Rh6BG304300

Polygalacturonase-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr6B
OG0016261
Physical Location & Seq
Reverse (-)
53459455 .. 53462783
3329 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh6BG304300.1

Sequence Viewer

Length: 1128 bp
ATGTTTCAGGCATTTCAGAAGGCGTGGCTGGAAGCTTGTTCCTCCAACGGAGCGGTGGTTCTTCTGGTGCCGCCCCACAGGAGCTATTTCGTTAAGCAATTCACATTCTCAGGCGCGCAATGCAAATCCCATATTACAATGCAGATCCAAGGAACGATAATGGCATTTGAGGATCCGAAAACCTACCATTTTCCAAATAAAAGTAAGCAGCAGTACTGGCTTACCTTTGAGAGGGTTCAGAACTTGGTGGTTGAAGGTCCTGGAACCATCAATGGCAACGGAGAAAAATGGTGGCAAAGCTCATGCAAACAAAACAATATAACTCGCACGCTGGTGCCCAATTGCAATAACGACGCACCAACTGCTGTAACCTTCAAGACGTGCAATAACTTGACGGTGCATAATCTGAATTTTGAAAAGGCACAGCGGAAGCATGTTTCGTTTGAAAATTGCACGGATGTTAAAGCTTCCCGTCTTAGAATAAATACATCAGAGGCTAGTCCCAACACTGATGGAATTCACGTTACAGAAACCAAGAACATCGACATTTCAATGAGTCGTATAAGCACAGGTGATGATTGTATATCCATTATGGGAGGATCCCAGAATGTTTATGTCGCAAACATAGCTTGCGGACCAGGCCATGGAATCAGCATTGGTAGCTTGGGAAGAGGTGGCTCAGAAGACCATGTTTCCGACGTAACAGTCTTTGGATCTAGGCTAACTGGAACCATGTATGGAGTGAGGATTAAGACATGGCCGGGAGGGTCAGGGTATGCAACCAACATCACATTTCAGATGATACAGATGGATAATGTGACCAACCCCATAATCATCGACCAAAACTACTGCGACACTGCAACCAAAGTCATCAACGGAGAATGCAAACCACCACCACTGCAGAAAAATACAGCAGTTAAAGTGCATAATGTTATGTACCAGAGCATAAATGGGACAGTTTCTAAGGACGGCCAAGCCATAGTATTTAATTGCAGCAGTGTTCCTGGTGCATGTGAGAAGATTGTGCTGGACGATGTTAGACTTGAGAAAGGAGGAGCTGCTGTATGCAGCAACGTCAAACCGACTTACAGCAGAGTAGATTTGCCCCTCAATCGATGCCCTAACTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00040 ko01100 map00040 map01100
Pfam Domains
Protein Families
Glyco_hydro_28

Protein Analysis

375

Amino Acids

41.04

Weight (kDa)

8.59

Isoelectric Point (pI)

37.44

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Glyco_hydro_28 PF00295 13 - 361 7.3e-87 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: OG0016261)

Species Orthologous Gene IDs
fragaria_vesca FvH4_2g20980
rosa_chinensis RchiOBHm_Chr6g0287361
rosa_laevigata RLG00000012495
rosa_multiflora Rmu_sc0007029.1_g000028
rosa_roxburghii Rroxscaffold_7G00181500
rosa_rugosa Rorug06G0187300 Rorug06G0187400 Rorug06G0187500 Rorug06G0187600.1
rosa_samantha Rh6AG298800 Rh6BG304300 Rh6CG305300 Rh6CG312900 Rh6DG296200
rosa_wichuraiana Rw6G025820

