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ATG5 autophagy related 5 [ Homo sapiens (human) ]

Gene ID: 9474, updated on 21-Apr-2019

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
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

Genomic context

See ATG5 in Genome Data Viewer
Location:
6q21
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (106184476..106325820, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (106632351..106773695, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RN7SK pseudogene 211 Neighboring gene PR/SET domain 1 Neighboring gene RNA, 7SL, cytoplasmic 47, pseudogene Neighboring gene RNA, U6 small nuclear 344, pseudogene Neighboring gene crystallin beta-gamma domain containing 1 Neighboring gene uncharacterized LOC105377924 Neighboring gene RNA, 5S ribosomal pseudogene 211

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 25
MedGen: C4539808 OMIM: 617584 GeneReviews: Not available
not available

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • Autophagy - animal, organism-specific biosystem (from KEGG)
    Autophagy - animal, organism-specific biosystemAutophagy (or macroautophagy) is a cellular catabolic pathway involving in protein degradation, organelle turnover, and non-selective breakdown of cytoplasmic components, which is evolutionarily cons...
  • Autophagy - animal, conserved biosystem (from KEGG)
    Autophagy - animal, conserved biosystemAutophagy (or macroautophagy) is a cellular catabolic pathway involving in protein degradation, organelle turnover, and non-selective breakdown of cytoplasmic components, which is evolutionarily cons...
  • Autophagy - other, organism-specific biosystem (from KEGG)
    Autophagy - other, organism-specific biosystemAutophagy is a degradative pathway for the removal of cytoplasmic materials in eukaryotic cells, and is characterized by the formation of a double-membrane structure called the autophagosome, either ...
  • Autophagy - other, conserved biosystem (from KEGG)
    Autophagy - other, conserved biosystemAutophagy is a degradative pathway for the removal of cytoplasmic materials in eukaryotic cells, and is characterized by the formation of a double-membrane structure called the autophagosome, either ...
  • Cellular responses to stress, organism-specific biosystem (from REACTOME)
    Cellular responses to stress, organism-specific biosystemCells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. The ability of cells and tissu...
  • Ferroptosis, organism-specific biosystem (from KEGG)
    Ferroptosis, organism-specific biosystemFerroptosis is a regulated form of cell death and characterized by a production of reactive oxygen species (ROS) from accumulated iron and lipid peroxidation. It can be induced by experimental compou...
  • Ferroptosis, conserved biosystem (from KEGG)
    Ferroptosis, conserved biosystemFerroptosis is a regulated form of cell death and characterized by a production of reactive oxygen species (ROS) from accumulated iron and lipid peroxidation. It can be induced by experimental compou...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Longevity regulating pathway, organism-specific biosystem (from KEGG)
    Longevity regulating pathway, organism-specific biosystemRegulation of longevity depends on genetic and environmental factors. Caloric restriction (CR), that is limiting food intake, is recognized in mammals as the best characterized and most reproducible ...
  • Longevity regulating pathway - multiple species, organism-specific biosystem (from KEGG)
    Longevity regulating pathway - multiple species, organism-specific biosystemAging is a complex process of accumulation of molecular, cellular, and organ damage, leading to loss of function and increased vulnerability to disease and death. Despite the complexity of aging, rec...
  • Longevity regulating pathway - multiple species, conserved biosystem (from KEGG)
    Longevity regulating pathway - multiple species, conserved biosystemAging is a complex process of accumulation of molecular, cellular, and organ damage, leading to loss of function and increased vulnerability to disease and death. Despite the complexity of aging, rec...
  • Macroautophagy, organism-specific biosystem (from REACTOME)
    Macroautophagy, organism-specific biosystemMacroautophagy (hereafter referred to as autophagy) acts as a buffer against starvation by liberating building materials and energy sources from cellular components. It has additional roles in embryo...
  • Mitophagy, organism-specific biosystem (from REACTOME)
    Mitophagy, organism-specific biosystemMitophagy is a specific form of autophagy where mitochondria are specifically targeted for degradation by autophagolysosomes.. In mammals there are a number of known mechanisms of mitophagy. One insu...
