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

Gene ID: 406730, updated on 14-Apr-2024

Summary

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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
Predicted to enable DNA-(apurinic or apyrimidinic site) endonuclease activity; double-stranded DNA 3'-5' exodeoxyribonuclease activity; and phosphoric diester hydrolase 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 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]
Orthologs
human mouse all
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Genomic context

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Location:
chromosome: 4
Exon count:
6
Annotation release Status Assembly Chr Location
106 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_007115.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101884589 Neighboring gene si:ch211-214j24.10 Neighboring gene si:dkey-14d8.1 Neighboring gene zgc:113263 Neighboring gene uncharacterized LOC108183607 Neighboring gene O-sialoglycoprotein endopeptidase

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Evolution of the redox function in mammalian apurinic/apyrimidinic endonuclease. Georgiadis MM, et al. Mutat Res, 2008 Aug 25. PMID 18579163, Free PMC Article
  2. DNA repair protein involved in heart and blood development. Wang Y, et al. Mol Cell Biol, 2006 Dec. PMID 16966376, Free PMC Article
  3. Insights into Mechanisms of Damage Recognition and Catalysis by APE1-like Enzymes. Bulygin AA, et al. Int J Mol Sci, 2022 Apr 14. PMID 35457179, Free PMC Article
  4. The Enigma of Substrate Recognition and Catalytic Efficiency of APE1-Like Enzymes. Davletgildeeva AT, et al. Front Cell Dev Biol, 2021. PMID 33842455, Free PMC Article
  5. Graphene oxide nanosheets induce DNA damage and activate the base excision repair (BER) signaling pathway both in vitro and in vivo. Lu CJ, et al. Chemosphere, 2017 Oct. PMID 28645083

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Clone Names

  • MGC113976

Gene Ontology Provided by ZFIN

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 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 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 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 
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
  
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; DNA-(apurinic or apyrimidinic site) lyase
Names
AP endonuclease 1
DNA-(apurinic or apyrimidinic site) endonuclease
apurinic/apyrimidinic endonuclease 1
NP_001315507.1
NP_001315508.1
NP_001315509.1
NP_998586.2
XP_021330658.1

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)

  1. 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

  2. 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

  3. 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

  4. 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

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007115.7 Reference GRCz11 Primary Assembly

    Range
    5333988..5339829
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021474983.1 → XP_021330658.1  DNA-(apurinic or apyrimidinic site) lyase isoform X1

    UniProtKB/Swiss-Prot
    A0MTA1, Q4V955, Q5RHZ7, Q7SXL6
    UniProtKB/TrEMBL
    A0A8M1PAH1, F1QTR9, Z4YHV8
    Conserved Domains (1) summary
    cd09087
    Location:86 → 339
    Ape1-like_AP-endo; Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A0MTA1.1 GenPept UniProtKB/Swiss-Prot:A0MTA1

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.