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

Gene ID: 27301, updated on 22-Aug-2021

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
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
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Genomic context

See APEX2 in Genome Data Viewer
Location:
Xp11.21
Exon count:
6
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (55000363..55009057)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (55026796..55035490)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes 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 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

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?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

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
PubMed 
enables double-stranded DNA 3'-5' exodeoxyribonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables endonuclease activity IEA
Inferred from Electronic Annotation
more info
 
enables phosphoric diester hydrolase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
involved_in cell cycle IEA
Inferred from Electronic Annotation
more info
 
involved_in nucleic acid phosphodiester bond hydrolysis IEA
Inferred from Electronic Annotation
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
PubMed 

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)

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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_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
    UniProtKB/TrEMBL
    E5KN95
    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: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

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