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

Gene ID: 242557, updated on 2-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 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

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