Rorug03G0031900

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
Reverse (-)
2522210 .. 2525207
2998 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug03G0031900.1

Sequence Viewer

Length: 534 bp
ATGTCTGCGGAATCAGCCAGCGCAATTCAGAGAAGCCAAGTTGATCTGATGGACTTCATAGATTGGTCTGGGGTTGAATGCCTCAACCAAAGCACCAGTCACTCTGTTGCTAACGCTCTTAAGCAGGGATACAGAGACGATGATGGTTTGAATCTAGAGAGTGATGCGGATGAGCAGCTTCTGATCTACATTCCTTTTCTTCAAGTCATTAAGCTGCACTCTATTGTCATCAAAGGACCTGAAGAGGAAGGTCCCAAGACAGTGAAGCTTTTTTCAAACAAGGAGCACATGGGTTTCAGCAATGTCAATGACTACCCGGCAAGTGACACAGTTGTTTTATCGCCTGATCATCTAAAGGGAAAACCAGTTGTTTTGAAGTATGTCAAATTTCAAAATGTTCGCAGCTTGACAATTTTCATTGAGGATAATCAGTCTGACTCAGAAATCACAAAAGTTCAAAAGATTGGCCTGGTTGGAACAACGGTGGAAACAACTGACATGAAGGGTTTGAAGAAGATTGAGGATGGACACTGA
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

177

Amino Acids

19.64

Weight (kDa)

4.97

Isoelectric Point (pI)