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 704
AccB1I GGYRCC 2 cut(s) 67, 334
AccB7I CCANNNNNTGG 1 cut(s) 644
AccBSI CCGCTC 1 cut(s) 53
AccII CGCG 1 cut(s) 116
AciI CCGC 4 cut(s) 53, 71, 427, 633
AclWI GGATC 6 cut(s) 139, 167, 180, 594, 607, 721
AcoI YGGCCR 2 cut(s) 758, 970
AcsI RAATTY 2 cut(s) 409, 516
AfaI GTAC 2 cut(s) 215, 938
AfiI CCNNNNNNNGG 2 cut(s) 231, 644
AgsI TTSAA 5 cut(s) 254, 376, 416, 446, 552
AjiI CACGTC 1 cut(s) 381
AjnI CCWGG 3 cut(s) 259, 637, 1003
AleI CACNNNNGTG 1 cut(s) 332
AloI GAACNNNNNNTCC 2 cut(s) 42, 74
AluBI AGCT 7 cut(s) 35, 84, 300, 467, 629, 663, 1058
AluI AGCT 7 cut(s) 35, 84, 300, 467, 629, 663, 1058
AlwI GGATC 6 cut(s) 139, 167, 180, 594, 607, 721
AoxI GGCC 3 cut(s) 640, 758, 970
ApeKI GCWGC 4 cut(s) 208, 993, 1058, 1068
ApoI RAATTY 2 cut(s) 409, 516
AspLEI GCGC 2 cut(s) 116, 118
AspS9I GGNCC 2 cut(s) 257, 635
AsuC2I CCSGG 1 cut(s) 762
AsuHPI GGTGA 1 cut(s) 584
AvaII GGWCC 2 cut(s) 257, 635
BaeGI GKGCMC 1 cut(s) 339
BamHI GGATCC 2 cut(s) 172, 599
BanI GGYRCC 2 cut(s) 67, 334
BbsI GAAGAC 1 cut(s) 690
BbvI GCAGC 4 cut(s) 220, 1005, 1045, 1080
BccI CCATC 3 cut(s) 275, 506, 802
BceAI ACGGC 1 cut(s) 985
BciT130I CCWGG 3 cut(s) 261, 639, 1005
BcnI CCSGG 1 cut(s) 762
BfaI CTAG 2 cut(s) 498, 717
BfmI CTRYAG 1 cut(s) 899
BisI GCNGC 5 cut(s) 71, 209, 994, 1059, 1069
BlsI GCNGC 5 cut(s) 72, 210, 995, 1060, 1070
BmcAI AGTACT 1 cut(s) 215
Bme1390I CCNGG 4 cut(s) 261, 639, 762, 1005
Bme18I GGWCC 2 cut(s) 257, 635
BmgBI CACGTC 1 cut(s) 381
BmgT120I GGNCC 2 cut(s) 257, 635
BmiI GGNNCC 6 cut(s) 69, 174, 265, 336, 601, 730
BmrFI CCNGG 4 cut(s) 261, 639, 762, 1005
BmsI GCATC 1 cut(s) 1106
BpiI GAAGAC 1 cut(s) 690
BpuEI CTTGAG 1 cut(s) 1064
BpuMI CCSGG 1 cut(s) 762
Bsa29I ATCGAT 1 cut(s) 1114
BsaJI CCNNGG 2 cut(s) 148, 643
BsaXI ACNNNNNCTCC 4 cut(s) 42, 72, 1047, 1077
Bsc4I CCNNNNNNNGG 2 cut(s) 231, 644
Bse1I ACTGG 2 cut(s) 221, 730
Bse3DI GCAATG 1 cut(s) 125
BseBI CCWGG 3 cut(s) 261, 639, 1005
BseCI ATCGAT 1 cut(s) 1114
BseDI CCNNGG 2 cut(s) 148, 643
BseGI GGATG 1 cut(s) 463
BseLI CCNNNNNNNGG 2 cut(s) 231, 644
BseMI GCAATG 1 cut(s) 125
BseMII CTCAG 2 cut(s) 123, 693
BseNI ACTGG 2 cut(s) 221, 730
BsePI GCGCGC 1 cut(s) 114
BseRI GAGGAG 1 cut(s) 1068
BseSI GKGCMC 1 cut(s) 339
BseXI GCAGC 4 cut(s) 220, 1005, 1045, 1080
Bsh1236I CGCG 1 cut(s) 116
BshFI GGCC 3 cut(s) 642, 760, 972
BshNI GGYRCC 2 cut(s) 67, 334
