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Aliases for ATG3 Gene

Aliases for ATG3 Gene

  • Autophagy Related 3 2 3 5
  • Autophagy-Related Protein 3 3 4
  • APG3-LIKE 3 4
  • APG3L 3 4
  • HApg3 3 4
  • APG3 3 4
  • ATG3 Autophagy Related 3 Homolog (S. Cerevisiae) 2
  • Ubiquitin-Like-Conjugating Enzyme ATG3 3
  • APG3 Autophagy 3-Like (S. Cerevisiae) 2
  • ATG3 Autophagy Related 3 Homolog 3
  • APG3 Autophagy 3-Like 3
  • Protein PC3-96 4
  • 2610016C12Rik 3
  • EC 6.3.2.- 4
  • PC3-96 3

External Ids for ATG3 Gene

Previous HGNC Symbols for ATG3 Gene

  • APG3L

Previous GeneCards Identifiers for ATG3 Gene

  • GC03M113735
  • GC03M112251
  • GC03M109636

Summaries for ATG3 Gene

Entrez Gene Summary for ATG3 Gene

  • This gene encodes a ubiquitin-like-conjugating enzyme and is a component of ubiquitination-like systems involved in autophagy, the process of degradation, turnover and recycling of cytoplasmic constituents in eukaryotic cells. This protein is known to play a role in regulation of autophagy during cell death. A pseudogene of this gene is located on chromosome 20. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]

GeneCards Summary for ATG3 Gene

ATG3 (Autophagy Related 3) is a Protein Coding gene. Diseases associated with ATG3 include Bardet-Biedl Syndrome 4. Among its related pathways are Cellular Senescence (REACTOME) and Autophagy Pathway. GO annotations related to this gene include enzyme binding and ubiquitin-like protein transferase activity.

UniProtKB/Swiss-Prot for ATG3 Gene

  • E2 conjugating enzyme required for the cytoplasm to vacuole transport (Cvt), autophagy, and mitochondrial homeostasis. Responsible for the E2-like covalent binding of phosphatidylethanolamine to the C-terminal Gly of ATG8-like proteins (GABARAP, GABARAPL1, GABARAPL2 or MAP1LC3A). The ATG12-ATG5 conjugate plays a role of an E3 and promotes the transfer of ATG8-like proteins from ATG3 to phosphatidylethanolamine (PE). This step is required for the membrane association of ATG8-like proteins. The formation of the ATG8-phosphatidylethanolamine conjugates is essential for autophagy and for the cytoplasm to vacuole transport (Cvt). Preferred substrate is MAP1LC3A. Also acts as an autocatalytic E2-like enzyme, catalyzing the conjugation of ATG12 to itself, ATG12 conjugation to ATG3 playing a role in mitochondrial homeostasis but not in autophagy. ATG7 (E1-like enzyme) facilitates this reaction by forming an E1-E2 complex with ATG3. Promotes primary ciliogenesis by removing OFD1 from centriolar satellites via the autophagic pathway.

Additional gene information for ATG3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ATG3 Gene

Genomics for ATG3 Gene

Regulatory Elements for ATG3 Gene

Enhancers for ATG3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03H112539 1.2 FANTOM5 ENCODE dbSUPER 10.1 +21.7 21729 0.9 JUNB BATF IKZF1 ETV6 ATF7 CREM RUNX3 SPI1 SLC35A5 CD200 C3orf52 MIR567 ATG3 ENSG00000279349
GH03H112555 0.9 FANTOM5 Ensembl 13.2 +6.2 6246 1.2 NFIL3 PRDM6 HLF ZNF843 SP7 SLC35A5 ATG3 MIR567 C3orf52 CD200 ENSG00000279349
GH03H112817 1.1 FANTOM5 Ensembl ENCODE 5.4 -256.3 -256302 1.7 ZNF316 MAFG CEBPB FOS NFE2 CEBPG MAFK CD200R1 CD200R1L ATG3 SLC35A5 ENSG00000242770
GH03H112357 1.6 FANTOM5 Ensembl ENCODE dbSUPER 2.3 +200.3 200286 8.9 JUN BMI1 BATF RELA GATA3 POLR2A ATF7 RUNX3 IKZF2 ZNF687 CD200 BTLA MIR567 C3orf52 LOC105374042 SLC9C1 ENSG00000261488 ATG3
GH03H112773 1.6 FANTOM5 Ensembl ENCODE dbSUPER 2.3 -215.0 -214989 7.3 NFIB JUN MAX CEBPG RFX5 GATA3 FOSL2 FOS TRIM24 RUNX3 CD200R1 ENSG00000242770 CD200R1L ATG3 LINC02042
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ATG3 on UCSC Golden Path with GeneCards custom track

