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Aliases for ATG4A Gene

Aliases for ATG4A Gene

  • Autophagy Related 4A Cysteine Peptidase 2 3 5
  • Autophagy-Related Cysteine Endopeptidase 2 3 4
  • Autophagy-Related Protein 4 Homolog A 3 4
  • HAPG4A 3 4
  • APG4A 3 4
  • AUTL2 3 4
  • AUT-Like 2, Cysteine Endopeptidase (S. Cerevisiae) 2
  • ATG4 Autophagy Related 4 Homolog A (S. Cerevisiae) 2
  • APG4 Autophagy 4 Homolog A (S. Cerevisiae) 2
  • Autophagy Related 4A, Cysteine Peptidase 2
  • ATG4 Autophagy Related 4 Homolog A 3
  • AUT-Like 2, Cysteine Endopeptidase 3
  • AUT-Like 2 Cysteine Endopeptidase 4
  • APG4 Autophagy 4 Homolog A 3
  • Cysteine Protease ATG4A 3
  • Autophagin 2 3
  • Autophagin-2 4
  • EC 3.4.22.- 4

External Ids for ATG4A Gene

Previous HGNC Symbols for ATG4A Gene

  • AUTL2
  • APG4A

Previous GeneCards Identifiers for ATG4A Gene

  • GC0XP107142
  • GC0XP107221
  • GC0XP107334
  • GC0XP096957

Summaries for ATG4A Gene

Entrez Gene Summary for ATG4A 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 encodes a member of the autophagin protein family. The encoded protein is also designated as a member of the C-54 family of cysteine proteases. [provided by RefSeq, Mar 2016]

GeneCards Summary for ATG4A Gene

ATG4A (Autophagy Related 4A Cysteine Peptidase) is a Protein Coding gene. Among its related pathways are Autophagy Pathway and Autophagy - animal. Gene Ontology (GO) annotations related to this gene include cysteine-type endopeptidase activity and cysteine-type peptidase activity. An important paralog of this gene is ATG4B.

UniProtKB/Swiss-Prot for ATG4A Gene

  • Cysteine protease required for the cytoplasm to vacuole transport (Cvt) and autophagy. Cleaves the C-terminal amino acid of ATG8 family proteins 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. Preferred substrate is GABARAPL2 followed by MAP1LC3A and GABARAP. Has also an activity of delipidating enzyme for the PE-conjugated forms.

Gene Wiki entry for ATG4A Gene

Additional gene information for ATG4A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ATG4A Gene

Genomics for ATG4A Gene

GeneHancer (GH) Regulatory Elements for ATG4A Gene

Promoters and enhancers for ATG4A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ108089 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 655.2 +2.3 2290 2.8 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF143 SP3 ATG4A PSMD10
GH0XJ108088 Promoter/Enhancer 1.3 EPDnew ENCODE 655.3 -0.2 -170 1.4 HDAC1 PKNOX1 ZBTB40 CHAMP1 TCF12 ATF7 CEBPB NCOA1 ATF4 NFIC ATG4A PSMD10 GC0XM108072
GH0XJ108072 Enhancer 0.8 Ensembl ENCODE 5 -16.7 -16660 0.3 CTCF PKNOX1 ZNF654 TRIM22 ZNF384 REST RAD21 YY1 ZNF148 ZNF335 GC0XM108072 VSIG1 ATG4A
GH0XJ107708 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 1.4 -374.6 -374604 10.9 HDGF PKNOX1 SMAD1 ARNT SIN3A YBX1 YY1 ZNF143 FOS JUNB TSC22D3 RBM41 MORC4 MID2 LOC101928335 ATG4A GC0XM107728 GC0XM107676
GH0XJ108070 Enhancer 0.6 ENCODE 4.7 -17.6 -17600 1.4 CTCF ZNF654 TRIM22 ZNF384 RAD21 YY1 ZNF335 FOS GC0XM108072 VSIG1 TEX13B ATG4A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATG4A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ATG4A gene promoter:
  • C/EBPbeta
  • COMP1
  • Nkx2-2
  • Nkx6-1
  • C/EBPalpha
  • POU2F1
  • POU2F1a
  • c-Myb
  • RORalpha1
  • Nkx3-1

Genomic Locations for ATG4A Gene

Genomic Locations for ATG4A Gene
chrX:108,088,916-108,154,671
(GRCh38/hg38)
Size:
65,756 bases
Orientation:
Plus strand
chrX:107,334,898-107,397,901
(GRCh37/hg19)
Size:
63,004 bases
Orientation:
Plus strand

Genomic View for ATG4A Gene

Genes around ATG4A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATG4A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATG4A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATG4A Gene

Proteins for ATG4A Gene

  • Protein details for ATG4A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WYN0-ATG4A_HUMAN
    Recommended name:
    Cysteine protease ATG4A
    Protein Accession:
    Q8WYN0
    Secondary Accessions:
    • A6NCH2
    • B2RAZ7
    • D3DUY0
    • O95534
    • Q5JYY9
    • Q5JYZ0
    • Q86VE5
    • Q96KQ0
    • Q96KQ1

