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

Gene ID: 328, updated on 4-Jan-2025

Summary

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

See APEX1 in Genome Data Viewer
Location:
14q11.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (20455226..20457767)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (14652129..14654670)
RS_2024_09 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

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

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

Interactions

General gene information

Gene Ontology Provided by GOA

Items 1 - 25 of 29
Function Evidence Code Pubs
enables 3'-5' exonuclease activity PubMed 
enables 3'-5' exonuclease activity PubMed 
enables 3'-5'-DNA exonuclease activity PubMed 
enables DNA binding PubMed 
enables DNA endonuclease activity  
enables DNA-(abasic site) binding PubMed 
enables DNA-(apurinic or apyrimidinic site) endonuclease activity  
enables DNA-(apurinic or apyrimidinic site) endonuclease activity PubMed 
enables DNA-(apurinic or apyrimidinic site) endonuclease activity PubMed 
enables RNA binding PubMed 
enables RNA-DNA hybrid ribonuclease activity PubMed 
enables chromatin DNA binding PubMed 
enables class II DNA-(apurinic or apyrimidinic site) endonuclease activity PubMed 
enables damaged DNA binding PubMed 
enables double-stranded DNA 3'-5' DNA exonuclease activity  
enables double-stranded DNA exodeoxyribonuclease activity PubMed 
enables double-stranded telomeric DNA binding PubMed 
enables endonuclease activity PubMed 
enables metal ion binding PubMed 
enables oxidoreductase activity PubMed 
enables phosphodiesterase I activity PubMed 
enables phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands PubMed 
enables phosphoric diester hydrolase activity  
enables phosphoric diester hydrolase activity PubMed 
enables protein binding PubMed 
enables site-specific endodeoxyribonuclease activity, specific for altered base PubMed 
enables transcription coactivator activity PubMed 
enables transcription corepressor activity PubMed 
enables uracil DNA N-glycosylase activity  
Items 1 - 25 of 29
Component Evidence Code Pubs
located_in centrosome  
located_in chromosome, telomeric region PubMed 
located_in cytoplasm PubMed 
located_in endoplasmic reticulum PubMed 
located_in mitochondrion PubMed 
located_in mitochondrion PubMed 
located_in nuclear speck PubMed 
located_in nucleolus PubMed 
located_in nucleoplasm PubMed 
located_in nucleoplasm  
is_active_in nucleus  
located_in nucleus PubMed 
located_in perinuclear region of cytoplasm PubMed 
located_in ribosome PubMed 

General protein information

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_001244249.2NP_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:62316
    Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases
  2. NM_001641.4NP_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:62316
    Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases
  3. NM_080648.3NP_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:62316
    Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases
  4. NM_080649.3NP_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:62316
    Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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)
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