Rorug03G0032000

Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double- stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000003
OG0005415
Physical Location & Seq
Forward (+)
2526886 .. 2527887
1002 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug03G0032000.1

Sequence Viewer

Length: 1002 bp
ATGGATATTAGAAACACTTGCCTAGCTTGTGGTAGTGGAGCCTTTAGGGGAGTTCTGGTCTACTGTAGTAAGTGCAAGGAGTATGCACAGCATGGATATTGCCTTGGAGTGTCAATAGACGAGTATGTTCGTCGTGGGCGTATTTGGTACTGTGAAGATTGCCAAGAGGTGAAGCCAGCTGCCTCTTTTTCCACTCATGATCTCGATGAATGTGAATCCATGGATACCGGAGAAGTGCTGCAAAGCACTCCTCCTTCTGCTGGGACAAGTAGTACCCCTGATGGTACCAACAAGAAATTGAAGGCCAAGAACACCAAGAAGCTGAAAAAGAAGAGTCAGAAGAAGAAATCCAATCAATCTGGATTTGTGGTTAAAAGTGTATTAGAGACAATACTTGAAGGTAATGAAGAGGCTGAAGATGAGGGCGCCGAAATCAATTGTGATGATGGTCACAAGCTTGGTAATGATCAAGAAGGCAATGGTCTTCAAAAAGATCAATTTGATGCCTCCGATGACACTACAGAAATAGATGAAGATGGCGATTCTACTCATGTTGCTGCTCAACCGGTTGCTATTCCAACTTGGAGGGGAAGCCTAAACATATTGAACAAAGTTAACTACAAGAACTTGAGAAATGAAACTATTAGTGGACTTGCTGCTCATCTCTCAAGCATAGCCTGCGCTAAAGTGTTGGAGGAGTCGAAATTTCTGAAGACACAGCTTGTCCCAGATTTGGTTCGTAGGACGGATGTGTGGCCAAAAGGCTATGACATGTGTGAAACTAGTGATCGGAGTATTGCCCTTTATTTTTTCCCCGACAGCGAAACAGATGAGAAGGATTTCAACAACTTGATGGGTAGCATGATGCAGGAGGATCTCGCTATGAGAGTTGATGTCGAAAACGCTGAGCTTTTGGTTTTCACTTCAAGCATGTTACCCAAGAAATATCAAAGAGTTAAGTCAAAGATGTATCTATGGGGAGTTTTTAAGGAAAAGTATTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko03030 ko03410 ko03450 map03030 map03410 map03450
Pfam Domains
Protein Families
XPG_I XPG_N

Protein Analysis

333

Amino Acids

37.22

Weight (kDa)

5.14

Isoelectric Point (pI)