Promoters for ATG3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000156574 446 3201 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 YY1 ZNF766 ZNF143

Genomic Locations for ATG3 Gene

Genomic Locations for ATG3 Gene
chr3:112,532,507-112,562,046
(GRCh38/hg38)
Size:
29,540 bases
Orientation:
Minus strand
chr3:112,251,356-112,280,893
(GRCh37/hg19)

Genomic View for ATG3 Gene

Genes around ATG3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATG3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATG3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATG3 Gene

Proteins for ATG3 Gene

  • Protein details for ATG3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NT62-ATG3_HUMAN
    Recommended name:
    Ubiquitin-like-conjugating enzyme ATG3
    Protein Accession:
    Q9NT62
    Secondary Accessions:
    • Q6PKC5
    • Q9H6L9

    Protein attributes for ATG3 Gene

    Size:
    314 amino acids
    Molecular mass:
    35864 Da
    Quaternary structure:
    • Interacts with ATG7 and ATG12. The complex, composed of ATG3 and ATG7, plays a role in the conjugation of ATG12 to ATG5. Interacts with FNBP1L.
    SequenceCaution:
    • Sequence=AAH02830.1; Type=Frameshift; Positions=290; Evidence={ECO:0000305}; Sequence=BAB15237.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for ATG3 Gene

    Alternative splice isoforms for ATG3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ATG3 Gene

Post-translational modifications for ATG3 Gene

  • Cleaved by CASP8 upon death ligand binding such as tumor necrosis factor-alpha. CASP8 cleavage blocks survival-related autophagy and favors apoptosis.
  • Conjugated to ATG12 at Lys-243. ATG12-conjugation plays a role in regulation of mitochondrial homeostasis and cell death, while it is not involved in PE-conjugation to ATG8-like proteins and autophagy.
  • Ubiquitination at posLast=1111
  • Modification sites at PhosphoSitePlus

Other Protein References for ATG3 Gene

No data available for DME Specific Peptides for ATG3 Gene

Domains & Families for ATG3 Gene

Gene Families for ATG3 Gene

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

Protein Domains for ATG3 Gene

Suggested Antigen Peptide Sequences for ATG3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NT62

UniProtKB/Swiss-Prot:

ATG3_HUMAN :
  • Belongs to the ATG3 family.
Family:
  • Belongs to the ATG3 family.
genes like me logo Genes that share domains with ATG3: view

Function for ATG3 Gene

Molecular function for ATG3 Gene

UniProtKB/Swiss-Prot Function:
E2 conjugating enzyme required for the cytoplasm to vacuole transport (Cvt), autophagy, and mitochondrial homeostasis. Responsible for the E2-like covalent binding of phosphatidylethanolamine to the C-terminal Gly of ATG8-like proteins (GABARAP, GABARAPL1, GABARAPL2 or MAP1LC3A). The ATG12-ATG5 conjugate plays a role of an E3 and promotes the transfer of ATG8-like proteins from ATG3 to phosphatidylethanolamine (PE). This step is required for the membrane association of ATG8-like proteins. The formation of the ATG8-phosphatidylethanolamine conjugates is essential for autophagy and for the cytoplasm to vacuole transport (Cvt). Preferred substrate is MAP1LC3A. Also acts as an autocatalytic E2-like enzyme, catalyzing the conjugation of ATG12 to itself, ATG12 conjugation to ATG3 playing a role in mitochondrial homeostasis but not in autophagy. ATG7 (E1-like enzyme) facilitates this reaction by forming an E1-E2 complex with ATG3. Promotes primary ciliogenesis by removing OFD1 from centriolar satellites via the autophagic pathway.

