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Aliases for APEX2 Gene

Aliases for APEX2 Gene

  • APEX Nuclease (Apurinic/Apyrimidinic Endonuclease) 2 2 3
  • AP Endonuclease XTH2 3 4
  • AP Endonuclease 2 3 4
  • APEXL2 3 4
  • APE2 3 4
  • XTH2 3 4
  • Apurinic/Apyrimidinic Endonuclease-Like 2 3
  • Apurinic-Apyrimidinic Endonuclease 2 4
  • Zinc Finger, GRF-Type Containing 2 3
  • GRF-Type Containing 2 2
  • APEX Nuclease-Like 2 4
  • APEX Nuclease 2 4
  • EC 4.2.99.18 4
  • Zinc Finger 2
  • EC 3.1.-.- 4
  • ZGRF2 3

External Ids for APEX2 Gene

Previous GeneCards Identifiers for APEX2 Gene

  • GC0XP051878
  • GC0XP052964
  • GC0XP053632
  • GC0XP053993
  • GC0XP054909
  • GC0XP052077

Summaries for APEX2 Gene

Entrez Gene Summary for APEX2 Gene

  • Apurinic/apyrimidinic (AP) sites occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by DNA glycosylases that remove specific abnormal bases. AP sites are pre-mutagenic lesions that can prevent normal DNA replication so the cell contains systems to identify and repair such sites. Class II AP endonucleases cleave the phosphodiester backbone 5' to the AP site. This gene encodes a protein shown to have a weak class II AP endonuclease activity. Most of the encoded protein is located in the nucleus but some is also present in mitochondria. This protein may play an important role in both nuclear and mitochondrial base excision repair. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2012]

GeneCards Summary for APEX2 Gene

APEX2 (APEX Nuclease (Apurinic/Apyrimidinic Endonuclease) 2) is a Protein Coding gene. Among its related pathways are Lagging Strand Synthesis. GO annotations related to this gene include nuclease activity and double-stranded DNA 3-5 exodeoxyribonuclease activity. An important paralog of this gene is APEX1.

UniProtKB/Swiss-Prot for APEX2 Gene

  • Function as a weak apurinic/apyrimidinic (AP) endodeoxyribonuclease in the DNA base excision repair (BER) pathway of DNA lesions induced by oxidative and alkylating agents. Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage, generating a single-strand break with 5-deoxyribose phosphate and 3-hydroxyl ends. Displays also double-stranded DNA 3-5 exonuclease, 3-phosphodiesterase activities. Shows robust 3-5 exonuclease activity on 3-recessed heteroduplex DNA and is able to remove mismatched nucleotides preferentially. Shows fairly strong 3-phosphodiesterase activity involved in the removal of 3-damaged termini formed in DNA by oxidative agents. In the nucleus functions in the PCNA-dependent BER pathway. Required for somatic hypermutation (SHM) and DNA cleavage step of class switch recombination (CSR) of immunoglobulin genes. Required for proper cell cycle progression during proliferation of peripheral lymphocytes.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for APEX2 Gene

Genomics for APEX2 Gene

Regulatory Elements for APEX2 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for APEX2 Gene

Chromosome:
X
Start:
55,000,323 bp from pter
End:
55,009,057 bp from pter
Size:
8,735 bases
Orientation:
Plus strand

Genomic View for APEX2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
GeneLoc Logo Gene Density

RefSeq DNA sequence for APEX2 Gene

Proteins for APEX2 Gene

  • Protein details for APEX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UBZ4-APEX2_HUMAN
    Recommended name:
    DNA-(apurinic or apyrimidinic site) lyase 2
    Protein Accession:
    Q9UBZ4
    Secondary Accessions:
    • Q9Y5X7

    Protein attributes for APEX2 Gene

    Size:
    518 amino acids
    Molecular mass:
    57401 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Note=Probably binds two magnesium or manganese ions per subunit.;
    Quaternary structure:
    • Interacts with PCNA; this interaction is triggered by reactive oxygen species and increased by misincorporation of uracil in nuclear DNA.

neXtProt entry for APEX2 Gene

Proteomics data for APEX2 Gene at MOPED

Post-translational modifications for APEX2 Gene

  • Ubiquitination at Lys 338, Lys 371, and Lys 457
  • Modification sites at PhosphoSitePlus

Other Protein References for APEX2 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for APEX2 Gene

Domains & Families for APEX2 Gene

Gene Families for APEX2 Gene

Protein Domains for APEX2 Gene

Graphical View of Domain Structure for InterPro Entry

Q9UBZ4

UniProtKB/Swiss-Prot:

APEX2_HUMAN :
  • Belongs to the DNA repair enzymes AP/ExoA family.
Family:
  • Belongs to the DNA repair enzymes AP/ExoA family.
genes like me logo Genes that share domains with APEX2: view

