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Aliases for ATG13 Gene

Aliases for ATG13 Gene

  • Autophagy Related 13 2 3 5
  • KIAA0652 2 3 4
  • ATG13 Autophagy Related 13 Homolog (S. Cerevisiae) 2
  • ATG13 Autophagy Related 13 Homolog 3
  • Autophagy-Related Protein 13 3
  • PARATARG8 3

External Ids for ATG13 Gene

Previous HGNC Symbols for ATG13 Gene

  • KIAA0652

Previous GeneCards Identifiers for ATG13 Gene

  • GC11P046345

Summaries for ATG13 Gene

Entrez Gene Summary for ATG13 Gene

  • The protein encoded by this gene is an autophagy factor and a target of the TOR kinase signaling pathway. The encoded protein is essential for autophagosome formation and mitophagy. [provided by RefSeq, Oct 2016]

GeneCards Summary for ATG13 Gene

ATG13 (Autophagy Related 13) is a Protein Coding gene. Among its related pathways are Autophagy Pathway and mTOR signaling pathway (Pathway Interaction Database). Gene Ontology (GO) annotations related to this gene include protein kinase binding.

UniProtKB/Swiss-Prot for ATG13 Gene

  • Autophagy factor required for autophagosome formation and mitophagy. Target of the TOR kinase signaling pathway that regulates autophagy through the control of the phosphorylation status of ATG13 and ULK1, and the regulation of the ATG13-ULK1-RB1CC1 complex. Through its regulation of ULK1 activity, plays a role in the regulation of the kinase activity of mTORC1 and cell proliferation.

Gene Wiki entry for ATG13 Gene

Additional gene information for ATG13 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ATG13 Gene

Genomics for ATG13 Gene

GeneHancer (GH) Regulatory Elements for ATG13 Gene

Promoters and enhancers for ATG13 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
GH11J046615 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 658.9 +0.2 204 4.6 HDGF ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 POLR2B ZNF213 ATG13 HARBI1 PIR50656 ENSG00000270060 ZNF408 DDB2 RPS10P19
GH11J046552 Enhancer 1.3 Ensembl ENCODE 19.5 -61.7 -61650 5.5 HDGF PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 SLC30A9 FOS ATG13 AMBRA1 HARBI1 CHRM4 MDK DGKZ C11orf49 ZNF408 MIR3160-1
GH11J046344 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 8.7 -267.4 -267370 10.4 HDGF SMAD1 FOXA2 ARNT SIN3A ZNF2 YY1 E2F8 ZNF143 SP3 GC11P046351 DGKZ C11orf49 LOC105376662 ENSG00000255314 SNORD67 ENSG00000255447 ENSG00000254514 MDK CHRM4
GH11J046559 Enhancer 0.9 Ensembl ENCODE 20.2 -56.2 -56224 3.2 HDGF IRF2 PKNOX1 ZBTB40 E4F1 IRF4 ZNF335 ZNF366 STAT2 ADNP ATG13 AMBRA1 HARBI1 CHRM4 MDK DGKZ MIR3160-1
GH11J046378 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 7.7 -236.7 -236743 4.6 PKNOX1 FOXA2 ZFP64 ARID4B SIN3A ZNF143 SP3 SP5 REST ZNF592 MDK ATG13 C11orf49 MIR4688 GC11P046351 DGKZ
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ATG13 on UCSC Golden Path with GeneCards custom track

Genomic Locations for ATG13 Gene

Genomic Locations for ATG13 Gene
chr11:46,617,276-46,676,019
(GRCh38/hg38)
Size:
58,744 bases
Orientation:
Plus strand
chr11:46,638,826-46,697,569
(GRCh37/hg19)

Genomic View for ATG13 Gene

Genes around ATG13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATG13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATG13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATG13 Gene

Proteins for ATG13 Gene

  • Protein details for ATG13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75143-ATG13_HUMAN
    Recommended name:
    Autophagy-related protein 13
    Protein Accession:
    O75143
    Secondary Accessions:
    • B4DFI4
    • D3DQQ1
    • D3DQQ2
    • E9PQZ8
    • Q53EN6
    • Q9BRL3
    • Q9H8B0

    Protein attributes for ATG13 Gene

    Size:
    517 amino acids
    Molecular mass:
    56572 Da
    Quaternary structure:
    • Part of a complex consisting of ATG13, ULK1 and RB1CC1 (PubMed:19597335, PubMed:19211835, PubMed:19225151, PubMed:24290141). Interacts with ATG101 (PubMed:19597335, PubMed:19287211, PubMed:26299944). Interacts with ULK1 (via C-terminus) (PubMed:19287211, PubMed:21855797, PubMed:18936157). Interacts with ULK2 (via C-terminus) (PubMed:19225151, PubMed:18936157). Interacts (via the LIR motif) with GABARAP, GABARAPL, GABARAPL2 (PubMed:23043107). Interacts (via the LIR motif) with MAP1LC3A, MAP1LC3B and MAP1LC3C (PubMed:24290141). Interacts with TAB2 and TAB3 (PubMed:21976705). Interacts with C9orf72 (PubMed:27334615).
    SequenceCaution:
    • Sequence=BAA31627.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAD97323.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for ATG13 Gene

