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ATG3 autophagy related 3 [ Homo sapiens (human) ]

Gene ID: 64422, updated on 3-Nov-2024

Summary

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Official Symbol
ATG3provided by HGNC
Official Full Name
autophagy related 3provided by HGNC
Primary source
HGNC:HGNC:20962
See related
Ensembl:ENSG00000144848 MIM:609606; AllianceGenome:HGNC:20962
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
APG3; APG3L; hApg3; PC3-96; APG3-LIKE
Summary
This gene encodes a ubiquitin-like-conjugating enzyme and is a component of ubiquitination-like systems involved in autophagy, the process of degradation, turnover and recycling of cytoplasmic constituents in eukaryotic cells. This protein is known to play a role in regulation of autophagy during cell death. A pseudogene of this gene is located on chromosome 20. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]
Expression
Ubiquitous expression in testis (RPKM 24.5), bone marrow (RPKM 17.6) and 25 other tissues See more
Orthologs
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Genomic context

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See ATG3 in Genome Data Viewer
Location:
3q13.2
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (112532510..112561962, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (115253546..115282997, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (112251357..112280809, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr3:112184939-112185454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:112192511-112193011 Neighboring gene B and T lymphocyte associated Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:112240775-112241275 Neighboring gene olfactory receptor family 7 subfamily E member 100 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20244 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:112279571-112280380 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:112280381-112281190 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112282811-112283620 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112283621-112284430 Neighboring gene solute carrier family 35 member A5 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_64338 Neighboring gene coiled-coil domain containing 80 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:112383725-112384298 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:112405169-112405758 Neighboring gene MAT2A pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Combination erlotinib-cisplatin and Atg3-mediated autophagy in erlotinib resistant lung cancer. Lee JG, et al. PLoS One, 2012. PMID 23119048, Free PMC Article
  2. Lentiviral vector-mediate ATG3 overexpression inhibits growth and promotes apoptosis of human SKM-1 cells. Wang L, et al. Mol Biol Rep, 2014. PMID 24420857
  3. An N-terminal conserved region in human Atg3 couples membrane curvature sensitivity to conjugase activity during autophagy. Ye Y, et al. Nat Commun, 2021 Jan 14. PMID 33446636, Free PMC Article
  4. Inhibition of ATG3 ameliorates liver steatosis by increasing mitochondrial function. da Silva Lima N, et al. J Hepatol, 2022 Jan. PMID 34555423
  5. Long non-coding RNA PVT1 promotes autophagy as ceRNA to target ATG3 by sponging microRNA-365 in hepatocellular carcinoma. Yang L, et al. Gene, 2019 May 20. PMID 30794914

See all (85) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Inhibition of ATG3 ameliorates liver steatosis by increasing mitochondrial function.
    Title: Inhibition of ATG3 ameliorates liver steatosis by increasing mitochondrial function.
  2. Overexpression of miR-431 attenuates hypoxia/reoxygenation-induced myocardial damage via autophagy-related 3.
    Title: Overexpression of miR-431 attenuates hypoxia/reoxygenation-induced myocardial damage via autophagy-related 3.
  3. An N-terminal conserved region in human Atg3 couples membrane curvature sensitivity to conjugase activity during autophagy.
    Title: An N-terminal conserved region in human Atg3 couples membrane curvature sensitivity to conjugase activity during autophagy.
  4. LncRNA NEAT1 promotes autophagy via regulating miR-204/ATG3 and enhanced cell resistance to sorafenib in hepatocellular carcinoma.
    Title: LncRNA NEAT1 promotes autophagy via regulating miR-204/ATG3 and enhanced cell resistance to sorafenib in hepatocellular carcinoma.
  5. Let-7c-3p Regulates Autophagy under Oxidative Stress by Targeting ATG3 in Lens Epithelial Cells.
    Title: Let-7c-3p Regulates Autophagy under Oxidative Stress by Targeting ATG3 in Lens Epithelial Cells.
  6. Study validated that miR-1 overexpression improved DDP sensitivity of NSCLC cells by inhibiting ATG3-mediated autophagy.
    Title: MicroRNA-1 overexpression increases chemosensitivity of non-small cell lung cancer cells by inhibiting autophagy related 3-mediated autophagy.
  7. We have also observed membrane aggregation induced by ATG3 in vitro, which could point to a more complex function of this protein in AP biogenesis. Moreover, in vitro GABARAP lipidation assays suggest that ATG3-membrane interaction could facilitate the lipidation of ATG8 homologues.
    Title: Human ATG3 binding to lipid bilayers: role of lipid geometry, and electric charge.
  8. Authors confirmed that the effect of PVT1 promoting autophagy was dependent on regulating ATG3 expression. Further investigations revealed that PVT1 could upregulate autophagy-related gene 3 (ATG3) expression by acting as an endogenous sponge of miR-365, which was an inhibitor gene on ATG3 protein by targeting 3'UTR of ATG3 mRNA.
    Title: Long non-coding RNA PVT1 promotes autophagy as ceRNA to target ATG3 by sponging microRNA-365 in hepatocellular carcinoma.
  9. this study identified an amino acid motif in ATG3 causing eIF5A dependency for its efficient translation
    Title: eIF5A is required for autophagy by mediating ATG3 translation.
  10. Results revealed that miR-16 was significantly downregulated, and ATG3 was significantly upregulated in non-small cell lung carcinoma (NSCLC) patient tissue samples. ATG3 was found to be a direct target of miR-16.
    Title: miR-16 mimics inhibit TGF-β1-induced epithelial-to-mesenchymal transition via activation of autophagy in non-small cell lung carcinoma cells.
Submit: New GeneRIF Correction See all GeneRIFs (24)

