apex1 APEX nuclease (multifunctional DNA repair enzyme) 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: apex1provided by ZNC
Official Full Name: APEX nuclease (multifunctional DNA repair enzyme) 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-040426-2761
See related: Ensembl:ENSDARG00000045843 AllianceGenome:ZFIN:ZDB-GENE-040426-2761
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: APEN; zap1; apex1a; zgc:66204; wu:fc13d11; hm:zehn1532
Summary: Enables DNA-(apurinic or apyrimidinic site) endonuclease activity. Acts upstream of or within several processes, including heart contraction; heart looping; and negative regulation of apoptotic process. Predicted to be located in endoplasmic reticulum; mitochondrion; and nuclear lumen. Predicted to be active in nucleus. Is expressed in head. Human ortholog(s) of this gene implicated in artery disease (multiple); 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, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 4

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	4	NC_007115.7 (5333988..5339829)
105	previous assembly	GRCz10 (GCF_000002035.5)	4	NC_007115.6 (5325418..5331259)

Chromosome 4 - NC_007115.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Knock-down of Apex1 not only resulted in reduction of expression of several major proteins in the BER pathway (Polb and Ogg1), and it also resulted in maldistribution and loss of four key brain transcription factors (fezf2, otx2, egr2a, and pax2a), leading to abnormal brain development.
Title: AP endonuclease 1 (Apex1) influences brain development linking oxidative stress and DNA repair.

Submit: New GeneRIF Correction

General gene information

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Markers

fb92g09.y1 (e-PCR)
- UniSTS:191765

fc13d11.x1 (e-PCR)
- UniSTS:203805

AI617415 (e-PCR)
- UniSTS:206170

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation 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	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables catalytic activity	IEA Inferred from Electronic Annotation more info
enables class II DNA-(apurinic or apyrimidinic site) endonuclease activity	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 3'-5' DNA exonuclease activity	IEA Inferred from Electronic Annotation more info
enables endodeoxyribonuclease activity, producing 5'-phosphomonoesters	IEA Inferred from Electronic Annotation more info
enables endonuclease activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity, acting on ester bonds	IEA Inferred from Electronic Annotation more info
enables lyase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nuclease activity	IEA Inferred from Electronic Annotation more info
NOT enables oxidoreductase activity	IDA Inferred from Direct Assay more info	PubMed
enables phosphoric diester hydrolase activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within DNA repair	IEA Inferred from Electronic Annotation more info
involved_in base-excision repair	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within heart contraction	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart looping	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression via chromosomal CpG island demethylation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation 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 nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nucleolus	IEA Inferred from Electronic Annotation 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

General protein information

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Preferred Names: DNA repair nuclease APEX1

Names: AP endonuclease 1; DNA-(apurinic or apyrimidinic site) endonuclease; DNA-(apurinic or apyrimidinic site) lyase; apurinic/apyrimidinic endonuclease 1

NP_001315507.1

EC 3.1.11.2

NP_001315508.1

EC 3.1.11.2

NP_001315509.1

EC 3.1.11.2

NP_998586.2

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.

mRNA and Protein(s)

NM_001328578.1 → NP_001315507.1 DNA repair nuclease APEX1 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

BX323558

UniProtKB/Swiss-Prot

A0MTA1, Q4V955, Q5RHZ7, Q7SXL6

UniProtKB/TrEMBL

A0A8M1PAH1, F1QTR9, Z4YHV8

Related

ENSDARP00000110718.3, ENSDART00000129398.3

Conserved Domains (1) summary

cd09087
Location:86 → 339

Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases
NM_001328579.1 → NP_001315508.1 DNA repair nuclease APEX1 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

BX323558

UniProtKB/Swiss-Prot

A0MTA1, Q4V955, Q5RHZ7, Q7SXL6

UniProtKB/TrEMBL

A0A0R4IWF9, A0A8M1P9D9

Related

ENSDARP00000138791.2, ENSDART00000163850.2

Conserved Domains (1) summary

cd09087
Location:85 → 338

Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases
NM_001328580.1 → NP_001315509.1 DNA repair nuclease APEX1 isoform 4

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks an alternate exon, uses an alternate in-frame splice junction, and begins translation at a downstream AUG compared to variant 1. The resulting isoform (4) is shorter at the N-terminus and lacks an internal aa compared to isoform 1.

Source sequence(s)

BX323558

UniProtKB/Swiss-Prot

A0MTA1, Q4V955, Q5RHZ7, Q7SXL6

UniProtKB/TrEMBL

A0A8M1P554

Conserved Domains (1) summary

cd09087
Location:54 → 307

Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases
NM_213421.2 → NP_998586.2 DNA repair nuclease APEX1 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate exon and begins translation at a downstream AUG compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.

Source sequence(s)

BX323558

UniProtKB/Swiss-Prot

A0MTA1, Q4V955, Q5RHZ7, Q7SXL6

UniProtKB/TrEMBL

A0A2R9YJQ0, A0A8M1PF57

Related

ENSDARP00000067373.6, ENSDART00000067374.8