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    ATG3 autophagy related 3 [ Homo sapiens (human) ]

    Gene ID: 64422, updated on 17-Jun-2024

    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
    NEW
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    Genomic context

    See ATG3 in Genome Data Viewer
    Location:
    3q13.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (112532510..112561962, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (115253546..115282997, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (112251357..112280809, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr3:112184939-112185454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:112192511-112193011 Neighboring gene B and T lymphocyte associated Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:112240775-112241275 Neighboring gene olfactory receptor family 7 subfamily E member 100 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20244 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:112279571-112280380 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:112280381-112281190 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112282811-112283620 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112283621-112284430 Neighboring gene solute carrier family 35 member A5 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_64338 Neighboring gene coiled-coil domain containing 80 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:112383725-112384298 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:112405169-112405758 Neighboring gene MAT2A pseudogene 1

    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

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ22125, MGC15201, DKFZp564M1178

    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 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 IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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

    Preferred Names
    ubiquitin-like-conjugating enzyme ATG3
    Names
    APG3 autophagy 3-like
    ATG3 autophagy related 3 homolog
    autophagy-related protein 3
    NP_001265641.1
    NP_071933.2
    XP_011511376.1

    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_001278712.2NP_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:8135
      Autophagy_N; Autophagocytosis associated protein (Atg3), N-terminal domain
      pfam03987
      Location:204265
      Autophagy_act_C; Autophagocytosis associated protein, active-site domain
    2. NM_022488.5NP_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:8135
      Autophagy_N; Autophagocytosis associated protein (Atg3), N-terminal domain
      pfam03987
      Location:38308
      Autophagy_act_C; Autophagocytosis associated protein, active-site domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      112532510..112561962 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011513074.1XP_011511376.1  ubiquitin-like-conjugating enzyme ATG3 isoform X1

      Conserved Domains (3) summary
      pfam03986
      Location:1248
      Autophagy_N; Autophagocytosis associated protein (Atg3), N-terminal domain
      pfam03987
      Location:117178
      Autophagy_act_C; Autophagocytosis associated protein, active-site domain
      pfam10381
      Location:199222
      Autophagy_C; Autophagocytosis associated protein C-terminal

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      115253546..115282997 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)