Rw3G007670

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_wichuraiana
Chr3
OG0005415
Physical Location & Seq
Forward (+)
7092163 .. 7098044
5882 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw3G007670.1

Sequence Viewer

Length: 1251 bp
ATGGGTATAAAGGGTTTAACGAAGCTGTTGGCGGACAATGCCCCAAAGTGCATGAAAGAGCAGAAATTCGAGAGCTATTTTGGCCGCAAGATTGCCATCGATGCCAGCATGAGCATTTATCAGTTCCTTATTGTTGTGGGAAGAACGGGGACTGAGATGCTCACTAATGAGGCTGGTGAAGTTACTAGTCATCTCCAAGGCATGTTTTCGCGGACTATTAGGCTTCTGGAAGCTGGGATTAAGCCGGTCTATGTTTTCGATGGGAAGCCTCCAGAGTTGAAAAGCCAAGAGCTGGCAAAGCGTTACTCAAAGAGAGTTGATGCTACTCAAGATTTGGCGACGGCCGTAGAGTCTGGCACTAAGGAAGACATTGAGAAATTCAGTAAACGGACGGTAAAGGTGACAAAGCAGCACAATGAAGACTGCAGAAGACTTTTAAGGCTCATGGGTGTACCTGTAATTGAGGCTCCCTCGGAAGCAGAGGCACAGTGTGCTGTACTTTGCAAGGCAGGAAAGGTTTATGCTGTGGCCTCAGAAGACATGGATTCCCTAACATTTGGAGCTCCTAAATTTCTTCGCCATTTGATGGATCCTAGCTCAAGAAAAATCCCAGTCATGGAATTTGATGTTGCTAAGGTTTTGGAGGAGCTAAATCTTACTATGGATCAATTCATTGACTTGTGCATACTCTCTGGATGTGATTATTGTGACAGCATTCGAGGTATTGGAGGTCAGACAGCTTTGAAGCTCATCCGCCAACATGGCTCCATAGAGAGTATACTGGAGAACATAAACAAAGAGAGGTACCAAATACCGGATAATTGGCCATATCAAGAGGCTAGGCGGCTTTTTAAGGAACCAGTTGCTTTAACCGATGACGAGCAACTGGAGCTTAAGTGGATTGCTCCAGATGAAGATGGGCTGATTTCCTTTCTGGTGAATGAAAATGGATTCAATAGTGACAGAGTGACTAAGGCTATAGAAAAGATTAAAGCAGCCAAGAACAAGTCATCACAGGGCAGACTTGAATCATTTTTCAAGCCAACTGCTACCACATCTGTACCCCTTAAACGGAAGGATAGCAAATGTGTACTTAAACACCCCAAACCGGCAATCAAGAATCAGATGTTCTCTGTACAAGATTGTAACTCATCTAGGCCCAATGTCATTGGCAGTCTAAGCCTGCCAATTTATAATTTGGGCGCCAATCATCTCATACCATTATCCAGAGGTGTTTGTTTTAGCACATGA
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

416

Amino Acids

46.47

Weight (kDa)

8.65

Isoelectric Point (pI)

