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Aliases for ATG4D Gene

Aliases for ATG4D Gene

  • Autophagy Related 4D, Cysteine Peptidase 2 3
  • APG4D 3 4 6
  • AUTL4 3 4 6
  • Autophagy-Related Cysteine Endopeptidase 4 3 4
  • Autophagy-Related Protein 4 Homolog D 3 4
  • AUT-Like 4 Cysteine Endopeptidase 3 4
  • Autophagin-4 3 4
  • AUT-Like 4, Cysteine Endopeptidase (S. Cerevisiae) 2
  • ATG4 Autophagy Related 4 Homolog D (S. Cerevisiae) 2
  • APG4 Autophagy 4 Homolog D (S. Cerevisiae) 2
  • Cysteine Protease Involved In Autophagy 3
  • ATG4 Autophagy Related 4 Homolog D 3
  • APG4 Autophagy 4 Homolog D 3
  • Cysteine Protease ATG4D 3
  • EC 3.4.22.- 4
  • EC 3.4.22 63
  • APG4-D 3

External Ids for ATG4D Gene

Previous HGNC Symbols for ATG4D Gene

  • AUTL4
  • APG4D

Previous GeneCards Identifiers for ATG4D Gene

  • GC19P010654
  • GC19P010232

Summaries for ATG4D Gene

Entrez Gene Summary for ATG4D Gene

  • Autophagy is the process by which endogenous proteins and damaged organelles are destroyed intracellularly. Autophagy is postulated to be essential for cell homeostasis and cell remodeling during differentiation, metamorphosis, non-apoptotic cell death, and aging. Reduced levels of autophagy have been described in some malignant tumors, and a role for autophagy in controlling the unregulated cell growth linked to cancer has been proposed. This gene belongs to the autophagy-related protein 4 (Atg4) family of C54 endopeptidases. Members of this family encode proteins that play a role in the biogenesis of autophagosomes, which sequester the cytosol and organelles for degradation by lysosomes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

GeneCards Summary for ATG4D Gene

ATG4D (Autophagy Related 4D, Cysteine Peptidase) is a Protein Coding gene. Among its related pathways are Regulation of autophagy. GO annotations related to this gene include cysteine-type endopeptidase activity. An important paralog of this gene is ATG4B.

UniProtKB/Swiss-Prot for ATG4D Gene

  • Cysteine protease ATG4D: Cysteine protease required for the cytoplasm to vacuole transport (Cvt) and autophagy. Cleaves the C-terminal amino acid of ATG8 family proteins MAP1LC3 and GABARAPL2, to reveal a C-terminal glycine. Exposure of the glycine at the C-terminus is essential for ATG8 proteins conjugation to phosphatidylethanolamine (PE) and insertion to membranes, which is necessary for autophagy. Has also an activity of delipidating enzyme for the PE-conjugated forms

  • Cysteine protease ATG4D, mitochondrial: Plays a role as an autophagy regulator that links mitochondrial dysfunction with apoptosis. The mitochondrial import of ATG4D during cellular stress and differentiation may play important roles in the regulation of mitochondrial physiology, ROS, mitophagy and cell viability

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ATG4D Gene

Genomics for ATG4D Gene

Regulatory Elements for ATG4D Gene

Transcription factor binding sites by QIAGEN in the ATG4D gene promoter:

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for ATG4D Gene

Start:
10,543,894 bp from pter
End:
10,553,423 bp from pter
Size:
9,530 bases
Orientation:
Plus strand

Genomic View for ATG4D Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for ATG4D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATG4D Gene

Proteins for ATG4D Gene

  • Protein details for ATG4D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86TL0-ATG4D_HUMAN
    Recommended name:
    Cysteine protease ATG4D
    Protein Accession:
    Q86TL0
    Secondary Accessions:
    • Q969K0

    Protein attributes for ATG4D Gene

    Size:
    474 amino acids
    Molecular mass:
    52922 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for ATG4D Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ATG4D Gene

Proteomics data for ATG4D Gene at MOPED

Post-translational modifications for ATG4D Gene

  • Cleaved by CASP3 during apoptosis which leads to increased activity. The cleavage by CASP3 reveals a cryptic mitochondrial targeting sequence immediately downstream of their canonical caspase cleavage sites which leads to mitochondroal import of the protein.
  • Ubiquitination at Lys281, Lys298, and Lys322
  • Modification sites at PhosphoSitePlus

