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    ATG4A autophagy related 4A, cysteine peptidase [ Homo sapiens (human) ]

    Gene ID: 115201, updated on 14-May-2013
    Official Symbol
    ATG4Aprovided by HGNC
    Official Full Name
    autophagy related 4A, cysteine peptidaseprovided by HGNC
    Primary source
    HGNC:16489
    Locus tag
    RP5-889N15.2
    See related
    Ensembl:ENSG00000101844; HPRD:06455; MIM:300663; Vega:OTTHUMG00000022176
    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
    APG4A; AUTL2
    Summary
    Autophagy is the process by which endogenous proteins and damaged organelles are destroyed intracellularly. Autophagy is postulated to be essential for cell homeostasis and cell remodeling during differentiation, metamorphosis, non-apoptotic cell death, and aging. Reduced levels of autophagy have been described in some malignant tumors, and a role for autophagy in controlling the unregulated cell growth linked to cancer has been proposed. This gene encodes a member of the autophagin protein family. The encoded protein is also designated as a member of the C-54 family of cysteine proteases. Transcript variants that encode distinct isoforms have been identified. [provided by RefSeq, Jul 2008]
    Location :
    Xq22.1-q22.3
    Sequence :
    Chromosome: X; NC_000023.10 (107334899..107397901)
    See ATG4A in Epigenomics, MapViewer

    Chromosome X - NC_000023.10Genomic Context describing neighboring genes Neighboring gene V-set and immunoglobulin domain containing 1 Neighboring gene proteasome (prosome, macropain) 26S subunit, non-ATPase, 10 Neighboring gene collagen, type IV, alpha 6 Neighboring gene collagen, type IV, alpha 5

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details

    Related articles in PubMed

    1. A systematic bioinformatics approach for selection of target and screening of ligand for malignant tumours suppressing APG4A gene on Xq22.1. Niranjan V, et al. Int J Comput Biol Drug Des, 2010. PMID 21297227.
    2. Kinetics comparisons of mammalian Atg4 homologues indicate selective preferences toward diverse Atg8 substrates. Li M, et al. J Biol Chem, 2011 Mar 4. PMID 21177865.
    3. Granulomas in Crohn's disease: are newly discovered genetic variants involved? Mazor Y, et al. J Crohns Colitis, 2010 Oct. PMID 21122541.
    4. MicroRNA-related genetic variations as predictors for risk of second primary tumor and/or recurrence in patients with early-stage head and neck cancer. Zhang X, et al. Carcinogenesis, 2010 Dec. PMID 20819778.
    5. Nix is a selective autophagy receptor for mitochondrial clearance. Novak I, et al. EMBO Rep, 2010 Jan. PMID 20010802.

    See all (14) citations in PubMed

    See citations in PubMed for homologs of this gene provided by HomoloGene

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. no association between SNP rs807185 and the presence of granulomas in Crohn's disease
      Title: Granulomas in Crohn's disease: are newly discovered genetic variants involved?
    2. statistical analysis of APG4A gene confirmed the characterisation of each protein-coding gene present in human genome Xq22.1
      Title: A systematic bioinformatics approach for selection of target and screening of ligand for malignant tumours suppressing APG4A gene on Xq22.1.
    3. Atg4B possessed the broadest spectrum against all substrates, followed by Atg4A for ATG8 substrates
      Title: Kinetics comparisons of mammalian Atg4 homologues indicate selective preferences toward diverse Atg8 substrates.
    4. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: MicroRNA-related genetic variations as predictors for risk of second primary tumor and/or recurrence in patients with early-stage head and neck cancer.
    5. HsApg4A cleaves the COOH terminus of GATE-16
      Title: The COOH terminus of GATE-16, an intra-Golgi transport modulator, is cleaved by the human cysteine protease HsApg4A.
    6. The cysteine protease HsAtg4 is identified as a direct target for oxidation by hydrogen peroxide, and a cysteine residue located near the HsAtg4 catalytic site as critical for this regulation.
      Title: Reactive oxygen species are essential for autophagy and specifically regulate the activity of Atg4.
    Submit: New GeneRIF Correction

    Review eQTL and phenotype association data in this region using PheGenI

    Products Interactant Other Gene Complex Source Pubs Description
    Q8WYN0 P60520 GABARAPL2    HPRD  PubMed  
    BioGRID:125418 BioGRID:123565 MAP1LC3B    BioGRID  PubMed Two-hybrid 

    Markers

    Genotypes

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    cysteine-type peptidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    proteolysis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Preferred Names
    cysteine protease ATG4A
    Names
    cysteine protease ATG4A
    hAPG4A
    autophagin 2
    autophagin-2
    APG4 autophagy 4 homolog A
    AUT-like 2 cysteine endopeptidase
    ATG4 autophagy related 4 homolog A
    AUT-like 2, cysteine endopeptidase
    autophagy-related protein 4 homolog A
    autophagy-related cysteine endopeptidase 2
    NP_443168.2
    NP_840054.1

    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_052936.3 → NP_443168.2  cysteine protease ATG4A isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is the predominant transcript and it encodes the longer isoform (a).
      Source sequence(s)
      AA648264, BC041862, BC061696
      Consensus CDS
      CCDS14538.1
      UniProtKB/Swiss-Prot
      Q8WYN0
      Related
      ENSP00000361306, OTTHUMP00000023821, ENST00000372232, OTTHUMT00000057860
      Conserved Domains (1) summary
      pfam03416
      Location:39 – 338
      Blast Score: 1190
      Peptidase_C54; Peptidase family C54