40.74

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
XPG_N PF00752 1 - 107 3.9e-29 XPG N-terminal domain
XPG_I PF00867 150 - 234 4e-32 XPG I-region
5_3_exonuc PF01367 220 - 268 1.7e-06 5'-3' exonuclease, C-terminal SAM fold
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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 1194
Acc65I GGTACC 1 cut(s) 804
AccB1I GGYRCC 2 cut(s) 804, 1202
AccB7I CCANNNNNTGG 2 cut(s) 292, 586
AccI GTMKAC 1 cut(s) 778
AccII CGCG 1 cut(s) 211
AciI CCGC 5 cut(s) 32, 85, 211, 754, 844
AclWI GGATC 3 cut(s) 584, 597, 672
AcoI YGGCCR 3 cut(s) 82, 342, 824
AcsI RAATTY 4 cut(s) 65, 377, 569, 620
AcyI GRCGYC 1 cut(s) 1203
AdeI CACNNNGTG 1 cut(s) 491
AfaI GTAC 6 cut(s) 453, 498, 806, 1062, 1092, 1137
AfiI CCNNNNNNNGG 6 cut(s) 292, 586, 616, 814, 1071, 1108
AflII CTTAAG 1 cut(s) 893
AgsI TTSAA 5 cut(s) 280, 745, 955, 1028, 1039
AhlI ACTAGT 1 cut(s) 185
Alw21I GWGCWC 1 cut(s) 565
AlwI GGATC 3 cut(s) 584, 597, 672
AoxI GGCC 5 cut(s) 82, 342, 528, 824, 1157
ApeKI GCWGC 2 cut(s) 409, 995
ApoI RAATTY 4 cut(s) 65, 377, 569, 620
Asp718I GGTACC 1 cut(s) 804
AspLEI GCGC 1 cut(s) 1205
AspS9I GGNCC 1 cut(s) 1158
AsuHPI GGTGA 3 cut(s) 188, 412, 949
BaeI ACNNNNGTAYC 2 cut(s) 1044, 1077
BalI TGGCCA 1 cut(s) 826
BamHI GGATCC 1 cut(s) 589
BanI GGYRCC 2 cut(s) 804, 1202
BanII GRGCYC 1 cut(s) 565
BbsI GAAGAC 4 cut(s) 372, 426, 436, 543
Bbv12I GWGCWC 1 cut(s) 565
BbvI GCAGC 2 cut(s) 421, 1007
BccI CCATC 4 cut(s) 104, 254, 580, 911
BceAI ACGGC 2 cut(s) 329, 357
BcuI ACTAGT 1 cut(s) 185
BfaI CTAG 4 cut(s) 186, 594, 840, 1155
BfmI CTRYAG 2 cut(s) 424, 978
BfoI RGCGCY 1 cut(s) 1206
BfrI CTTAAG 1 cut(s) 893
BglI GCCNNNNNGGC 1 cut(s) 762
BisI GCNGC 4 cut(s) 85, 410, 845, 996
BlsI GCNGC 4 cut(s) 86, 411, 846, 997
BmgT120I GGNCC 1 cut(s) 1158
BmiI GGNNCC 6 cut(s) 468, 591, 766, 806, 858, 1204
BmrI ACTGGG 1 cut(s) 605
BmsI GCATC 3 cut(s) 91, 147, 310
BmuI ACTGGG 1 cut(s) 605
BpiI GAAGAC 4 cut(s) 372, 426, 436, 543
BplI GAGNNNNNCTC 2 cut(s) 455, 487
BpmI CTGGAG 4 cut(s) 255, 803, 891, 908
Bpu10I CCTNAGC 1 cut(s) 633
BpuEI CTTGAG 2 cut(s) 312, 583
Bsa29I ATCGAT 1 cut(s) 99
BsaBI GATNNNNATC 1 cut(s) 95
BsaHI GRCGYC 1 cut(s) 1203
BsaJI CCNNGG 2 cut(s) 196, 471
BsaWI WCCGGW 1 cut(s) 814
BsaXI ACNNNNNCTCC 2 cut(s) 881, 911
Bsc4I CCNNNNNNNGG 6 cut(s) 292, 586, 616, 814, 1071, 1108
Bse118I RCCGGY 2 cut(s) 244, 1108
Bse1I ACTGG 4 cut(s) 611, 786, 860, 891
Bse8I GATNNNNATC 1 cut(s) 95
BseCI ATCGAT 1 cut(s) 99
BseDI CCNNGG 2 cut(s) 196, 471
BseGI GGATG 2 cut(s) 701, 750
BseJI GATNNNNATC 1 cut(s) 95
BseLI CCNNNNNNNGG 6 cut(s) 292, 586, 616, 814, 1071, 1108
