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Aliases for APEX2 Gene

Aliases for APEX2 Gene

  • Apurinic/Apyrimidinic Endodeoxyribonuclease 2 2 3 5
  • APEX Nuclease (Apurinic/Apyrimidinic Endonuclease) 2 2 3
  • Zinc Finger, GRF-Type Containing 2 2 3
  • AP Endonuclease XTH2 3 4
  • AP Endonuclease 2 3 4
  • APEXL2 3 4
  • APE2 3 4
  • XTH2 3 4
  • DNA-(Apurinic Or Apyrimidinic Site) Lyase 2 3
  • Apurinic/Apyrimidinic Endonuclease-Like 2 3
  • Apurinic-Apyrimidinic Endonuclease 2 4
  • APEX Nuclease-Like 2 4
  • APEX Nuclease 2 4
  • EC 4.2.99.18 4
  • 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 (Apurinic/Apyrimidinic Endodeoxyribonuclease 2) is a Protein Coding gene. Among its related pathways are Telomere C-strand (Lagging Strand) Synthesis. Gene Ontology (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.

Additional gene information for APEX2 Gene

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

Genomics for APEX2 Gene

GeneHancer (GH) Regulatory Elements for APEX2 Gene

Promoters and enhancers for APEX2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XI054999 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 565.4 +0.2 182 2.6 HDGF PKNOX1 ATF1 ARID4B SIN3A YY1 POLR2B ELK1 ATF7 SP3 APEX2 PFKFB1 PHF8 GNL3L PAGE2B
GH0XI054998 Promoter 0.5 EPDnew 550.8 -1.8 -1756 0.1 APEX2 PFKFB1 PIR44979
GH0XI054042 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 24.1 -956.0 -955974 3.9 PKNOX1 CLOCK FOXA2 ARNT NEUROD1 SIN3A FEZF1 DMAP1 ZNF2 YY1 PHF8 KDM5C ACTG1P10 SMC1A KANTR ENSG00000233250 TSPYL2 APEX2 GPR173 MAGED2
GH0XI055006 Enhancer 1.2 Ensembl ENCODE dbSUPER 6.1 +7.9 7900 3.4 ELF3 FOXA2 JUN MAX CEBPG RAD21 ZBTB40 YY1 POLR2A VEZF1 TRO PFKFB1 APEX2 ALAS2 PAGE2B
GH0XI055003 Enhancer 0.4 ENCODE dbSUPER 0.8 +3.9 3867 1.6 APEX2 PAGE2B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around APEX2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the APEX2 gene promoter:

Genomic Locations for APEX2 Gene

Genomic Locations for APEX2 Gene
chrX:55,000,323-55,009,057
(GRCh38/hg38)
Size:
8,735 bases
Orientation:
Plus strand
chrX:55,026,780-55,035,490
(GRCh37/hg19)

Genomic View for APEX2 Gene

Genes around APEX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
APEX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for APEX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene 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;
    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

Post-translational modifications for APEX2 Gene

  • Ubiquitination at posLast=338338, Lys371, and Lys457
  • Modification sites at PhosphoSitePlus

Other Protein References for APEX2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for APEX2 Gene

Domains & Families for APEX2 Gene

Gene Families for APEX2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

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 IEA --
GO:0004519 endonuclease activity IEA --
GO:0004527 exonuclease activity 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:

Clone Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for APEX2 gene
Compartment Confidence
nucleus 5
mitochondrion 4
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (3)
  • Nucleus (3)
  • Vesicles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for APEX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA --
GO:0005622 intracellular IEA --
GO:0005634 nucleus IDA,IBA --
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IEA --
genes like me logo Genes that share ontologies with APEX2: view

Pathways & Interactions for APEX2 Gene

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

Pathways by source for APEX2 Gene

1 KEGG pathway for APEX2 Gene

Gene Ontology (GO) - Biological Process for APEX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006281 DNA repair IEA --
GO:0006284 base-excision repair IBA --
GO:0006310 DNA recombination IEA --
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0007049 cell cycle 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

(1) ApexBio Compounds for APEX2 Gene

Compound Action Cas Number
CRT0044876 6960-45-8
genes like me logo Genes that share compounds with APEX2: view

Drug Products

Transcripts for APEX2 Gene

mRNA/cDNA for APEX2 Gene

Unigene Clusters for APEX2 Gene

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

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE for APEX2 Gene

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



NURSA nuclear receptor signaling pathways regulating expression of APEX2 Gene:

APEX2

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.

Evidence on tissue expression from TISSUES for APEX2 Gene

  • Bone marrow(4.2)
  • Lung(4.2)
genes like me logo Genes that share expression patterns with APEX2: view

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 , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia APEX2 34 33
  • 95.78 (n)
OneToOne
dog
(Canis familiaris)
Mammalia APEX2 34 33
  • 87.9 (n)
OneToOne
cow
(Bos Taurus)
Mammalia APEX2 33 34
  • 87.81 (n)
mouse
(Mus musculus)
Mammalia Apex2 16 34 33
  • 83.33 (n)
rat
(Rattus norvegicus)
Mammalia Apex2 33
  • 83.01 (n)
oppossum
(Monodelphis domestica)
Mammalia APEX2 34
  • 57 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia APEX2 34
  • 50 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia APEX2 34
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia apex2 33
  • 57.79 (n)
zebrafish
(Danio rerio)
Actinopterygii apex2 33 34
  • 54.91 (n)
APEX2 (2 of 2) 34
  • 43 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes APN2 34 36
  • 19 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G36050 33
  • 50.49 (n)
rice
(Oryza sativa)
Liliopsida Os09g0536000 33
  • 47.5 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU01961 33
  • 47.98 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes apn2 33
  • 46.14 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 40 (a)
OneToOne
Species where no ortholog for APEX2 was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs1000994387 -- 55,001,028(+) A/G intron_variant
rs1002177796 -- 55,002,695(+) T/C intron_variant
rs1002242249 -- 55,001,515(+) T/A intron_variant
rs1002478846 -- 55,004,307(+) G/C intron_variant
rs1002514685 -- 55,004,697(+) C/T intron_variant

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

Variant ID Type Subtype PubMed ID
esv2740175 CNV deletion 23290073
esv3573984 CNV loss 25503493
nsv435891 CNV deletion 17901297

Variation tolerance for APEX2 Gene

Residual Variation Intolerance Score: 86.1% 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)

Additional Variant Information for APEX2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
APEX2

SNP Genotyping and Copy Number Assay Products

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

Disorders for APEX2 Gene

Additional Disease Information for APEX2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for APEX2 Gene.

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 research 2001) 2 3 4 22 58
  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 research 2009) 3 4 22 58
  3. Human Ape2 protein has a 3'-5' exonuclease activity that acts preferentially on mismatched base pairs. (PMID: 16687656) Burkovics P … Haracska L (Nucleic acids research 2006) 3 4 22 58
  4. Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing. (PMID: 20843780) Wang W … Scharfe C (Nucleic acids research 2011) 3 4 58
  5. Variation within DNA repair pathway genes and risk of multiple sclerosis. (PMID: 20522537) Briggs FB … International Multiple Sclerosis Genetics Consortium (American journal of epidemiology 2010) 3 44 58

Products for APEX2 Gene

Sources for APEX2 Gene

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