Function for APEX2 Gene

Molecular function for APEX2 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
pH dependence: Optimum pH is 6.0-8.0. {ECO:0000269 PubMed:16687656};
UniProtKB/Swiss-Prot CatalyticActivity:
The C-O-P bond 3 to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3-terminal unsaturated sugar and a product with a terminal 5-phosphate.
UniProtKB/Swiss-Prot EnzymeRegulation:
3-5 exonuclease activity is activated by sodium and manganese. 3-5 exonuclease and 3-phosphodiesterase activities are stimulated in presence of PCNA
UniProtKB/Swiss-Prot Function:
Function as a weak apurinic/apyrimidinic (AP) endodeoxyribonuclease in the DNA base excision repair (BER) pathway of DNA lesions induced by oxidative and alkylating agents. Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage, generating a single-strand break with 5-deoxyribose phosphate and 3-hydroxyl ends. Displays also double-stranded DNA 3-5 exonuclease, 3-phosphodiesterase activities. Shows robust 3-5 exonuclease activity on 3-recessed heteroduplex DNA and is able to remove mismatched nucleotides preferentially. Shows fairly strong 3-phosphodiesterase activity involved in the removal of 3-damaged termini formed in DNA by oxidative agents. In the nucleus functions in the PCNA-dependent BER pathway. Required for somatic hypermutation (SHM) and DNA cleavage step of class switch recombination (CSR) of immunoglobulin genes. Required for proper cell cycle progression during proliferation of peripheral lymphocytes.

Enzyme Numbers (IUBMB) for APEX2 Gene

Gene Ontology (GO) - Molecular Function for APEX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003906 DNA-(apurinic or apyrimidinic site) lyase activity IBA --
GO:0004518 nuclease activity --
GO:0004519 endonuclease activity --
GO:0008270 zinc ion binding IEA --
genes like me logo Genes that share ontologies with APEX2: view
genes like me logo Genes that share phenotypes with APEX2: view

Animal Models for APEX2 Gene

MGI Knock Outs for APEX2:

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for APEX2

In Situ Assay Products

Flow Cytometry Products

No data available for Transcription Factor Targets and HOMER Transcription for APEX2 Gene

Localization for APEX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for APEX2 Gene

Nucleus. Cytoplasm. Mitochondrion. Note=Together with PCNA, is redistributed in discrete nuclear foci in presence of oxidative DNA damaging agents.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for APEX2 Gene COMPARTMENTS Subcellular localization image for APEX2 gene
Compartment Confidence
nucleus 4
mitochondrion 2

Gene Ontology (GO) - Cellular Components for APEX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular --
GO:0005634 nucleus IDA --
GO:0005730 nucleolus IDA --
GO:0005739 mitochondrion --
GO:0005743 mitochondrial inner membrane IEA --
genes like me logo Genes that share ontologies with APEX2: view

Pathways & Interactions for APEX2 Gene

SuperPathways for APEX2 Gene

Superpath Contained pathways
1 Lagging Strand Synthesis
genes like me logo Genes that share pathways with APEX2: view

Pathways by source for APEX2 Gene

1 KEGG pathway for APEX2 Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for APEX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006281 DNA repair --
GO:0006284 base-excision repair IBA --
GO:0006310 DNA recombination IEA --
GO:0007049 cell cycle IEA --
GO:0090305 nucleic acid phosphodiester bond hydrolysis IEA --
genes like me logo Genes that share ontologies with APEX2: view

No data available for SIGNOR curated interactions for APEX2 Gene

Drugs & Compounds for APEX2 Gene

(1) Drugs for APEX2 Gene - From: ApexBio

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
CRT0044876 Pharma 0
genes like me logo Genes that share compounds with APEX2: view

Transcripts for APEX2 Gene

mRNA/cDNA for APEX2 Gene

Unigene Clusters for APEX2 Gene

APEX nuclease (apurinic/apyrimidinic endonuclease) 2:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for APEX2

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for APEX2 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b
SP1:
SP2: -

Relevant External Links for APEX2 Gene

GeneLoc Exon Structure for
APEX2
ECgene alternative splicing isoforms for
APEX2

Expression for APEX2 Gene

mRNA expression in normal human tissues for APEX2 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for APEX2 Gene



SOURCE GeneReport for Unigene cluster for APEX2 Gene Hs.659558

mRNA Expression by UniProt/SwissProt for APEX2 Gene

Q9UBZ4-APEX2_HUMAN
Tissue specificity: Highly expressed in brain and kidney. Weakly expressed in the fetal brain.
genes like me logo Genes that share expression patterns with APEX2: view

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues and Protein tissue co-expression partners for APEX2 Gene

