Apex1 apurinic/apyrimidinic endodeoxyribonuclease 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Apex1provided by RGD
Official Full Name: apurinic/apyrimidinic endodeoxyribonuclease 1provided by RGD
Primary source: RGD:2126
See related: EnsemblRapid:ENSRNOG00000009663 AllianceGenome:RGD:2126
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: APE; Apex; REF-1
Summary: Enables NF-kappaB binding activity and endoribonuclease activity. Involved in several processes, including cellular response to organonitrogen compound; negative regulation of smooth muscle cell migration; and positive regulation of G1/S transition of mitotic cell cycle. Located in mitochondrion and nucleus. Part of transcription regulator complex. Biomarker of brain ischemia; lung disease; status epilepticus; and visual epilepsy. Human ortholog(s) of this gene implicated in breast cancer; female reproductive organ cancer (multiple); spina bifida; and urinary bladder cancer. Orthologous to human APEX1 (apurinic/apyrimidinic endodeoxyribonuclease 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Adrenal (RPKM 361.2), Testes (RPKM 265.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 15p14

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	15	NC_086033.1 (26618146..26620330)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	15	NC_051350.1 (24144595..24146785)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	15	NC_005114.4 (27849943..27852083)

Chromosome 15 - NC_086033.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Apurinic/apyrimidinic endonuclease 1 regulates palmitic acid-mediated apoptosis in cardiomyocytes via endoplasmic reticulum stress.
Title: Apurinic/apyrimidinic endonuclease 1 regulates palmitic acid-mediated apoptosis in cardiomyocytes via endoplasmic reticulum stress.
Our findings provide an insight into the PTEN and APE1 overexpression protects against cardiac hypoxia/reoxygenation injury, which may be through inducing the PINK1/Parkin-mediated mitophagy.
Title: PTEN-mediated mitophagy and APE1 overexpression protects against cardiac hypoxia/reoxygenation injury.
Changes in APE1 expression and sub-cellular distribution are implicated in inflammatory pain mechanisms mediated by APE1 redox functions.
Title: APE1/Ref-1 redox function contributes to inflammatory pain sensitization.
Study shows that genetically enhancing apurinic/apyrimidinic endonuclease expression or treatment with the small molecule, E3330, increases DNA repair.
Title: DNA damage mediates changes in neuronal sensitivity induced by the inflammatory mediators, MCP-1 and LPS, and can be reversed by enhancing the DNA repair function of APE1.
Our findings provided valuable insights into the redox function of APE1/Ref-1 in preventing Pi-induced VSMC calcification by inhibiting oxidative stress and osteoblastic differentiation, resulting in prevention of altered osteoblastic phenotypes in VSMCs.
Title: APE1/Ref-1 Inhibits Phosphate-Induced Calcification and Osteoblastic Phenotype Changes in Vascular Smooth Muscle Cells.
The results of this study suggest that Ape1 protects against neuron death by activating the ERK1/2 signaling pathway.
Title: Ape1 protects against MPP+-induced neurotoxicity through ERK1/2 signaling in PC12 cells.
altered expression and/or subcellular distribution of APE1/Ref-1 in activated astrocytes regulated the neuroinflammatory response to excitotoxin and endotoxin insults used in model of neurodegenerative brain diseases.
Title: The anti-inflammatory role of extranuclear apurinic/apyrimidinic endonuclease 1/redox effector factor-1 in reactive astrocytes.
This study suggests that a new function of GLP-1 is to elevate DNA repair by inducing the expression of the DNA repair protein APE1.
Title: Activation of GLP-1 Receptor Enhances Neuronal Base Excision Repair via PI3K-AKT-Induced Expression of Apurinic/Apyrimidinic Endonuclease 1.
In summary, APE1 is regulated at different levels after acute and chronic UUO. Thus, our results suggest that DNA repair activity is regulated in response to progressive (7 days) obstruction and that APE1 potentially could play a role in the development of fibrosis in kidney disease.
Title: Unilateral ureteral obstruction induces DNA repair by APE1.
Ape1 expression was initially high and then gradually reduced along with the tooth development.
Title: Inhibition of Ape1 Redox Activity Promotes Odonto/osteogenic Differentiation of Dental Papilla Cells.

Submit: New GeneRIF Correction See all GeneRIFs (32)