  • Mitophagy - animal, organism-specific biosystem (from KEGG)
    Mitophagy - animal, organism-specific biosystemMitochondria act as the energy powerhouse of the cell, and are essential for eukaryotic cells to grow and function normally. However, deleterious byproducts of oxidative phosphorylation process calle...
  • Mitophagy - animal, conserved biosystem (from KEGG)
    Mitophagy - animal, conserved biosystemMitochondria act as the energy powerhouse of the cell, and are essential for eukaryotic cells to grow and function normally. However, deleterious byproducts of oxidative phosphorylation process calle...
  • NOD-like receptor signaling pathway, organism-specific biosystem (from KEGG)
    NOD-like receptor signaling pathway, organism-specific biosystemSpecific families of pattern recognition receptors are responsible for detecting various pathogens and generating innate immune responses. The intracellular NOD-like receptor (NLR) family contains mo...
  • NOD-like receptor signaling pathway, conserved biosystem (from KEGG)
    NOD-like receptor signaling pathway, conserved biosystemSpecific families of pattern recognition receptors are responsible for detecting various pathogens and generating innate immune responses. The intracellular NOD-like receptor (NLR) family contains mo...
  • Nanoparticle triggered autophagic cell death, organism-specific biosystem (from WikiPathways)
    Nanoparticle triggered autophagic cell death, organism-specific biosystemProgrammed cell death: autophagic cell death. Autophagy (self-eating) is a survival mechanism deployed by cells to cope with conditions of nutrient deprivation. However, unrestrained autophagy can re...
  • Negative regulators of RIG-I/MDA5 signaling, organism-specific biosystem (from REACTOME)
    Negative regulators of RIG-I/MDA5 signaling, organism-specific biosystemAs with other cytokine systems, production of type I IFN is a transient process, and can be hazardous to the host if unregulated, resulting in chronic cellular toxicity or inflammatory and autoimmune...
  • Pink/Parkin Mediated Mitophagy, organism-specific biosystem (from REACTOME)
    Pink/Parkin Mediated Mitophagy, organism-specific biosystemThis is the process of selective removal of damaged mitochondria by autophagosomes and subsequent catabolism by lysosomes. In healthy mitochondria, PINK1 is imported to the inner mitochondrial membra...
  • RIG-I-like Receptor Signaling, organism-specific biosystem (from WikiPathways)
    RIG-I-like Receptor Signaling, organism-specific biosystemViral pathogen RNA are recognized by host helicases called RIG-I-like receptors (RLRs) that include DDX58 (RIG-I), DHX58 (LGP2), IFIH1 (MDA5), SNW1, and DDX17. These RLR proteins then go on to initia...
  • RIG-I-like receptor signaling pathway, organism-specific biosystem (from KEGG)
    RIG-I-like receptor signaling pathway, organism-specific biosystemSpecific families of pattern recognition receptors are responsible for detecting viral pathogens and generating innate immune responses. Non-self RNA appearing in a cell as a result of intracellular ...
  • RIG-I-like receptor signaling pathway, conserved biosystem (from KEGG)
    RIG-I-like receptor signaling pathway, conserved biosystemSpecific families of pattern recognition receptors are responsible for detecting viral pathogens and generating innate immune responses. Non-self RNA appearing in a cell as a result of intracellular ...
  • RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways, organism-specific biosystem (from REACTOME)
    RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways, organism-specific biosystemRIG-I-like helicases (RLHs) the retinoic acid inducible gene-I (RIG-I) and melanoma differentiation associated gene 5 (MDA5) are RNA helicases that recognize viral RNA present within the cytoplasm. F...
  • Senescence and Autophagy in Cancer, organism-specific biosystem (from WikiPathways)
    Senescence and Autophagy in Cancer, organism-specific biosystemSenescense and Autophagy Pathways in Cancer
  • Shigellosis, organism-specific biosystem (from KEGG)
    Shigellosis, organism-specific biosystemShigellosis, or bacillary dysentery, is an intestinal infection caused by Shigella, a genus of enterobacteria. Shigella are potential food-borne pathogens that are capable of colonizing the intestina...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
aggrephagy IMP
Inferred from Mutant Phenotype
more info
PubMed 
antigen processing and presentation of endogenous antigen IEA
Inferred from Electronic Annotation
more info
 
