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

    Gene ID: 328, updated on 25-Jan-2022

    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
    NEW
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    Genomic context

    See APEX1 in Genome Data Viewer
    Location:
    14q11.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    109.20211119 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (20455226..20457767)
    105.20201022 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 phosphatidylinositol-4,5-bisphosphate 4-phosphatase 1 Neighboring gene purine nucleoside phosphorylase Neighboring gene ribonuclease A family member 10 (inactive)

    Genomic regions, transcripts, and products

    Expression

    • 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

    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

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    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'-exodeoxyribonuclease activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
    PubMed 
    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 NF-kappaB binding IEA
    Inferred from Electronic Annotation
    more info
     
    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' exodeoxyribonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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 endodeoxyribonuclease activity TAS
    Traceable Author Statement
    more info
     
    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
    PubMed 
    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 protein-containing complex binding IEA
    Inferred from Electronic Annotation
    more info
     
    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, endonucleolytic IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in DNA demethylation 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 RNA phosphodiester bond hydrolysis, endonucleolytic IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in aging IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in base-excision repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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 cellular response to cAMP IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to hydrogen peroxide IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to peptide hormone stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of smooth muscle cell migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of G1/S transition of mitotic cell cycle IEA
    Inferred from Electronic Annotation
    more info
     
    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 response to xenobiotic stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    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
    PubMed 
    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 
    part_of transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    DNA-(apurinic or apyrimidinic site) endonuclease
    Names
    AP endonuclease class I
    AP lyase
    APEX nuclease (multifunctional DNA repair enzyme) 1
    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)

    NEW Try the new Transcript table

    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-(apurinic or apyrimidinic site) endonuclease

      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
      UniProtKB/TrEMBL
      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-(apurinic or apyrimidinic site) endonuclease

      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
      UniProtKB/TrEMBL
      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-(apurinic or apyrimidinic site) endonuclease

      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
      UniProtKB/TrEMBL
      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-(apurinic or apyrimidinic site) endonuclease

      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
      UniProtKB/TrEMBL
      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: Homo sapiens Updated Annotation Release 109.20211119

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p13 Primary Assembly

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