Rorug06G0451200

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
GWHBQTZ00000006
OG0015406
Physical Location & Seq
Forward (+)
58057107 .. 58059304
2198 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug06G0451200.1

Sequence Viewer

Length: 1020 bp
ATGAAATCATTGCAAACGACCTTTGTGATTTTCAGCTTCTTCTACTCTCTGGATGTTCTTGTGCTTTCTTCCCGTACAATTTCCTCCGATCCTTGTGATCCTACAGCTCAGCAGGACCCAAGAACTCTCCGCGCGGACCAACTAACAGTCCTCATCAATGGCTACTCTGAGTCACGCATCCCTCTCCTCCAATCCATTGTCACCACATATGCAGCCTCTTCTCTGGTGTCATCAATTCTTGTACTTTGGGGAAACCCTTCAACCCCATCCCAAACCTTGGCCCAACTTGCCCACAATCTCACACATTCCTCGTTTGGCTTTAATAGCATCTCCTTAATCCGCCAATCATCAAACAGTCTCAATAACCGGTTCCTCCCCAGACCCTCAATTAAGACCCGAGCTGTGTTGGTGTGTGATGATGACGTTGAAGTTGATTCCAAATCCTTTGAATTTGCATTTAAAATGTGGGGATCGAATCCTGATCGTCTCATTGGGTTCTTTGTCAGATCACATGACATAGACTTATCGAAGAAAGAGTGGATTTATACTATGCATCCAGACAAGTACTCAATCATGCTCACTAAGTTTATGATTTTGAAAAGTAAGTATTTGTTTCAGTACAGCTGTGCAAGAGGGCCTGTGATGGCCAACATGAGGAAGATTGTGGATAAGATGCATAATTGCGAGGACATATTAATGAATTTTGTGGTCGCGGATGAGGTAAATGCAGGACCTATATTGGTGGGTGCCAAGAGGGCCAGGGATTGGGGGGATGCACGCAATGATCATGATCATATGGATGGTCAAGGACGGCGAGGATTGATTGGGGAGGTTGCTCAGGTGGGTTTGAGTAGTAGGAAAGAGAAGCATAGGAAGAGAAGAGGGGAGTGTATAGGTGAGTTTCATAGGGTCTTGGGGAGAATGCCTCTGAGGTATAGTTATGGGAAGGTTGTCGATTCTGTTGGTGAACAAGGGCTGTGTCAAAAAGGAGGGAAATTGGTGCTTTGTGATCAATCATAG
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

339

Amino Acids

38.17

Weight (kDa)

9.19

Isoelectric Point (pI)

41.79

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Glyco_transf_64 PF09258 48 - 321 2.4e-75 Glycosyl transferase family 64 domain
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: OG0015406)

Species Orthologous Gene IDs
arabidopsis_thaliana AT5G07990
fragaria_vesca FvH4_5g14010
malus_domestica MD06G1201700.v1.1 MD14G1210700.v1.1
prunus_persica Prupe.5G203600_v2.0.a1
pyrus_communis pycom06g17760 pycom14g17410
rosa_chinensis RchiOBHm_Chr7g0182961
rosa_laevigata RLG00000005095
rosa_multiflora Rmu_sc0000014.1_g000019
rosa_roxburghii Rroxscaffold_3G00270940
rosa_rugosa Rorug06G0451200
rosa_samantha Rh7AG054400 Rh7BG054000 Rh7CG055500
rosa_wichuraiana Rw7G004440