Orthologs for APEX2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for APEX2 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia APEX2 35
  • 87.81 (n)
  • 85.6 (a)
APEX2 36
  • 86 (a)
OneToOne
dog
(Canis familiaris)
Mammalia APEX2 35
  • 87.9 (n)
  • 85.83 (a)
APEX2 36
  • 85 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Apex2 35
  • 83.33 (n)
  • 79.65 (a)
Apex2 16
Apex2 36
  • 80 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia APEX2 35
  • 95.78 (n)
  • 94.85 (a)
APEX2 36
  • 96 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Apex2 35
  • 83.01 (n)
  • 79.65 (a)
oppossum
(Monodelphis domestica)
Mammalia APEX2 36
  • 57 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia APEX2 36
  • 50 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia APEX2 36
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia apex2 35
  • 57.79 (n)
  • 54.92 (a)
zebrafish
(Danio rerio)
Actinopterygii apex2 35
  • 54.91 (n)
  • 51.81 (a)
apex2 36
  • 44 (a)
OneToMany
APEX2 (2 of 2) 36
  • 43 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes APN2 36
  • 19 (a)
OneToMany
APN2 38
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G36050 35
  • 50.49 (n)
  • 44.15 (a)
rice
(Oryza sativa)
Liliopsida Os09g0536000 35
  • 47.5 (n)
  • 41.82 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU01961 35
  • 47.98 (n)
  • 38.63 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes apn2 35
  • 46.14 (n)
  • 38.19 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 40 (a)
OneToOne
Species with no ortholog for APEX2:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for APEX2 Gene

ENSEMBL:
Gene Tree for APEX2 (if available)
TreeFam:
Gene Tree for APEX2 (if available)

Paralogs for APEX2 Gene

Paralogs for APEX2 Gene

genes like me logo Genes that share paralogs with APEX2: view

Variants for APEX2 Gene

Sequence variations from dbSNP and Humsavar for APEX2 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
rs1883158 -- 55,004,028(-) gtcta(C/T)tgaat intron-variant
rs2301416 -, - 55,002,430(-) TTACC(A/C/G)GATCT intron-variant, reference, missense
rs2301417 -- 55,002,417(-) TGCTG(C/T)GTGAG intron-variant, reference, synonymous-codon
rs2858764 -- 55,007,490(-) AGCTG(G/T)CCTCA utr-variant-3-prime
rs2858765 -- 55,007,075(-) GGGGA(A/G)GGCTG reference, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for APEX2 Gene

Variant ID Type Subtype PubMed ID
nsv435891 CNV Deletion 17901297
esv2740175 CNV Deletion 23290073

Variation tolerance for APEX2 Gene

Residual Variation Intolerance Score: 86.09% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.40; 27.54% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for APEX2 Gene

HapMap Linkage Disequilibrium report
APEX2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for APEX2 Gene

Disorders for APEX2 Gene

Relevant External Links for APEX2

Genetic Association Database (GAD)
APEX2
Human Genome Epidemiology (HuGE) Navigator
APEX2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
APEX2
genes like me logo Genes that share disorders with APEX2: view

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for APEX2 Gene

Publications for APEX2 Gene

  1. Human APE2 protein is mostly localized in the nuclei and to some extent in the mitochondria, while nuclear APE2 is partly associated with proliferating cell nuclear antigen. (PMID: 11376153) Tsuchimoto D. … Nakabeppu Y. (Nucleic Acids Res. 2001) 2 23 67
  2. Role of PCNA-dependent stimulation of 3'-phosphodiesterase and 3'-5' exonuclease activities of human Ape2 in repair of oxidative DNA damage. (PMID: 19443450) Burkovics P. … Haracska L. (Nucleic Acids Res. 2009) 23 67
  3. The roles of APE1, APE2, DNA polymerase beta and mismatch repair in creating S region DNA breaks during antibody class switch. (PMID: 19010771) Schrader C.E. … Stavnezer J. (Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2009) 23 67
  4. Human Ape2 protein has a 3'-5' exonuclease activity that acts preferentially on mismatched base pairs. (PMID: 16687656) Burkovics P. … Haracska L. (Nucleic Acids Res. 2006) 23 67
  5. Biological significance of the defense mechanisms against oxidative damage in nucleic acids caused by reactive oxygen species: from mitochondria to nuclei. (PMID: 15126288) Nakabeppu Y. … Sakumi K. (Ann. N. Y. Acad. Sci. 2004) 23 67

Products for APEX2 Gene

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat
  • Pathway & Disease-focused RT² Profiler PCR Arrays
  • QIAGEN qRT-PCR Assays for microRNAs that regulate APEX2
    • QuantiTect SYBR Green Assays in human,mouse,rat
    • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
    • QuantiFast Probe-based Assays in human,mouse,rat
    • Predesigned siRNA for gene silencing in human,mouse,rat for APEX2
    • Block miRNA regulation of APEX2 using miScript Target Protectors

    Sources for APEX2 Gene

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