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    Atg4d autophagy related 4D, cysteine peptidase [ Mus musculus (house mouse) ]

    Gene ID: 235040, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Atg4dprovided by MGI
    Official Full Name
    autophagy related 4D, cysteine peptidaseprovided by MGI
    Primary source
    MGI:MGI:2444308
    See related
    Ensembl:ENSMUSG00000002820 AllianceGenome:MGI:2444308
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Apg4d; Autl4; APG4-D; Atg4dl; 9830134P12Rik
    Summary
    Predicted to enable cysteine-type endopeptidase activity; cysteine-type exopeptidase activity; and protein-phosphatidylethanolamide deconjugating activity. Involved in protein delipidation. Predicted to be located in mitochondrion and nucleoplasm. Predicted to be active in cytoplasm. Is expressed in central nervous system and retina. Orthologous to human ATG4D (autophagy related 4D cysteine peptidase). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in duodenum adult (RPKM 44.0), colon adult (RPKM 34.3) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Atg4d in Genome Data Viewer
    Location:
    9 A3; 9 7.75 cM
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (21176496..21186133)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (21265205..21274837)

    Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 16754 Neighboring gene STARR-seq mESC enhancer starr_23486 Neighboring gene kelch-like ECH-associated protein 1 Neighboring gene STARR-positive B cell enhancer ABC_E8278 Neighboring gene sphingosine-1-phosphate receptor 5 Neighboring gene STARR-positive B cell enhancer mm9_chr9:21069491-21069792 Neighboring gene KRI1 homolog Neighboring gene cyclin dependent kinase inhibitor 2D Neighboring gene adaptor protein complex AP-1, mu 2 subunit

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. ATG4D is the main ATG8 delipidating enzyme in mammalian cells and protects against cerebellar neurodegeneration. Tamargo-Gómez I, et al. Cell Death Differ, 2021 Sep. PMID 33795848, Free PMC Article
    2. Mutations in Spliceosomal Genes PPIL1 and PRP17 Cause Neurodegenerative Pontocerebellar Hypoplasia with Microcephaly. Chai G, et al. Neuron, 2021 Jan 20. PMID 33220177, Free PMC Article
    3. BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. Magdaleno S, et al. PLoS Biol, 2006 Apr. PMID 16602821, Free PMC Article
    4. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Watahiki A, et al. Nat Methods, 2004 Dec. PMID 15782199
    5. Large-scale gene trapping in C57BL/6N mouse embryonic stem cells. Hansen GM, et al. Genome Res, 2008 Oct. PMID 18799693, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Gene trapped (1) 

    General gene information

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    Homology

    Clone Names

    • MGC31226

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables cysteine-type endopeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cysteine-type exopeptidase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables cysteine-type peptidase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables cysteine-type peptidase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein-phosphatidylethanolamide deconjugating activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein-phosphatidylethanolamide deconjugating activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in aggrephagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 autophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in autophagy ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in mitophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mitophagy ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in piecemeal microautophagy of the nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein delipidation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein delipidation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein localization to phagophore assembly site ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein localization to phagophore assembly site ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proteolysis ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrial matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    cysteine protease ATG4D
    Names
    APG4 (ATG4) autophagy-related homolog D
    AUT-like 4, cysteine endopeptidase
    autophagin-4
    autophagy-related 4D
    autophagy-related cysteine endopeptidase 4
    autophagy-related protein 4 homolog D
    cysteine protease involved in autophagy APG4-D
    NP_705811.8
    XP_006510248.1
    XP_017168790.1
    XP_036010754.1

    NCBI Reference Sequences (RefSeq)

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    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_153583.10 → NP_705811.8  cysteine protease ATG4D precursor

      See identical proteins and their annotated locations for NP_705811.8

      Status: VALIDATED

      Source sequence(s)
      AK036282, AK036571, BB857077
      Consensus CDS
      CCDS22899.1
      UniProtKB/Swiss-Prot
      Q8BGV9, Q8C4N9, Q8K0Q2
      UniProtKB/TrEMBL
      Q3U4N6
      Related
      ENSMUSP00000068450.4, ENSMUST00000065005.5
      Conserved Domains (1) summary
      pfam03416
      Location:110 → 411
      Peptidase_C54; Peptidase family C54

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000075.7 Reference GRCm39 C57BL/6J

      Range
      21176496..21186133
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006510185.4 → XP_006510248.1  cysteine protease ATG4D isoform X2

      Conserved Domains (1) summary
      pfam03416
      Location:1 → 267
      Peptidase_C54; Peptidase family C54

    2. XM_017313301.3 → XP_017168790.1  cysteine protease ATG4D isoform X1

      UniProtKB/TrEMBL
      Q3U4N6
      Related
      ENSMUST00000216826.2
      Conserved Domains (1) summary
      pfam03416
      Location:109 → 402
      Peptidase_C54; Peptidase family C54

    3. XM_036154861.1 → XP_036010754.1  cysteine protease ATG4D isoform X2

      Conserved Domains (1) summary
      pfam03416
      Location:1 → 267
      Peptidase_C54; Peptidase family C54
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BGV9.1 GenPept UniProtKB/Swiss-Prot:Q8BGV9

    Gene LinkOut

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

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