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    Atg4c autophagy related 4C, cysteine peptidase [ Mus musculus (house mouse) ]

    Gene ID: 242557, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Atg4cprovided by MGI
    Official Full Name
    autophagy related 4C, cysteine peptidaseprovided by MGI
    Primary source
    MGI:MGI:2651854
    See related
    Ensembl:ENSMUSG00000028550 AllianceGenome:MGI:2651854
    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
    Apg4c; Autl1; Apg4-C; Atg4cl
    Summary
    Predicted to enable cysteine-type endopeptidase activity and protein-phosphatidylethanolamide deconjugating activity. Predicted to be involved in macroautophagy; protein delipidation; and protein processing. Predicted to be active in cytoplasm. Is expressed in central nervous system and retina. Orthologous to human ATG4C (autophagy related 4C cysteine peptidase). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in cortex adult (RPKM 2.2), frontal lobe adult (RPKM 1.8) and 26 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Atg4c in Genome Data Viewer
    Location:
    4 C6; 4 45.61 cM
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (99077181..99185495)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (99189159..99297258)

    Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene dedicator of cytokinesis 7 Neighboring gene STARR-seq mESC enhancer starr_10863 Neighboring gene angiopoietin-like 3 Neighboring gene ribosomal protein S4, X-linked pseudogene Neighboring gene STARR-seq mESC enhancer starr_10865 Neighboring gene STARR-positive B cell enhancer mm9_chr4:98849339-98849639 Neighboring gene STARR-seq mESC enhancer starr_10866 Neighboring gene predicted gene 10305 Neighboring gene predicted gene, 35379 Neighboring gene predicted gene, 35537

    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. Analysis of ATG4C function in vivo. Tamargo-Gómez I, et al. Autophagy, 2023 Nov. PMID 37459465, Free PMC Article
    2. Transient receptor potential vanilloid 1 activation induces autophagy in thymocytes through ROS-regulated AMPK and Atg4C pathways. Farfariello V, et al. J Leukoc Biol, 2012 Sep. PMID 22753949
    3. Control of autophagy by oncogenes and tumor suppressor genes. Maiuri MC, et al. Cell Death Differ, 2009 Jan. PMID 18806760
    4. Cell-Type-Specific Gene Expression in Developing Mouse Neocortex: Intermediate Progenitors Implicated in Axon Development. Bedogni F, et al. Front Mol Neurosci, 2021. PMID 34321999, Free PMC Article
    5. 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

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Analysis of ATG4C function in vivo.
      Title: Analysis of ATG4C function in vivo.
    2. we demonstrated for the first time that triggering of TRPV1 induces autophagy in mouse thymocytes resulting in AMPK activation and increased Atg4C mRNA expression
      Title: Transient receptor potential vanilloid 1 activation induces autophagy in thymocytes through ROS-regulated AMPK and Atg4C pathways.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Gene trapped (1) 
    • Targeted (1) 

    General gene information

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    Markers

    Homology

    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 endopeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cysteine-type endopeptidase 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 autophagosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in autophagosome assembly IEA
    Inferred from Electronic Annotation
    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 piecemeal microautophagy of the nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein delipidation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein delipidation 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 cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    cysteine protease ATG4C
    Names
    APG4 (ATG4) autophagy-related homolog C
    AUT-like 1, cysteine endopeptidase
    AUT-like 3 cysteine endopeptidase
    autophagin 3
    autophagy-related 4C
    autophagy-related cysteine endopeptidase 3
    autophagy-related protein 4 homolog C
    cysteine protease involved in autophagy
    NP_001139439.1
    NP_778194.3
    XP_006503134.1
    XP_006503135.1
    XP_006503136.1
    XP_030109415.1
    XP_030109417.1
    XP_036020021.1

    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_001145967.1 → NP_001139439.1  cysteine protease ATG4C

      See identical proteins and their annotated locations for NP_001139439.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants encode the same protein.
      Source sequence(s)
      AK134838, BB851037, BC058981
      Consensus CDS
      CCDS18382.1
      UniProtKB/Swiss-Prot
      B1ASJ9, Q6PD25, Q811C2
      UniProtKB/TrEMBL
      Q3UYA5
      Related
      ENSMUSP00000137035.2, ENSMUST00000180278.2
      Conserved Domains (1) summary
      pfam03416
      Location:77 → 395
      Peptidase_C54; Peptidase family C54

    2. NM_175029.3 → NP_778194.3  cysteine protease ATG4C

      See identical proteins and their annotated locations for NP_778194.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants encode the same protein.
      Source sequence(s)
      AK134838, BC058981
      Consensus CDS
      CCDS18382.1
      UniProtKB/Swiss-Prot
      B1ASJ9, Q6PD25, Q811C2
      UniProtKB/TrEMBL
      Q3UYA5
      Related
      ENSMUSP00000030279.9, ENSMUST00000030279.15
      Conserved Domains (1) summary
      pfam03416
      Location:77 → 395
      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_000070.7 Reference GRCm39 C57BL/6J

      Range
      99077181..99185495
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006503072.5 → XP_006503135.1  cysteine protease ATG4C isoform X2

      UniProtKB/TrEMBL
      Q3UYA5
      Conserved Domains (1) summary
      pfam03416
      Location:76 → 343
      Peptidase_C54; Peptidase family C54

    2. XM_006503073.5 → XP_006503136.1  cysteine protease ATG4C isoform X3

      Conserved Domains (1) summary
      pfam03416
      Location:76 → 311
      Peptidase_C54; Peptidase family C54

    3. XM_006503071.5 → XP_006503134.1  cysteine protease ATG4C isoform X1

      UniProtKB/TrEMBL
      Q3UYA5
      Conserved Domains (1) summary
      pfam03416
      Location:56 → 380
      Peptidase_C54; Peptidase family C54

    4. XM_036164128.1 → XP_036020021.1  cysteine protease ATG4C isoform X2

      UniProtKB/TrEMBL
      Q3UYA5
      Conserved Domains (1) summary
      pfam03416
      Location:76 → 343
      Peptidase_C54; Peptidase family C54

    5. XM_030253557.2 → XP_030109417.1  cysteine protease ATG4C isoform X3

      Conserved Domains (1) summary
      pfam03416
      Location:76 → 311
      Peptidase_C54; Peptidase family C54

    6. XM_030253555.2 → XP_030109415.1  cysteine protease ATG4C isoform X1

      UniProtKB/TrEMBL
      Q3UYA5
      Conserved Domains (1) summary
      pfam03416
      Location:56 → 380
      Peptidase_C54; Peptidase family C54

    RNA

    1. XR_376316.5 RNA Sequence

    2. XR_867860.4 RNA Sequence

    3. XR_867862.4 RNA Sequence

    4. XR_867864.4 RNA Sequence

    5. XR_867865.4 RNA Sequence

    6. XR_003954943.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q811C2.2 GenPept UniProtKB/Swiss-Prot:Q811C2

    Gene LinkOut

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