    2. NM_178270.2 → NP_840054.1  cysteine protease ATG4A isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame segment when compared to variant 1, resulting in a shorter protein (isoform b) compared to isoform a.
      Source sequence(s)
      AA648264, AJ320509, BC041862, BC061696
      Consensus CDS
      CCDS14539.1
      UniProtKB/Swiss-Prot
      Q8WYN0
      Related
      ENSP00000298131, OTTHUMP00000023822, ENST00000345734, OTTHUMT00000057861
      Conserved Domains (1) summary
      pfam03416
      Location:39 – 276
      Blast Score: 901
      Peptidase_C54; Peptidase family C54

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

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

    Reference GRCh37.p10 Primary Assembly

    Genomic

    1. NC_000023.10 Reference GRCh37.p10 Primary Assembly

      Range
      107334899..107397901
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000155.1 Alternate HuRef

      Range
      96957585..97020331
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.0

    Genomic

    1. NC_018934.1 Alternate CHM1_1.0

      Range
      107306609..107369566
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_178271.1: Suppressed sequence

      Description
      NM_178271.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    genomic ABBA01035973.1 None
    genomic ABBA01035974.1 None
    genomic ABBA01035975.1 None
    genomic ABBA01035976.1 None
    genomic ABBA01035977.1 None
    genomic ABBA01035978.1 None
    genomic ABBA01035979.1 None
    genomic ABBA01035980.1 None
    genomic AL031177.1 (44647..107649) None
    genomic AMYH01022835.1 (43670..106627) None
    genomic CH471120.2 EAX02689.1
      EAX02690.1
      EAX02691.1
      EAX02692.1
      EAX02693.1
      EAX02694.1
      EAX02695.1
      EAX02696.1
    mRNA AA648264.1 None
    mRNA AB066214.1 BAB83889.1
    mRNA AJ320508.1 CAC69076.1
    mRNA AJ320509.1 CAC69077.1
    mRNA AJ504651.1 CAD43218.1
    mRNA AK054927.1 None
    mRNA AK123287.1 None
    mRNA AK293533.1 BAG57015.1
    mRNA AK314429.1 BAG37044.1
    mRNA BC041862.1 AAH41862.1
    mRNA BC061696.1 AAH61696.1
    mRNA BM541631.1 None
    other-genetic HQ447703.1 ADQ32188.1
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WYN0.1 GenPept UniProtKB/Swiss-Prot:Q8WYN0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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      Supplemental Content

      Table of contents

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        BioSystems
      • CCDS
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      • Conserved Domains
        Conserved Domain Database Links between Entrez Gene and Conserved Domain Database (CDD) are calculated from the domains annotated by the CDD group on Reference Sequence proteins.
      • dbVar
        Link from Gene to dbVar
      • EST
        Link to related EST entry
      • Full text in PMC
        PMC links
      • Full text in PMC_nucleotide
        Full text in PubMedCentral identified from shared sequence links
      • Genome
        Genome records having the gene annotated on corresponding genomic reference sequence.
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        Related GEO
      • HomoloGene
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        These links are maintained by the Map Viewer group and are provided when a GeneID is annotated on a map for the same species.
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        Link to related Nucleotide entry
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        Related Probe entry
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        Link to related protein entry
      • PubChem Compound
        PubChem Compounds
      • PubChem Substance
        PubChem Substances
      • PubMed
        Links between Gene and PubMed are the result of the following: 1. Manual curation within NCBI. Part of the process of generating a REVIEWED RefSeq is an analysis of the current literature. Papers that are seminal in defining the gene, its sequence, and its function are added to the record at that time. Alert users point out gaps or errors in papers associated with a Gene record. These messages are reviewed and implemented as required. 2. Integration of information from other public databases. Gene integrates gene-citation from resources external to NCBI such as model organism-specific databases, Gene Ontology (GO), groups curating interactions, and sequence databases. The assumption in using these source is that they report citations specific to a gene in a known species. Gene does not process citations from OMIM automatically, because many of citations in OMIM refer to studies of genes in species other than human.
      • PubMed (GeneRIF)
        GeneRIF -- Gene Reference Into Function Staff of the Index Section in the National Library of Medicine review the current literature. When they find articles focused on the structure and function of a gene, they write a brief summary of the impact of the paper and make the connection between the citation (PubMed) and Gene. An interface exists for interested users to submit such data as well. http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html
      • PubMed (OMIM)
        Links are provided when Gene has a link to a record in OMIM, and OMIM explicitly cites these publications in PubMed.
      • PubMed(nucleotide/PMC)
        Citations in PubMed identified from shared sequence and PMC links.
      • RefSeq Proteins
        Link to Protein RefSeqs
      • RefSeq RNAs
        Link to Nucleotide RefSeq RNAs
      • SNP
        Related SNP records
      • SNP: GeneView
        SNPs linked from GeneView
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        Gene Genotype Report
      • Taxonomy
        Link to related taxonomy entry
      • UniGene
        Links are provided between Gene and UniGene when both databases calculate links to the same mRNA record (gi).
      • UniSTS
        Related UniSTS records

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