    Protein attributes for ATG4A Gene

    Size:
    398 amino acids
    Molecular mass:
    45378 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for ATG4A Gene

    Alternative splice isoforms for ATG4A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ATG4A Gene

Post-translational modifications for ATG4A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ATG4A Gene

Domains & Families for ATG4A Gene

Gene Families for ATG4A Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for ATG4A Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ATG4A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8WYN0

UniProtKB/Swiss-Prot:

ATG4A_HUMAN :
  • Belongs to the peptidase C54 family.
Family:
  • Belongs to the peptidase C54 family.
genes like me logo Genes that share domains with ATG4A: view

Function for ATG4A Gene

Molecular function for ATG4A Gene

UniProtKB/Swiss-Prot Function:
Cysteine protease required for the cytoplasm to vacuole transport (Cvt) and autophagy. Cleaves the C-terminal amino acid of ATG8 family proteins 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. Preferred substrate is GABARAPL2 followed by MAP1LC3A and GABARAP. Has also an activity of delipidating enzyme for the PE-conjugated forms.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by N-ethylmaleimide. Redox-regulated during autophagy since reducing conditions activate ATG4A whereas an oxidizing environment such as the presence of H(2)O(2) inhibits its activity.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=33.9 uM for MAP1LC3B {ECO:0000269 PubMed:21177865, ECO:0000269 PubMed:22302004}; KM=20.8 uM for GABARAP {ECO:0000269 PubMed:21177865, ECO:0000269 PubMed:22302004}; KM=36.7 uM for GABARAPL1 {ECO:0000269 PubMed:21177865, ECO:0000269 PubMed:22302004}; KM=15.7 uM for GABARAPL2 {ECO:0000269 PubMed:21177865, ECO:0000269 PubMed:22302004};

Enzyme Numbers (IUBMB) for ATG4A Gene

Gene Ontology (GO) - Molecular Function for ATG4A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004197 cysteine-type endopeptidase activity IBA,IEA --
GO:0005515 protein binding IPI 25416956
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IDA,IEA 12473658
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with ATG4A: view
genes like me logo Genes that share phenotypes with ATG4A: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATG4A

Clone Products

  • Addgene plasmids for ATG4A

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ATG4A Gene

Localization for ATG4A Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATG4A Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ATG4A gene
Compartment Confidence
cytosol 5
nucleus 3
cytoskeleton 2
mitochondrion 1
peroxisome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (2)
  • Microtubules (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ATG4A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,ISS 12446702
GO:0005829 cytosol IBA --
genes like me logo Genes that share ontologies with ATG4A: view

Pathways & Interactions for ATG4A Gene

genes like me logo Genes that share pathways with ATG4A: view

Pathways by source for ATG4A Gene

1 GeneTex pathway for ATG4A Gene
1 BioSystems pathway for ATG4A Gene
2 Reactome pathways for ATG4A Gene
2 KEGG pathways for ATG4A Gene
1 R&D Systems pathway for ATG4A Gene

Gene Ontology (GO) - Biological Process for ATG4A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000045 autophagosome assembly IBA --
GO:0000422 autophagy of mitochondrion IBA --
GO:0006501 C-terminal protein lipidation IBA --
GO:0006508 proteolysis IEA,IDA 12473658
GO:0006612 protein targeting to membrane IBA --
genes like me logo Genes that share ontologies with ATG4A: view

No data available for SIGNOR curated interactions for ATG4A Gene

Drugs & Compounds for ATG4A Gene

(8) Drugs for ATG4A Gene - From:

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Nimodipine Approved, Investigational Pharma Potentiation, Activator Ca2+ channel blocker (L-type) 27
Omeprazole Approved, Investigational, Vet_approved Pharma Activator H+,K+-ATPase inhibitor 373
Nocodazole Experimental Pharma Tubulin production inhibitor,anti-neoplastic agent, Microtubule inhibitor 0
Chloroquine diphosphate Pharma Antimalarial drug 154
Dexamethasone (DHAP) Pharma Glucocorticoidan;ti-inflammatory 0
genes like me logo Genes that share compounds with ATG4A: view

Transcripts for ATG4A Gene

Unigene Clusters for ATG4A Gene

Autophagy related 4A, cysteine peptidase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATG4A

Clone Products

  • Addgene plasmids for ATG4A

Alternative Splicing Database (ASD) splice patterns (SP) for ATG4A Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15
SP1: - - - -
SP2: - - - - - -
SP3: - - - - - -
SP4: - - - -
SP5: - - - - -
SP6: - -
SP7: - -
SP8:
SP9: -

Relevant External Links for ATG4A Gene

GeneLoc Exon Structure for
ATG4A
ECgene alternative splicing isoforms for
ATG4A

Expression for ATG4A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ATG4A Gene

Protein differential expression in normal tissues from HIPED for ATG4A Gene

This gene is overexpressed in Saliva (37.1), Pancreas (19.5), and Gallbladder (9.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ATG4A Gene



NURSA nuclear receptor signaling pathways regulating expression of ATG4A Gene:

ATG4A

SOURCE GeneReport for Unigene cluster for ATG4A Gene:

Hs.8763

mRNA Expression by UniProt/SwissProt for ATG4A Gene:

Q8WYN0-ATG4A_HUMAN
Tissue specificity: Widely expressed, at a low level, and the highest expression is observed in skeletal muscle and brain. Also detected in fetal liver.

