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APEX1 apurinic/apyrimidinic endodeoxyribonuclease 1 [ Homo sapiens (human) ]

Gene ID: 328, updated on 14-Apr-2024

Summary

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Official Symbol
APEX1provided by HGNC
Official Full Name
apurinic/apyrimidinic endodeoxyribonuclease 1provided by HGNC
Primary source
HGNC:HGNC:587
See related
Ensembl:ENSG00000100823 MIM:107748; AllianceGenome:HGNC:587
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
APE; APX; APE1; APEN; APEX; HAP1; REF1
Summary
The APEX gene encodes the major AP endonuclease in human cells. It encodes the APEX endonuclease, a DNA repair enzyme with apurinic/apyrimidinic (AP) activity. Such AP activity sites occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by DNA glycosylases that remove specific abnormal bases. The AP sites are the most frequent pre-mutagenic lesions that can prevent normal DNA replication. Splice variants have been found for this gene; all encode the same protein. Disruptions in the biological functions related to APEX are associated with many various malignancies and neurodegenerative diseases.[provided by RefSeq, Dec 2019]
Expression
Ubiquitous expression in ovary (RPKM 68.7), endometrium (RPKM 60.6) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
14q11.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (20455226..20457767)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (14652129..14654670)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (20923385..20925926)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene solute carrier family 12 member 3 pseudogene Neighboring gene OSGEP/APEX1 bi-directional promoter region Neighboring gene O-sialoglycoprotein endopeptidase Neighboring gene Sharpr-MPRA regulatory region 9617 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:20928913-20929879 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:20929880-20930845 Neighboring gene phosphatidylinositol-4,5-bisphosphate 4-phosphatase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:20937332-20937836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8079 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:20945841-20946029 Neighboring gene purine nucleoside phosphorylase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8080 Neighboring gene ribonuclease A family member 10 (inactive)

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Dual Function of Secreted APE1/Ref-1 in TNBC Tumorigenesis: An Apoptotic Initiator and a Regulator of Chronic Inflammatory Signaling. Choi S, et al. Int J Mol Sci, 2022 Aug 12. PMID 36012284, Free PMC Article
  2. Conformational Rearrangements Regulating the DNA Repair Protein APE1. Komaniecka N, et al. Int J Mol Sci, 2022 Jul 20. PMID 35887361, Free PMC Article
  3. Idiopathic sudden sensorineural hearing loss: A critique on corticosteroid therapy. Murray DH, et al. Hear Res, 2022 Sep 1. PMID 35816890
  4. APEX1 regulates alternative splicing of key tumorigenesis genes in non-small-cell lung cancer. Peng L, et al. BMC Med Genomics, 2022 Jul 2. PMID 35780128, Free PMC Article
  5. Effect of DNA Methylation on the 3'→5' Exonuclease Activity of Major Human Abasic Site Endonuclease APEX1. Endutkin AV, et al. Biochemistry (Mosc), 2022 Jan. PMID 35491018

See all (705) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) promotes stress granule formation via YBX1 phosphorylation in ovarian cancer.
    Title: Apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) promotes stress granule formation via YBX1 phosphorylation in ovarian cancer.
  2. Investigation of APE1 and OGG1 expression in chronic hemodialysis patients.
    Title: Investigation of APE1 and OGG1 expression in chronic hemodialysis patients.
  3. In vitro and In vivo evidence demonstrating chronic absence of Ref-1 Cysteine 65 impacts Ref-1 folding configuration, redox signaling, proliferation and metastasis in pancreatic cancer.
    Title: In vitro and In vivo evidence demonstrating chronic absence of Ref-1 Cysteine 65 impacts Ref-1 folding configuration, redox signaling, proliferation and metastasis in pancreatic cancer.
  4. Back-Up Base Excision DNA Repair in Human Cells Deficient in the Major AP Endonuclease, APE1.
    Title: Back-Up Base Excision DNA Repair in Human Cells Deficient in the Major AP Endonuclease, APE1.
  5. Coordination between human DNA polymerase beta and apurinic/apyrimidinic endonuclease 1 in the course of DNA repair.
    Title: Coordination between human DNA polymerase β and apurinic/apyrimidinic endonuclease 1 in the course of DNA repair.
  6. Expression of Apurinic/Apyrimidinic Endonuclease 1 in Colorectal Cancer and its Relation to Tumor Progression and Prognosis.
    Title: Expression of Apurinic/Apyrimidinic Endonuclease 1 in Colorectal Cancer and its Relation to Tumor Progression and Prognosis.
  7. APE1-dependent base excision repair of DNA photodimers in human cells.
    Title: APE1-dependent base excision repair of DNA photodimers in human cells.
  8. JNK mediates cell death by promoting the ubiquitination of the apurinic/apyrimidinic endonuclease APE1.
    Title: JNK mediates cell death by promoting the ubiquitination of the apurinic/apyrimidinic endonuclease APE1.
  9. AUF1 Recognizes 8-Oxo-Guanosine Embedded in DNA and Stimulates APE1 Endoribonuclease Activity.
    Title: AUF1 Recognizes 8-Oxo-Guanosine Embedded in DNA and Stimulates APE1 Endoribonuclease Activity.
  10. APE1 promotes embryonic stem cell proliferation and teratoma formation by regulating GDNF/GFRalpha1 axis.
    Title: APE1 promotes embryonic stem cell proliferation and teratoma formation by regulating GDNF/GFRα1 axis.
Submit: New GeneRIF Correction See all GeneRIFs (513)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
SiRNA-mediated knockdown of one of the components of the SET complex, APE1, inhibits HIV-1 infection with significantly reduced levels of integrated HIV-1 DNA and viral production in HeLa-CD4 cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, APEX nuclease 1 (APEX1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with APEX1 is increased by RRE PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 3'-5' exonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables 3'-5' exonuclease activity TAS
Traceable Author Statement
more info
 PubMed 
enables 3'-5'-DNA exonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA endonuclease activity TAS
Traceable Author Statement
more info
  
