ATG3 autophagy related 3 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

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_000003.12 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?

Inhibition of ATG3 ameliorates liver steatosis by increasing mitochondrial function.
Title: Inhibition of ATG3 ameliorates liver steatosis by increasing mitochondrial function.
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.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G20743 (e-PCR)
- UniSTS:57200

A006E19 (e-PCR)
- UniSTS:57201

WI-22015 (e-PCR)
- UniSTS:74098

RH120928 (e-PCR)
- UniSTS:133788

GDB:372310 (e-PCR)
- UniSTS:27092

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

EC 2.3.2.-

NP_071933.2

EC 2.3.2.-

XP_011511376.1

EC 2.3.2.-

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_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
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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

112532510..112561962 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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