Enzyme Numbers (IUBMB) for ATG3 Gene

Phenotypes From GWAS Catalog for ATG3 Gene

Gene Ontology (GO) - Molecular Function for ATG3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11825910
GO:0016874 ligase activity IEA --
GO:0019776 Atg8 ligase activity ISS --
GO:0019777 Atg12 transferase activity ISS --
GO:0019787 ubiquitin-like protein transferase activity IDA 11825910
genes like me logo Genes that share ontologies with ATG3: view
genes like me logo Genes that share phenotypes with ATG3: view

Animal Models for ATG3 Gene

MGI Knock Outs for ATG3:

Animal Model Products

miRNA for ATG3 Gene

miRTarBase miRNAs that target ATG3

Clone Products

  • Addgene plasmids for ATG3

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ATG3 Gene

Localization for ATG3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATG3 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 ATG3 gene
Compartment Confidence
cytosol 5
plasma membrane 2
mitochondrion 2
lysosome 2
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Plasma membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ATG3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000153 cytoplasmic ubiquitin ligase complex IPI 11825910
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with ATG3: view

Pathways & Interactions for ATG3 Gene

genes like me logo Genes that share pathways with ATG3: view

Pathways by source for ATG3 Gene

1 GeneTex pathway for ATG3 Gene
2 Reactome pathways for ATG3 Gene
1 R&D Systems pathway for ATG3 Gene

SIGNOR curated interactions for ATG3 Gene

Activates:
Is activated by:

Gene Ontology (GO) - Biological Process for ATG3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000045 autophagosome assembly ISS --
GO:0000422 mitophagy IBA --
GO:0006464 cellular protein modification process IDA 11825910
GO:0006612 protein targeting to membrane ISS --
GO:0006810 transport IEA --
genes like me logo Genes that share ontologies with ATG3: view

Drugs & Compounds for ATG3 Gene

(6) Drugs for ATG3 Gene - From: ApexBio

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Nimodipine Approved Pharma Potentiation, Activator 27
Omeprazole Approved, Investigational, Vet_approved Pharma Activator H+,K+-ATPase inhibitor 355
Dexamethasone (DHAP) Pharma Glucocorticoidan;ti-inflammatory 0
Sulfacetamide Sodium Pharma Sulfonamide antibiotic 0
Trifluoperazine 2HCl Pharma 0

(6) ApexBio Compounds for ATG3 Gene

Compound Action Cas Number
Dexamethasone (DHAP) Glucocorticoidan;ti-inflammatory 1950-02-2
Divalproex Sodium Epilepsy/migraines/bipolar disorder medicine 76584-70-8
Nimodipine 66085-59-4
Omeprazole H+,K+-ATPase inhibitor 73590-58-6
Sulfacetamide Sodium Sulfonamide antibiotic 127-56-0
Trifluoperazine 2HCl 440-17-5
genes like me logo Genes that share compounds with ATG3: view

Drug Products

Transcripts for ATG3 Gene

Unigene Clusters for ATG3 Gene

Autophagy related 3:
Representative Sequences:

Clone Products

  • Addgene plasmids for ATG3

Alternative Splicing Database (ASD) splice patterns (SP) for ATG3 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13
SP1: -
SP2:
SP3: - -
SP4: - -
SP5: -

Relevant External Links for ATG3 Gene

GeneLoc Exon Structure for
ATG3
ECgene alternative splicing isoforms for
ATG3

Expression for ATG3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ATG3 Gene

Protein differential expression in normal tissues from HIPED for ATG3 Gene

This gene is overexpressed in Testis (9.7) and Bone marrow stromal cell (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for ATG3 Gene



Protein tissue co-expression partners for ATG3 Gene

NURSA nuclear receptor signaling pathways regulating expression of ATG3 Gene:

ATG3

SOURCE GeneReport for Unigene cluster for ATG3 Gene:

Hs.477126

mRNA Expression by UniProt/SwissProt for ATG3 Gene:

Q9NT62-ATG3_HUMAN
Tissue specificity: Widely expressed, with a highest expression in heart, skeletal muscle, kidney, liver and placenta.

Evidence on tissue expression from TISSUES for ATG3 Gene

  • Nervous system(4.8)
  • Lung(4.4)
  • Eye(4.2)
  • Liver(2.4)
  • Spleen(2.1)
genes like me logo Genes that share expression patterns with ATG3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for ATG3 Gene

