2 cut(s) 512, 1034
BseYI CCCAGC 1 cut(s) 193
Bsh1285I CGRYCG 1 cut(s) 825
BshFI GGCC 6 cut(s) 134, 152, 170, 235, 251, 407
BshNI GGYRCC 2 cut(s) 861, 966
BsiEI CGRYCG 1 cut(s) 825
BsiHKCI CYCGRG 1 cut(s) 610
BsiSI CCGG 3 cut(s) 198, 411, 1047
BslFI GGGAC 2 cut(s) 176, 269
BslI CCNNNNNNNGG 4 cut(s) 673, 764, 765, 871
BsmFI GGGAC 2 cut(s) 176, 269
BsnI GGCC 6 cut(s) 134, 152, 170, 235, 251, 407
BsoBI CYCGRG 1 cut(s) 610
Bsp1286I GDGCHC 1 cut(s) 866
Bsp143I GATC 3 cut(s) 822, 832, 981
BspACI CCGC 1 cut(s) 429
BspANI GGCC 6 cut(s) 134, 152, 170, 235, 251, 407
BspCNI CTCAG 3 cut(s) 68, 726, 1017
BspLI GGNNCC 3 cut(s) 100, 863, 968
BspMAI CTGCAG 1 cut(s) 73
BspT107I GGYRCC 2 cut(s) 861, 966
BsrDI GCAATG 2 cut(s) 223, 264
BsrFI RCCGGY 1 cut(s) 1046
BsrI ACTGG 6 cut(s) 326, 391, 447, 759, 769, 993
BssAI RCCGGY 1 cut(s) 1046
BssECI CCNNGG 8 cut(s) 129, 165, 177, 361, 609, 847, 865, 916
BssMI GATC 3 cut(s) 822, 832, 981
BssNI GRCGYC 1 cut(s) 615
BssT1I CCWWGG 1 cut(s) 129
Bst2UI CCWGG 4 cut(s) 299, 668, 849, 867
Bst4CI ACNGT 3 cut(s) 697, 706, 956
BstACI GRCGYC 1 cut(s) 615
BstAPI GCANNNNNTGC 1 cut(s) 420
BstC8I GCNNGC 2 cut(s) 271, 427
BstDEI CTNAG 5 cut(s) 55, 633, 734, 774, 1004
BstDSI CCRYGG 2 cut(s) 361, 916
BstEII GGTNACC 1 cut(s) 349
BstENI CCTNNNNNAGG 1 cut(s) 671
BstF5I GGATG 5 cut(s) 152, 485, 682, 912, 997
BstHHI GCGC 1 cut(s) 425
BstKTI GATC 3 cut(s) 825, 835, 984
BstMBI GATC 3 cut(s) 822, 832, 981
BstMCI CGRYCG 1 cut(s) 825
BstMWI GCNNNNNNNGC 4 cut(s) 270, 420, 431, 1028
BstNI CCWGG 4 cut(s) 299, 668, 849, 867
BstNSI RCATGY 2 cut(s) 341, 797
BstPI GGTNACC 1 cut(s) 349
BstSCI CCNGG 4 cut(s) 297, 666, 847, 865
BstSFI CTRYAG 1 cut(s) 69
BstSLI GKGCMC 1 cut(s) 866
BstV1I GCAGC 2 cut(s) 512, 1034
BstV2I GAAGAC 2 cut(s) 37, 760
BstXI CCANNNNNNTGG 1 cut(s) 1049
BsuRI GGCC 6 cut(s) 134, 152, 170, 235, 251, 407
BtgI CCRYGG 2 cut(s) 361, 916
BtrI CACGTC 2 cut(s) 598, 898
BtsCI GGATG 5 cut(s) 152, 485, 682, 912, 997
BtsIMutI CAGTG 3 cut(s) 384, 440, 986
Cac8I GCNNGC 2 cut(s) 271, 427
CfoI GCGC 1 cut(s) 425
Cfr10I RCCGGY 1 cut(s) 1046
Cfr13I GGNCC 4 cut(s) 150, 233, 249, 664
CseI GACGC 1 cut(s) 604
CsiI ACCWGGT 1 cut(s) 297
Csp6I GTAC 3 cut(s) 720, 762, 967
CviAII CATG 7 cut(s) 237, 338, 747, 794, 802, 1035, 1043
CviQI GTAC 3 cut(s) 720, 762, 967