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

EBI GWAS Catalog

Description
Rank-based genome-wide analysis reveals the association of ryanodine receptor-2 gene variants with childhood asthma among human populations.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ22125, MGC15201, DKFZp564M1178

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables Atg12 transferase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables Atg8-family conjugating enzyme activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables Atg8-family conjugating enzyme activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables Atg8-family conjugating enzyme activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables Atg8-family ligase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin-like protein transferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in autophagosome assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in autophagosome assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in autophagosome assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in autophagy of mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in glycophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitochondrial fragmentation involved in apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of phagocytosis IEA
Inferred from Electronic Annotation
more info
  
involved_in nucleophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein targeting to membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in protein ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of cilium assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of Atg12-Atg5-Atg16 complex IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in phagophore assembly site IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
ubiquitin-like-conjugating enzyme ATG3
Names
APG3 autophagy 3-like
ATG3 autophagy related 3 homolog
autophagy-related protein 3
NP_001265641.1
NP_071933.2
XP_011511376.1

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_001278712.2 → NP_001265641.1  ubiquitin-like-conjugating enzyme ATG3 isoform 2

    See identical proteins and their annotated locations for NP_001265641.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains a 3' terminal exon that extends past a splice site that is used in variant 1 that results in an early stop codon and a different 3' UTR, compared to variant 1. It encodes a protein which is shorter at the C-terminus (isoform 2), compared to isoform 1.
    Source sequence(s)
    AA448974, AC092692, AK025778, AK308919, BC002830
    Consensus CDS
    CCDS63721.1
    UniProtKB/Swiss-Prot
    Q9NT62
    Related
    ENSP00000385943.2, ENST00000402314.6
    Conserved Domains (2) summary
    pfam03986
    Location:8 → 135
    Autophagy_N; Autophagocytosis associated protein (Atg3), N-terminal domain
    pfam03987
    Location:204 → 265
    Autophagy_act_C; Autophagocytosis associated protein, active-site domain

  2. NM_022488.5 → NP_071933.2  ubiquitin-like-conjugating enzyme ATG3 isoform 1

    See identical proteins and their annotated locations for NP_071933.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC092692, AW408464, BC024221, DC311625
    Consensus CDS
    CCDS2966.1
    UniProtKB/Swiss-Prot
    C9JNW8, Q6PKC5, Q9H6L9, Q9NT62
    Related
    ENSP00000283290.5, ENST00000283290.10
    Conserved Domains (2) summary
    pfam03986
    Location:8 → 135
    Autophagy_N; Autophagocytosis associated protein (Atg3), N-terminal domain
    pfam03987
    Location:38 → 308
    Autophagy_act_C; Autophagocytosis associated protein, active-site domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    112532510..112561962 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513074.1 → XP_011511376.1  ubiquitin-like-conjugating enzyme ATG3 isoform X1

    Conserved Domains (3) summary
    pfam03986
    Location:12 → 48
    Autophagy_N; Autophagocytosis associated protein (Atg3), N-terminal domain
    pfam03987
    Location:117 → 178
    Autophagy_act_C; Autophagocytosis associated protein, active-site domain
    pfam10381
    Location:199 → 222
    Autophagy_C; Autophagocytosis associated protein C-terminal

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    115253546..115282997 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NT62.1 GenPept UniProtKB/Swiss-Prot:Q9NT62

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