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    Atg4d autophagy related 4D, cysteine peptidase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 686505, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Atg4dprovided by RGD
    Official Full Name
    autophagy related 4D, cysteine peptidaseprovided by RGD
    Primary source
    RGD:1596392
    See related
    EnsemblRapid:ENSRNOG00000047625 AllianceGenome:RGD:1596392
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    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; cysteine-type exopeptidase activity; and protein-phosphatidylethanolamide deconjugating activity. Predicted to be involved in macroautophagy; protein delipidation; and protein processing. Predicted to be located in mitochondrion and nucleoplasm. Predicted to be active in cytoplasm. Orthologous to human ATG4D (autophagy related 4D cysteine peptidase). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Spleen (RPKM 186.2), Heart (RPKM 167.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Atg4d in Genome Data Viewer
    Location:
    8q13
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (28083902..28093491)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (19807733..19817321)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (22291445..22301331)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene Kelch-like ECH-associated protein 1 Neighboring gene sphingosine-1-phosphate receptor 5 Neighboring gene KRI1 homolog Neighboring gene cyclin dependent kinase inhibitor 2D Neighboring gene adaptor related protein complex 1 subunit mu 2

    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 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
    3. Hepatic interferon regulatory factor 8 expression mediates liver ischemia/reperfusion injury in mice. Shi G, et al. Biochem Pharmacol, 2021 Oct. PMID 34400126
    4. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    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 exopeptidase 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 mitophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in piecemeal microautophagy of the nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein delipidation IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 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
    		  
    located_in mitochondrion 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
    ATG4 autophagy related 4 homolog D
    autophagy-related 4D
    NP_001094483.2
    XP_038938087.1

    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_001101013.2 → NP_001094483.2  cysteine protease ATG4D

      See identical proteins and their annotated locations for NP_001094483.2

      Status: VALIDATED

      Source sequence(s)
      BC168141, BG371460, DY318309
      UniProtKB/TrEMBL
      A6JNQ6, B4F756, M0R5T6
      Related
      ENSRNOP00000064764.1, ENSRNOT00000075174.4
      Conserved Domains (1) summary
      pfam03416
      Location:110 → 410
      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_086026.1 Reference GRCr8

      Range
      28083902..28093491
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039082159.2 → XP_038938087.1  cysteine protease ATG4D isoform X1

      UniProtKB/TrEMBL
      A6JNQ8
      Conserved Domains (1) summary
      pfam03416
      Location:34 → 233
      Peptidase_C54; Peptidase family C54

    RNA

    1. XR_005487922.2 RNA Sequence

    2. XR_005487923.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

    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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