enables DNA-(abasic site) binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables DNA-(apurinic or apyrimidinic site) endonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-(apurinic or apyrimidinic site) endonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-(apurinic or apyrimidinic site) endonuclease activity TAS
Traceable Author Statement
more info
 PubMed 
enables RNA binding HDA PubMed 
enables RNA-DNA hybrid ribonuclease activity TAS
Traceable Author Statement
more info
 PubMed 
enables chromatin DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables class II DNA-(apurinic or apyrimidinic site) endonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables damaged DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables double-stranded DNA 3'-5' DNA exonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables double-stranded DNA exodeoxyribonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables double-stranded telomeric DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables endonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables oxidoreductase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphodiesterase I activity TAS
Traceable Author Statement
more info
 PubMed 
enables phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphoric diester hydrolase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphoric diester hydrolase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables site-specific endodeoxyribonuclease activity, specific for altered base IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription coactivator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription corepressor activity TAS
Traceable Author Statement
more info
 PubMed 
enables uracil DNA N-glycosylase activity TAS
Traceable Author Statement
more info
  
Process Evidence Code Pubs
involved_in DNA catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA recombination IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in base-excision repair IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in base-excision repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in base-excision repair, gap-filling TAS
Traceable Author Statement
more info
  
involved_in cell redox homeostasis IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of gene expression via chromosomal CpG island demethylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of apoptotic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of mRNA stability IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in telomere maintenance IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in telomere maintenance via base-excision repair IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in centrosome IDA
Inferred from Direct Assay
more info
  
located_in chromosome, telomeric region IC
Inferred by Curator
more info
 PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum TAS
Traceable Author Statement
more info
 PubMed 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in ribosome TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
DNA repair nuclease/redox regulator APEX1
Names
AP endonuclease class I
AP lyase
APEX nuclease (multifunctional DNA repair enzyme) 1
DNA-(apurinic or apyrimidinic site) endonuclease
DNA-(apurinic or apyrimidinic site) lyase
apurinic-apyrimidinic endonuclease 1
apurinic/apyrimidinic (abasic) endonuclease
deoxyribonuclease (apurinic or apyrimidinic)
protein REF-1
redox factor-1
NP_001231178.1
NP_001632.2
NP_542379.1
NP_542380.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008718.1 RefSeqGene

    Range
    5096..7637
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001244249.2 → NP_001231178.1  DNA repair nuclease/redox regulator APEX1

    See identical proteins and their annotated locations for NP_001231178.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses a donor splice site for exon 1 downstream of that used by variant 3.
    Source sequence(s)
    AI554786, AK291100, CB139337
    Consensus CDS
    CCDS9550.1
    UniProtKB/Swiss-Prot
    P27695, Q969L5, Q99775
    UniProtKB/TrEMBL
    G3V3M6, Q5TZP7
    Conserved Domains (1) summary
    cd09087
    Location:62 → 316
    Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases

  2. NM_001641.4 → NP_001632.2  DNA repair nuclease/redox regulator APEX1

    See identical proteins and their annotated locations for NP_001632.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) contains the full-length first exon and is the longest transcript.
    Source sequence(s)
    AI554786, AK291100
    Consensus CDS
    CCDS9550.1
    UniProtKB/Swiss-Prot
    P27695, Q969L5, Q99775
    UniProtKB/TrEMBL
    G3V3M6, Q5TZP7
    Related
    ENSP00000216714.3, ENST00000216714.8
    Conserved Domains (1) summary
    cd09087
    Location:62 → 316
    Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases

  3. NM_080648.3 → NP_542379.1  DNA repair nuclease/redox regulator APEX1

    See identical proteins and their annotated locations for NP_542379.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses a different donor splice site for exon 1 when compared to variant 1.
    Source sequence(s)
    AL355075, BC004979
    Consensus CDS
    CCDS9550.1
    UniProtKB/Swiss-Prot
    P27695, Q969L5, Q99775
    UniProtKB/TrEMBL
    G3V3M6, Q5TZP7
    Related
    ENSP00000381111.4, ENST00000398030.8
    Conserved Domains (1) summary
    cd09087
    Location:62 → 316
    Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases

  4. NM_080649.3 → NP_542380.1  DNA repair nuclease/redox regulator APEX1

    See identical proteins and their annotated locations for NP_542380.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses a donor splice site for exon 1 downstream of that used by variant 2.
    Source sequence(s)
    BC095428
    Consensus CDS
    CCDS9550.1
    UniProtKB/Swiss-Prot
    P27695, Q969L5, Q99775
    UniProtKB/TrEMBL
    G3V3M6, Q5TZP7
    Related
    ENSP00000451979.1, ENST00000555414.5
    Conserved Domains (1) summary
    cd09087
    Location:62 → 316
    Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    20455226..20457767
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791796.1 Reference GRCh38.p14 PATCHES

    Range
    657907..660448
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    14652129..14654670
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P27695.2 GenPept UniProtKB/Swiss-Prot:P27695

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