Evidence on tissue expression from TISSUES for ATG4A Gene

  • Kidney(4.2)
genes like me logo Genes that share expression patterns with ATG4A: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for ATG4A Gene

Orthologs for ATG4A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ATG4A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ATG4A 34 33
  • 99.66 (n)
OneToOne
cow
(Bos Taurus)
Mammalia ATG4A 34 33
  • 92.63 (n)
OneToOne
dog
(Canis familiaris)
Mammalia ATG4A 34 33
  • 92.38 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Atg4al1 33
  • 91.54 (n)
mouse
(Mus musculus)
Mammalia Atg4a 16 34 33
  • 90.44 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia ATG4A 34
  • 80 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia ATG4A 34
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves ATG4A 34 33
  • 76.68 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ATG4A 34
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia atg4a 33
  • 73.14 (n)
Str.4065 33
zebrafish
(Danio rerio)
Actinopterygii atg4a 34 33
  • 69.25 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Atg4 34 33
  • 52.89 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008497 33
  • 51.55 (n)
worm
(Caenorhabditis elegans)
Secernentea atg-4.1 34 33
  • 50.38 (n)
OneToMany
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D19536g 33
  • 48.27 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ABL191W 33
  • 45.77 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ATG4 34 33
  • 45.48 (n)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G59950 33
  • 47.35 (n)
rice
(Oryza sativa)
Liliopsida Os04g0682000 33
  • 46.1 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2997 34
  • 40 (a)
OneToMany
Species where no ortholog for ATG4A was found in the sources mined by GeneCards:
  • 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)
  • 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)
  • 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 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for ATG4A Gene

ENSEMBL:
Gene Tree for ATG4A (if available)
TreeFam:
Gene Tree for ATG4A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ATG4A: view image

Paralogs for ATG4A Gene

Paralogs for ATG4A Gene

(2) SIMAP similar genes for ATG4A Gene using alignment to 5 proteins:

  • ATG4A_HUMAN
  • F5H3G3_HUMAN
  • F8W7J2_HUMAN
  • G5E979_HUMAN
  • H7BYM2_HUMAN

Pseudogenes.org Pseudogenes for ATG4A Gene

genes like me logo Genes that share paralogs with ATG4A: view

Variants for ATG4A Gene

Sequence variations from dbSNP and Humsavar for ATG4A Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1000125068 -- 108,096,156(+) T/C intron_variant
rs1000168904 -- 108,115,773(+) C/G intron_variant
rs1000210757 -- 108,146,605(+) C/T intron_variant
rs1000220135 -- 108,129,513(+) A/G intron_variant
rs1000279749 -- 108,115,359(+) A/G intron_variant

Variation tolerance for ATG4A Gene

Residual Variation Intolerance Score: 34.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.11; 38.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATG4A Gene

Human Gene Mutation Database (HGMD)
ATG4A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ATG4A

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for ATG4A Gene

Disorders for ATG4A Gene

Additional Disease Information for ATG4A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for ATG4A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ATG4A Gene

Publications for ATG4A Gene

  1. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy. (PMID: 12446702) Mariño G … López-Otín C (The Journal of biological chemistry 2003) 2 3 4 58
  2. The COOH terminus of GATE-16, an intra-Golgi transport modulator, is cleaved by the human cysteine protease HsApg4A. (PMID: 12473658) Scherz-Shouval R … Elazar Z (The Journal of biological chemistry 2003) 2 3 4 58
  3. Kinetics comparisons of mammalian Atg4 homologues indicate selective preferences toward diverse Atg8 substrates. (PMID: 21177865) Li M … Yin XM (The Journal of biological chemistry 2011) 3 4 58
  4. MicroRNA-related genetic variations as predictors for risk of second primary tumor and/or recurrence in patients with early-stage head and neck cancer. (PMID: 20819778) Zhang X … Wu X (Carcinogenesis 2010) 3 44 58
  5. Reactive oxygen species are essential for autophagy and specifically regulate the activity of Atg4. (PMID: 17347651) Scherz-Shouval R … Elazar Z (The EMBO journal 2007) 3 4 58

Products for ATG4A Gene

Sources for ATG4A Gene

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