Rh5BG152400

Polygalacturonase QRT3

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5B
OG0016157
Physical Location & Seq
Reverse (-)
15571802 .. 15572881
1080 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5BG152400.1

Sequence Viewer

Length: 1080 bp
ATGAACATATATGATCATAACAAACAGATACAAGGAGGAACGCTGCGAGCCTCTGAAACATTTCCCGGTGACCGCCACCTAGTCGAATTATGGTCTGCAAATTCTCAAAAGCTTGGGGAAAAAACCTCCATCACCAATCAATTCTTCTTTGATAAAAAAGTCGAAGGCGGTGTAGGAATCTACTACGAAGACATCACCTTTAGAGATATACTATTCGATTCAAGCTTCAGAGGAGGAGGCATTTTCATAGTCGATTCAGCTCGAGTTCGCATAACCAATTGCTTCTTCCTACACTTCACAACACAAGGGATTCTAGTCGAAAAGGGCCACGAAACCTACATATCAAACACCTTCTTGGGACAACACTCCACAGTTGGTGGCGACAAAGGTGAGAGGGGATTTACCGGCACAGCCATCGATCTTGCTAGCAATGACAATGCCGTAACTGATGTCGTAATATTTTCAGCTGAAATTGGGATTGTGTTAAGGGGTCAGGCTAACATGGTCACAGGGGTACATTGTTATAACAAGGCAACTGGCTTTGGGGGTATAGGTATTTTGGTAAAGTTAGCAGGAAACTCACAAACTAGAATTGACAATTGCTACTTGGATTTCAATGCTATTGTCATGGAAGACCCAGTTCAAGTTCATGTGACCAATGGGTTCTTTTTGGGTGATGCTAATGTGGTGTTGAAATCTGTCAATGGCAAGATTCTAGGGTTAAATATTGTGAACAATATGTTCACTGGGAACCCTAGAAGTACTGTTCCCATGGTTCAATTAGATGGGCAATTTGGGGACATTGATCAAGTGGTGATTGACCAGAACAATGTGATTGGGATGAGCTTGAAATCAACGGTAGGGAGACTAAGTGTGGAGGGGAATGGCACCAAATGGGTGGCTGATTTTTCTTCCCAGTTGGTCTTTCCCAACCGGATTAATCATTTTCAGTATTCTTTACATACAAAAGGGGAAACCAAGTTTACTACACATGCTGTGACAAATGTATCGAACAATGTGGTGGTTGTGGAGAGTCAAAATGAGGTAGATGGTGTGGTTTCTCTAGTTGTTCACCAGTAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
Beta_helix

Protein Analysis

359

Amino Acids

39.21

Weight (kDa)

5.74

Isoelectric Point (pI)

16.95

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this protein.
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: OG0016157)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G20040
fragaria_vesca FvH4_3g12830
malus_domestica MD05G1247600.v1.1
prunus_persica Prupe.4G116400_v2.0.a1
pyrus_communis pycom05g22370
rosa_chinensis RchiOBHm_Chr5g0020771
rosa_laevigata RLG00000032561
rosa_multiflora Rmu_sc0002527.1_g000005
rosa_roxburghii Rroxscaffold_1G00057530
rosa_rugosa Rorug05G0062800
rosa_samantha Rh5AG152700 Rh5BG152400 Rh5CG164000 Rh5DG151900
rosa_wichuraiana Rw5G013540