    Alternative splice isoforms for ATG13 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ATG13 Gene

Post-translational modifications for ATG13 Gene

  • Phosphorylated by ULK1, ULK2 and mTOR. Phosphorylation status depends on nutrient-rich conditions; dephosphorylated during starvation or following treatment with rapamycin. ULK1-mediated phosphorylation of ATG13 at Ser-355 is required for efficient clearance of depolarized mitochondria.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ATG13 Gene

Domains & Families for ATG13 Gene

Gene Families for ATG13 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins

Protein Domains for ATG13 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ATG13 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O75143

UniProtKB/Swiss-Prot:

ATG13_HUMAN :
  • The LIR motif (LC3-interacting region) is required for the interaction with the ATG8 family proteins GABARAP, GABARAPL, GABARAPL2, and MAP1LC3A.
  • Belongs to the ATG13 family. Metazoan subfamily.
Domain:
  • The LIR motif (LC3-interacting region) is required for the interaction with the ATG8 family proteins GABARAP, GABARAPL, GABARAPL2, and MAP1LC3A.
Family:
  • Belongs to the ATG13 family. Metazoan subfamily.
genes like me logo Genes that share domains with ATG13: view

Function for ATG13 Gene

Molecular function for ATG13 Gene

UniProtKB/Swiss-Prot Function:
Autophagy factor required for autophagosome formation and mitophagy. Target of the TOR kinase signaling pathway that regulates autophagy through the control of the phosphorylation status of ATG13 and ULK1, and the regulation of the ATG13-ULK1-RB1CC1 complex. Through its regulation of ULK1 activity, plays a role in the regulation of the kinase activity of mTORC1 and cell proliferation.

Phenotypes From GWAS Catalog for ATG13 Gene

Gene Ontology (GO) - Molecular Function for ATG13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19211835
GO:0019887 protein kinase regulator activity IBA --
GO:0019901 protein kinase binding IPI 18936157
genes like me logo Genes that share ontologies with ATG13: view
genes like me logo Genes that share phenotypes with ATG13: view

Animal Model Products

Clone Products

  • Addgene plasmids for ATG13

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ATG13 Gene

Localization for ATG13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATG13 Gene

Cytoplasm, cytosol. Preautophagosomal structure. Note=Under starvation conditions, is localized to puncate structures primarily representing the isolation membrane; the isolation membrane sequesters a portion of the cytoplasm resulting in autophagosome formation. {ECO:0000269 PubMed:19211835}.

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 ATG13 gene
Compartment Confidence
mitochondrion 5
endoplasmic reticulum 4
cytosol 4
nucleus 3
plasma membrane 2
lysosome 2
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ATG13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000407 phagophore assembly site ISS --
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IDA 21855797
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0005829 cytosol TAS,IBA --
genes like me logo Genes that share ontologies with ATG13: view

Pathways & Interactions for ATG13 Gene

genes like me logo Genes that share pathways with ATG13: view

Pathways by source for ATG13 Gene

1 R&D Systems pathway for ATG13 Gene

SIGNOR curated interactions for ATG13 Gene

Activates:
Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for ATG13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000045 autophagosome assembly IMP 19211835
GO:0000422 autophagy of mitochondrion IBA --
GO:0000423 mitophagy IEA --
GO:0006914 autophagy IEA --
GO:0016236 macroautophagy TAS --
genes like me logo Genes that share ontologies with ATG13: view

Drugs & Compounds for ATG13 Gene

No Compound Related Data Available

Transcripts for ATG13 Gene

Unigene Clusters for ATG13 Gene

Autophagy related 13:
Representative Sequences:

Clone Products

  • Addgene plasmids for ATG13

Alternative Splicing Database (ASD) splice patterns (SP) for ATG13 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c · 4d · 4e ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a ·
SP1: - - - - - - - - - - - - - -
SP2: - - - - - - - - - - - - -
SP3: - - - - - - - - - - - - - -
SP4: - - - - - - - - - - - -
SP5: - - - - - - - -
SP6: - - - - - - - - - -
SP7: - - - - - - - - - - -
SP8: - - - - - - - - - -
SP9: - - - - -
SP10: - - - - - - -
SP11: - - - - - - - - -
SP12:
SP13: - - - - - - - - - - -
SP14: - -
SP15: - - - - -
SP16: - - - - - - - -
SP17: - - - - - - - - -
SP18:
SP19:
SP20:
SP21: - - - - - - - - - - - - - - -
SP22: - - - - - - -
SP23: - - - - - - - -
SP24: - - - -
SP25: -
SP26: - -
SP27: - - - - - -
SP28: - - - -
SP29:
SP30:
SP31:

ExUns: 13b ^ 14 ^ 15a · 15b ^ 16a · 16b · 16c ^ 17 ^ 18a · 18b ^ 19 ^ 20 ^ 21a · 21b ^ 22 ^ 23a · 23b ^ 24 ^ 25
SP1: - -
SP2: - - - -
SP3: - - -
SP4: - - - -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19: - - - -
SP20: -
SP21:
SP22:
SP23:
SP24:
SP25:
SP26:
SP27:
SP28:
SP29:
SP30: - - - - - - - - - - -
SP31:

Relevant External Links for ATG13 Gene

GeneLoc Exon Structure for
ATG13
ECgene alternative splicing isoforms for
ATG13

Expression for ATG13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ATG13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ATG13 Gene

This gene is overexpressed in Neutrophil (25.9), Monocytes (16.6), and Testis (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ATG13 Gene



Protein tissue co-expression partners for ATG13 Gene

NURSA nuclear receptor signaling pathways regulating expression of ATG13 Gene:

ATG13

SOURCE GeneReport for Unigene cluster for ATG13 Gene:

Hs.127403

Evidence on tissue expression from TISSUES for ATG13 Gene

  • Nervous system(5)
  • Lung(4.5)
  • Muscle(4.4)
  • Thyroid gland(4.3)
  • Liver(4.2)
  • Eye(2.5)
  • Intestine(2.5)
genes like me logo Genes that share expression patterns with ATG13: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ATG13 Gene

Orthologs for ATG13 Gene

This gene was present in the common ancestor of animals.

Orthologs for ATG13 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ATG13 34 33
  • 97.55 (n)
OneToOne
dog
(Canis familiaris)
Mammalia ATG13 34 33
  • 93.7 (n)
OneToOne
cow
(Bos Taurus)
Mammalia ATG13 34 33
  • 89.86 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Atg13 33
  • 88.36 (n)
mouse
(Mus musculus)
Mammalia Atg13 16 34 33
  • 87.09 (n)
oppossum
(Monodelphis domestica)
Mammalia ATG13 34
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ATG13 34
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves ATG13 34 33
  • 83.66 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ATG13 34
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia atg13 33
  • 71.26 (n)
Str.15163 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.17897 33
zebrafish
(Danio rerio)
Actinopterygii atg13 34 33
  • 69.78 (n)
OneToOne
zgc63526 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1013 33
fruit fly
(Drosophila melanogaster)
Insecta Atg13 34
  • 30 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea atg-13 34
  • 26 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 50 (a)
OneToOne
Species where no ortholog for ATG13 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • 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)
  • 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 ATG13 Gene

ENSEMBL:
Gene Tree for ATG13 (if available)
TreeFam:
Gene Tree for ATG13 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ATG13: view image

Paralogs for ATG13 Gene

No data available for Paralogs for ATG13 Gene

Variants for ATG13 Gene

Sequence variations from dbSNP and Humsavar for ATG13 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs193920809 uncertain-significance, Malignant tumor of prostate 46,672,254(+) G/C splice_acceptor_variant
rs1000017961 -- 46,655,561(+) A/G intron_variant
rs1000029630 -- 46,636,892(+) C/G genic_upstream_transcript_variant, intron_variant
rs1000037324 -- 46,652,941(+) A/G intron_variant
rs1000073983 -- 46,649,677(+) G/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ATG13 Gene

Variant ID Type Subtype PubMed ID
esv3626191 CNV gain 21293372
esv993220 OTHER inversion 20482838
nsv38662 CNV deletion 16902084

Variation tolerance for ATG13 Gene

Residual Variation Intolerance Score: 70.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.49; 43.66% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATG13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ATG13

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATG13 Gene

Disorders for ATG13 Gene

Additional Disease Information for ATG13

No disorders were found for ATG13 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ATG13 Gene

Publications for ATG13 Gene

  1. Structure of the Human Atg13-Atg101 HORMA Heterodimer: an Interaction Hub within the ULK1 Complex. (PMID: 26299944) Qi S … Hurley JH (Structure (London, England : 1993) 2015) 3 4 58
  2. Structural basis of the autophagy-related LC3/Atg13 LIR complex: recognition and interaction mechanism. (PMID: 24290141) Suzuki H … Wakatsuki S (Structure (London, England : 1993) 2014) 3 4 58
  3. ATG8 family proteins act as scaffolds for assembly of the ULK complex: sequence requirements for LC3-interacting region (LIR) motifs. (PMID: 23043107) Alemu EA … Johansen T (The Journal of biological chemistry 2012) 3 4 58
  4. TGFβ-activated kinase 1 (TAK1)-binding proteins (TAB) 2 and 3 negatively regulate autophagy. (PMID: 21976705) Takaesu G … Yoshimura A (Journal of biochemistry 2012) 3 4 58
  5. Hsp90-Cdc37 chaperone complex regulates Ulk1- and Atg13-mediated mitophagy. (PMID: 21855797) Joo JH … Kundu M (Molecular cell 2011) 3 4 58

Products for ATG13 Gene

Sources for ATG13 Gene

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