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 746
AccB7I CCANNNNNTGG 2 cut(s) 277, 765
AccII CGCG 3 cut(s) 132, 134, 713
AciI CCGC 4 cut(s) 130, 134, 340, 713
AclWI GGATC 3 cut(s) 83, 92, 478
AcoI YGGCCR 1 cut(s) 645
AcsI RAATTY 2 cut(s) 449, 700
AfaI GTAC 4 cut(s) 76, 243, 566, 620
AfiI CCNNNNNNNGG 3 cut(s) 277, 654, 765
AgeI ACCGGT 1 cut(s) 366
AgsI TTSAA 4 cut(s) 261, 428, 449, 598
AjnI CCWGG 1 cut(s) 758
AluBI AGCT 4 cut(s) 36, 107, 401, 624
AluI AGCT 4 cut(s) 36, 107, 401, 624
Alw26I GTCTC 2 cut(s) 362, 491
AlwI GGATC 3 cut(s) 83, 92, 478
Ama87I CYCGRG 1 cut(s) 396
AoxI GGCC 4 cut(s) 279, 635, 645, 756
ApeKI GCWGC 1 cut(s) 212
ApoI RAATTY 2 cut(s) 449, 700
AseI ATTAAT 1 cut(s) 695
AsiGI ACCGGT 1 cut(s) 366
Asp700I GAANNNNTTC 1 cut(s) 256
AspLEI GCGC 1 cut(s) 134
AspS9I GGNCC 6 cut(s) 115, 136, 280, 635, 731, 756
AsuHPI GGTGA 3 cut(s) 193, 908, 977
AvaI CYCGRG 1 cut(s) 396
AvaII GGWCC 3 cut(s) 115, 136, 731
BalI TGGCCA 1 cut(s) 647
BanI GGYRCC 1 cut(s) 746
BbvI GCAGC 1 cut(s) 224
BccI CCATC 3 cut(s) 274, 637, 794
BceAI ACGGC 1 cut(s) 827
BciT130I CCWGG 1 cut(s) 760
BclI TGATCA 3 cut(s) 784, 790, 1009
BcoDI GTCTC 2 cut(s) 362, 491
BfmI CTRYAG 1 cut(s) 102
BglI GCCNNNNNGGC 1 cut(s) 755
BisI GCNGC 1 cut(s) 213
BlpI GCTNAGC 1 cut(s) 108
BlsI GCNGC 1 cut(s) 214
BmcAI AGTACT 1 cut(s) 566
Bme1390I CCNGG 1 cut(s) 760
Bme18I GGWCC 3 cut(s) 115, 136, 731
BmeT110I CYCGRG 1 cut(s) 396
BmgT120I GGNCC 6 cut(s) 115, 136, 280, 635, 731, 756
BmiI GGNNCC 3 cut(s) 117, 371, 748
BmrFI CCNGG 1 cut(s) 760
BmsI GCATC 5 cut(s) 186, 336, 562, 663, 763
BplI GAGNNNNNCTC 2 cut(s) 910, 942
Bpu10I CCTNAGC 1 cut(s) 837
Bpu1102I GCTNAGC 1 cut(s) 108
BsaBI GATNNNNATC 1 cut(s) 789
BsaJI CCNNGG 2 cut(s) 276, 759
BsaWI WCCGGW 1 cut(s) 366
Bsc4I CCNNNNNNNGG 3 cut(s) 277, 654, 765
Bse118I RCCGGY 1 cut(s) 366
Bse3DI GCAATG 2 cut(s) 8, 787
Bse8I GATNNNNATC 1 cut(s) 789
BseBI CCWGG 1 cut(s) 760
BseDI CCNNGG 2 cut(s) 276, 759
BseGI GGATG 7 cut(s) 58, 177, 266, 553, 721, 778, 805
BseJI GATNNNNATC 1 cut(s) 789
BseLI CCNNNNNNNGG 3 cut(s) 277, 654, 765
BseMI GCAATG 2 cut(s) 8, 787
BseMII CTCAG 4 cut(s) 122, 159, 851, 920
BseRI GAGGAG 1 cut(s) 176
BseXI GCAGC 1 cut(s) 224
