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    APEX2 apurinic/apyrimidinic endodeoxyribonuclease 2 [ Homo sapiens (human) ]

    Gene ID: 27301, updated on 17-Jun-2024

    Summary

    Official Symbol
    APEX2provided by HGNC
    Official Full Name
    apurinic/apyrimidinic endodeoxyribonuclease 2provided by HGNC
    Primary source
    HGNC:HGNC:17889
    See related
    Ensembl:ENSG00000169188 MIM:300773; AllianceGenome:HGNC:17889
    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
    APE2; XTH2; ZGRF2; APEXL2
    Summary
    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]
    Expression
    Ubiquitous expression in placenta (RPKM 8.8), lymph node (RPKM 8.7) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See APEX2 in Genome Data Viewer
    Location:
    Xp11.21
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (55000363..55009057)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (54293489..54302183)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (55026796..55035490)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chrX:54962395-54962556 Neighboring gene small nucleolar RNA, H/ACA box 11G Neighboring gene trophinin Neighboring gene 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:54977103-54977603 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20865 Neighboring gene Sharpr-MPRA regulatory regions 2439 and 5762 Neighboring gene ALAS2 intronic erythroid enhancer Neighboring gene ALAS2 intron 1 and 3 erythroid regulatory elements Neighboring gene 5'-aminolevulinate synthase 2 Neighboring gene PAGE family member 2B Neighboring gene HDGFL3 pseudogene 1 Neighboring gene PAGE family member 2

    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?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA-(apurinic or apyrimidinic site) endonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables double-stranded DNA 3'-5' DNA exonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables endonuclease activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables phosphoric diester hydrolase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in DNA recombination IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in base-excision repair IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    DNA-(apurinic or apyrimidinic site) endonuclease 2
    Names
    AP endonuclease 2
    AP endonuclease XTH2
    APEX nuclease (apurinic/apyrimidinic endonuclease) 2
    DNA-(apurinic or apyrimidinic site) lyase 2
    apurinic/apyrimidinic endonuclease-like 2
    zinc finger, GRF-type containing 2
    NP_001258677.1
    NP_055296.2

    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_012568.1 RefSeqGene

      Range
      5017..13711
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001271748.2NP_001258677.1  DNA-(apurinic or apyrimidinic site) endonuclease 2 isoform 2

      See identical proteins and their annotated locations for NP_001258677.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks a 5' exon compared to variant 1. This variant represents translation initiation at a downstream AUG compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a weak Kozak sequence and a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream AUG. The encoded protein (isoform 2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK301555, AK316186, AL020991, BM795632, BP363514
      UniProtKB/TrEMBL
      B4DWI9, B7ZA71
      Conserved Domains (2) summary
      pfam06839
      Location:296343
      zf-GRF; GRF zinc finger
      cl00490
      Location:1140
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
    2. NM_014481.4NP_055296.2  DNA-(apurinic or apyrimidinic site) endonuclease 2 isoform 1

      See identical proteins and their annotated locations for NP_055296.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL020991, BC002959, BM795632, BP363514
      Consensus CDS
      CCDS14365.1
      UniProtKB/Swiss-Prot
      Q9UBZ4, Q9Y5X7
      UniProtKB/TrEMBL
      E5KN95, E5KNB2, E5KNC9
      Related
      ENSP00000364126.3, ENST00000374987.4
      Conserved Domains (3) summary
      cd09088
      Location:3311
      Ape2-like_AP-endo; Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases
      pfam06839
      Location:467514
      zf-GRF; GRF zinc finger
      cl27087
      Location:347449
      SPOR; Sporulation related domain

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      55000363..55009057
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      54293489..54302183
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)