apoptotic process IEA
Inferred from Electronic Annotation
more info
 
autophagosome assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
autophagy IMP
Inferred from Mutant Phenotype
more info
PubMed 
autophagy ISS
Inferred from Sequence or Structural Similarity
more info
 
autophagy of host cells involved in interaction with symbiont IGI
Inferred from Genetic Interaction
more info
PubMed 
blood vessel remodeling IEA
Inferred from Electronic Annotation
more info
 
cellular homeostasis IEA
Inferred from Electronic Annotation
more info
 
cellular response to nitrosative stress IEA
Inferred from Electronic Annotation
more info
 
heart contraction IEA
Inferred from Electronic Annotation
more info
 
macroautophagy TAS
Traceable Author Statement
more info
 
negative regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cell death IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of histone H4-K16 acetylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of phagocytosis IEA
Inferred from Electronic Annotation
more info
 
negative regulation of protein ubiquitination IEA
Inferred from Electronic Annotation
more info
 
negative regulation of reactive oxygen species metabolic process IEA
Inferred from Electronic Annotation
more info
 
negative stranded viral RNA replication IEA
Inferred from Electronic Annotation
more info
 
negative thymic T cell selection IEA
Inferred from Electronic Annotation
more info
 
otolith development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of mucus secretion IEA
Inferred from Electronic Annotation
more info
 
post-translational protein modification ISS
Inferred from Sequence or Structural Similarity
more info
 
protein lipidation involved in autophagosome assembly IEA
Inferred from Electronic Annotation
more info
 
regulation of cilium assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cytokine secretion involved in immune response IEA
Inferred from Electronic Annotation
more info
 
regulation of release of sequestered calcium ion into cytosol IEA
Inferred from Electronic Annotation
more info
 
response to drug IEA
Inferred from Electronic Annotation
more info
 
response to fungus IEA
Inferred from Electronic Annotation
more info
 
vasodilation IEA
Inferred from Electronic Annotation
more info
 
ventricular cardiac muscle cell development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Mitochondria-associated ER Membrane IEA
Inferred from Electronic Annotation
more info
 
autophagosome IDA
Inferred from Direct Assay
more info
PubMed 
axoneme ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosol TAS
Traceable Author Statement
more info
 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
phagocytic vesicle membrane TAS
Traceable Author Statement
more info
 
phagophore assembly site membrane ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001286106.1NP_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)
    BC002699, BX537904, CR749386, HY168998
    Consensus CDS
    CCDS5055.1
    UniProtKB/Swiss-Prot
    Q9H1Y0
    UniProtKB/TrEMBL
    A9UGY9, Q7Z3H3
    Related
    ENSP00000343313.3, ENST00000343245.7
    Conserved Domains (1) summary
    pfam04106
    Location:79270
    APG5; Autophagy protein Apg5
  2. NM_001286107.1NP_001273036.1  autophagy protein 5 isoform b precursor

    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/Swiss-Prot
    Q9H1Y0
    UniProtKB/TrEMBL
    Q7Z3H3
    Related
    ENSP00000490493.1, ENST00000635758.2
    Conserved Domains (1) summary
    pfam04106
    Location:1192
    APG5; Autophagy protein Apg5
  3. NM_001286108.1NP_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:79189
    APG5; Autophagy protein Apg5
  4. NM_001286111.1NP_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/Swiss-Prot
    Q9H1Y0
    UniProtKB/TrEMBL
    Q7Z3H3
    Related
    ENSP00000353884.4, ENST00000360666.6
  5. NM_004849.4NP_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
    Q9H1Y0
    UniProtKB/TrEMBL
    A9UGY9, Q7Z3H3
    Related
    ENSP00000358072.3, ENST00000369076.8
    Conserved Domains (1) summary
    pfam04106
    Location:79270
    APG5; Autophagy protein Apg5

RNA

  1. 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
  2. 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

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    106184476..106325820 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024446590.1XP_024302358.1  autophagy protein 5 isoform X1

    Conserved Domains (1) summary
    pfam04106
    Location:1192
    APG5; Autophagy protein Apg5

RNA

  1. XR_001743757.2 RNA Sequence

    Related
    ENST00000369070.5
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