MD04G1184400.v1.1

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
malus_domestica
Chr04
OG0005415
Physical Location & Seq
Reverse (-)
27531921 .. 27536842
4922 bp
Loading structure...
UTR
Exon/CDS
Intron
MD04G1184400.v1.1.491

Sequence Viewer

Length: 1152 bp
ATGGGTATAAAGGGTTTAACGAAGCTGCTGGCGGACAATGCCCCGAAGGCCATGAAGGAGCAGAAATTCGAGAGCTATTTCGGCCGAAAGATCGCCATCGATGCCAGCATGAGCATTTACCAGTTCCTTATTGTTGTGGGAAGGACTGGGACTGAGATGCTCACCAATGAGGCTGGTGAAGTTACTAGTCATCTGCAAGGCATGTTTTCACGGACGATTAGGCTTCTGGAAGCTGGAATTAAACCACTCTATGTTTTCGATGGGAAGCCTCCAGAATTGAAGAAACAAGAGCTGGCAAAGCGTTACTCAAAGAGGGCAGATGCCACTGATGATTTGGCAGCGGCTGTGGAGGATGGTAATAAGGAAGACATTGAGAAGTACAGTAAACGAACAGTAAAGGTGACAAAGCAGCACAATGATGACTGCAAAAGACTTCTAAGGCTCATGGGGGTACCTGTAGTTGAGGCTCCCTCAGAAGCAGAGGCACAGTGTGCTGTACTTTGCAAATCAGGAAAGGTTTATGCTGTGGCCTCTGAAGACATGGATTCTCTTACATTTGGAGCGCCTAGGTTTCTTCGTCATTTGATGGATCCTAGCTCAAGGAAAATCCCTGTCATGGAATTCGATATTGCTAAGGTGTTGGAGGAGCTAAATCTTACCATGGATCAATTCATTGACTTGTGCATTCTGTCCGGATGTGATTATTGTGACAGCATTCGAGGGATTGGAGGACAGACAGCTTTGAAGCTCATCCGTCAGCATGGCTCCATTGAGAATATACTCGAGAACATAAACAAAGAAAGGTACCAAATACCAGAGGAGTGGCCCTATCAAGAGGCTCGGAGACTTTTTAAGGAACCAGTTGCTTTATCTGATGAAGAACAAGTTGAGATTAAATGGACAGCGCCAGATGAAGAAGGACTAATTGCATTTTTGGTGAATGAAAATGGATTTAACAGTGACAGAGTGGCAAAGGCAATAGAAAAAATTAAAGCAGCCAAGAACAAGTCATCGCAAGGAAGACTTGAATCATTTTTCAAGCCGACTGCTAACCCATCTGTACCCATTAAACGAAAGGAAACACCACAAAGCACGGCTAAAGAAACTGCGAACAAAAAGGCAAAAGCTGGTGGCGGTAGAAAGAAAAAATAG
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

384

Amino Acids

42.81

Weight (kDa)

8.77

Isoelectric Point (pI)

