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

Gene ID: 235040, updated on 18-Feb-2023

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 peptidase activity. Predicted to be involved in proteolysis. Predicted to act upstream of or within apoptotic process; autophagy; and protein transport. Predicted to be located in mitochondrion and nucleoplasm. Is expressed in central nervous system and retina. Orthologous to human ATG4D (autophagy related 4D cysteine peptidase). [provided by Alliance of Genome Resources, Apr 2022]
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; 9 A3
Exon count:
10
Annotation release Status Assembly Chr Location
109 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 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 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 (17) 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)
  • Gene trapped (1) 
  • Endonuclease-mediated (1) 

General gene information

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Homology

Clone Names

  • MGC31226

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables cysteine-type peptidase activity ISO
Inferred from Sequence Orthology
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables peptidase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in autophagy ISO
Inferred from Sequence Orthology
more info
  
involved_in mitophagy ISO
Inferred from Sequence Orthology
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
  
acts_upstream_of_or_within protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in proteolysis ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrion ISO
Inferred from Sequence Orthology
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, Q8K0Q2
    Related
    ENSMUSP00000068450.4, ENSMUST00000065005.5
    Conserved Domains (1) summary
    pfam03416
    Location:110 → 411
    Peptidase_C54; Peptidase family C54

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

    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

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