BshVI ATCGAT 1 cut(s) 1114
BsiSI CCGG 1 cut(s) 761
BslFI GGGAC 2 cut(s) 486, 967
BslI CCNNNNNNNGG 2 cut(s) 231, 644
BsmFI GGGAC 2 cut(s) 486, 967
BsmI GAATGC 1 cut(s) 887
BsnI GGCC 3 cut(s) 642, 760, 972
Bsp1286I GDGCHC 1 cut(s) 339
Bsp143I GATC 4 cut(s) 144, 172, 599, 713
Bsp19I CCATGG 1 cut(s) 643
BspACI CCGC 4 cut(s) 53, 71, 427, 633
BspANI GGCC 3 cut(s) 642, 760, 972
BspCNI CTCAG 2 cut(s) 122, 692
BspDI ATCGAT 1 cut(s) 1114
BspFNI CGCG 1 cut(s) 116
BspLI GGNNCC 6 cut(s) 69, 174, 265, 336, 601, 730
BspMAI CTGCAG 1 cut(s) 903
BspPI GGATC 6 cut(s) 139, 167, 180, 594, 607, 721
BspT107I GGYRCC 2 cut(s) 67, 334
BsrBI CCGCTC 1 cut(s) 53
BsrDI GCAATG 1 cut(s) 125
BsrI ACTGG 2 cut(s) 221, 730
BssECI CCNNGG 2 cut(s) 148, 643
BssHII GCGCGC 1 cut(s) 114
BssMI GATC 4 cut(s) 144, 172, 599, 713
BssT1I CCWWGG 2 cut(s) 148, 643
Bst2UI CCWGG 3 cut(s) 261, 639, 1005
Bst4CI ACNGT 3 cut(s) 397, 706, 958
Bst6I CTCTTC 1 cut(s) 664
BstAPI GCANNNNNTGC 1 cut(s) 362
BstC8I GCNNGC 3 cut(s) 116, 329, 631
BstDEI CTNAG 4 cut(s) 109, 476, 679, 963
BstDSI CCRYGG 1 cut(s) 643
BstENI CCTNNNNNAGG 1 cut(s) 229
BstF5I GGATG 1 cut(s) 463
BstFNI CGCG 1 cut(s) 116
BstHHI GCGC 2 cut(s) 116, 118
BstKTI GATC 4 cut(s) 147, 175, 602, 716
BstMBI GATC 4 cut(s) 144, 172, 599, 713
BstMWI GCNNNNNNNGC 6 cut(s) 120, 217, 362, 626, 639, 660
BstNI CCWGG 3 cut(s) 261, 639, 1005
BstNSI RCATGY 2 cut(s) 437, 1014
BstSCI CCNGG 4 cut(s) 259, 637, 760, 1003
BstSFI CTRYAG 1 cut(s) 899
BstSLI GKGCMC 1 cut(s) 339
BstUI CGCG 1 cut(s) 116
BstV1I GCAGC 4 cut(s) 220, 1005, 1045, 1080
BstV2I GAAGAC 1 cut(s) 690
BstX2I RGATCY 4 cut(s) 144, 172, 599, 713
BstYI RGATCY 4 cut(s) 144, 172, 599, 713
Bsu15I ATCGAT 1 cut(s) 1114
BsuRI GGCC 3 cut(s) 642, 760, 972
BsuTUI ATCGAT 1 cut(s) 1114
BtgI CCRYGG 1 cut(s) 643
BtrI CACGTC 1 cut(s) 381
BtsCI GGATG 1 cut(s) 463
BtsI GCAGTG 3 cut(s) 855, 896, 1003
BtsIMutI CAGTG 4 cut(s) 507, 855, 896, 1003
Cac8I GCNNGC 3 cut(s) 116, 329, 631
CfoI GCGC 2 cut(s) 116, 118
Cfr13I GGNCC 2 cut(s) 257, 635
ClaI ATCGAT 1 cut(s) 1114
CseI GACGC 1 cut(s) 362
Csp6I GTAC 2 cut(s) 214, 937
CviAII CATG 7 cut(s) 303, 434, 644, 689, 733, 756, 1011
CviQI GTAC 2 cut(s) 214, 937
DdeI CTNAG 4 cut(s) 109, 476, 679, 963
DpnI GATC 4 cut(s) 146, 174, 601, 715
DpnII GATC 4 cut(s) 144, 172, 599, 713
DrdI GACNNNNNNGTC 1 cut(s) 704
DseDI GACNNNNNNGTC 1 cut(s) 704
EaeI YGGCCR 2 cut(s) 758, 970