44.64

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
XPG_N PF00752 1 - 107 1.4e-29 XPG N-terminal domain
XPG_I PF00867 150 - 234 1.5e-32 XPG I-region
5_3_exonuc PF01367 220 - 267 5.5e-07 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
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 2 cut(s) 451, 804
AccB1I GGYRCC 2 cut(s) 451, 804
AccIII TCCGGA 1 cut(s) 692
AciI CCGC 3 cut(s) 32, 341, 1134
AclWI GGATC 3 cut(s) 584, 597, 672
AcoI YGGCCR 1 cut(s) 82
AcsI RAATTY 2 cut(s) 65, 620
AcuI CTGAAG 1 cut(s) 555
AdeI CACNNNGTG 1 cut(s) 491
AfaI GTAC 5 cut(s) 380, 453, 498, 806, 1062
AfiI CCNNNNNNNGG 1 cut(s) 616
AgsI TTSAA 4 cut(s) 280, 745, 1028, 1039
AhlI ACTAGT 1 cut(s) 185
AluBI AGCT 9 cut(s) 25, 75, 233, 292, 597, 649, 740, 748, 1127
AluI AGCT 9 cut(s) 25, 75, 233, 292, 597, 649, 740, 748, 1127
Alw26I GTCTC 1 cut(s) 838
AlwI GGATC 3 cut(s) 584, 597, 672
AlwNI CAGNNNCTG 1 cut(s) 344
Ama87I CYCGRG 1 cut(s) 782
Aor13HI TCCGGA 1 cut(s) 692
AoxI GGCC 4 cut(s) 48, 82, 528, 824
ApeKI GCWGC 4 cut(s) 25, 338, 409, 995
ApoI RAATTY 2 cut(s) 65, 620
Asp718I GGTACC 2 cut(s) 451, 804
AspA2I CCTAGG 1 cut(s) 566
AspLEI GCGC 2 cut(s) 565, 907
AspS9I GGNCC 1 cut(s) 825
AsuHPI GGTGA 4 cut(s) 154, 188, 412, 949
AvaI CYCGRG 1 cut(s) 782
AvrII CCTAGG 1 cut(s) 566
BamHI GGATCC 1 cut(s) 589
BanI GGYRCC 2 cut(s) 451, 804
BbsI GAAGAC 3 cut(s) 372, 543, 1027
BbvI GCAGC 4 cut(s) 12, 350, 421, 1007
BccI CCATC 5 cut(s) 104, 254, 347, 580, 1063
BceAI ACGGC 1 cut(s) 1110
BcoDI GTCTC 1 cut(s) 838
BcuI ACTAGT 1 cut(s) 185
BfaI CTAG 3 cut(s) 186, 567, 594
BfmI CTRYAG 1 cut(s) 456
BfoI RGCGCY 2 cut(s) 566, 908
BglI GCCNNNNNGGC 1 cut(s) 47
BisI GCNGC 5 cut(s) 26, 339, 342, 410, 996
BlnI CCTAGG 1 cut(s) 566
BlsI GCNGC 5 cut(s) 27, 340, 343, 411, 997
BmeT110I CYCGRG 1 cut(s) 782
BmgT120I GGNCC 1 cut(s) 825
BmiI GGNNCC 6 cut(s) 453, 468, 591, 766, 806, 858
BmrI ACTGGG 1 cut(s) 156
BmsI GCATC 3 cut(s) 91, 147, 310
BmuI ACTGGG 1 cut(s) 156
BpiI GAAGAC 3 cut(s) 372, 543, 1027
BplI GAGNNNNNCTC 2 cut(s) 455, 487
BpmI CTGGAG 1 cut(s) 255
Bpu10I CCTNAGC 1 cut(s) 633
BpuEI CTTGAG 1 cut(s) 583
Bsa29I ATCGAT 1 cut(s) 99
BsaBI GATNNNNATC 1 cut(s) 95
BsaJI CCNNGG 2 cut(s) 566, 660
BsaWI WCCGGW 1 cut(s) 692
Bsc4I CCNNNNNNNGG 1 cut(s) 616
Bse1I ACTGG 3 cut(s) 121, 151, 860
