ATG5 autophagy related 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ATG5provided by HGNC
Official Full Name: autophagy related 5provided by HGNC
Primary source: HGNC:HGNC:589
See related: Ensembl:ENSG00000057663 MIM:604261; AllianceGenome:HGNC:589
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: ASP; APG5; APG5L; hAPG5; SCAR25; APG5-LIKE
Summary: The protein encoded by this gene, in combination with autophagy protein 12, functions as an E1-like activating enzyme in a ubiquitin-like conjugating system. The encoded protein is involved in several cellular processes, including autophagic vesicle formation, mitochondrial quality control after oxidative damage, negative regulation of the innate antiviral immune response, lymphocyte development and proliferation, MHC II antigen presentation, adipocyte differentiation, and apoptosis. Several transcript variants encoding different protein isoforms have been found for this gene. [provided by RefSeq, Sep 2015]
Expression: Ubiquitous expression in thyroid (RPKM 11.9), adrenal (RPKM 11.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6q21

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (106184476..106325760, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (107360315..107501922, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (106632351..106773635, complement)

Chromosome 6 - NC_000006.12 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

ATG5 nonautophagically regulates inflammation and differentiation in mouse embryonic stem cells.
Title: ATG5 nonautophagically regulates inflammation and differentiation in mouse embryonic stem cells.
Autophagy-related protein 5 (ATG5) interacts with bone marrow stromal cell antigen 2 (BST2) to stimulate HBV replication through antagonizing the antiviral activity of BST2.
Title: Autophagy-related protein 5 (ATG5) interacts with bone marrow stromal cell antigen 2 (BST2) to stimulate HBV replication through antagonizing the antiviral activity of BST2.
Autophagy related gene 5 polymorphism rs17587319 (C/G) in asthmatic patients in North Indian population.
Title: Autophagy related gene 5 polymorphism rs17587319 (C/G) in asthmatic patients in North Indian population.
Autophagy-related 5 in acute ischemic stroke: Variation and linkage with neurofunction, and survival.
Title: Autophagy-related 5 in acute ischemic stroke: Variation and linkage with neurofunction, and survival.
Serum autophagy-related gene 5 level in stroke patients: correlation with CD4+ T cells and cognition impairment during a 3-year follow-up.
Title: Serum autophagy-related gene 5 level in stroke patients: correlation with CD4+ T cells and cognition impairment during a 3-year follow-up.
MIR222HG/LIN28B/ATG5 Axis Drives M2 Macrophage Polarization and Proliferation of Hepatocellular Carcinoma Cells.
Title: MIR222HG/LIN28B/ATG5 Axis Drives M2 Macrophage Polarization and Proliferation of Hepatocellular Carcinoma Cells.
Association of ATG16L1 and ATG5 gene polymorphisms with susceptibility to hepatitis B virus infection and progression to HCC in central China.
Title: Association of ATG16L1 and ATG5 gene polymorphisms with susceptibility to hepatitis B virus infection and progression to HCC in central China.
LncRNA TEX41 promotes the proliferation and migration of squamous cell carcinoma cells by upregulating Atg5 via sponging miR-153-3p.
Title: LncRNA TEX41 promotes the proliferation and migration of squamous cell carcinoma cells by upregulating Atg5 via sponging miR-153-3p.
Comparative Genetic Analysis of the Promoters of the ATG16L1 and ATG5 Genes Associated with Sporadic Parkinson's Disease.
Title: Comparative Genetic Analysis of the Promoters of the ATG16L1 and ATG5 Genes Associated with Sporadic Parkinson's Disease.
TRIM45 aggravates microglia pyroptosis via Atg5/NLRP3 axis in septic encephalopathy.
Title: TRIM45 aggravates microglia pyroptosis via Atg5/NLRP3 axis in septic encephalopathy.