General gene information

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Markers

RH94450 (e-PCR)
- UniSTS:119698

RH140031 (e-PCR)
- UniSTS:222113

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 3'-5' exonuclease activity	ISO Inferred from Sequence Orthology more info
enables 3'-5' exonuclease activity	ISS Inferred from Sequence or Structural Similarity more info
enables 3'-5'-DNA exonuclease activity	IEA Inferred from Electronic Annotation more info
enables 3'-5'-DNA exonuclease activity	ISO Inferred from Sequence Orthology more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-(abasic site) binding	IEA Inferred from Electronic Annotation more info
enables DNA-(abasic site) binding	ISO Inferred from Sequence Orthology more info
enables DNA-(abasic site) binding	ISS Inferred from Sequence or Structural Similarity more info
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	ISO Inferred from Sequence Orthology more info
enables DNA-(apurinic or apyrimidinic site) endonuclease activity	ISS Inferred from Sequence or Structural Similarity more info
enables NF-kappaB binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA endonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables chromatin DNA binding	IEA Inferred from Electronic Annotation more info
enables chromatin DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables class II DNA-(apurinic or apyrimidinic site) endonuclease activity	IEA Inferred from Electronic Annotation more info
enables class II DNA-(apurinic or apyrimidinic site) endonuclease activity	ISO Inferred from Sequence Orthology more info
enables class II DNA-(apurinic or apyrimidinic site) endonuclease activity	ISS Inferred from Sequence or Structural Similarity more info
enables damaged DNA binding	ISO Inferred from Sequence Orthology more info
enables damaged DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables double-stranded DNA 3'-5' DNA exonuclease activity	IBA Inferred from Biological aspect of Ancestor more info
enables double-stranded DNA exodeoxyribonuclease activity	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA exodeoxyribonuclease activity	ISO Inferred from Sequence Orthology more info
enables double-stranded telomeric DNA binding	IEA Inferred from Electronic Annotation more info
enables double-stranded telomeric DNA binding	ISO Inferred from Sequence Orthology more info
enables endonuclease activity	IEA Inferred from Electronic Annotation more info
enables endonuclease activity	ISO Inferred from Sequence Orthology more info
enables exonuclease activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info
enables oxidoreductase activity	ISO Inferred from Sequence Orthology more info
enables oxidoreductase activity	ISS Inferred from Sequence or Structural Similarity more info
enables phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands	IEA Inferred from Electronic Annotation more info
enables phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands	ISO Inferred from Sequence Orthology more info
enables phosphoric diester hydrolase activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphoric diester hydrolase activity	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed
enables site-specific endodeoxyribonuclease activity, specific for altered base	IEA Inferred from Electronic Annotation more info
enables site-specific endodeoxyribonuclease activity, specific for altered base	ISO Inferred from Sequence Orthology more info
enables site-specific endodeoxyribonuclease activity, specific for altered base	ISS Inferred from Sequence or Structural Similarity more info
enables transcription coactivator activity	IEA Inferred from Electronic Annotation more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in DNA catabolic process	IEA Inferred from Electronic Annotation more info
involved_in DNA catabolic process	ISO Inferred from Sequence Orthology more info
involved_in DNA recombination	IEA Inferred from Electronic Annotation more info
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in DNA repair	ISO Inferred from Sequence Orthology more info
involved_in DNA repair	ISS Inferred from Sequence or Structural Similarity more info
involved_in base-excision repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in base-excision repair	ISO Inferred from Sequence Orthology more info
involved_in cell redox homeostasis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell redox homeostasis	ISO Inferred from Sequence Orthology more info
involved_in cellular response to cAMP	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to hydrogen peroxide	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to hydrogen peroxide	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to organonitrogen compound	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to peptide hormone stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in negative regulation of smooth muscle cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of G1/S transition of mitotic cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression via chromosomal CpG island demethylation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression via chromosomal CpG island demethylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression via chromosomal CpG island demethylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of mRNA stability	IEA Inferred from Electronic Annotation more info
involved_in regulation of mRNA stability	ISO Inferred from Sequence Orthology more info
involved_in regulation of mRNA stability	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in telomere maintenance	ISO Inferred from Sequence Orthology more info
involved_in telomere maintenance via base-excision repair	IEA Inferred from Electronic Annotation more info
involved_in telomere maintenance via base-excision repair	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in centrosome	IEA Inferred from Electronic Annotation more info
located_in centrosome	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
part_of transcription regulator complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: DNA repair nuclease/redox regulator APEX1; DNA-(apurinic or apyrimidinic site) endonuclease

Names: AP endonuclease 1; APEN; APEX nuclease (multifunctional DNA repair enzyme) 1; APEX nuclease 1; DNA-(apurinic or apyrimidinic site) lyase; apurinic/apyrimidinic endonuclease 1; redox factor-1

NP_077062.1

EC 3.1.11.2

XP_006251975.1

EC 3.1.11.2

XP_017455294.1

EC 3.1.11.2

XP_063130745.1

EC 3.1.11.2

XP_063130746.1

EC 3.1.11.2

XP_063130747.1

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.

mRNA and Protein(s)

NM_024148.1 → NP_077062.1 DNA repair nuclease/redox regulator APEX1

See identical proteins and their annotated locations for NP_077062.1

Status: PROVISIONAL

Source sequence(s)

D44495

UniProtKB/Swiss-Prot

P43138, Q548N9

UniProtKB/TrEMBL

A6KEC1, A6KEC2

Related

ENSRNOP00000068673.2, ENSRNOT00000087958.3

Conserved Domains (1) summary

cd09087
Location:61 → 315

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

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086033.1 Reference GRCr8

Range

26618146..26620330

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006251913.3 → XP_006251975.1 DNA-(apurinic or apyrimidinic site) endonuclease isoform X2

See identical proteins and their annotated locations for XP_006251975.1

UniProtKB/Swiss-Prot

P43138, Q548N9

UniProtKB/TrEMBL

A6KEC1, A6KEC2

Conserved Domains (1) summary

cd09087
Location:61 → 315

Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases
XM_063274676.1 → XP_063130746.1 DNA-(apurinic or apyrimidinic site) endonuclease isoform X2

UniProtKB/Swiss-Prot

P43138, Q548N9

UniProtKB/TrEMBL

A6KEC1, A6KEC2
XM_063274675.1 → XP_063130745.1 DNA-(apurinic or apyrimidinic site) endonuclease isoform X1

UniProtKB/TrEMBL

A6KEC2
XM_063274677.1 → XP_063130747.1 DNA-(apurinic or apyrimidinic site) endonuclease isoform X3

UniProtKB/TrEMBL

A0A8L2Q612, A0A8L2QZQ5

Related

ENSRNOP00000013176.4, ENSRNOT00000013176.7
XM_017599805.3 → XP_017455294.1 DNA-(apurinic or apyrimidinic site) endonuclease isoform X3

UniProtKB/TrEMBL

A0A8L2Q612, A0A8L2QZQ5