Bse8I GATNNNNATC 1 cut(s) 95
BseAI TCCGGA 1 cut(s) 692
BseCI ATCGAT 1 cut(s) 99
BseDI CCNNGG 2 cut(s) 566, 660
BseGI GGATG 3 cut(s) 358, 701, 750
BseJI GATNNNNATC 1 cut(s) 95
BseLI CCNNNNNNNGG 1 cut(s) 616
BseMII CTCAG 2 cut(s) 144, 486
BseNI ACTGG 3 cut(s) 121, 151, 860
BseRI GAGGAG 2 cut(s) 659, 833
BseX3I CGGCCG 1 cut(s) 82
BseXI GCAGC 4 cut(s) 12, 350, 421, 1007
Bsh1285I CGRYCG 1 cut(s) 85
BshFI GGCC 4 cut(s) 50, 84, 530, 826
BshNI GGYRCC 2 cut(s) 451, 804
BshVI ATCGAT 1 cut(s) 99
BsiEI CGRYCG 1 cut(s) 85
BsiHKCI CYCGRG 1 cut(s) 782
BsiSI CCGG 1 cut(s) 693
BslFI GGGAC 1 cut(s) 163
BslI CCNNNNNNNGG 1 cut(s) 616
BsmAI GTCTC 1 cut(s) 838
BsmFI GGGAC 1 cut(s) 163
BsmI GAATGC 2 cut(s) 684, 714
BsnI GGCC 4 cut(s) 50, 84, 530, 826
BsoBI CYCGRG 1 cut(s) 782
Bsp13I TCCGGA 1 cut(s) 692
Bsp143I GATC 3 cut(s) 90, 589, 664
Bsp19I CCATGG 1 cut(s) 660
BspACI CCGC 3 cut(s) 32, 341, 1134
BspANI GGCC 4 cut(s) 50, 84, 530, 826
BspCNI CTCAG 2 cut(s) 145, 485
BspDI ATCGAT 1 cut(s) 99
BspEI TCCGGA 1 cut(s) 692
BspLI GGNNCC 6 cut(s) 453, 468, 591, 766, 806, 858
BspPI GGATC 3 cut(s) 584, 597, 672
BspT107I GGYRCC 2 cut(s) 451, 804
BsrI ACTGG 3 cut(s) 121, 151, 860
BssECI CCNNGG 2 cut(s) 566, 660
BssMI GATC 3 cut(s) 90, 589, 664
BssT1I CCWWGG 2 cut(s) 566, 660
Bst4CI ACNGT 4 cut(s) 383, 394, 489, 959
BstAPI GCANNNNNTGC 1 cut(s) 491
BstC8I GCNNGC 3 cut(s) 30, 106, 294
BstDEI CTNAG 4 cut(s) 153, 437, 472, 633
BstDSI CCRYGG 1 cut(s) 660
BstF5I GGATG 3 cut(s) 358, 701, 750
BstH2I RGCGCY 2 cut(s) 566, 908
BstHHI GCGC 2 cut(s) 565, 907
BstKTI GATC 3 cut(s) 93, 592, 667
BstMAI GTCTC 1 cut(s) 838
BstMBI GATC 3 cut(s) 90, 589, 664
BstMCI CGRYCG 1 cut(s) 85
BstMWI GCNNNNNNNGC 6 cut(s) 38, 47, 81, 101, 298, 491
BstNSI RCATGY 1 cut(s) 205
BstSFI CTRYAG 1 cut(s) 456
BstV1I GCAGC 4 cut(s) 12, 350, 421, 1007
BstV2I GAAGAC 3 cut(s) 372, 543, 1027
BstX2I RGATCY 1 cut(s) 589
BstXI CCANNNNNNTGG 1 cut(s) 822
BstYI RGATCY 1 cut(s) 589
BstZI CGGCCG 1 cut(s) 82
Bsu15I ATCGAT 1 cut(s) 99
BsuRI GGCC 4 cut(s) 50, 84, 530, 826
BsuTUI ATCGAT 1 cut(s) 99
BtgI CCRYGG 1 cut(s) 660
BtgZI GCGATG 1 cut(s) 996
BtsCI GGATG 3 cut(s) 358, 701, 750
BtsIMutI CAGTG 3 cut(s) 324, 494, 964
Cac8I GCNNGC 3 cut(s) 30, 106, 294
CaiI CAGNNNCTG 1 cut(s) 344
CfoI GCGC 2 cut(s) 565, 907
Cfr13I GGNCC 1 cut(s) 825