BseMII CTCAG 2 cut(s) 144, 546
BseNI ACTGG 4 cut(s) 611, 786, 860, 891
BseRI GAGGAG 1 cut(s) 659
BseX3I CGGCCG 1 cut(s) 342
BseXI GCAGC 2 cut(s) 421, 1007
BseYI CCCAGC 1 cut(s) 233
Bsh1236I CGCG 1 cut(s) 211
Bsh1285I CGRYCG 1 cut(s) 345
BshFI GGCC 5 cut(s) 84, 344, 530, 826, 1159
BshNI GGYRCC 2 cut(s) 804, 1202
BshVI ATCGAT 1 cut(s) 99
BsiEI CGRYCG 1 cut(s) 345
BsiHKAI GWGCWC 1 cut(s) 565
BsiSI CCGG 3 cut(s) 245, 815, 1109
BslFI GGGAC 1 cut(s) 163
BslI CCNNNNNNNGG 6 cut(s) 292, 586, 616, 814, 1071, 1108
BsmFI GGGAC 1 cut(s) 163
BsmI GAATGC 1 cut(s) 714
BsnI GGCC 5 cut(s) 84, 344, 530, 826, 1159
Bsp1286I GDGCHC 1 cut(s) 565
Bsp1407I TGTACA 1 cut(s) 1135
Bsp143I GATC 2 cut(s) 589, 664
BspACI CCGC 5 cut(s) 32, 85, 211, 754, 844
BspANI GGCC 5 cut(s) 84, 344, 530, 826, 1159
BspCNI CTCAG 2 cut(s) 145, 545
BspDI ATCGAT 1 cut(s) 99
BspFNI CGCG 1 cut(s) 211
BspLI GGNNCC 6 cut(s) 468, 591, 766, 806, 858, 1204
BspMAI CTGCAG 1 cut(s) 428
BspPI GGATC 3 cut(s) 584, 597, 672
BspT107I GGYRCC 2 cut(s) 804, 1202
BspTI CTTAAG 1 cut(s) 893
BsrFI RCCGGY 2 cut(s) 244, 1108
BsrGI TGTACA 1 cut(s) 1135
BsrI ACTGG 4 cut(s) 611, 786, 860, 891
BssAI RCCGGY 2 cut(s) 244, 1108
BssECI CCNNGG 2 cut(s) 196, 471
BssMI GATC 2 cut(s) 589, 664
BssNAI GTATAC 1 cut(s) 779
BssNI GRCGYC 1 cut(s) 1203
BssT1I CCWWGG 1 cut(s) 196
Bst1107I GTATAC 1 cut(s) 779
Bst4CI ACNGT 2 cut(s) 394, 489
BstACI GRCGYC 1 cut(s) 1203
BstAFI CTTAAG 1 cut(s) 893
BstAPI GCANNNNNTGC 1 cut(s) 491
BstAUI TGTACA 1 cut(s) 1135
BstC8I GCNNGC 3 cut(s) 106, 294, 1184
BstDEI CTNAG 6 cut(s) 153, 360, 532, 633, 972, 1178
BstF5I GGATG 2 cut(s) 701, 750
BstFNI CGCG 1 cut(s) 211
BstH2I RGCGCY 1 cut(s) 1206
BstHHI GCGC 1 cut(s) 1205
BstKTI GATC 2 cut(s) 592, 667
BstMBI GATC 2 cut(s) 589, 664
BstMCI CGRYCG 1 cut(s) 345
BstMWI GCNNNNNNNGC 8 cut(s) 38, 81, 101, 298, 491, 762, 889, 1179
BstNSI RCATGY 1 cut(s) 205
BstSFI CTRYAG 2 cut(s) 424, 978
BstUI CGCG 1 cut(s) 211
BstV1I GCAGC 2 cut(s) 421, 1007
BstV2I GAAGAC 4 cut(s) 372, 426, 436, 543
BstX2I RGATCY 1 cut(s) 589
BstYI RGATCY 1 cut(s) 589
BstZ17I GTATAC 1 cut(s) 779
BstZI CGGCCG 1 cut(s) 342
Bsu15I ATCGAT 1 cut(s) 99
BsuRI GGCC 5 cut(s) 84, 344, 530, 826, 1159
BsuTUI ATCGAT 1 cut(s) 99
BtsCI GGATG 2 cut(s) 701, 750
BtsIMutI CAGTG 1 cut(s) 494
Cac8I GCNNGC 3 cut(s) 106, 294, 1184
CfoI GCGC 1 cut(s) 1205
Cfr10I RCCGGY 2 cut(s) 244, 1108
Cfr13I GGNCC 1 cut(s) 1158
ClaI ATCGAT 1 cut(s) 99
Csp6I GTAC 6 cut(s) 452, 497, 805, 1061, 1091, 1136
CviAII CATG 8 cut(s) 52, 109, 202, 445, 541, 616, 761, 1248
CviQI GTAC 6 cut(s) 452, 497, 805, 1061, 1091, 1136