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 525
AccB1I GGYRCC 1 cut(s) 887
AciI CCGC 2 cut(s) 73, 168
AcsI RAATTY 1 cut(s) 100
AcuI CTGAAG 1 cut(s) 211
AfaI GTAC 2 cut(s) 516, 763
AgsI TTSAA 6 cut(s) 222, 616, 644, 694, 779, 850
AjuI GAANNNNNNNTTGG 4 cut(s) 128, 160, 269, 301
AluBI AGCT 5 cut(s) 112, 225, 260, 467, 846
AluI AGCT 5 cut(s) 112, 225, 260, 467, 846
Alw26I GTCTC 1 cut(s) 859
Ama87I CYCGRG 1 cut(s) 261
AoxI GGCC 1 cut(s) 325
ApeKI GCWGC 1 cut(s) 43
ApoI RAATTY 1 cut(s) 100
AseI ATTAAT 1 cut(s) 939
Asp700I GAANNNNTTC 1 cut(s) 60
AspS9I GGNCC 1 cut(s) 325
AsuC2I CCSGG 1 cut(s) 66
AsuHPI GGTGA 7 cut(s) 80, 124, 187, 401, 686, 826, 1064
AsuNHI GCTAGC 1 cut(s) 425
AvaI CYCGRG 1 cut(s) 261
BaeI ACNNNNGTAYC 2 cut(s) 990, 1023
BanI GGYRCC 1 cut(s) 887
BbsI GAAGAC 2 cut(s) 195, 639
BbvI GCAGC 1 cut(s) 30
BccI CCATC 4 cut(s) 137, 422, 779, 1043
BceAI ACGGC 1 cut(s) 425
BcgI CGANNNNNNTGC 2 cut(s) 397, 431
BclI TGATCA 2 cut(s) 13, 805
BcnI CCSGG 1 cut(s) 66
BcoDI GTCTC 1 cut(s) 859
BfaI CTAG 7 cut(s) 80, 314, 426, 588, 716, 756, 1064
BisI GCNGC 1 cut(s) 44
BlsI GCNGC 1 cut(s) 45
BmcAI AGTACT 1 cut(s) 763
Bme1390I CCNGG 1 cut(s) 66
BmeT110I CYCGRG 1 cut(s) 261
BmgT120I GGNCC 1 cut(s) 325
BmiI GGNNCC 2 cut(s) 752, 889
BmrFI CCNGG 1 cut(s) 66
BmrI ACTGGG 3 cut(s) 632, 756, 910
BmsI GCATC 1 cut(s) 667
BmtI GCTAGC 1 cut(s) 429
BmuI ACTGGG 3 cut(s) 632, 756, 910
BpiI GAAGAC 2 cut(s) 195, 639
BpuMI CCSGG 1 cut(s) 66
Bsa29I ATCGAT 1 cut(s) 417
BsaJI CCNNGG 1 cut(s) 771
BsaWI WCCGGW 1 cut(s) 933
BsaXI ACNNNNNCTCC 2 cut(s) 856, 886
Bse118I RCCGGY 1 cut(s) 404
Bse1I ACTGG 5 cut(s) 541, 638, 751, 916, 1075
Bse3DI GCAATG 1 cut(s) 436
BseCI ATCGAT 1 cut(s) 417
BseDI CCNNGG 1 cut(s) 771
BseGI GGATG 1 cut(s) 846
BseMI GCAATG 1 cut(s) 436
BseNI ACTGG 5 cut(s) 541, 638, 751, 916, 1075
BseRI GAGGAG 2 cut(s) 246, 249
BseXI GCAGC 1 cut(s) 30
BshFI GGCC 1 cut(s) 327
BshNI GGYRCC 1 cut(s) 887
BshVI ATCGAT 1 cut(s) 417
BsiHKCI CYCGRG 1 cut(s) 261
BsiSI CCGG 3 cut(s) 66, 405, 934
BslFI GGGAC 2 cut(s) 372, 812
BsmAI GTCTC 1 cut(s) 859
BsmFI GGGAC 2 cut(s) 372, 812
BsnI GGCC 1 cut(s) 327
BsoBI CYCGRG 1 cut(s) 261
Bsp143I GATC 3 cut(s) 13, 418, 805
Bsp19I CCATGG 1 cut(s) 771
BspACI CCGC 2 cut(s) 73, 168
BspANI GGCC 1 cut(s) 327
BspDI ATCGAT 1 cut(s) 417
BspLI GGNNCC 2 cut(s) 752, 889
BspOI GCTAGC 1 cut(s) 429
BspT107I GGYRCC 1 cut(s) 887
BsrDI GCAATG 1 cut(s) 436