ClaI ATCGAT 1 cut(s) 99
Csp6I GTAC 5 cut(s) 379, 452, 497, 805, 1061
CviAII CATG 8 cut(s) 52, 109, 202, 445, 541, 616, 661, 761
CviQI GTAC 5 cut(s) 379, 452, 497, 805, 1061
DdeI CTNAG 4 cut(s) 153, 437, 472, 633
DpnI GATC 3 cut(s) 92, 591, 666
DpnII GATC 3 cut(s) 90, 589, 664
DraIII CACNNNGTG 1 cut(s) 491
EaeI YGGCCR 1 cut(s) 82
EagI CGGCCG 1 cut(s) 82
EciI GGCGGA 1 cut(s) 47
EclXI CGGCCG 1 cut(s) 82
Eco130I CCWWGG 2 cut(s) 566, 660
Eco52I CGGCCG 1 cut(s) 82
Eco57I CTGAAG 1 cut(s) 555
Eco88I CYCGRG 1 cut(s) 782
EcoRI GAATTC 1 cut(s) 620
EcoT14I CCWWGG 2 cut(s) 566, 660
ErhI CCWWGG 2 cut(s) 566, 660
FaeI CATG 8 cut(s) 55, 112, 205, 448, 544, 619, 664, 764
FalI AAGNNNNNCTT 2 cut(s) 1008, 1040
FaqI GGGAC 1 cut(s) 163
FatI CATG 8 cut(s) 51, 108, 201, 444, 540, 615, 660, 760
Fnu4HI GCNGC 5 cut(s) 26, 339, 342, 410, 996
FokI GGATG 3 cut(s) 365, 708, 737
Fsp4HI GCNGC 5 cut(s) 26, 339, 342, 410, 996
FspBI CTAG 3 cut(s) 186, 567, 594
GlaI GCGC 2 cut(s) 564, 906
GluI GCNGC 5 cut(s) 26, 339, 342, 410, 996
GsuI CTGGAG 1 cut(s) 255
HaeII RGCGCY 2 cut(s) 566, 908
HaeIII GGCC 4 cut(s) 50, 84, 530, 826
HapII CCGG 1 cut(s) 693
HhaI GCGC 2 cut(s) 565, 907
Hin1II CATG 8 cut(s) 55, 112, 205, 448, 544, 619, 664, 764
Hin6I GCGC 2 cut(s) 563, 905
HinP1I GCGC 2 cut(s) 563, 905
HinfI GANTC 2 cut(s) 545, 1028
HpaII CCGG 1 cut(s) 693
HphI GGTGA 4 cut(s) 154, 188, 412, 949
Hpy166II GTNNAC 1 cut(s) 386
Hpy188I TCNGA 4 cut(s) 475, 535, 843, 874
Hpy188III TCNNGA 7 cut(s) 70, 227, 272, 510, 693, 784, 833
Hpy8I GTNNAC 1 cut(s) 386
HpyAV CCTTC 4 cut(s) 40, 49, 135, 911
HpyCH4III ACNGT 4 cut(s) 383, 394, 489, 959
HpyCH4V TGCA 5 cut(s) 196, 426, 504, 684, 929
HpyF10VI GCNNNNNNNGC 6 cut(s) 38, 47, 81, 101, 298, 491
HpyF3I CTNAG 4 cut(s) 153, 437, 472, 633
Hsp92II CATG 8 cut(s) 55, 112, 205, 448, 544, 619, 664, 764
HspAI GCGC 2 cut(s) 563, 905
Kpn2I TCCGGA 1 cut(s) 692
KpnI GGTACC 2 cut(s) 455, 808
Kzo9I GATC 3 cut(s) 90, 589, 664
LmnI GCTCC 5 cut(s) 58, 472, 560, 646, 770
Lsp1109I GCAGC 4 cut(s) 12, 350, 421, 1007
LweI GCATC 3 cut(s) 91, 147, 310
MaeI CTAG 3 cut(s) 186, 567, 594
MaeIII GTNAC 5 cut(s) 181, 302, 400, 707, 959
MalI GATC 3 cut(s) 92, 591, 666
MboI GATC 3 cut(s) 90, 589, 664
MboII GAAGA 7 cut(s) 292, 377, 548, 566, 890, 926, 1032
MflI RGATCY 1 cut(s) 589