Bsh1236I CGCG 3 cut(s) 132, 134, 713
BshFI GGCC 4 cut(s) 281, 637, 647, 758
BshNI GGYRCC 1 cut(s) 746
BshTI ACCGGT 1 cut(s) 366
BsiHKCI CYCGRG 1 cut(s) 396
BsiSI CCGG 1 cut(s) 367
BslI CCNNNNNNNGG 3 cut(s) 277, 654, 765
BsmAI GTCTC 2 cut(s) 362, 491
BsmBI CGTCTC 1 cut(s) 491
BsmI GAATGC 1 cut(s) 927
BsnI GGCC 4 cut(s) 281, 637, 647, 758
BsoBI CYCGRG 1 cut(s) 396
Bsp143I GATC 8 cut(s) 88, 97, 470, 481, 506, 784, 790, 1009
Bsp1720I GCTNAGC 1 cut(s) 108
BspACI CCGC 4 cut(s) 130, 134, 340, 713
BspANI GGCC 4 cut(s) 281, 637, 647, 758
BspCNI CTCAG 4 cut(s) 121, 160, 850, 921
BspFNI CGCG 3 cut(s) 132, 134, 713
BspHI TCATGA 1 cut(s) 787
BspLI GGNNCC 3 cut(s) 117, 371, 748
BspPI GGATC 3 cut(s) 83, 92, 478
BspT107I GGYRCC 1 cut(s) 746
BsrDI GCAATG 2 cut(s) 8, 787
BsrFI RCCGGY 1 cut(s) 366
BssAI RCCGGY 1 cut(s) 366
BssECI CCNNGG 2 cut(s) 276, 759
BssMI GATC 8 cut(s) 88, 97, 470, 481, 506, 784, 790, 1009
BssT1I CCWWGG 1 cut(s) 276
Bst2UI CCWGG 1 cut(s) 760
Bst4CI ACNGT 2 cut(s) 148, 356
Bst6I CTCTTC 3 cut(s) 223, 869, 874
BstC8I GCNNGC 1 cut(s) 778
BstDEI CTNAG 5 cut(s) 108, 168, 582, 837, 929
BstF5I GGATG 7 cut(s) 58, 177, 266, 553, 721, 778, 805
BstFNI CGCG 3 cut(s) 132, 134, 713
BstHHI GCGC 1 cut(s) 134
BstKTI GATC 8 cut(s) 91, 100, 473, 484, 509, 787, 793, 1012
BstMAI GTCTC 2 cut(s) 362, 491
BstMBI GATC 8 cut(s) 88, 97, 470, 481, 506, 784, 790, 1009
BstMWI GCNNNNNNNGC 3 cut(s) 287, 324, 755
BstNI CCWGG 1 cut(s) 760
BstSCI CCNGG 1 cut(s) 758
BstSFI CTRYAG 1 cut(s) 102
BstUI CGCG 3 cut(s) 132, 134, 713
BstV1I GCAGC 1 cut(s) 224
BsuRI GGCC 4 cut(s) 281, 637, 647, 758
BtsCI GGATG 7 cut(s) 58, 177, 266, 553, 721, 778, 805
Cac8I GCNNGC 1 cut(s) 778
CciI TCATGA 1 cut(s) 787
CfoI GCGC 1 cut(s) 134
Cfr10I RCCGGY 1 cut(s) 366
Cfr13I GGNCC 6 cut(s) 115, 136, 280, 635, 731, 756
Csp6I GTAC 4 cut(s) 75, 242, 565, 619
CspAI ACCGGT 1 cut(s) 366
CviAII CATG 4 cut(s) 512, 574, 652, 788
CviQI GTAC 4 cut(s) 75, 242, 565, 619
DdeI CTNAG 5 cut(s) 108, 168, 582, 837, 929
DpnI GATC 8 cut(s) 90, 99, 472, 483, 508, 786, 792, 1011
DpnII GATC 8 cut(s) 88, 97, 470, 481, 506, 784, 790, 1009
DraI TTTAAA 1 cut(s) 460
EaeI YGGCCR 1 cut(s) 645
Eam1104I CTCTTC 3 cut(s) 223, 869, 874
EarI CTCTTC 3 cut(s) 223, 869, 874