Eam1104I CTCTTC 1 cut(s) 664
EarI CTCTTC 1 cut(s) 664
Eco130I CCWWGG 2 cut(s) 148, 643
Eco47I GGWCC 2 cut(s) 257, 635
EcoNI CCTNNNNNAGG 1 cut(s) 229
EcoO109I RGGNCCY 1 cut(s) 257
EcoRI GAATTC 1 cut(s) 516
EcoRII CCWGG 3 cut(s) 259, 637, 1003
EcoT14I CCWWGG 2 cut(s) 148, 643
ErhI CCWWGG 2 cut(s) 148, 643
FaeI CATG 7 cut(s) 306, 437, 647, 692, 736, 759, 1014
FaqI GGGAC 2 cut(s) 486, 967
FatI CATG 7 cut(s) 302, 433, 643, 688, 732, 755, 1010
Fnu4HI GCNGC 5 cut(s) 71, 209, 994, 1059, 1069
FokI GGATG 1 cut(s) 470
Fsp4HI GCNGC 5 cut(s) 71, 209, 994, 1059, 1069
FspBI CTAG 2 cut(s) 498, 717
GlaI GCGC 2 cut(s) 115, 117
GluI GCNGC 5 cut(s) 71, 209, 994, 1059, 1069
HaeIII GGCC 3 cut(s) 642, 760, 972
HapII CCGG 1 cut(s) 761
HgaI GACGC 1 cut(s) 362
HhaI GCGC 2 cut(s) 116, 118
Hin1II CATG 7 cut(s) 306, 437, 647, 692, 736, 759, 1014
Hin6I GCGC 2 cut(s) 114, 116
HinP1I GCGC 2 cut(s) 114, 116
HindIII AAGCTT 2 cut(s) 33, 465
HinfI GANTC 2 cut(s) 556, 648
HpaII CCGG 1 cut(s) 761
HphI GGTGA 1 cut(s) 584
Hpy188I TCNGA 8 cut(s) 18, 177, 240, 408, 493, 682, 697, 798
Hpy188III TCNNGA 1 cut(s) 376
Hpy99I CGWCG 2 cut(s) 356, 701
HpyAV CCTTC 3 cut(s) 13, 248, 382
HpyCH4III ACNGT 3 cut(s) 397, 706, 958
HpyCH4IV ACGT 4 cut(s) 380, 522, 699, 1074
HpyF10VI GCNNNNNNNGC 6 cut(s) 120, 217, 362, 626, 639, 660
HpyF3I CTNAG 4 cut(s) 109, 476, 679, 963
HpySE526I ACGT 4 cut(s) 380, 522, 699, 1074
Hsp92II CATG 7 cut(s) 306, 437, 647, 692, 736, 759, 1014
HspAI GCGC 2 cut(s) 114, 116
Kzo9I GATC 4 cut(s) 144, 172, 599, 713
LmnI GCTCC 3 cut(s) 50, 81, 1055
Lsp1109I GCAGC 4 cut(s) 220, 1005, 1045, 1080
LweI GCATC 1 cut(s) 1106
MaeI CTAG 2 cut(s) 498, 717
MaeII ACGT 4 cut(s) 380, 522, 699, 1074
MaeIII GTNAC 4 cut(s) 367, 523, 700, 817
MalI GATC 4 cut(s) 146, 174, 601, 715
MbiI CCGCTC 1 cut(s) 53
MboI GATC 4 cut(s) 144, 172, 599, 713
MboII GAAGA 4 cut(s) 53, 681, 695, 1030
MfeI CAATTG 1 cut(s) 340
MflI RGATCY 4 cut(s) 144, 172, 599, 713
MhlI GDGCHC 1 cut(s) 339
MluCI AATT 6 cut(s) 98, 340, 409, 448, 516, 988
MlyI GAGTC 1 cut(s) 565
MmeI TCCRAC 2 cut(s) 69, 720
MseI TTAA 5 cut(s) 93, 462, 750, 918, 987
MslI CAYNNNNRTG 2 cut(s) 332, 551
MspA1I CMGCKG 1 cut(s) 427
MspI CCGG 1 cut(s) 761
MspR9I CCNGG 4 cut(s) 261, 639, 762, 1005
MunI CAATTG 1 cut(s) 340
Mva1269I GAATGC 1 cut(s) 887
MvaI CCWGG 3 cut(s) 261, 639, 1005
MvnI CGCG 1 cut(s) 116
MwoI GCNNNNNNNGC 6 cut(s) 120, 217, 362, 626, 639, 660