40.17

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PITH PF06201 8 - 173 4.5e-54 PITH domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 2 cut(s) 8, 167
AcsI RAATTY 1 cut(s) 386
AcuI CTGAAG 1 cut(s) 261
AflII CTTAAG 1 cut(s) 119
AgsI TTSAA 8 cut(s) 77, 151, 203, 276, 376, 392, 458, 511
AjnI CCWGG 1 cut(s) 468
AluBI AGCT 4 cut(s) 178, 214, 268, 405
AluI AGCT 4 cut(s) 178, 214, 268, 405
Alw21I GWGCWC 1 cut(s) 288
Alw26I GTCTC 1 cut(s) 129
AlwNI CAGNNNCTG 1 cut(s) 181
AoxI GGCC 1 cut(s) 466
ApeKI GCWGC 3 cut(s) 175, 214, 402
ApoI RAATTY 1 cut(s) 386
ArsI GACNNNNNNTTYG 2 cut(s) 82, 114
AspLEI GCGC 1 cut(s) 23
AspS9I GGNCC 2 cut(s) 236, 251
AsuC2I CCSGG 1 cut(s) 317
AvaII GGWCC 2 cut(s) 236, 251
Bbv12I GWGCWC 1 cut(s) 288
BbvI GCAGC 3 cut(s) 187, 201, 414
BccI CCATC 3 cut(s) 43, 137, 518
BciT130I CCWGG 1 cut(s) 470
BciVI GTATCC 1 cut(s) 122
BclI TGATCA 1 cut(s) 346
BcnI CCSGG 1 cut(s) 317
BcoDI GTCTC 1 cut(s) 129
BfaI CTAG 1 cut(s) 155
BfrI CTTAAG 1 cut(s) 119
BfuI GTATCC 1 cut(s) 122
BisI GCNGC 3 cut(s) 176, 215, 403
BlsI GCNGC 3 cut(s) 177, 216, 404
Bme1390I CCNGG 2 cut(s) 317, 470
Bme18I GGWCC 2 cut(s) 236, 251
BmgT120I GGNCC 2 cut(s) 236, 251
BmiI GGNNCC 1 cut(s) 253
BmrFI CCNGG 2 cut(s) 317, 470
BmsI GCATC 1 cut(s) 154
BpuMI CCSGG 1 cut(s) 317
Bse1I ACTGG 2 cut(s) 96, 365
Bse3DI GCAATG 1 cut(s) 307
BseBI CCWGG 1 cut(s) 470
BseGI GGATG 2 cut(s) 175, 529
BseMI GCAATG 1 cut(s) 307
BseMII CTCAG 1 cut(s) 453
BseNI ACTGG 2 cut(s) 96, 365
BseXI GCAGC 3 cut(s) 187, 201, 414
BsgI GTGCAG 1 cut(s) 200
BshFI GGCC 1 cut(s) 468
BsiHKAI GWGCWC 1 cut(s) 288
BsiSI CCGG 1 cut(s) 317
BslFI GGGAC 1 cut(s) 237
BsmAI GTCTC 1 cut(s) 129
BsmBI CGTCTC 1 cut(s) 129
BsmFI GGGAC 1 cut(s) 237
BsmI GAATGC 1 cut(s) 83
BsnI GGCC 1 cut(s) 468
Bsp1286I GDGCHC 1 cut(s) 288
Bsp143I GATC 3 cut(s) 43, 183, 346
BspACI CCGC 2 cut(s) 8, 167
BspANI GGCC 1 cut(s) 468
BspCNI CTCAG 1 cut(s) 452
BspLI GGNNCC 1 cut(s) 253
BspTI CTTAAG 1 cut(s) 119
BsrDI GCAATG 1 cut(s) 307
BsrI ACTGG 2 cut(s) 96, 365
BssMI GATC 3 cut(s) 43, 183, 346
Bst2UI CCWGG 1 cut(s) 470
Bst4CI ACNGT 3 cut(s) 262, 331, 484
Bst6I CTCTTC 1 cut(s) 237
BstAFI CTTAAG 1 cut(s) 119
BstC8I GCNNGC 1 cut(s) 19
BstDEI CTNAG 1 cut(s) 439
BstF5I GGATG 2 cut(s) 175, 529
BstHHI GCGC 1 cut(s) 23
BstKTI GATC 3 cut(s) 46, 186, 349
BstMAI GTCTC 1 cut(s) 129
BstMBI GATC 3 cut(s) 43, 183, 346
BstMWI GCNNNNNNNGC 1 cut(s) 14
BstNI CCWGG 1 cut(s) 470
BstSCI CCNGG 2 cut(s) 315, 468
BstV1I GCAGC 3 cut(s) 187, 201, 414
BsuI GTATCC 1 cut(s) 122
BsuRI GGCC 1 cut(s) 468
BtsCI GGATG 2 cut(s) 175, 529
BtsIMutI CAGTG 2 cut(s) 267, 529
Cac8I GCNNGC 1 cut(s) 19
CaiI CAGNNNCTG 1 cut(s) 181
CfoI GCGC 1 cut(s) 23
Cfr13I GGNCC 2 cut(s) 236, 251
CviAII CATG 2 cut(s) 289, 499
CviJI RGCY 7 cut(s) 17, 36, 178, 214, 268, 405, 468
CviKI_1 RGCY 7 cut(s) 17, 36, 178, 214, 268, 405, 468
DdeI CTNAG 1 cut(s) 439
DpnI GATC 3 cut(s) 45, 185, 348
DpnII GATC 3 cut(s) 43, 183, 346
Eam1104I CTCTTC 1 cut(s) 237
EarI CTCTTC 1 cut(s) 237
Eco47I GGWCC 2 cut(s) 236, 251
Eco57I CTGAAG 1 cut(s) 261
