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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 Cellular Senescence and mTOR signalling. 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

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

Genomics for ATG13 Gene

Regulatory Elements for ATG13 Gene

Enhancers for ATG13 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
GH11F046552 1.3 Ensembl ENCODE 19.5 -61.7 -61681 5.6 HDGF PKNOX1 CREB3L1 MLX ARID4B SIN3A DMAP1 SLC30A9 FOS SP5 ATG13 AMBRA1 HARBI1 CHRM4 MDK DGKZ C11orf49 ZNF408 MIR3160-1
GH11F046559 1 Ensembl ENCODE 20.2 -56.4 -56358 3.4 HDGF KLF1 IRF2 PKNOX1 ZNF366 STAT2 ADNP PRDM10 ZNF600 STAT1 ATG13 AMBRA1 HARBI1 CHRM4 MDK DGKZ MIR3160-1
GH11F046520 1.1 Ensembl ENCODE 18.3 -95.1 -95121 3.3 PKNOX1 ARNT ZNF2 RAD21 GATA2 ZNF366 SCRT2 FOS MIXL1 CEBPB ATG13 MDK DGKZ CHRM4 HARBI1 C11orf49 ZNF408 AMBRA1 MIR3160-1
GH11F046647 0.9 Ensembl ENCODE 16.9 +32.0 31961 2.8 CTCF NFIA JUN SIN3A RAD21 ATF2 NR2F2 JUND POLR2A ZBTB48 ATG13 ARHGAP1 ZNF408 HARBI1 F2 AMBRA1 CHRM4 SNORD67 CKAP5 LRP4
GH11F046491 0.7 ENCODE 18.2 -124.9 -124882 1.4 SIN3A MAFG RAD21 MAFF ZNF766 ZNF316 ZNF692 PRDM10 MAFK EMSY ATG13 HARBI1 MIR3160-1 AMBRA1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ATG13 on UCSC Golden Path with GeneCards custom track

Promoters for ATG13 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000108991 624 2601 HDGF CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 SP3 SP5

Genomic Location for ATG13 Gene

Chromosome:
11
Start:
46,617,276 bp from pter
End:
46,676,019 bp from pter
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).
    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

Other Protein References for ATG13 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ATG13 Gene

Domains & Families for ATG13 Gene

Gene Families for ATG13 Gene

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.

Gene Ontology (GO) - Molecular Function for ATG13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19211835
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

Flow Cytometry Products

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

Gene Ontology (GO) - Cellular Components for ATG13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000407 pre-autophagosomal structure ISS --
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IDA 21855797
GO:0005829 cytosol IBA,TAS --
GO:1990316 ATG1/ULK1 kinase complex IEA,IPI 19211835
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

2 GeneTex pathways for ATG13 Gene
2 BioSystems pathways for ATG13 Gene
2 Reactome pathways for ATG13 Gene
2 KEGG pathways 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:0006914 autophagy IEA --
GO:0016236 macroautophagy TAS --
GO:0098779 mitophagy in response to mitochondrial depolarization IEA --
GO:1903955 positive regulation of protein targeting to mitochondrion IMP 24270810
genes like me logo Genes that share ontologies with ATG13: view

Transcripts for ATG13 Gene

Unigene Clusters for ATG13 Gene

Autophagy related 13:
Representative Sequences:

Flow Cytometry Products

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 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, PaxDb, 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
genes like me logo Genes that share expression patterns with ATG13: view

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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 35
  • 97.55 (n)
dog
(Canis familiaris)
Mammalia ATG13 34 35
  • 93.7 (n)
cow
(Bos Taurus)
Mammalia ATG13 34 35
  • 89.86 (n)
rat
(Rattus norvegicus)
Mammalia Atg13 34
  • 88.36 (n)
mouse
(Mus musculus)
Mammalia Atg13 34 16 35
  • 87.09 (n)
oppossum
(Monodelphis domestica)
Mammalia ATG13 35
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ATG13 35
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves ATG13 34 35
  • 83.66 (n)
lizard
(Anolis carolinensis)
Reptilia ATG13 35
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia atg13 34
  • 71.26 (n)
Str.15163 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.17897 34
zebrafish
(Danio rerio)
Actinopterygii atg13 34 35
  • 69.78 (n)
zgc63526 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1013 34
fruit fly
(Drosophila melanogaster)
Insecta Atg13 35
  • 30 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea atg-13 35
  • 26 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 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)

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 Sequence Context AA Info Type
rs193920809 Uncertain significance 46,672,254(+) GTACA(C/G)GACTC splice-acceptor-variant
rs10645429 -- 46,634,502(+) AGCAG(-/TCC)TCCTG intron-variant, upstream-variant-2KB
rs10679682 -- 46,662,034(+) TGAAC(-/AT)ATATG intron-variant
rs10714909 -- 46,628,939(+) TTTTC(-/T)TTTTT intron-variant
rs10769204 -- 46,654,807(+) AAAAC(C/T)CGAAA intron-variant

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

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

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)

Relevant External Links for ATG13 Gene

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

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

Disorders for ATG13 Gene

Relevant External Links for ATG13

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 J.H. (Structure 2015) 3 4 64
  2. Structural basis of the autophagy-related LC3/Atg13 LIR complex: recognition and interaction mechanism. (PMID: 24290141) Suzuki H. … Wakatsuki S. (Structure 2014) 3 4 64
  3. ATG8 family proteins act as scaffolds for assembly of the ULK complex: sequence requirements for LC3-interacting region (LIR) motifs. (PMID: 23043107) Alemu E.A. … Johansen T. (J. Biol. Chem. 2012) 3 4 64
  4. TGFbeta-activated kinase 1 (TAK1)-binding proteins (TAB) 2 and 3 negatively regulate autophagy. (PMID: 21976705) Takaesu G. … Yoshimura A. (J. Biochem. 2012) 3 4 64
  5. Hsp90-Cdc37 chaperone complex regulates Ulk1- and Atg13-mediated mitophagy. (PMID: 21855797) Joo J.H. … Kundu M. (Mol. Cell 2011) 3 4 64

Products for ATG13 Gene

Sources for ATG13 Gene

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