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    Atg4c autophagy related 4C, cysteine peptidase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 313391, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Atg4cprovided by RGD
    Official Full Name
    autophagy related 4C, cysteine peptidaseprovided by RGD
    Primary source
    RGD:1598323
    See related
    EnsemblRapid:ENSRNOG00000008767 AllianceGenome:RGD:1598323
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    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. Orthologous to human ATG4C (autophagy related 4C cysteine peptidase). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Liver (RPKM 107.0), Brain (RPKM 106.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Atg4c in Genome Data Viewer
    Location:
    5q33
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (118977594..119050894)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (113867218..113935534)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (117861517..117932116)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene dedicator of cytokinesis 7 Neighboring gene noelin-like Neighboring gene ribosomal protein L15, pseudogene 14 Neighboring gene cytochrome c oxidase assembly factor 3 homolog, mitochondrial-like Neighboring gene uncharacterized LOC102556219

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. 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, Free PMC Article
    2. LC3 conjugation system in mammalian autophagy. Tanida I, et al. Int J Biochem Cell Biol, 2004 Dec. PMID 15325588, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables cysteine-type endopeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    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 protein-phosphatidylethanolamide deconjugating activity IBA
    Inferred from Biological aspect of Ancestor
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in autophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    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 processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein transport 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
    		  

    General protein information

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    Preferred Names
    cysteine protease ATG4C
    Names
    ATG4 autophagy related 4 homolog C
    autophagy-related 4C
    NP_001101418.1
    XP_038965839.1
    XP_038965840.1
    XP_038965841.1
    XP_038965842.1
    XP_038965843.1
    XP_038965844.1
    XP_063143722.1

    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_001107948.1 → NP_001101418.1  cysteine protease ATG4C

      See identical proteins and their annotated locations for NP_001101418.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473998
      UniProtKB/TrEMBL
      A0A8I5ZXZ8, A6JRL6, F1M3M0
      Related
      ENSRNOP00000106807.1, ENSRNOT00000146775.1
      Conserved Domains (1) summary
      pfam03416
      Location:76 → 395
      Peptidase_C54; Peptidase family C54

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086023.1 Reference GRCr8

      Range
      118977594..119050894
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039109912.2 → XP_038965840.1  cysteine protease ATG4C isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZXZ8, A6JRL6, F1M3M0
      Conserved Domains (1) summary
      pfam03416
      Location:76 → 395
      Peptidase_C54; Peptidase family C54

    2. XM_039109911.2 → XP_038965839.1  cysteine protease ATG4C isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZXZ8, A6JRL6, F1M3M0
      Related
      ENSRNOP00000011631.8, ENSRNOT00000011631.8
      Conserved Domains (1) summary
      pfam03416
      Location:76 → 395
      Peptidase_C54; Peptidase family C54

    3. XM_039109915.2 → XP_038965843.1  cysteine protease ATG4C isoform X4

      UniProtKB/TrEMBL
      F1M3M0
      Conserved Domains (1) summary
      pfam03416
      Location:76 → 343
      Peptidase_C54; Peptidase family C54

    4. XM_039109913.2 → XP_038965841.1  cysteine protease ATG4C isoform X2

      UniProtKB/TrEMBL
      A0A8I5Y0E2, A0A8I6AKI4
      Related
      ENSRNOP00000076527.1, ENSRNOT00000104305.2
      Conserved Domains (1) summary
      pfam03416
      Location:48 → 367
      Peptidase_C54; Peptidase family C54

    5. XM_039109914.2 → XP_038965842.1  cysteine protease ATG4C isoform X3

      UniProtKB/TrEMBL
      F1M3M0
      Related
      ENSRNOP00000084390.2, ENSRNOT00000116538.2
      Conserved Domains (1) summary
      pfam03416
      Location:76 → 395
      Peptidase_C54; Peptidase family C54

    6. XM_063287652.1 → XP_063143722.1  cysteine protease ATG4C isoform X5

    7. XM_039109916.2 → XP_038965844.1  cysteine protease ATG4C isoform X5

      Conserved Domains (1) summary
      pfam03416
      Location:76 → 315
      Peptidase_C54; Peptidase family C54
    Nucleotide Protein Strain
    Heading Accession and Version

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