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

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: mouse all
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Genomic context

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_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

APEX2-based Proximity Labeling of Atox1 Identifies CRIP2 as a Nuclear Copper-binding Protein that Regulates Autophagy Activation.
Title: APEX2-based Proximity Labeling of Atox1 Identifies CRIP2 as a Nuclear Copper-binding Protein that Regulates Autophagy Activation.
An APEX2 proximity ligation method for mapping interactions with the nuclear lamina.
Title: An APEX2 proximity ligation method for mapping interactions with the nuclear lamina.
Genomic alterations and abnormal expression of APE2 in multiple cancers.
Title: Genomic alterations and abnormal expression of APE2 in multiple cancers.
Authors now show by immunoelectron microscopy that VAPB also localizes to the inner nuclear membrane (INM). Using a modified enhanced ascorbate peroxidase 2 (APEX2) approach with rapamycin-dependent targeting of the peroxidase to a protein of interest, we searched for proteins that are in close proximity to VAPB, particularly at the INM.
Title: Proteomic mapping by rapamycin-dependent targeting of APEX2 identifies binding partners of VAPB at the inner nuclear membrane.
we propose a two-step APE1/APE2-mediated mechanism for DNA single-strand breaks (SSBs) end resection that couples DNA damage response with SSB repair in a eukaryotic system.
Title: APE1 senses DNA single-strand breaks for repair and signaling.
we describe the use of Clustered Regularly Interspaced Short Palindromic Repeats and an engineered ascorbate peroxidase 2 (APEX2) system to investigate local chromatin interactions (CAPLOCUS). We showed that with specific small-guide RNA targets, CAPLOCUS could efficiently identify both repetitive genomic regions and single-copy genomic locus with high resolution.
Title: Determination of local chromatin interactions using a combined CRISPR and peroxidase APEX2 system.
Identified APEX2 and FEN1 as synthetic lethal genes with both BRCA1 and BRCA2 loss of function in tumor cell lines.
Title: Genetic Screens Reveal FEN1 and APEX2 as BRCA2 Synthetic Lethal Targets.
Single-Strand Break End Resection in Genome Integrity: Mechanism and Regulation by APE2.
Title: Single-Strand Break End Resection in Genome Integrity: Mechanism and Regulation by APE2.
Observational study of gene-disease association. (HuGE Navigator)
Title: Variation within DNA repair pathway genes and risk of multiple sclerosis.
Ape2 may be involved in repair of oxidative DNA damage and PCNA-dependent repair synthesis.
Title: Role of PCNA-dependent stimulation of 3'-phosphodiesterase and 3'-5' exonuclease activities of human Ape2 in repair of oxidative DNA damage.

Submit: New GeneRIF Correction See all GeneRIFs (13)

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

APEX2_705 (e-PCR)
- UniSTS:276998

APEX2_V75 (e-PCR)
- UniSTS:276998

MARC_5951-5952:997299472:1 (e-PCR)
- UniSTS:269620

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
involved_in cell cycle	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

General protein information

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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

EC 3.1.11.2

NP_055296.2

EC 3.1.11.2

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

NG_012568.1 RefSeqGene

Range

5017..13711

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001271748.2 → NP_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:296 → 343

zf-GRF; GRF zinc finger

cl00490
Location:1 → 140

EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
NM_014481.4 → NP_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:3 → 311

Ape2-like_AP-endo; Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases

pfam06839
Location:467 → 514

zf-GRF; GRF zinc finger

cl27087
Location:347 → 449

SPOR; Sporulation related domain