EcoO109I RGGNCCY 2 cut(s) 236, 251
EcoRII CCWGG 1 cut(s) 468
Esp3I CGTCTC 1 cut(s) 129
FaeI CATG 2 cut(s) 292, 502
FaiI YATR 4 cut(s) 59, 290, 381, 500
FaqI GGGAC 1 cut(s) 237
FatI CATG 2 cut(s) 288, 498
FbaI TGATCA 1 cut(s) 346
Fnu4HI GCNGC 3 cut(s) 176, 215, 403
FokI GGATG 1 cut(s) 182
Fsp4HI GCNGC 3 cut(s) 176, 215, 403
FspBI CTAG 1 cut(s) 155
GlaI GCGC 1 cut(s) 22
GluI GCNGC 3 cut(s) 176, 215, 403
HaeIII GGCC 1 cut(s) 468
HapII CCGG 1 cut(s) 317
HhaI GCGC 1 cut(s) 23
Hin1II CATG 2 cut(s) 292, 502
Hin6I GCGC 1 cut(s) 21
HinP1I GCGC 1 cut(s) 21
HindIII AAGCTT 1 cut(s) 266
HinfI GANTC 3 cut(s) 11, 151, 437
HpaII CCGG 1 cut(s) 317
Hpy188I TCNGA 5 cut(s) 30, 48, 183, 436, 442
Hpy188III TCNNGA 1 cut(s) 155
HpyAV CCTTC 2 cut(s) 242, 496
HpyCH4III ACNGT 3 cut(s) 262, 331, 484
HpyCH4V TGCA 1 cut(s) 217
HpyF10VI GCNNNNNNNGC 1 cut(s) 14
HpyF3I CTNAG 1 cut(s) 439
Hsp92II CATG 2 cut(s) 292, 502
HspAI GCGC 1 cut(s) 21
Ksp22I TGATCA 1 cut(s) 346
Kzo9I GATC 3 cut(s) 43, 183, 346
LmnI GCTCC 1 cut(s) 283
Lsp1109I GCAGC 3 cut(s) 187, 201, 414
LweI GCATC 1 cut(s) 154
MaeI CTAG 1 cut(s) 155
MaeIII GTNAC 2 cut(s) 98, 323
MalI GATC 3 cut(s) 45, 185, 348
MboI GATC 3 cut(s) 43, 183, 346
MboII GAAGA 4 cut(s) 191, 254, 523, 526
MhlI GDGCHC 1 cut(s) 288
MluCI AATT 3 cut(s) 24, 386, 411
MlyI GAGTC 1 cut(s) 431
MmeI TCCRAC 1 cut(s) 454
MnlI CCTC 4 cut(s) 92, 238, 415, 514
MseI TTAA 2 cut(s) 120, 210
MspCI CTTAAG 1 cut(s) 119
MspI CCGG 1 cut(s) 317
MspR9I CCNGG 2 cut(s) 317, 470
Mva1269I GAATGC 1 cut(s) 83
MvaI CCWGG 1 cut(s) 470
MwoI GCNNNNNNNGC 1 cut(s) 14
NciI CCSGG 1 cut(s) 317
NdeII GATC 3 cut(s) 43, 183, 346
NlaIII CATG 2 cut(s) 292, 502
NlaIV GGNNCC 1 cut(s) 253
NmuCI GTSAC 2 cut(s) 98, 323
PctI GAATGC 1 cut(s) 83
PfeI GAWTC 2 cut(s) 11, 151
PkrI GCNGC 3 cut(s) 177, 216, 404
PleI GAGTC 1 cut(s) 431
PpsI GAGTC 1 cut(s) 431
PpuMI RGGWCCY 2 cut(s) 236, 251
Psp5II RGGWCCY 2 cut(s) 236, 251
Psp6I CCWGG 1 cut(s) 468
PspGI CCWGG 1 cut(s) 468
PspN4I GGNNCC 1 cut(s) 253
PspPI GGNCC 2 cut(s) 236, 251
PspPPI RGGWCCY 2 cut(s) 236, 251
PstNI CAGNNNCTG 1 cut(s) 181
SaqAI TTAA 2 cut(s) 120, 210
SatI GCNGC 3 cut(s) 176, 215, 403
Sau3AI GATC 3 cut(s) 43, 183, 346
Sau96I GGNCC 2 cut(s) 236, 251
SchI GAGTC 1 cut(s) 431
ScrFI CCNGG 2 cut(s) 317, 470
SduI GDGCHC 1 cut(s) 288
SetI ASST 6 cut(s) 180, 216, 241, 253, 270, 407
SfaNI GCATC 1 cut(s) 154
SinI GGWCC 2 cut(s) 236, 251
SmlI CTYRAG 1 cut(s) 119
SmoI CTYRAG 1 cut(s) 119
Sse9I AATT 3 cut(s) 24, 386, 411
SsiI CCGC 2 cut(s) 8, 167
SspMI CTAG 1 cut(s) 155
StyD4I CCNGG 2 cut(s) 315, 468
TaaI ACNGT 3 cut(s) 262, 331, 484
TasI AATT 3 cut(s) 24, 386, 411
TfiI GAWTC 2 cut(s) 11, 151
Tru1I TTAA 2 cut(s) 120, 210
Tru9I TTAA 2 cut(s) 120, 210
TscAI CASTG 1 cut(s) 267
TseFI GTSAC 2 cut(s) 98, 323
TseI GCWGC 3 cut(s) 175, 214, 402
Tsp45I GTSAC 2 cut(s) 98, 323
TspDTI ATGAA 3 cut(s) 46, 406, 515
TspRI CASTG 1 cut(s) 267
Vha464I CTTAAG 1 cut(s) 119
VpaK11BI GGWCC 2 cut(s) 236, 251
XapI RAATTY 1 cut(s) 386
XbaI TCTAGA 1 cut(s) 154
XspI CTAG 1 cut(s) 155
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.