Submit: New GeneRIF Correction See all GeneRIFs (167)

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

Associated conditions

Description	Tests
Spinocerebellar ataxia, autosomal recessive 25 MedGen: C4539808 OMIM: 617584 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
A systemic sclerosis and systemic lupus erythematosus pan-meta-GWAS reveals new shared susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetics of rheumatoid arthritis contributes to biology and drug discovery. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians. 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

STS-N94345 (e-PCR)
- UniSTS:69927

WI-20363 (e-PCR)
- UniSTS:82998

Atg5 (e-PCR), detects polymorphism
- UniSTS:526933

RH78069 (e-PCR)
- UniSTS:52851

RH93335 (e-PCR)
- UniSTS:89477

EST6B12 (e-PCR)
- UniSTS:263392

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables Atg8-family ligase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in aggrephagy	IBA Inferred from Biological aspect of Ancestor more info
involved_in aggrephagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in antigen processing and presentation of endogenous antigen	IEA Inferred from Electronic Annotation more info
involved_in autophagosome assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in autophagosome assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in autophagosome assembly	ISO Inferred from Sequence Orthology more info
involved_in autophagosome assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in autophagy	IGI Inferred from Genetic Interaction more info	PubMed
involved_in autophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in autophagy	ISS Inferred from Sequence or Structural Similarity more info
involved_in axonal transport	IEA Inferred from Electronic Annotation more info
involved_in blood vessel remodeling	IEA Inferred from Electronic Annotation more info
involved_in cardiac muscle cell apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in cellular response to nitrogen starvation	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to nitrosative stress	IEA Inferred from Electronic Annotation more info
involved_in chaperone-mediated autophagy	IEA Inferred from Electronic Annotation more info
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in defense response to virus	IEA Inferred from Electronic Annotation more info
involved_in heart contraction	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in macroautophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in macroautophagy	ISO Inferred from Sequence Orthology more info
involved_in mitophagy	IBA Inferred from Biological aspect of Ancestor more info
involved_in mucus secretion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of autophagic cell death	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cardiac muscle cell apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of defense response to virus	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of innate immune response	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of phagocytosis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of reactive oxygen species metabolic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of type I interferon production	ISO Inferred from Sequence Orthology more info
involved_in negative stranded viral RNA replication	IEA Inferred from Electronic Annotation more info
involved_in negative thymic T cell selection	IEA Inferred from Electronic Annotation more info
involved_in otolith development	IEA Inferred from Electronic Annotation more info
involved_in piecemeal microautophagy of the nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of mucus secretion	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of stress granule assembly	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of viral translation	IDA Inferred from Direct Assay more info	PubMed
involved_in post-translational protein modification	ISS Inferred from Sequence or Structural Similarity more info
involved_in postsynaptic modulation of chemical synaptic transmission	IEA Inferred from Electronic Annotation more info
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in regulation of autophagosome maturation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cilium assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cytokine production involved in immune response	IEA Inferred from Electronic Annotation more info
involved_in regulation of postsynaptic membrane neurotransmitter receptor levels	IEA Inferred from Electronic Annotation more info
involved_in regulation of release of sequestered calcium ion into cytosol	IEA Inferred from Electronic Annotation more info
involved_in response to fluoride	IEA Inferred from Electronic Annotation more info
involved_in response to fungus	IEA Inferred from Electronic Annotation more info
involved_in response to iron(II) ion	IEA Inferred from Electronic Annotation more info
involved_in response to xenobiotic stimulus	IEA Inferred from Electronic Annotation more info
involved_in vasodilation	IEA Inferred from Electronic Annotation more info
involved_in ventricular cardiac muscle cell development	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of Atg12-Atg5-Atg16 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Atg12-Atg5-Atg16 complex	IPI Inferred from Physical Interaction more info	PubMed
located_in Schaffer collateral - CA1 synapse	IEA Inferred from Electronic Annotation more info
is_active_in autophagosome	IBA Inferred from Biological aspect of Ancestor more info
located_in autophagosome	IDA Inferred from Direct Assay more info	PubMed
located_in axon	IEA Inferred from Electronic Annotation more info
located_in axoneme	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	TAS Traceable Author Statement more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondria-associated endoplasmic reticulum membrane contact site	IEA Inferred from Electronic Annotation more info
located_in phagocytic vesicle membrane	TAS Traceable Author Statement more info
is_active_in phagophore	IBA Inferred from Biological aspect of Ancestor more info
is_active_in phagophore assembly site membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in phagophore assembly site membrane	ISO Inferred from Sequence Orthology more info
located_in phagophore assembly site membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in postsynapse	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	NAS Non-traceable Author Statement more info	PubMed
part_of transferase complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: autophagy protein 5

Names: APG5 autophagy 5-like; ATG5 autophagy related 5 homolog; apoptosis-specific protein

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_001286106.2 → NP_001273035.1 autophagy protein 5 isoform a

See identical proteins and their annotated locations for NP_001273035.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode isoform a.