DdeI CTNAG 5 cut(s) 55, 633, 734, 774, 1004
DpnI GATC 3 cut(s) 824, 834, 983
DpnII GATC 3 cut(s) 822, 832, 981
EaeI YGGCCR 1 cut(s) 168
Eco130I CCWWGG 1 cut(s) 129
Eco147I AGGCCT 2 cut(s) 134, 407
Eco47I GGWCC 1 cut(s) 664
Eco88I CYCGRG 1 cut(s) 610
Eco91I GGTNACC 1 cut(s) 349
EcoNI CCTNNNNNAGG 1 cut(s) 671
EcoO109I RGGNCCY 1 cut(s) 664
EcoO65I GGTNACC 1 cut(s) 349
EcoRI GAATTC 1 cut(s) 366
EcoRII CCWGG 4 cut(s) 297, 666, 847, 865
EcoT14I CCWWGG 1 cut(s) 129
ErhI CCWWGG 1 cut(s) 129
FaeI CATG 7 cut(s) 240, 341, 750, 797, 805, 1038, 1046
FaqI GGGAC 2 cut(s) 176, 269
FatI CATG 7 cut(s) 236, 337, 746, 793, 801, 1034, 1042
FbaI TGATCA 1 cut(s) 832
Fnu4HI GCNGC 2 cut(s) 526, 1023
FokI GGATG 5 cut(s) 159, 472, 689, 899, 1004
Fsp4HI GCNGC 2 cut(s) 526, 1023
FspBI CTAG 1 cut(s) 963
GlaI GCGC 1 cut(s) 424
GluI GCNGC 2 cut(s) 526, 1023
GsaI CCCAGC 1 cut(s) 197
GsuI CTGGAG 2 cut(s) 464, 689
HaeIII GGCC 6 cut(s) 134, 152, 170, 235, 251, 407
HapII CCGG 3 cut(s) 198, 411, 1047
HgaI GACGC 1 cut(s) 604
HhaI GCGC 1 cut(s) 425
Hin1I GRCGYC 1 cut(s) 615
Hin1II CATG 7 cut(s) 240, 341, 750, 797, 805, 1038, 1046
Hin6I GCGC 1 cut(s) 423
HinP1I GCGC 1 cut(s) 423
HindIII AAGCTT 2 cut(s) 156, 1029
HinfI GANTC 3 cut(s) 122, 591, 738
HpaII CCGG 3 cut(s) 198, 411, 1047
Hpy188I TCNGA 2 cut(s) 735, 822
Hpy188III TCNNGA 4 cut(s) 144, 371, 472, 879
Hpy99I CGWCG 1 cut(s) 284
HpyAV CCTTC 3 cut(s) 145, 195, 297
HpyCH4III ACNGT 3 cut(s) 697, 706, 956
HpyCH4IV ACGT 2 cut(s) 597, 897
HpyCH4V TGCA 7 cut(s) 71, 240, 402, 528, 544, 641, 685
HpyF10VI GCNNNNNNNGC 4 cut(s) 270, 420, 431, 1028
HpyF3I CTNAG 5 cut(s) 55, 633, 734, 774, 1004
HpySE526I ACGT 2 cut(s) 597, 897
Hsp92I GRCGYC 1 cut(s) 615
Hsp92II CATG 7 cut(s) 240, 341, 750, 797, 805, 1038, 1046
HspAI GCGC 1 cut(s) 423
KpnI GGTACC 1 cut(s) 970
Ksp22I TGATCA 1 cut(s) 832
Kzo9I GATC 3 cut(s) 822, 832, 981
LmnI GCTCC 2 cut(s) 98, 431
Lsp1109I GCAGC 2 cut(s) 512, 1034
MabI ACCWGGT 1 cut(s) 297
MaeI CTAG 1 cut(s) 963
MaeII ACGT 2 cut(s) 597, 897
MalI GATC 3 cut(s) 824, 834, 983
MboI GATC 3 cut(s) 822, 832, 981
MboII GAAGA 2 cut(s) 37, 765
MhlI GDGCHC 1 cut(s) 866
MluCI AATT 5 cut(s) 91, 366, 838, 888, 947
MlyI GAGTC 1 cut(s) 116
MmeI TCCRAC 2 cut(s) 477, 814
MnlI CCTC 8 cut(s) 29, 175, 187, 418, 574, 619, 664, 667
MslI CAYNNNNRTG 3 cut(s) 342, 470, 1047
