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ATG5 autophagy related 5 [ Homo sapiens (human) ]

Gene ID: 9474, updated on 7-Aug-2022

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
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Genomic context

See ATG5 in Genome Data Viewer
Location:
6q21
Exon count:
11
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (106184476..106325760, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (107360315..107501922, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (106632351..106773635, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene PR/SET domain 1 Neighboring gene Sharpr-MPRA regulatory region 9287 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 Functions

What's a GeneRIF?

Phenotypes

Associated conditions

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

EBI GWAS Catalog

Description
A systemic sclerosis and systemic lupus erythematosus pan-meta-GWAS reveals new shared susceptibility loci.
EBI GWAS Catalog
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
EBI GWAS Catalog
Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus.
EBI GWAS 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.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in C-terminal protein lipidation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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 autophagy of mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in autophagy of nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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 establishment of localization in cell IEA
Inferred from Electronic Annotation
more info
 
involved_in heart contraction IEA
Inferred from Electronic Annotation
more info
 
involved_in macroautophagy IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in mucus secretion IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of cardiac muscle cell apoptotic process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of cell death IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of defense response to virus IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of histone H4-K16 acetylation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of innate immune response IEA
Inferred from Electronic Annotation
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 IEA
Inferred from Electronic Annotation
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 positive regulation of mucus secretion 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 protein lipidation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in protein lipidation involved in autophagosome assembly 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 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
PubMed 
part_of Atg12-Atg5-Atg16 complex IPI
Inferred from Physical Interaction
more info
PubMed 
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 membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in mitochondria-associated endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
located_in phagocytic vesicle membrane TAS
Traceable Author Statement
more info
 
is_active_in phagophore assembly site membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in phagophore assembly site membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
part_of protein-containing complex IC
Inferred by Curator
more info
PubMed 

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)

NEW Try the new Transcript table

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_001286106.2NP_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
    Q9H1Y0, Q9HCZ7
    UniProtKB/TrEMBL
    A9UGY9, Q7Z3H3
    Related
    ENSP00000343313.3, ENST00000343245.7
    Conserved Domains (1) summary
    pfam04106
    Location:79270
    APG5; Autophagy protein Apg5
  2. NM_001286107.2NP_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_001286108.2NP_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_001286111.2NP_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, Q9HCZ7
    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
    Related
    ENST00000369070.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    106184476..106325760 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (1) summary
    pfam04106
    Location:1192
    APG5; Autophagy protein Apg5
  2. XM_047419574.1XP_047275530.1  autophagy protein 5 isoform X3

  3. XM_047419573.1XP_047275529.1  autophagy protein 5 isoform X1

    Related
    ENSP00000495958.1, ENST00000646025.1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    107360315..107501922 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)