38.87

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PHD PF00628 7 - 54 3.5e-06 PHD-finger
SPOC_AIPP2 PF23121 195 - 329 2.7e-42 AIPP2, SPOC-like domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc65I GGTACC 1 cut(s) 284
AccB1I GGYRCC 2 cut(s) 284, 425
AccI GTMKAC 1 cut(s) 60
AclWI GGATC 1 cut(s) 882
AcoI YGGCCR 1 cut(s) 755
AcsI RAATTY 1 cut(s) 704
AcuI CTGAAG 2 cut(s) 435, 731
AcyI GRCGYC 1 cut(s) 426
AfaI GTAC 3 cut(s) 149, 274, 286
AfiI CCNNNNNNNGG 2 cut(s) 260, 733
AflIII ACRYGT 1 cut(s) 771
AgeI ACCGGT 1 cut(s) 565
AgsI TTSAA 6 cut(s) 301, 398, 488, 607, 844, 927
AhlI ACTAGT 1 cut(s) 782
AluBI AGCT 6 cut(s) 26, 179, 322, 457, 721, 910
AluI AGCT 6 cut(s) 26, 179, 322, 457, 721, 910
Alw26I GTCTC 1 cut(s) 380
AlwI GGATC 1 cut(s) 882
AoxI GGCC 2 cut(s) 303, 755
ApeKI GCWGC 4 cut(s) 179, 238, 557, 656
ApoI RAATTY 1 cut(s) 704
AsiGI ACCGGT 1 cut(s) 565
Asp700I GAANNNNTTC 1 cut(s) 839
Asp718I GGTACC 1 cut(s) 284
AspLEI GCGC 2 cut(s) 428, 683
AsuHPI GGTGA 1 cut(s) 181
BalI TGGCCA 1 cut(s) 757
BanI GGYRCC 2 cut(s) 284, 425
BbsI GAAGAC 2 cut(s) 476, 719
BbvI GCAGC 4 cut(s) 166, 225, 544, 643
BccI CCATC 4 cut(s) 275, 440, 530, 847
BciVI GTATCC 1 cut(s) 217
BclI TGATCA 1 cut(s) 466
BcoDI GTCTC 1 cut(s) 380
BcuI ACTAGT 1 cut(s) 782
BfaI CTAG 2 cut(s) 23, 783
BfmI CTRYAG 2 cut(s) 64, 519
BfoI RGCGCY 1 cut(s) 429
BfuI GTATCC 1 cut(s) 217
BisI GCNGC 4 cut(s) 180, 239, 558, 657
BlpI GCTNAGC 1 cut(s) 906
BlsI GCNGC 4 cut(s) 181, 240, 559, 658
BmiI GGNNCC 3 cut(s) 40, 286, 427
BmsI GCATC 2 cut(s) 493, 855
BpiI GAAGAC 2 cut(s) 476, 719
Bpu1102I GCTNAGC 1 cut(s) 906
BpuEI CTTGAG 2 cut(s) 649, 652
BsaHI GRCGYC 1 cut(s) 426
BsaJI CCNNGG 2 cut(s) 103, 219
BsaWI WCCGGW 2 cut(s) 227, 565
BsaXI ACNNNNNCTCC 2 cut(s) 42, 72
Bsc4I CCNNNNNNNGG 2 cut(s) 260, 733
Bse118I RCCGGY 1 cut(s) 565
Bse3DI GCAATG 1 cut(s) 484
BseDI CCNNGG 2 cut(s) 103, 219
BseGI GGATG 1 cut(s) 754
BseLI CCNNNNNNNGG 2 cut(s) 260, 733
BseMI GCAATG 1 cut(s) 484
BseMII CTCAG 1 cut(s) 897
BseRI GAGGAG 2 cut(s) 240, 710
BseXI GCAGC 4 cut(s) 166, 225, 544, 643
BseYI CCCAGC 1 cut(s) 260
BshFI GGCC 2 cut(s) 305, 757
BshNI GGYRCC 2 cut(s) 284, 425
BshTI ACCGGT 1 cut(s) 565
BsiSI CCGG 2 cut(s) 228, 566
BslFI GGGAC 2 cut(s) 277, 710
BslI CCNNNNNNNGG 2 cut(s) 260, 733
BsmAI GTCTC 1 cut(s) 380
BsmFI GGGAC 2 cut(s) 277, 710
BsnI GGCC 2 cut(s) 305, 757
Bsp143I GATC 5 cut(s) 199, 466, 493, 787, 874
Bsp1720I GCTNAGC 1 cut(s) 906
Bsp19I CCATGG 1 cut(s) 219
BspANI GGCC 2 cut(s) 305, 757
BspCNI CTCAG 1 cut(s) 898
BspHI TCATGA 1 cut(s) 196
BspLI GGNNCC 3 cut(s) 40, 286, 427
BspPI GGATC 1 cut(s) 882
BspT107I GGYRCC 2 cut(s) 284, 425
BsrDI GCAATG 1 cut(s) 484
BsrFI RCCGGY 1 cut(s) 565
BssAI RCCGGY 1 cut(s) 565
BssECI CCNNGG 2 cut(s) 103, 219
BssMI GATC 5 cut(s) 199, 466, 493, 787, 874
BssNI GRCGYC 1 cut(s) 426