BsrFI RCCGGY 1 cut(s) 404
BsrI ACTGG 5 cut(s) 541, 638, 751, 916, 1075
BssAI RCCGGY 1 cut(s) 404
BssECI CCNNGG 1 cut(s) 771
BssMI GATC 3 cut(s) 13, 418, 805
BssT1I CCWWGG 1 cut(s) 771
Bst4CI ACNGT 3 cut(s) 373, 766, 859
BstC8I GCNNGC 2 cut(s) 48, 427
BstDEI CTNAG 1 cut(s) 869
BstDSI CCRYGG 1 cut(s) 771
BstEII GGTNACC 1 cut(s) 68
BstF5I GGATG 1 cut(s) 846
BstKTI GATC 3 cut(s) 16, 421, 808
BstMAI GTCTC 1 cut(s) 859
BstMBI GATC 3 cut(s) 13, 418, 805
BstNSI RCATGY 1 cut(s) 995
BstPI GGTNACC 1 cut(s) 68
BstSCI CCNGG 1 cut(s) 64
BstV1I GCAGC 1 cut(s) 30
BstV2I GAAGAC 2 cut(s) 195, 639
BstXI CCANNNNNNTGG 1 cut(s) 898
Bsu15I ATCGAT 1 cut(s) 417
BsuRI GGCC 1 cut(s) 327
BsuTUI ATCGAT 1 cut(s) 417
BtgI CCRYGG 1 cut(s) 771
BtsCI GGATG 1 cut(s) 846
BtsIMutI CAGTG 1 cut(s) 744
Cac8I GCNNGC 2 cut(s) 48, 427
Cfr10I RCCGGY 1 cut(s) 404
Cfr13I GGNCC 1 cut(s) 325
ClaI ATCGAT 1 cut(s) 417
Csp6I GTAC 2 cut(s) 515, 762
CviAII CATG 5 cut(s) 502, 628, 650, 772, 992
CviQI GTAC 2 cut(s) 515, 762
DdeI CTNAG 1 cut(s) 869
DpnI GATC 3 cut(s) 15, 420, 807
DpnII GATC 3 cut(s) 13, 418, 805
Eco130I CCWWGG 1 cut(s) 771
Eco57I CTGAAG 1 cut(s) 211
Eco88I CYCGRG 1 cut(s) 261
Eco91I GGTNACC 1 cut(s) 68
EcoO65I GGTNACC 1 cut(s) 68
EcoT14I CCWWGG 1 cut(s) 771
ErhI CCWWGG 1 cut(s) 771
FaeI CATG 5 cut(s) 505, 631, 653, 775, 995
FaqI GGGAC 2 cut(s) 372, 812
FatI CATG 5 cut(s) 501, 627, 649, 771, 991
FbaI TGATCA 2 cut(s) 13, 805
Fnu4HI GCNGC 1 cut(s) 44
FokI GGATG 1 cut(s) 853
Fsp4HI GCNGC 1 cut(s) 44
FspBI CTAG 7 cut(s) 80, 314, 426, 588, 716, 756, 1064
GluI GCNGC 1 cut(s) 44
HaeIII GGCC 1 cut(s) 327
HapII CCGG 3 cut(s) 66, 405, 934
Hin1II CATG 5 cut(s) 505, 631, 653, 775, 995
HindIII AAGCTT 2 cut(s) 110, 223
HinfI GANTC 6 cut(s) 177, 218, 254, 310, 712, 1033
HpaII CCGG 3 cut(s) 66, 405, 934
HphI GGTGA 7 cut(s) 80, 124, 187, 401, 686, 826, 1064
Hpy166II GTNNAC 4 cut(s) 733, 744, 984, 1072
Hpy188I TCNGA 2 cut(s) 55, 230
Hpy8I GTNNAC 4 cut(s) 733, 744, 984, 1072
HpyAV CCTTC 2 cut(s) 158, 361
HpyCH4III ACNGT 3 cut(s) 373, 766, 859
HpyCH4V TGCA 1 cut(s) 98
HpyF3I CTNAG 1 cut(s) 869
Hsp92II CATG 5 cut(s) 505, 631, 653, 775, 995
Ksp22I TGATCA 2 cut(s) 13, 805
Kzo9I GATC 3 cut(s) 13, 418, 805
Lsp1109I GCAGC 1 cut(s) 30
LweI GCATC 1 cut(s) 667
MaeI CTAG 7 cut(s) 80, 314, 426, 588, 716, 756, 1064
MaeIII GTNAC 5 cut(s) 68, 442, 505, 652, 997
MalI GATC 3 cut(s) 15, 420, 807