EciI GGCGGA 1 cut(s) 329
Eco130I CCWWGG 1 cut(s) 276
Eco47I GGWCC 3 cut(s) 115, 136, 731
Eco88I CYCGRG 1 cut(s) 396
EcoO109I RGGNCCY 3 cut(s) 115, 635, 731
EcoRII CCWGG 1 cut(s) 758
EcoT14I CCWWGG 1 cut(s) 276
EcoT22I ATGCAT 2 cut(s) 555, 678
ErhI CCWWGG 1 cut(s) 276
Esp3I CGTCTC 1 cut(s) 491
FaeI CATG 4 cut(s) 515, 577, 655, 791
FatI CATG 4 cut(s) 511, 573, 651, 787
FauNDI CATATG 2 cut(s) 208, 795
FbaI TGATCA 3 cut(s) 784, 790, 1009
Fnu4HI GCNGC 1 cut(s) 213
FokI GGATG 7 cut(s) 65, 164, 253, 540, 728, 785, 812
Fsp4HI GCNGC 1 cut(s) 213
GlaI GCGC 1 cut(s) 133
GluI GCNGC 1 cut(s) 213
HaeIII GGCC 4 cut(s) 281, 637, 647, 758
HapII CCGG 1 cut(s) 367
HhaI GCGC 1 cut(s) 134
Hin1II CATG 4 cut(s) 515, 577, 655, 791
Hin6I GCGC 1 cut(s) 132
HinP1I GCGC 1 cut(s) 132
HinfI GANTC 4 cut(s) 170, 434, 475, 956
HpaII CCGG 1 cut(s) 367
HphI GGTGA 3 cut(s) 193, 908, 977
Hpy166II GTNNAC 1 cut(s) 968
Hpy188I TCNGA 4 cut(s) 88, 169, 506, 930
Hpy188III TCNNGA 4 cut(s) 50, 479, 557, 788
Hpy8I GTNNAC 1 cut(s) 968
HpyAV CCTTC 2 cut(s) 267, 940
HpyCH4III ACNGT 2 cut(s) 148, 356
HpyCH4IV ACGT 1 cut(s) 423
HpyCH4V TGCA 8 cut(s) 13, 212, 455, 553, 629, 676, 728, 776
HpyF10VI GCNNNNNNNGC 3 cut(s) 287, 324, 755
HpyF3I CTNAG 5 cut(s) 108, 168, 582, 837, 929
HpySE526I ACGT 1 cut(s) 423
Hsp92II CATG 4 cut(s) 515, 577, 655, 791
HspAI GCGC 1 cut(s) 132
Ksp22I TGATCA 3 cut(s) 784, 790, 1009
Kzo9I GATC 8 cut(s) 88, 97, 470, 481, 506, 784, 790, 1009
Lsp1109I GCAGC 1 cut(s) 224
LweI GCATC 5 cut(s) 186, 336, 562, 663, 763
MaeII ACGT 1 cut(s) 423
MaeIII GTNAC 2 cut(s) 171, 199
MalI GATC 8 cut(s) 90, 99, 472, 483, 508, 786, 792, 1011
MboI GATC 8 cut(s) 88, 97, 470, 481, 506, 784, 790, 1009
MboII GAAGA 7 cut(s) 31, 60, 210, 541, 670, 886, 891
MlsI TGGCCA 1 cut(s) 647
MluCI AATT 7 cut(s) 78, 234, 387, 449, 679, 700, 995
MluNI TGGCCA 1 cut(s) 647
MlyI GAGTC 1 cut(s) 179
Mox20I TGGCCA 1 cut(s) 647
Mph1103I ATGCAT 2 cut(s) 555, 678
MroXI GAANNNNTTC 1 cut(s) 256
MscI TGGCCA 1 cut(s) 647
MseI TTAA 5 cut(s) 321, 335, 390, 459, 695
MslI CAYNNNNRTG 2 cut(s) 695, 798
Msp20I TGGCCA 1 cut(s) 647
MspA1I CMGCKG 1 cut(s) 624
MspI CCGG 1 cut(s) 367
MspR9I CCNGG 1 cut(s) 760
Mva1269I GAATGC 1 cut(s) 927