NciI CCSGG 1 cut(s) 762
NcoI CCATGG 1 cut(s) 643
NdeII GATC 4 cut(s) 144, 172, 599, 713
NlaIII CATG 7 cut(s) 306, 437, 647, 692, 736, 759, 1014
NlaIV GGNNCC 6 cut(s) 69, 174, 265, 336, 601, 730
NmuCI GTSAC 1 cut(s) 817
NspI RCATGY 2 cut(s) 437, 1014
OliI CACNNNNGTG 1 cut(s) 332
PauI GCGCGC 1 cut(s) 114
PctI GAATGC 1 cut(s) 887
PfeI GAWTC 1 cut(s) 648
PflMI CCANNNNNTGG 1 cut(s) 644
PfoI TCCNGGA 1 cut(s) 259
PkrI GCNGC 5 cut(s) 72, 210, 995, 1060, 1070
PleI GAGTC 1 cut(s) 564
PpsI GAGTC 1 cut(s) 564
PpuMI RGGWCCY 1 cut(s) 257
Psp5II RGGWCCY 1 cut(s) 257
Psp6I CCWGG 3 cut(s) 259, 637, 1003
PspGI CCWGG 3 cut(s) 259, 637, 1003
PspN4I GGNNCC 6 cut(s) 69, 174, 265, 336, 601, 730
PspPI GGNCC 2 cut(s) 257, 635
PspPPI RGGWCCY 1 cut(s) 257
PstI CTGCAG 1 cut(s) 903
PsuI RGATCY 4 cut(s) 144, 172, 599, 713
PteI GCGCGC 1 cut(s) 114
RsaI GTAC 2 cut(s) 215, 938
RsaNI GTAC 2 cut(s) 214, 937
RseI CAYNNNNRTG 2 cut(s) 332, 551
SaqAI TTAA 5 cut(s) 93, 462, 750, 918, 987
SatI GCNGC 5 cut(s) 71, 209, 994, 1059, 1069
Sau3AI GATC 4 cut(s) 144, 172, 599, 713
Sau96I GGNCC 2 cut(s) 257, 635
ScaI AGTACT 1 cut(s) 215
SchI GAGTC 1 cut(s) 565
ScrFI CCNGG 4 cut(s) 261, 639, 762, 1005
SduI GDGCHC 1 cut(s) 339
SfaNI GCATC 1 cut(s) 1106
SfcI CTRYAG 1 cut(s) 899
SinI GGWCC 2 cut(s) 257, 635
SmiMI CAYNNNNRTG 2 cut(s) 332, 551
SmlI CTYRAG 1 cut(s) 1043
SmoI CTYRAG 1 cut(s) 1043
Sse9I AATT 6 cut(s) 98, 340, 409, 448, 516, 988
SsiI CCGC 4 cut(s) 53, 71, 427, 633
SspMI CTAG 2 cut(s) 498, 717
StyD4I CCNGG 4 cut(s) 259, 637, 760, 1003
StyI CCWWGG 2 cut(s) 148, 643
TaaI ACNGT 3 cut(s) 397, 706, 958
TaiI ACGT 4 cut(s) 383, 525, 702, 1077
TaqI TCGA 3 cut(s) 543, 837, 1114
TasI AATT 6 cut(s) 98, 340, 409, 448, 516, 988
TatI WGTACW 1 cut(s) 213
TauI GCSGC 1 cut(s) 73
TfiI GAWTC 1 cut(s) 648
Tru1I TTAA 5 cut(s) 93, 462, 750, 918, 987
Tru9I TTAA 5 cut(s) 93, 462, 750, 918, 987
TscAI CASTG 4 cut(s) 514, 862, 903, 1003
TseFI GTSAC 1 cut(s) 817
TseI GCWGC 4 cut(s) 208, 993, 1058, 1068
Tsp45I GTSAC 1 cut(s) 817
TspGWI ACGGA 4 cut(s) 63, 294, 470, 891
TspRI CASTG 4 cut(s) 514, 862, 903, 1003
Van91I CCANNNNNTGG 1 cut(s) 644
VpaK11BI GGWCC 2 cut(s) 257, 635
XagI CCTNNNNNAGG 1 cut(s) 229
XapI RAATTY 2 cut(s) 409, 516
XceI RCATGY 2 cut(s) 437, 1014
XcmI CCANNNNNNNNNTGG 2 cut(s) 52, 947
XspI CTAG 2 cut(s) 498, 717
ZrmI AGTACT 1 cut(s) 215
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.