Orthologs for ATG3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ATG3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ATG3 33 34
  • 99.47 (n)
dog
(Canis familiaris)
Mammalia -- 34
  • 97 (a)
OneToMany
ATG3 33
  • 94.09 (n)
-- 34
  • 77 (a)
OneToMany
cow
(Bos Taurus)
Mammalia ATG3 33 34
  • 95.01 (n)
mouse
(Mus musculus)
Mammalia Atg3 33 16 34
  • 92.36 (n)
rat
(Rattus norvegicus)
Mammalia Atg3 33
  • 90.55 (n)
oppossum
(Monodelphis domestica)
Mammalia ATG3 34
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 88 (a)
OneToMany
-- 34
  • 61 (a)
OneToMany
chicken
(Gallus gallus)
Aves ATG3 33 34
  • 84.56 (n)
lizard
(Anolis carolinensis)
Reptilia ATG3 34
  • 91 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia atg3 33
  • 79.96 (n)
Str.602 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.12629 33
zebrafish
(Danio rerio)
Actinopterygii apg3l 34 33
  • 77.07 (n)
OneToOne
wufb15g12 33
fruit fly
(Drosophila melanogaster)
Insecta Aut1 33 34
  • 63.46 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011582 33
  • 60.86 (n)
worm
(Caenorhabditis elegans)
Secernentea atg-3 33 34
  • 58.11 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ATG3 34 36
  • 35 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons ATG3 33
  • 57.61 (n)
soybean
(Glycine max)
eudicotyledons Gma.1721 33
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.6805 33
rice
(Oryza sativa)
Liliopsida Os01g0200000 33
  • 57.5 (n)
Os.27665 33
barley
(Hordeum vulgare)
Liliopsida Hv.2402 33
wheat
(Triticum aestivum)
Liliopsida Ta.21403 33
corn
(Zea mays)
Liliopsida Zm.4250 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1702 34
  • 66 (a)
OneToOne
Species where no ortholog for ATG3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for ATG3 Gene

ENSEMBL:
Gene Tree for ATG3 (if available)
TreeFam:
Gene Tree for ATG3 (if available)

Paralogs for ATG3 Gene

Pseudogenes.org Pseudogenes for ATG3 Gene

genes like me logo Genes that share paralogs with ATG3: view

No data available for Paralogs for ATG3 Gene

Variants for ATG3 Gene

Sequence variations from dbSNP and Humsavar for ATG3 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs1000058179 -- 112,550,255(+) TTCCC(C/T)TGTAG reference, missense, utr-variant-5-prime
rs1000184299 -- 112,539,317(+) CCTCT(C/G)TGACT intron-variant
rs1000242591 -- 112,546,185(+) AAAAC(C/T)TATCT intron-variant
rs1000378189 -- 112,537,740(+) CTCAT(C/G)ATAGC reference, missense
rs1000598261 -- 112,560,717(+) TAGAA(A/G)TTTAC intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for ATG3 Gene

Variant ID Type Subtype PubMed ID
nsv591301 CNV loss 21841781
nsv591300 CNV gain 21841781
nsv591293 CNV loss 21841781
nsv1005323 CNV gain 25217958
esv3429488 CNV insertion 20981092
esv3379928 CNV insertion 20981092
esv3308297 CNV mobile element insertion 20981092
dgv4840n100 CNV gain 25217958

Variation tolerance for ATG3 Gene

Residual Variation Intolerance Score: 30% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.14; 23.08% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ATG3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ATG3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATG3 Gene

Disorders for ATG3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for ATG3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
bardet-biedl syndrome 4
  • bbs4
- elite association - COSMIC cancer census association via MalaCards
Search ATG3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for ATG3

Genetic Association Database (GAD)
ATG3
Human Genome Epidemiology (HuGE) Navigator
ATG3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
ATG3
genes like me logo Genes that share disorders with ATG3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ATG3 Gene

Publications for ATG3 Gene

  1. Human Apg3p/Aut1p homologue is an authentic E2 enzyme for multiple substrates, GATE-16, GABARAP, and MAP-LC3, and facilitates the conjugation of hApg12p to hApg5p. (PMID: 11825910) Tanida I … Kominami E (The Journal of biological chemistry 2002) 2 3 4 22 60
  2. Cleavage of Atg3 protein by caspase-8 regulates autophagy during receptor-activated cell death. (PMID: 22644571) Oral O … Gozuacik D (Apoptosis : an international journal on programmed cell death 2012) 3 4 60
  3. ATG12 conjugation to ATG3 regulates mitochondrial homeostasis and cell death. (PMID: 20723759) Radoshevich L … Debnath J (Cell 2010) 3 4 60
  4. Age at onset in Huntington's disease is modified by the autophagy pathway: implication of the V471A polymorphism in Atg7. (PMID: 20697744) Metzger S … Nguyen HP (Human genetics 2010) 3 45 60
  5. A novel hybrid yeast-human network analysis reveals an essential role for FNBP1L in antibacterial autophagy. (PMID: 19342671) Huett A … Xavier RJ (Journal of immunology (Baltimore, Md. : 1950) 2009) 3 4 60

Products for ATG3 Gene

  • Addgene plasmids for ATG3

Sources for ATG3 Gene

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