BssT1I CCWWGG 2 cut(s) 103, 219
Bst4CI ACNGT 2 cut(s) 65, 152
Bst6I CTCTTC 2 cut(s) 326, 402
BstACI GRCGYC 1 cut(s) 426
BstAPI GCANNNNNTGC 1 cut(s) 678
BstC8I GCNNGC 2 cut(s) 177, 679
BstDEI CTNAG 1 cut(s) 906
BstDSI CCRYGG 1 cut(s) 219
BstF5I GGATG 1 cut(s) 754
BstH2I RGCGCY 1 cut(s) 429
BstHHI GCGC 2 cut(s) 428, 683
BstKTI GATC 5 cut(s) 202, 469, 496, 790, 877
BstMAI GTCTC 1 cut(s) 380
BstMBI GATC 5 cut(s) 199, 466, 493, 787, 874
BstMWI GCNNNNNNNGC 1 cut(s) 678
BstNSI RCATGY 2 cut(s) 775, 934
BstSFI CTRYAG 2 cut(s) 64, 519
BstV1I GCAGC 4 cut(s) 166, 225, 544, 643
BstV2I GAAGAC 2 cut(s) 476, 719
BstX2I RGATCY 1 cut(s) 874
BstYI RGATCY 1 cut(s) 874
BsuI GTATCC 1 cut(s) 217
BsuRI GGCC 2 cut(s) 305, 757
BtgI CCRYGG 1 cut(s) 219
BtsCI GGATG 1 cut(s) 754
Cac8I GCNNGC 2 cut(s) 177, 679
CciI TCATGA 1 cut(s) 196
CfoI GCGC 2 cut(s) 428, 683
Cfr10I RCCGGY 1 cut(s) 565
Csp6I GTAC 3 cut(s) 148, 273, 285
CspAI ACCGGT 1 cut(s) 565
CviAII CATG 7 cut(s) 92, 197, 220, 551, 772, 862, 931
CviQI GTAC 3 cut(s) 148, 273, 285
DdeI CTNAG 1 cut(s) 906
DinI GGCGCC 1 cut(s) 427
DpnI GATC 5 cut(s) 201, 468, 495, 789, 876
DpnII GATC 5 cut(s) 199, 466, 493, 787, 874
EaeI YGGCCR 1 cut(s) 755
Eam1104I CTCTTC 2 cut(s) 326, 402
EarI CTCTTC 2 cut(s) 326, 402
Eco130I CCWWGG 2 cut(s) 103, 219
Eco57I CTGAAG 2 cut(s) 435, 731
EcoT14I CCWWGG 2 cut(s) 103, 219
EgeI GGCGCC 1 cut(s) 427
EheI GGCGCC 1 cut(s) 427
ErhI CCWWGG 2 cut(s) 103, 219
FaeI CATG 7 cut(s) 95, 200, 223, 554, 775, 865, 934
FaqI GGGAC 2 cut(s) 277, 710
FatI CATG 7 cut(s) 91, 196, 219, 550, 771, 861, 930
FbaI TGATCA 1 cut(s) 466
FblI GTMKAC 1 cut(s) 60
Fnu4HI GCNGC 4 cut(s) 180, 239, 558, 657
FokI GGATG 1 cut(s) 761
Fsp4HI GCNGC 4 cut(s) 180, 239, 558, 657
FspBI CTAG 2 cut(s) 23, 783
GlaI GCGC 2 cut(s) 427, 682
GluI GCNGC 4 cut(s) 180, 239, 558, 657
GsaI CCCAGC 1 cut(s) 264
HaeII RGCGCY 1 cut(s) 429
HaeIII GGCC 2 cut(s) 305, 757
HapII CCGG 2 cut(s) 228, 566
HhaI GCGC 2 cut(s) 428, 683
Hin1I GRCGYC 1 cut(s) 426
Hin1II CATG 7 cut(s) 95, 200, 223, 554, 775, 865, 934
Hin6I GCGC 2 cut(s) 426, 681
HinP1I GCGC 2 cut(s) 426, 681
HincII GTYRAC 1 cut(s) 616
HindII GTYRAC 1 cut(s) 616
HindIII AAGCTT 1 cut(s) 455
HinfI GANTC 4 cut(s) 215, 334, 542, 698
HpaI GTTAAC 1 cut(s) 616
HpaII CCGG 2 cut(s) 228, 566
HphI GGTGA 1 cut(s) 181
Hpy166II GTNNAC 3 cut(s) 61, 616, 650
Hpy188I TCNGA 4 cut(s) 339, 511, 711, 792
Hpy188III TCNNGA 4 cut(s) 197, 203, 360, 470
Hpy8I GTNNAC 3 cut(s) 61, 616, 650
Hpy99I CGWCG 1 cut(s) 135
HpyAV CCTTC 5 cut(s) 264, 295, 392, 467, 829
HpyCH4III ACNGT 2 cut(s) 65, 152
HpyCH4V TGCA 4 cut(s) 75, 86, 241, 868
HpyF10VI GCNNNNNNNGC 1 cut(s) 678
HpyF3I CTNAG 1 cut(s) 906
Hsp92I GRCGYC 1 cut(s) 426
Hsp92II CATG 7 cut(s) 95, 200, 223, 554, 775, 865, 934
HspAI GCGC 2 cut(s) 426, 681
KasI GGCGCC 1 cut(s) 425