DdeI CTNAG 6 cut(s) 153, 360, 532, 633, 972, 1178
DinI GGCGCC 1 cut(s) 1204
DpnI GATC 2 cut(s) 591, 666
DpnII GATC 2 cut(s) 589, 664
DraIII CACNNNGTG 1 cut(s) 491
EaeI YGGCCR 3 cut(s) 82, 342, 824
EagI CGGCCG 1 cut(s) 342
EciI GGCGGA 2 cut(s) 47, 743
Ecl136II GAGCTC 1 cut(s) 563
EclXI CGGCCG 1 cut(s) 342
Eco130I CCWWGG 1 cut(s) 196
Eco24I GRGCYC 1 cut(s) 565
Eco52I CGGCCG 1 cut(s) 342
Eco53kI GAGCTC 1 cut(s) 563
EcoICRI GAGCTC 1 cut(s) 563
EcoT14I CCWWGG 1 cut(s) 196
EcoT38I GRGCYC 1 cut(s) 565
EgeI GGCGCC 1 cut(s) 1204
EheI GGCGCC 1 cut(s) 1204
ErhI CCWWGG 1 cut(s) 196
FaeI CATG 8 cut(s) 55, 112, 205, 448, 544, 619, 764, 1251
FaqI GGGAC 1 cut(s) 163
FatI CATG 8 cut(s) 51, 108, 201, 444, 540, 615, 760, 1247
FblI GTMKAC 1 cut(s) 778
Fnu4HI GCNGC 4 cut(s) 85, 410, 845, 996
FokI GGATG 2 cut(s) 708, 737
FriOI GRGCYC 1 cut(s) 565
Fsp4HI GCNGC 4 cut(s) 85, 410, 845, 996
FspBI CTAG 4 cut(s) 186, 594, 840, 1155
GlaI GCGC 1 cut(s) 1204
GluI GCNGC 4 cut(s) 85, 410, 845, 996
GsaI CCCAGC 1 cut(s) 237
GsuI CTGGAG 4 cut(s) 255, 803, 891, 908
HaeII RGCGCY 1 cut(s) 1206
HaeIII GGCC 5 cut(s) 84, 344, 530, 826, 1159
HapII CCGG 3 cut(s) 245, 815, 1109
HhaI GCGC 1 cut(s) 1205
Hin1I GRCGYC 1 cut(s) 1203
Hin1II CATG 8 cut(s) 55, 112, 205, 448, 544, 619, 764, 1251
Hin6I GCGC 1 cut(s) 1203
HinP1I GCGC 1 cut(s) 1203
HinfI GANTC 5 cut(s) 350, 545, 951, 1028, 1120
HpaII CCGG 3 cut(s) 245, 815, 1109
HphI GGTGA 3 cut(s) 188, 412, 949
Hpy166II GTNNAC 4 cut(s) 386, 452, 779, 1091
Hpy188I TCNGA 4 cut(s) 475, 535, 735, 1125
Hpy8I GTNNAC 4 cut(s) 386, 452, 779, 1091
Hpy99I CGWCG 1 cut(s) 343
HpyAV CCTTC 1 cut(s) 1069
HpyCH4III ACNGT 2 cut(s) 394, 489
HpyCH4V TGCA 4 cut(s) 51, 426, 504, 684
HpyF10VI GCNNNNNNNGC 8 cut(s) 38, 81, 101, 298, 491, 762, 889, 1179
HpyF3I CTNAG 6 cut(s) 153, 360, 532, 633, 972, 1178
Hsp92I GRCGYC 1 cut(s) 1203
Hsp92II CATG 8 cut(s) 55, 112, 205, 448, 544, 619, 764, 1251
HspAI GCGC 1 cut(s) 1203
KasI GGCGCC 1 cut(s) 1202
KpnI GGTACC 1 cut(s) 808
Kzo9I GATC 2 cut(s) 589, 664
LmnI GCTCC 7 cut(s) 472, 560, 568, 646, 770, 889, 910
Lsp1109I GCAGC 2 cut(s) 421, 1007
LweI GCATC 3 cut(s) 91, 147, 310
MaeI CTAG 4 cut(s) 186, 594, 840, 1155
MaeIII GTNAC 7 cut(s) 181, 302, 400, 707, 959, 967, 1145
MalI GATC 2 cut(s) 591, 666
MboI GATC 2 cut(s) 589, 664
MboII GAAGA 7 cut(s) 153, 377, 431, 441, 548, 566, 926
MflI RGATCY 1 cut(s) 589
MhlI GDGCHC 1 cut(s) 565
MlsI TGGCCA 1 cut(s) 826
MluCI AATT 9 cut(s) 65, 377, 459, 569, 620, 668, 820, 1188, 1195
MluNI TGGCCA 1 cut(s) 826
Mly113I GGCGCC 1 cut(s) 1203
MlyI GAGTC 1 cut(s) 359