MluCI AATT 7 cut(s) 65, 237, 275, 620, 668, 924, 987
MmeI TCCRAC 1 cut(s) 621
MroI TCCGGA 1 cut(s) 692
MseI TTAA 7 cut(s) 17, 240, 852, 894, 954, 990, 1068
MslI CAYNNNNRTG 1 cut(s) 417
MspA1I CMGCKG 1 cut(s) 341
MspI CCGG 1 cut(s) 693
Mva1269I GAATGC 2 cut(s) 684, 714
MwoI GCNNNNNNNGC 6 cut(s) 38, 47, 81, 101, 298, 491
NcoI CCATGG 1 cut(s) 660
NdeII GATC 3 cut(s) 90, 589, 664
NlaIII CATG 8 cut(s) 55, 112, 205, 448, 544, 619, 664, 764
NlaIV GGNNCC 6 cut(s) 453, 468, 591, 766, 806, 858
NmuCI GTSAC 3 cut(s) 400, 707, 959
NspI RCATGY 1 cut(s) 205
PaeR7I CTCGAG 1 cut(s) 782
PctI GAATGC 2 cut(s) 684, 714
PfeI GAWTC 2 cut(s) 545, 1028
PkrI GCNGC 5 cut(s) 27, 340, 343, 411, 997
PspN4I GGNNCC 6 cut(s) 453, 468, 591, 766, 806, 858
PspPI GGNCC 1 cut(s) 825
PstNI CAGNNNCTG 1 cut(s) 344
PsuI RGATCY 1 cut(s) 589
RsaI GTAC 5 cut(s) 380, 453, 498, 806, 1062
RsaNI GTAC 5 cut(s) 379, 452, 497, 805, 1061
RseI CAYNNNNRTG 1 cut(s) 417
SaqAI TTAA 7 cut(s) 17, 240, 852, 894, 954, 990, 1068
SatI GCNGC 5 cut(s) 26, 339, 342, 410, 996
Sau3AI GATC 3 cut(s) 90, 589, 664
Sau96I GGNCC 1 cut(s) 825
SfaNI GCATC 3 cut(s) 91, 147, 310
SfcI CTRYAG 1 cut(s) 456
Sfr274I CTCGAG 1 cut(s) 782
SlaI CTCGAG 1 cut(s) 782
SmiMI CAYNNNNRTG 1 cut(s) 417
SmlI CTYRAG 2 cut(s) 598, 782
SmoI CTYRAG 2 cut(s) 598, 782
SpeI ACTAGT 1 cut(s) 185
Sse9I AATT 7 cut(s) 65, 237, 275, 620, 668, 924, 987
SsiI CCGC 3 cut(s) 32, 341, 1134
SspMI CTAG 3 cut(s) 186, 567, 594
StyI CCWWGG 2 cut(s) 566, 660
TaaI ACNGT 4 cut(s) 383, 394, 489, 959
TaqI TCGA 6 cut(s) 69, 99, 258, 624, 718, 783
TasI AATT 7 cut(s) 65, 237, 275, 620, 668, 924, 987
TatI WGTACW 2 cut(s) 378, 496
TauI GCSGC 1 cut(s) 344
TfiI GAWTC 2 cut(s) 545, 1028
Tru1I TTAA 7 cut(s) 17, 240, 852, 894, 954, 990, 1068
Tru9I TTAA 7 cut(s) 17, 240, 852, 894, 954, 990, 1068
TscAI CASTG 3 cut(s) 331, 494, 964
TseFI GTSAC 3 cut(s) 400, 707, 959
TseI GCWGC 4 cut(s) 25, 338, 409, 995
Tsp45I GTSAC 3 cut(s) 400, 707, 959
TspDTI ATGAA 5 cut(s) 68, 661, 891, 927, 957
TspGWI ACGGA 2 cut(s) 226, 743
TspRI CASTG 3 cut(s) 331, 494, 964
XapI RAATTY 2 cut(s) 65, 620
XceI RCATGY 1 cut(s) 205
XcmI CCANNNNNNNNNTGG 1 cut(s) 331
XhoI CTCGAG 1 cut(s) 782
XmaJI CCTAGG 1 cut(s) 566
XspI CTAG 3 cut(s) 186, 567, 594
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.