MvaI CCWGG 1 cut(s) 760
MvnI CGCG 3 cut(s) 132, 134, 713
MwoI GCNNNNNNNGC 3 cut(s) 287, 324, 755
NdeI CATATG 2 cut(s) 208, 795
NdeII GATC 8 cut(s) 88, 97, 470, 481, 506, 784, 790, 1009
NlaIII CATG 4 cut(s) 515, 577, 655, 791
NlaIV GGNNCC 3 cut(s) 117, 371, 748
NmuCI GTSAC 2 cut(s) 171, 199
NsiI ATGCAT 2 cut(s) 555, 678
PagI TCATGA 1 cut(s) 787
PctI GAATGC 1 cut(s) 927
PdmI GAANNNNTTC 1 cut(s) 256
PfeI GAWTC 3 cut(s) 434, 475, 956
PflMI CCANNNNNTGG 2 cut(s) 277, 765
PinAI ACCGGT 1 cut(s) 366
PkrI GCNGC 1 cut(s) 214
PleI GAGTC 1 cut(s) 178
PpsI GAGTC 1 cut(s) 178
PpuMI RGGWCCY 2 cut(s) 115, 731
PshBI ATTAAT 1 cut(s) 695
Psp5II RGGWCCY 2 cut(s) 115, 731
Psp6I CCWGG 1 cut(s) 758
PspGI CCWGG 1 cut(s) 758
PspN4I GGNNCC 3 cut(s) 117, 371, 748
PspPI GGNCC 6 cut(s) 115, 136, 280, 635, 731, 756
PspPPI RGGWCCY 2 cut(s) 115, 731
PvuII CAGCTG 1 cut(s) 624
RsaI GTAC 4 cut(s) 76, 243, 566, 620
RsaNI GTAC 4 cut(s) 75, 242, 565, 619
RseI CAYNNNNRTG 2 cut(s) 695, 798
SaqAI TTAA 5 cut(s) 321, 335, 390, 459, 695
SatI GCNGC 1 cut(s) 213
Sau3AI GATC 8 cut(s) 88, 97, 470, 481, 506, 784, 790, 1009
Sau96I GGNCC 6 cut(s) 115, 136, 280, 635, 731, 756
ScaI AGTACT 1 cut(s) 566
SchI GAGTC 1 cut(s) 179
ScrFI CCNGG 1 cut(s) 760
SfaNI GCATC 5 cut(s) 186, 336, 562, 663, 763
SfcI CTRYAG 1 cut(s) 102
SinI GGWCC 3 cut(s) 115, 136, 731
SmiMI CAYNNNNRTG 2 cut(s) 695, 798
Sse9I AATT 7 cut(s) 78, 234, 387, 449, 679, 700, 995
SsiI CCGC 4 cut(s) 130, 134, 340, 713
StyD4I CCNGG 1 cut(s) 758
StyI CCWWGG 1 cut(s) 276
TaaI ACNGT 2 cut(s) 148, 356
TaiI ACGT 1 cut(s) 426
TaqI TCGA 3 cut(s) 473, 527, 954
TasI AATT 7 cut(s) 78, 234, 387, 449, 679, 700, 995
TatI WGTACW 3 cut(s) 241, 564, 618
TfiI GAWTC 3 cut(s) 434, 475, 956
Tru1I TTAA 5 cut(s) 321, 335, 390, 459, 695
Tru9I TTAA 5 cut(s) 321, 335, 390, 459, 695
TseFI GTSAC 2 cut(s) 171, 199
TseI GCWGC 1 cut(s) 212
Tsp45I GTSAC 2 cut(s) 171, 199
TspDTI ATGAA 3 cut(s) 17, 713, 893
Van91I CCANNNNNTGG 2 cut(s) 277, 765
VpaK11BI GGWCC 3 cut(s) 115, 136, 731
VspI ATTAAT 1 cut(s) 695
XapI RAATTY 2 cut(s) 449, 700
XmnI GAANNNNTTC 1 cut(s) 256
ZrmI AGTACT 1 cut(s) 566
Zsp2I ATGCAT 2 cut(s) 555, 678
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.