Mox20I TGGCCA 1 cut(s) 826
MscI TGGCCA 1 cut(s) 826
MseI TTAA 9 cut(s) 17, 240, 437, 852, 869, 894, 990, 1068, 1095
Msp20I TGGCCA 1 cut(s) 826
MspCI CTTAAG 1 cut(s) 893
MspI CCGG 3 cut(s) 245, 815, 1109
Mva1269I GAATGC 1 cut(s) 714
MvnI CGCG 1 cut(s) 211
MwoI GCNNNNNNNGC 8 cut(s) 38, 81, 101, 298, 491, 762, 889, 1179
NarI GGCGCC 1 cut(s) 1203
NdeII GATC 2 cut(s) 589, 664
NlaIII CATG 8 cut(s) 55, 112, 205, 448, 544, 619, 764, 1251
NlaIV GGNNCC 6 cut(s) 468, 591, 766, 806, 858, 1204
NmuCI GTSAC 4 cut(s) 400, 707, 959, 967
NspI RCATGY 1 cut(s) 205
PctI GAATGC 1 cut(s) 714
PfeI GAWTC 4 cut(s) 545, 951, 1028, 1120
PflMI CCANNNNNTGG 2 cut(s) 292, 586
PkrI GCNGC 4 cut(s) 86, 411, 846, 997
PleI GAGTC 1 cut(s) 358
PluTI GGCGCC 1 cut(s) 1206
PpsI GAGTC 1 cut(s) 358
PsiI TTATAA 1 cut(s) 1194
Psp124BI GAGCTC 1 cut(s) 565
PspFI CCCAGC 1 cut(s) 233
PspN4I GGNNCC 6 cut(s) 468, 591, 766, 806, 858, 1204
PspPI GGNCC 1 cut(s) 1158
PstI CTGCAG 1 cut(s) 428
PsuI RGATCY 1 cut(s) 589
RsaI GTAC 6 cut(s) 453, 498, 806, 1062, 1092, 1137
RsaNI GTAC 6 cut(s) 452, 497, 805, 1061, 1091, 1136
SacI GAGCTC 1 cut(s) 565
SaqAI TTAA 9 cut(s) 17, 240, 437, 852, 869, 894, 990, 1068, 1095
SatI GCNGC 4 cut(s) 85, 410, 845, 996
Sau3AI GATC 2 cut(s) 589, 664
Sau96I GGNCC 1 cut(s) 1158
SchI GAGTC 1 cut(s) 359
SduI GDGCHC 1 cut(s) 565
SfaNI GCATC 3 cut(s) 91, 147, 310
SfcI CTRYAG 2 cut(s) 424, 978
SfoI GGCGCC 1 cut(s) 1204
SmlI CTYRAG 3 cut(s) 327, 598, 893
SmoI CTYRAG 3 cut(s) 327, 598, 893
SpeI ACTAGT 1 cut(s) 185
Sse9I AATT 9 cut(s) 65, 377, 459, 569, 620, 668, 820, 1188, 1195
SsiI CCGC 5 cut(s) 32, 85, 211, 754, 844
SspDI GGCGCC 1 cut(s) 1202
SspMI CTAG 4 cut(s) 186, 594, 840, 1155
SstI GAGCTC 1 cut(s) 565
StyI CCWWGG 1 cut(s) 196
TaaI ACNGT 2 cut(s) 394, 489
TaqI TCGA 4 cut(s) 69, 99, 258, 718
TasI AATT 9 cut(s) 65, 377, 459, 569, 620, 668, 820, 1188, 1195
TatI WGTACW 3 cut(s) 496, 1090, 1135
TauI GCSGC 2 cut(s) 87, 847
TfiI GAWTC 4 cut(s) 545, 951, 1028, 1120
Tru1I TTAA 9 cut(s) 17, 240, 437, 852, 869, 894, 990, 1068, 1095
Tru9I TTAA 9 cut(s) 17, 240, 437, 852, 869, 894, 990, 1068, 1095
TscAI CASTG 1 cut(s) 494
TseFI GTSAC 4 cut(s) 400, 707, 959, 967
TseI GCWGC 2 cut(s) 409, 995
Tsp45I GTSAC 4 cut(s) 400, 707, 959, 967
TspDTI ATGAA 5 cut(s) 68, 432, 661, 927, 957
TspGWI ACGGA 2 cut(s) 403, 1087
TspRI CASTG 1 cut(s) 494
Van91I CCANNNNNTGG 2 cut(s) 292, 586
Vha464I CTTAAG 1 cut(s) 893
XapI RAATTY 4 cut(s) 65, 377, 569, 620
XceI RCATGY 1 cut(s) 205
XmiI GTMKAC 1 cut(s) 778
XspI CTAG 4 cut(s) 186, 594, 840, 1155
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.