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] See more...

Aliases for ATG13 Gene

Aliases for ATG13 Gene

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

External Ids for ATG13 Gene

Previous HGNC Symbols for ATG13 Gene

  • KIAA0652

Previous GeneCards Identifiers for ATG13 Gene

  • GC11P046638
  • GC11P046345
  • GC11P046619

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. Diseases associated with ATG13 include Danon Disease and Tuberous Sclerosis 1. Among its related pathways are Autophagy - animal and Longevity regulating pathway. Gene Ontology (GO) annotations related to this gene include protein kinase binding.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification 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 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 508.8 +0.3 260 4.4 HNRNPK ZBTB40 ZNF217 EP300 CTCF NRF1 TCF12 POLR2G SP1 NCOR1 ATG13 HARBI1 lnc-ZNF408-5 piR-56657 ZNF408
GH11J046512 Enhancer 1.3 FANTOM5 Ensembl ENCODE 19.9 -95.6 -95575 19 CTCF USF1 NCOR1 JUND TCF7 TRIM28 REST MYC RCOR1 RAD21 piR-57460-080 ATG13 ZNF408 ENSG00000270060 AMBRA1 MDK DGKZ CHRM4 DDB2 HARBI1
GH11J046344 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 8.7 -267.4 -267413 10.5 RXRA ZBTB40 EP300 CTCF NRF1 MYC SP1 PHF8 PHB2 ZIC2 DGKZ C11orf49 MDK CHRM4 CREB3L1 LINC02489 AMBRA1 PACSIN3 ATG13 ZNF408
GH11J046552 Enhancer 1 ENCODE 19.5 -61.7 -61650 5.5 EP300 FOXK2 ZBTB40 ZNF217 TCF12 NCOR1 JUND FOS ZIC2 TCF7 ATG13 AMBRA1 HARBI1 CHRM4 MDK DGKZ C11orf49 ZNF408 lnc-HARBI1-1 piR-57133-075
GH11J046639 Enhancer 1 Ensembl ENCODE dbSUPER 19.6 +23.0 22999 2.5 FOXA2 SPI1 CREM FOXP1 ZNF664 GLIS1 ZNF792 POLR2A HNF4A ARNT ATG13 ZNF408 HARBI1 AMBRA1 F2 ARHGAP1 SNORD67 CKAP5 lnc-ARHGAP1-1 lnc-ZNF408-5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATG13 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ATG13

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)
Size:
58,744 bases
Orientation:
Plus strand

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=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=BAD97323.1; Type=Erroneous initiation; Note=Extended N-terminus.; 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
  • Transporters

Protein Domains for ATG13 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ATG13 Gene

GenScript: Design optimal peptide antigens:
  • Autophagy-related protein 13 (ATG13_HUMAN)
  • cDNA FLJ59492 (B4DFI4_HUMAN)

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 21873635
GO:0019901 protein kinase binding IPI,IBA 18936157
genes like me logo Genes that share ontologies with ATG13: view
genes like me logo Genes that share phenotypes with ATG13: view

Animal Models for ATG13 Gene

MGI Knock Outs for ATG13:
  • Atg13 Atg13<tm2b(EUCOMM)Hmgu>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATG13

Clone Products

  • Addgene plasmids for ATG13

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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
plasma membrane 3
nucleus 3
lysosome 3
extracellular 2
cytoskeleton 2
peroxisome 2
endosome 2
golgi apparatus 2

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 --
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
2 GeneTex pathways 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 21873635
GO:0000423 mitophagy IBA 21873635
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

mRNA/cDNA for ATG13 Gene

51 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
30 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATG13

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

Expression for ATG13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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 31 30
  • 97.55 (n)
OneToOne
dog
(Canis familiaris)
Mammalia ATG13 31 30
  • 93.7 (n)
OneToOne
cow
(Bos Taurus)
Mammalia ATG13 31 30
  • 89.86 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Atg13 30
  • 88.36 (n)
mouse
(Mus musculus)
Mammalia Atg13 17 31 30
  • 87.09 (n)
oppossum
(Monodelphis domestica)
Mammalia ATG13 31
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ATG13 31
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves ATG13 31 30
  • 83.66 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ATG13 31
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia atg13 30
  • 71.26 (n)
Str.15163 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.17897 30
zebrafish
(Danio rerio)
Actinopterygii atg13 31 30
  • 69.78 (n)
OneToOne
zgc63526 30
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1013 30
fruit fly
(Drosophila melanogaster)
Insecta Atg13 31
  • 30 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea atg-13 31
  • 26 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ATG13 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
779141 Benign: not provided 46,667,803(+) T/C NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
789796 Benign: not provided 46,645,398(+) T/A NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT
rs193920809 Uncertain Significance: Malignant tumor of prostate 46,672,254(+) G/C SPLICE_ACCEPTOR_VARIANT

Additional dbSNP identifiers (rs#s) for ATG13 Gene

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

MalaCards: The human disease database

(2) MalaCards diseases for ATG13 Gene - From: DISEASES

Disorder Aliases PubMed IDs
danon disease
  • vacuolar cardiomyopathy and myopathy, x-linked
tuberous sclerosis 1
  • ts
- elite association - COSMIC cancer census association via MalaCards
Search ATG13 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for ATG13

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

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

Publications for ATG13 Gene

  1. The C9orf72 protein interacts with Rab1a and the ULK1 complex to regulate initiation of autophagy. (PMID: 27334615) Webster CP … De Vos KJ (The EMBO journal 2016) 3 4 54
  2. 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 54
  3. 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 54
  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 54
  5. 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 54

Products for ATG13 Gene

Sources for ATG13 Gene