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    ATG12 autophagy related 12 [ Homo sapiens (human) ]

    Gene ID: 9140, updated on 9-Dec-2024

    Summary

    Official Symbol
    ATG12provided by HGNC
    Official Full Name
    autophagy related 12provided by HGNC
    Primary source
    HGNC:HGNC:588
    See related
    Ensembl:ENSG00000145782 MIM:609608; AllianceGenome:HGNC:588
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    APG12; FBR93; APG12L; HAPG12
    Summary
    Autophagy is a process of bulk protein degradation in which cytoplasmic components, including organelles, are enclosed in double-membrane structures called autophagosomes and delivered to lysosomes or vacuoles for degradation. ATG12 is the human homolog of a yeast protein involved in autophagy (Mizushima et al., 1998 [PubMed 9852036]).[supplied by OMIM, Mar 2008]
    Expression
    Ubiquitous expression in brain (RPKM 8.9), fat (RPKM 8.2) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See ATG12 in Genome Data Viewer
    Location:
    5q22.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (115828200..115841565, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (116340597..116353961, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (115163897..115177262, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene RNA, U2 small nuclear 49, pseudogene Neighboring gene Sharpr-MPRA regulatory region 14872 Neighboring gene uncharacterized LOC124901049 Neighboring gene cysteine dioxygenase type 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:115176125-115176625 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:115176629-115177530 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16255 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22939 Neighboring gene adaptor related protein complex 3 subunit sigma 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:115216191-115216388 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:115265650-115266849 Neighboring gene lincRNA adipogenesis and lipogenesis associated

    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?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of autophagy related 12 homolog (ATG12) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    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
    contributes_to Atg8-family ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein tag activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in autophagosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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 autophagosome maturation IBA
    Inferred from Biological aspect of Ancestor
    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 macroautophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in macroautophagy ISO
    Inferred from Sequence Orthology
    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 type I interferon production ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in piecemeal microautophagy of the nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of viral translation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of autophagosome maturation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 autophagosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in autophagosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    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
     
    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
     
    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
    ubiquitin-like protein ATG12
    Names
    APG12 autophagy 12-like
    ATG12 autophagy related 12 homolog
    Apg12 (autophagy, yeast) homolog

    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_001277783.2NP_001264712.1  ubiquitin-like protein ATG12 isoform 2

      See identical proteins and their annotated locations for NP_001264712.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks an exon in the coding region compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC026449, BC011033
      Consensus CDS
      CCDS64222.1
      UniProtKB/Swiss-Prot
      O94817
      Related
      ENSP00000425164.1, ENST00000500945.2
    2. NM_004707.4NP_004698.3  ubiquitin-like protein ATG12 isoform 1

      See identical proteins and their annotated locations for NP_004698.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer protein (isoform 1).
      Source sequence(s)
      AC026449, BC012266, DB530852
      Consensus CDS
      CCDS4122.2
      UniProtKB/Swiss-Prot
      O94817, Q6PJV2
      UniProtKB/TrEMBL
      B2R8C8
      Related
      ENSP00000425107.1, ENST00000509910.2
      Conserved Domains (1) summary
      pfam04110
      Location:54140
      APG12; Ubiquitin-like autophagy protein Apg12

    RNA

    1. NR_033362.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) includes an additional internal exon in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC026449, CN400030, DA005347, DB530852
    2. NR_033363.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) includes an additional internal exon in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC026449, CB995198, DA005347, DB530852
    3. NR_073603.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains two alternate exons compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC026449, AK313320

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      115828200..115841565 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      116340597..116353961 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NR_073604.1: Suppressed sequence

      Description
      NR_073604.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.