KpnI GGTACC 1 cut(s) 288
Ksp22I TGATCA 1 cut(s) 466
KspAI GTTAAC 1 cut(s) 616
Kzo9I GATC 5 cut(s) 199, 466, 493, 787, 874
LmnI GCTCC 1 cut(s) 38
Lsp1109I GCAGC 4 cut(s) 166, 225, 544, 643
LweI GCATC 2 cut(s) 493, 855
MaeI CTAG 2 cut(s) 23, 783
MaeIII GTNAC 2 cut(s) 449, 933
MalI GATC 5 cut(s) 201, 468, 495, 789, 876
MboI GATC 5 cut(s) 199, 466, 493, 787, 874
MboII GAAGA 9 cut(s) 167, 343, 352, 355, 419, 428, 476, 545, 724
MfeI CAATTG 1 cut(s) 436
MflI RGATCY 1 cut(s) 874
MlsI TGGCCA 1 cut(s) 757
MluCI AATT 4 cut(s) 296, 436, 497, 704
MluNI TGGCCA 1 cut(s) 757
Mly113I GGCGCC 1 cut(s) 426
MlyI GAGTC 2 cut(s) 343, 707
MmeI TCCRAC 2 cut(s) 602, 672
MnlI CCTC 9 cut(s) 160, 193, 261, 403, 415, 517, 579, 688, 865
Mox20I TGGCCA 1 cut(s) 757
MroXI GAANNNNTTC 1 cut(s) 839
MscI TGGCCA 1 cut(s) 757
MseI TTAA 5 cut(s) 372, 615, 957, 987, 1000
Msp20I TGGCCA 1 cut(s) 757
MspA1I CMGCKG 1 cut(s) 179
MspI CCGG 2 cut(s) 228, 566
MunI CAATTG 1 cut(s) 436
MwoI GCNNNNNNNGC 1 cut(s) 678
NarI GGCGCC 1 cut(s) 426
NcoI CCATGG 1 cut(s) 219
NdeII GATC 5 cut(s) 199, 466, 493, 787, 874
NlaIII CATG 7 cut(s) 95, 200, 223, 554, 775, 865, 934
NlaIV GGNNCC 3 cut(s) 40, 286, 427
NmuCI GTSAC 1 cut(s) 449
NspI RCATGY 2 cut(s) 775, 934
PagI TCATGA 1 cut(s) 196
PciI ACATGT 1 cut(s) 771
PcsI WCGNNNNNNNCGW 1 cut(s) 136
PdmI GAANNNNTTC 1 cut(s) 839
PfeI GAWTC 2 cut(s) 215, 542
PinAI ACCGGT 1 cut(s) 565
PkrI GCNGC 4 cut(s) 181, 240, 559, 658
PleI GAGTC 2 cut(s) 342, 706
PluTI GGCGCC 1 cut(s) 429
PpsI GAGTC 2 cut(s) 342, 706
PscI ACATGT 1 cut(s) 771
PspFI CCCAGC 1 cut(s) 260
PspN4I GGNNCC 3 cut(s) 40, 286, 427
PsuI RGATCY 1 cut(s) 874
PvuII CAGCTG 1 cut(s) 179
RsaI GTAC 3 cut(s) 149, 274, 286
RsaNI GTAC 3 cut(s) 148, 273, 285
SaqAI TTAA 5 cut(s) 372, 615, 957, 987, 1000
SatI GCNGC 4 cut(s) 180, 239, 558, 657
Sau3AI GATC 5 cut(s) 199, 466, 493, 787, 874
SchI GAGTC 2 cut(s) 343, 707
SetI ASST 8 cut(s) 28, 171, 181, 324, 403, 459, 723, 912
SfaNI GCATC 2 cut(s) 493, 855
SfcI CTRYAG 2 cut(s) 64, 519
SfoI GGCGCC 1 cut(s) 427
SmlI CTYRAG 2 cut(s) 628, 667
SmoI CTYRAG 2 cut(s) 628, 667
SpeI ACTAGT 1 cut(s) 782
Sse9I AATT 4 cut(s) 296, 436, 497, 704
SspDI GGCGCC 1 cut(s) 425
SspMI CTAG 2 cut(s) 23, 783
StyI CCWWGG 2 cut(s) 103, 219
TaaI ACNGT 2 cut(s) 65, 152
TaqI TCGA 3 cut(s) 204, 701, 897
TasI AATT 4 cut(s) 296, 436, 497, 704
TfiI GAWTC 2 cut(s) 215, 542
Tru1I TTAA 5 cut(s) 372, 615, 957, 987, 1000
Tru9I TTAA 5 cut(s) 372, 615, 957, 987, 1000
TseFI GTSAC 1 cut(s) 449
TseI GCWGC 4 cut(s) 179, 238, 557, 656
Tsp45I GTSAC 1 cut(s) 449
TspDTI ATGAA 4 cut(s) 222, 420, 546, 651
TspGWI ACGGA 1 cut(s) 761
XapI RAATTY 1 cut(s) 704
XceI RCATGY 2 cut(s) 775, 934
XmiI GTMKAC 1 cut(s) 60
XmnI GAANNNNTTC 1 cut(s) 839
XspI CTAG 2 cut(s) 23, 783
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.