Domains for ATG4D Gene

Protein Domains for ATG4D Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ATG4D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q86TL0

UniProtKB/Swiss-Prot:

ATG4D_HUMAN :
  • Q86TL0
Domain:
  • Residues 64 to 103 constitute a cryptic mitochondrial transit peptide which is revealed after cleavage by caspase of residues 1 to 63 upon oxidative stress and cell death. It acts then as a functional transit peptide, and allows the import of the cleaved protein into the mitochondria (PubMed:22441018).
Family:
  • Belongs to the peptidase C54 family.
genes like me logo Genes that share domains with ATG4D: view

No data available for Gene Families for ATG4D Gene

Function for ATG4D Gene

Molecular function for ATG4D Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties: Kinetic parameters: KM=13.1 uM for MAP1LC3B {ECO:0000269 PubMed:21177865}; KM=7.2 uM for GABARAPL2 {ECO:0000269 PubMed:21177865};
UniProtKB/Swiss-Prot EnzymeRegulation: Inhibited by N-ethylmaleimide
UniProtKB/Swiss-Prot Function: Cysteine protease ATG4D: Cysteine protease required for the cytoplasm to vacuole transport (Cvt) and autophagy. Cleaves the C-terminal amino acid of ATG8 family proteins MAP1LC3 and GABARAPL2, to reveal a C-terminal glycine. Exposure of the glycine at the C-terminus is essential for ATG8 proteins conjugation to phosphatidylethanolamine (PE) and insertion to membranes, which is necessary for autophagy. Has also an activity of delipidating enzyme for the PE-conjugated forms
UniProtKB/Swiss-Prot Function: Cysteine protease ATG4D, mitochondrial: Plays a role as an autophagy regulator that links mitochondrial dysfunction with apoptosis. The mitochondrial import of ATG4D during cellular stress and differentiation may play important roles in the regulation of mitochondrial physiology, ROS, mitophagy and cell viability

Enzyme Numbers (IUBMB) for ATG4D Gene

Gene Ontology (GO) - Molecular Function for ATG4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004197 cysteine-type endopeptidase activity ISS 12446702
GO:0008234 cysteine-type peptidase activity --
genes like me logo Genes that share ontologies with ATG4D: view

Animal Model Products

CRISPR Products

No data available for Phenotypes , Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for ATG4D Gene

Localization for ATG4D Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATG4D Gene

Cysteine protease ATG4D: Cytoplasm.
Cysteine protease ATG4D, mitochondrial: Cytoplasm. Mitochondrion matrix. Note=Imported into mitochondrial matrix after cleavage by CASP3 during oxidative stress and cell death.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for ATG4D Gene COMPARTMENTS Subcellular localization image for ATG4D gene
Compartment Confidence
cytosol 2
nucleus 2
vacuole 2
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for ATG4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm ISS 12446702
GO:0005739 mitochondrion --
GO:0005759 mitochondrial matrix IEA --
GO:0005829 cytosol IBA --
genes like me logo Genes that share ontologies with ATG4D: view

Pathways for ATG4D Gene

SuperPathways for ATG4D Gene

Superpath Contained pathways
1 Regulation of autophagy
genes like me logo Genes that share pathways with ATG4D: view

Pathways by source for ATG4D Gene

1 KEGG pathway for ATG4D Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for ATG4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000045 autophagic vacuole assembly IBA --
GO:0000422 mitochondrion degradation IBA --
GO:0006501 C-terminal protein lipidation IBA --
GO:0006508 proteolysis --
GO:0006612 protein targeting to membrane IBA --
genes like me logo Genes that share ontologies with ATG4D: view

Transcripts for ATG4D Gene

Unigene Clusters for ATG4D Gene

Autophagy related 4D, cysteine peptidase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for ATG4D

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for ATG4D Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3a · 3b · 3c ^ 4a · 4b · 4c · 4d · 4e · 4f ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b ^ 9 ^ 10
SP1:
SP2: - - -
SP3:
SP4: - - - -
SP5: - - -
SP6: -
SP7:
SP8:
SP9:

Relevant External Links for ATG4D Gene

GeneLoc Exon Structure for
ATG4D
ECgene alternative splicing isoforms for
ATG4D

Expression for ATG4D Gene

mRNA expression in normal human tissues for ATG4D Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for ATG4D Gene

SOURCE GeneReport for Unigene cluster for ATG4D Gene Hs.512799

mRNA Expression by UniProt/SwissProt for ATG4D Gene

Q86TL0-ATG4D_HUMAN
Tissue specificity: Mainly expressed in skeletal muscle and, to a lower extent, in testis.
genes like me logo Genes that share expressions with ATG4D: view

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for ATG4D Gene

Orthologs for ATG4D Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for ATG4D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ATG4D 35
  • 99.08 (n)
  • 99.25 (a)
ATG4D 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia ATG4D 35
  • 88.91 (n)
  • 91.53 (a)
ATG4D 36
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia ATG4D 35
  • 89.92 (n)
  • 93.02 (a)
ATG4D 36
  • 95 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Atg4d 35
  • 83.33 (n)
  • 85.44 (a)
Atg4d 16
Atg4d 36
  • 86 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia ATG4D 36
  • 72 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ATG4D 36
  • 72 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Atg4d 35
  • 83.51 (n)
  • 85.84 (a)
lizard
(Anolis carolinensis)
Reptilia ATG4D 36
  • 57 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia atg4d 35
  • 59.93 (n)
  • 57.14 (a)
zebrafish
(Danio rerio)
Actinopterygii atg4da 36
  • 51 (a)
OneToMany
atg4db 36
  • 41 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004023 35
  • 56.96 (n)
  • 50.82 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG6194 35
  • 53.43 (n)
  • 49.12 (a)
CG6194 36
  • 31 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea atg-4.2 35
  • 46.18 (n)
  • 38.53 (a)
atg-4.2 36
  • 27 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ATG4 36
  • 21 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.753 36
  • 30 (a)
OneToMany
Species with no ortholog for ATG4D:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for ATG4D Gene

ENSEMBL:
Gene Tree for ATG4D (if available)
TreeFam:
Gene Tree for ATG4D (if available)

Paralogs for ATG4D Gene

Paralogs for ATG4D Gene

genes like me logo Genes that share paralogs with ATG4D: view

Variants for ATG4D Gene

Sequence variations from dbSNP and Humsavar for ATG4D Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type MAF
rs2288869 -- 10,544,355(-) CCGAC(A/G)CCCCC intron-variant
rs2304165 -- 10,548,983(-) CGCAC(A/G)GGCAC reference, synonymous-codon, nc-transcript-variant
rs2360750 -- 10,545,766(-) CTTTA(C/G)CTTGC intron-variant
rs3816042 -- 10,549,059(-) GGAGG(C/T)GTCCT intron-variant
rs7258433 -- 10,543,787(+) GCGGG(A/G)AGGCG upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for ATG4D Gene

Variant ID Type Subtype PubMed ID
dgv3725n71 CNV Loss 21882294
nsv833744 CNV Loss 17160897
nsv911042 CNV Loss 21882294
dgv3727n71 CNV Loss 21882294
nsv833745 CNV Loss 17160897
nsv911045 CNV Loss 21882294
nsv911046 CNV Loss 21882294

Relevant External Links for ATG4D Gene

HapMap Linkage Disequilibrium report
ATG4D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATG4D Gene

Disorders for ATG4D Gene

No disorders were found for ATG4D Gene.

No data available for UniProtKB/Swiss-Prot for ATG4D Gene

Publications for ATG4D Gene

  1. Caspase cleavage of Atg4D stimulates GABARAP-L1 processing and triggers mitochondrial targeting and apoptosis. (PMID: 19549685) Betin V.M. … Lane J.D. (J. Cell. Sci. 2009) 3 4 23
  2. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy. (PMID: 12446702) Marino G. … Lopez-Otin C. (J. Biol. Chem. 2003) 2 3 4
  3. A cryptic mitochondrial targeting motif in Atg4D links caspase cleavage with mitochondrial import and oxidative stress. (PMID: 22441018) Betin V.M. … Lane J.D. (Autophagy 2012) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  5. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PMID: 17207965) Lamesch P. … Vidal M. (Genomics 2007) 3

Products for ATG4D Gene

Sources for ATG4D Gene

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