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

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: mouse all
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Genomic context

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_000014.9 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 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?

Nanoscale Interaction of Endonuclease APE1 with DNA.
Title: Nanoscale Interaction of Endonuclease APE1 with DNA.
Live-cell imaging of human apurinic/apyrimidinic endonuclease 1 in the nucleus and nucleolus using a chaperone@DNA probe.
Title: Live-cell imaging of human apurinic/apyrimidinic endonuclease 1 in the nucleus and nucleolus using a chaperone@DNA probe.
APE1 inhibition enhances ferroptotic cell death and contributes to hepatocellular carcinoma therapy.
Title: APE1 inhibition enhances ferroptotic cell death and contributes to hepatocellular carcinoma therapy.
Apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) promotes stress granule formation via YBX1 phosphorylation in ovarian cancer.
Title: Apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) promotes stress granule formation via YBX1 phosphorylation in ovarian cancer.
Investigation of APE1 and OGG1 expression in chronic hemodialysis patients.
Title: Investigation of APE1 and OGG1 expression in chronic hemodialysis patients.
In vitro and In vivo evidence demonstrating chronic absence of Ref-1 Cysteine 65 impacts Ref-1 folding configuration, redox signaling, proliferation and metastasis in pancreatic cancer.
Title: In vitro and In vivo evidence demonstrating chronic absence of Ref-1 Cysteine 65 impacts Ref-1 folding configuration, redox signaling, proliferation and metastasis in pancreatic cancer.
Back-Up Base Excision DNA Repair in Human Cells Deficient in the Major AP Endonuclease, APE1.
Title: Back-Up Base Excision DNA Repair in Human Cells Deficient in the Major AP Endonuclease, APE1.
Coordination between human DNA polymerase beta and apurinic/apyrimidinic endonuclease 1 in the course of DNA repair.
Title: Coordination between human DNA polymerase β and apurinic/apyrimidinic endonuclease 1 in the course of DNA repair.
Expression of Apurinic/Apyrimidinic Endonuclease 1 in Colorectal Cancer and its Relation to Tumor Progression and Prognosis.
Title: Expression of Apurinic/Apyrimidinic Endonuclease 1 in Colorectal Cancer and its Relation to Tumor Progression and Prognosis.
APE1-dependent base excision repair of DNA photodimers in human cells.
Title: APE1-dependent base excision repair of DNA photodimers in human cells.

Submit: New GeneRIF Correction See all GeneRIFs (516)

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)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D2S2636 (e-PCR)
- UniSTS:70413

WI-18729 (e-PCR)
- UniSTS:63042

SHGC-36712 (e-PCR)
- UniSTS:60513

APEX1_1488.2 (e-PCR)
- UniSTS:280445

GDB:451907 (e-PCR)
- UniSTS:157388

APEX (e-PCR)
- UniSTS:479967

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'-DNA exonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA endonuclease activity	TAS Traceable Author Statement more info
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
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 RNA binding	HDA more info	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' DNA exonuclease activity	IBA Inferred from Biological aspect of Ancestor more info
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 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
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 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	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 base-excision repair	IBA Inferred from Biological aspect of Ancestor more info
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 negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression via chromosomal CpG island demethylation	IDA Inferred from Direct Assay more info	PubMed
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 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	HTP 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
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

General protein information

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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

EC 3.1.11.2

NP_001632.2

EC 3.1.11.2

NP_542379.1

EC 3.1.11.2

NP_542380.1

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_008718.1 RefSeqGene

Range

5096..7637

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001244249.2 → NP_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:62 → 316

Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases
NM_001641.4 → NP_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:62 → 316

Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases
NM_080648.3 → NP_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:62 → 316

Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases
NM_080649.3 → NP_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:62 → 316

Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases