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    ATG5 autophagy related 5 [ Homo sapiens (human) ]

    Gene ID: 9474, updated on 27-Nov-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See ATG5 in Genome Data Viewer
    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_000006.12Genomic Context describing neighboring genes Neighboring gene RN7SK pseudogene 211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17429 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:106441121-106441655 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:106442725-106443257 Neighboring gene NANOG hESC enhancer GRCh37_chr6:106462748-106463464 Neighboring gene PR/SET domain 1 Neighboring gene NANOG hESC enhancer GRCh37_chr6:106511809-106512319 Neighboring gene NANOG hESC enhancer GRCh37_chr6:106528405-106528951 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24877 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:106533839-106534558 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:106546043-106547242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:106552649-106553363 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:106553364-106554077 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:106582537-106583736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24878 Neighboring gene Sharpr-MPRA regulatory region 9287 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:106611080-106611926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:106611927-106612773 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:106614661-106615396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17430 Neighboring gene MPRA-validated peak6001 silencer Neighboring gene RNA, 7SL, cytoplasmic 47, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:106771297-106771797 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:106770796-106771296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24885 Neighboring gene RNA, U6 small nuclear 344, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17431 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:106808598-106809464 Neighboring gene crystallin beta-gamma domain containing 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:106895745-106896246 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
    not available

    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

    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

    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
      O60875, Q5JVR2, Q68DI4, Q9H1Y0, Q9H2B8, Q9HCZ7
      UniProtKB/TrEMBL
      A9UGY9, B3KMH8
      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

      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: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/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
      O60875, Q5JVR2, Q68DI4, Q9H1Y0, Q9H2B8, Q9HCZ7
      UniProtKB/TrEMBL
      A9UGY9, B3KMH8
      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: 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_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

      UniProtKB/TrEMBL
      B7Z5Y6
      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

      UniProtKB/TrEMBL
      A0A2R8Y718
      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)

    mRNA and Protein(s)

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

    2. XM_054356851.1XP_054212826.1  autophagy protein 5 isoform X3

    3. XM_054356849.1XP_054212824.1  autophagy protein 5 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y718