Source sequence(s)

AL138917, BC002699, BX537904, CR749386, HY168998

Consensus CDS

CCDS5055.1

UniProtKB/Swiss-Prot

O60875, Q5JVR2, Q68DI4, Q9H1Y0, Q9H2B8, Q9HCZ7

UniProtKB/TrEMBL

A9UGY9, B3KMH8

Related

ENSP00000343313.3, ENST00000343245.7

Conserved Domains (1) summary

pfam04106
Location:79 → 270

APG5; Autophagy protein Apg5
NM_001286107.2 → NP_001273036.1 autophagy protein 5 isoform b

See identical proteins and their annotated locations for NP_001273036.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an exon in the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform a.

Source sequence(s)

BP297166, BX537904, CR749386

Consensus CDS

CCDS69159.1

UniProtKB/TrEMBL

B7Z5Y6

Related

ENSP00000490493.1, ENST00000635758.2

Conserved Domains (1) summary

pfam04106
Location:1 → 192

APG5; Autophagy protein Apg5
NM_001286108.2 → NP_001273037.1 autophagy protein 5 isoform c

See identical proteins and their annotated locations for NP_001273037.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate splice site that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (c) has a distinct C-terminus and is shorter than isoform a.

Source sequence(s)

AK315800, BP297166, BX537904, Y11588

UniProtKB/Swiss-Prot

Q9H1Y0

UniProtKB/TrEMBL

Q7Z3H3

Conserved Domains (1) summary

pfam04106
Location:79 → 189

APG5; Autophagy protein Apg5
NM_001286111.2 → NP_001273040.1 autophagy protein 5 isoform d

See identical proteins and their annotated locations for NP_001273040.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks three alternate exons in the 5' coding region, which results in a frameshift in the remaining coding region, compared to variant 1. The encoded isoform (d) has the same N-terminus but is otherwise distinct and shorter than isoform a.

Source sequence(s)

BP297166, BX537904, Y11588

Consensus CDS

CCDS75498.1

UniProtKB/TrEMBL

Q7Z3H3

Related

ENSP00000353884.4, ENST00000360666.6
NM_004849.4 → NP_004840.1 autophagy protein 5 isoform a

See identical proteins and their annotated locations for NP_004840.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Both variants 1 and 2 encode isoform a.

Source sequence(s)

BX537904, Y11588

Consensus CDS

CCDS5055.1

UniProtKB/Swiss-Prot

O60875, Q5JVR2, Q68DI4, Q9H1Y0, Q9H2B8, Q9HCZ7

UniProtKB/TrEMBL

A9UGY9, B3KMH8

Related

ENSP00000358072.3, ENST00000369076.8

Conserved Domains (1) summary

pfam04106
Location:79 → 270

APG5; Autophagy protein Apg5

RNA

NR_104402.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks the 5' exon and an internal exon, compared to variant 1. This variant is represented as non-coding because use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

BP297166, BX537904, JQ918353, Y11588
NR_104403.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (7) lacks the 5' exon and two internal exons, compared to variant 1. This variant is represented as non-coding because use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

BP297166, BX537904, JQ918354, Y11588

Related

ENST00000369070.5

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_000006.12 Reference GRCh38.p14 Primary Assembly

Range

106184476..106325760 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_024446590.2 → XP_024302358.1 autophagy protein 5 isoform X2

UniProtKB/TrEMBL

B7Z5Y6

Conserved Domains (1) summary

pfam04106
Location:1 → 192

APG5; Autophagy protein Apg5
XM_047419574.1 → XP_047275530.1 autophagy protein 5 isoform X3

UniProtKB/TrEMBL

B7Z5Y6
XM_047419573.1 → XP_047275529.1 autophagy protein 5 isoform X1

UniProtKB/TrEMBL

A0A2R8Y718

Related

ENSP00000495958.1, ENST00000646025.1

Alternate T2T-CHM13v2.0

Genomic

NC_060930.1 Alternate T2T-CHM13v2.0

Range

107360315..107501922 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054356850.1 → XP_054212825.1 autophagy protein 5 isoform X2

UniProtKB/TrEMBL

B7Z5Y6
XM_054356851.1 → XP_054212826.1 autophagy protein 5 isoform X3

UniProtKB/TrEMBL

B7Z5Y6
XM_054356849.1 → XP_054212824.1 autophagy protein 5 isoform X1

UniProtKB/TrEMBL

A0A2R8Y718