MspA1I CMGCKG 2 cut(s) 429, 1058
MspI CCGG 3 cut(s) 198, 411, 1047
MspR9I CCNGG 4 cut(s) 299, 668, 849, 867
MvaI CCWGG 4 cut(s) 299, 668, 849, 867
MwoI GCNNNNNNNGC 4 cut(s) 270, 420, 431, 1028
NdeII GATC 3 cut(s) 822, 832, 981
NlaIII CATG 7 cut(s) 240, 341, 750, 797, 805, 1038, 1046
NlaIV GGNNCC 3 cut(s) 100, 863, 968
NmeAIII GCCGAG 1 cut(s) 146
NmuCI GTSAC 6 cut(s) 73, 481, 569, 616, 893, 898
NspI RCATGY 2 cut(s) 341, 797
PceI AGGCCT 2 cut(s) 134, 407
PfeI GAWTC 2 cut(s) 591, 738
PkrI GCNGC 2 cut(s) 527, 1024
Ple19I CGATCG 1 cut(s) 825
PleI GAGTC 1 cut(s) 116
PpsI GAGTC 1 cut(s) 116
PpuMI RGGWCCY 1 cut(s) 664
Psp5II RGGWCCY 1 cut(s) 664
Psp6I CCWGG 4 cut(s) 297, 666, 847, 865
PspEI GGTNACC 1 cut(s) 349
PspFI CCCAGC 1 cut(s) 193
PspGI CCWGG 4 cut(s) 297, 666, 847, 865
PspN4I GGNNCC 3 cut(s) 100, 863, 968
PspPI GGNCC 4 cut(s) 150, 233, 249, 664
PspPPI RGGWCCY 1 cut(s) 664
PstI CTGCAG 1 cut(s) 73
PvuI CGATCG 1 cut(s) 825
PvuII CAGCTG 1 cut(s) 1058
RsaI GTAC 3 cut(s) 721, 763, 968
RsaNI GTAC 3 cut(s) 720, 762, 967
RseI CAYNNNNRTG 3 cut(s) 342, 470, 1047
SatI GCNGC 2 cut(s) 526, 1023
Sau3AI GATC 3 cut(s) 822, 832, 981
Sau96I GGNCC 4 cut(s) 150, 233, 249, 664
ScaI AGTACT 1 cut(s) 763
SchI GAGTC 1 cut(s) 116
ScrFI CCNGG 4 cut(s) 299, 668, 849, 867
SduI GDGCHC 1 cut(s) 866
SexAI ACCWGGT 1 cut(s) 297
SfcI CTRYAG 1 cut(s) 69
SinI GGWCC 1 cut(s) 664
SmiMI CAYNNNNRTG 3 cut(s) 342, 470, 1047
Sse9I AATT 5 cut(s) 91, 366, 838, 888, 947
SseBI AGGCCT 2 cut(s) 134, 407
SsiI CCGC 1 cut(s) 429
SspMI CTAG 1 cut(s) 963
StuI AGGCCT 2 cut(s) 134, 407
StyD4I CCNGG 4 cut(s) 297, 666, 847, 865
StyI CCWWGG 1 cut(s) 129
TaaI ACNGT 3 cut(s) 697, 706, 956
TaiI ACGT 2 cut(s) 600, 900
TaqI TCGA 2 cut(s) 458, 951
TaqII GACCGA 1 cut(s) 169
TasI AATT 5 cut(s) 91, 366, 838, 888, 947
TatI WGTACW 1 cut(s) 761
TfiI GAWTC 2 cut(s) 591, 738
TscAI CASTG 3 cut(s) 391, 447, 993
TseFI GTSAC 6 cut(s) 73, 481, 569, 616, 893, 898
TseI GCWGC 2 cut(s) 525, 1022
Tsp45I GTSAC 6 cut(s) 73, 481, 569, 616, 893, 898
TspDTI ATGAA 3 cut(s) 37, 279, 1023
TspGWI ACGGA 1 cut(s) 390
TspRI CASTG 3 cut(s) 391, 447, 993
VpaK11BI GGWCC 1 cut(s) 664
XagI CCTNNNNNAGG 1 cut(s) 671
XapI RAATTY 2 cut(s) 366, 947
XceI RCATGY 2 cut(s) 341, 797
XspI CTAG 1 cut(s) 963
ZrmI AGTACT 1 cut(s) 763
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.