MboI GATC 3 cut(s) 13, 418, 805
MboII GAAGA 5 cut(s) 136, 200, 277, 644, 903
MfeI CAATTG 2 cut(s) 277, 598
MluCI AATT 9 cut(s) 86, 100, 140, 277, 471, 591, 598, 779, 791
MlyI GAGTC 1 cut(s) 1042
MnlI CCTC 9 cut(s) 29, 61, 136, 224, 227, 230, 387, 871, 1036
MroXI GAANNNNTTC 1 cut(s) 60
MseI TTAA 3 cut(s) 485, 722, 939
MspA1I CMGCKG 1 cut(s) 467
MspI CCGG 3 cut(s) 66, 405, 934
MspR9I CCNGG 1 cut(s) 66
MunI CAATTG 2 cut(s) 277, 598
NciI CCSGG 1 cut(s) 66
NcoI CCATGG 1 cut(s) 771
NdeII GATC 3 cut(s) 13, 418, 805
NheI GCTAGC 1 cut(s) 425
NlaIII CATG 5 cut(s) 505, 631, 653, 775, 995
NlaIV GGNNCC 2 cut(s) 752, 889
NmuCI GTSAC 4 cut(s) 68, 505, 652, 997
NspI RCATGY 1 cut(s) 995
PaeR7I CTCGAG 1 cut(s) 261
PdmI GAANNNNTTC 1 cut(s) 60
PfeI GAWTC 5 cut(s) 177, 218, 254, 310, 712
PkrI GCNGC 1 cut(s) 45
PleI GAGTC 1 cut(s) 1041
PpsI GAGTC 1 cut(s) 1041
PshBI ATTAAT 1 cut(s) 939
PsiI TTATAA 1 cut(s) 525
PspEI GGTNACC 1 cut(s) 68
PspN4I GGNNCC 2 cut(s) 752, 889
PspPI GGNCC 1 cut(s) 325
PspXI VCTCGAGB 1 cut(s) 261
PvuII CAGCTG 1 cut(s) 467
RsaI GTAC 2 cut(s) 516, 763
RsaNI GTAC 2 cut(s) 515, 762
SaqAI TTAA 3 cut(s) 485, 722, 939
SatI GCNGC 1 cut(s) 44
Sau3AI GATC 3 cut(s) 13, 418, 805
Sau96I GGNCC 1 cut(s) 325
ScaI AGTACT 1 cut(s) 763
SchI GAGTC 1 cut(s) 1042
ScrFI CCNGG 1 cut(s) 66
SfaNI GCATC 1 cut(s) 667
Sfr274I CTCGAG 1 cut(s) 261
SlaI CTCGAG 1 cut(s) 261
SmlI CTYRAG 1 cut(s) 261
SmoI CTYRAG 1 cut(s) 261
Sse9I AATT 9 cut(s) 86, 100, 140, 277, 471, 591, 598, 779, 791
SsiI CCGC 2 cut(s) 73, 168
SspI AATATT 2 cut(s) 459, 727
SspMI CTAG 7 cut(s) 80, 314, 426, 588, 716, 756, 1064
StyD4I CCNGG 1 cut(s) 64
StyI CCWWGG 1 cut(s) 771
TaaI ACNGT 3 cut(s) 373, 766, 859
TaqI TCGA 8 cut(s) 84, 162, 216, 252, 262, 318, 417, 1010
TasI AATT 9 cut(s) 86, 100, 140, 277, 471, 591, 598, 779, 791
TatI WGTACW 1 cut(s) 761
TfiI GAWTC 5 cut(s) 177, 218, 254, 310, 712
Tru1I TTAA 3 cut(s) 485, 722, 939
Tru9I TTAA 3 cut(s) 485, 722, 939
TscAI CASTG 1 cut(s) 751
TseFI GTSAC 4 cut(s) 68, 505, 652, 997
TseI GCWGC 1 cut(s) 43
Tsp45I GTSAC 4 cut(s) 68, 505, 652, 997
TspDTI ATGAA 3 cut(s) 17, 235, 638
TspRI CASTG 1 cut(s) 751
VspI ATTAAT 1 cut(s) 939
XapI RAATTY 1 cut(s) 100
XceI RCATGY 1 cut(s) 995
XhoI CTCGAG 1 cut(s) 261
XmnI GAANNNNTTC 1 cut(s) 60
XspI CTAG 7 cut(s) 80, 314, 426, 588, 716, 756, 1064
ZrmI AGTACT 1 cut(s) 763
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.