This gene encodes a coiled-coil domain-containing protein. The encoded protein functions as a receptor for ubiquitin-coated bacteria and plays an important role in innate immunity by mediating macroautophagy. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012] See more...

Aliases for CALCOCO2 Gene

Aliases for CALCOCO2 Gene

  • Calcium Binding And Coiled-Coil Domain 2 2 3 5
  • Calcium-Binding And Coiled-Coil Domain-Containing Protein 2 3 4
  • Antigen Nuclear Dot 52 KDa Protein 3 4
  • Nuclear Domain 10 Protein NDP52 3 4
  • Nuclear Domain 10 Protein 52 3 4
  • Nuclear Dot Protein 52 3 4
  • NDP52 3 4

External Ids for CALCOCO2 Gene

Previous GeneCards Identifiers for CALCOCO2 Gene

  • GC17P044264
  • GC17P046908
  • GC17P042276

Summaries for CALCOCO2 Gene

Entrez Gene Summary for CALCOCO2 Gene

  • This gene encodes a coiled-coil domain-containing protein. The encoded protein functions as a receptor for ubiquitin-coated bacteria and plays an important role in innate immunity by mediating macroautophagy. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]

GeneCards Summary for CALCOCO2 Gene

CALCOCO2 (Calcium Binding And Coiled-Coil Domain 2) is a Protein Coding gene. Diseases associated with CALCOCO2 include Influenza. Among its related pathways are Measles and Mitophagy - animal. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity. An important paralog of this gene is TAX1BP1.

UniProtKB/Swiss-Prot Summary for CALCOCO2 Gene

  • Xenophagy-specific receptor required for autophagy-mediated intracellular bacteria degradation. Acts as an effector protein of galectin-sensed membrane damage that restricts the proliferation of infecting pathogens such as Salmonella typhimurium upon entry into the cytosol by targeting LGALS8-associated bacteria for autophagy (PubMed:22246324). Initially orchestrates bacteria targeting to autophagosomes and subsequently ensures pathogen degradation by regulating pathogen-containing autophagosome maturation (PubMed:23022382, PubMed:25771791). Bacteria targeting to autophagosomes relies on its interaction with MAP1LC3A, MAP1LC3B and/or GABARAPL2, whereas regulation of pathogen-containing autophagosome maturation requires the interaction with MAP3LC3C (PubMed:23022382, PubMed:25771791). May play a role in ruffle formation and actin cytoskeleton organization and seems to negatively regulate constitutive secretion (PubMed:17635994).

Gene Wiki entry for CALCOCO2 Gene

Additional gene information for CALCOCO2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CALCOCO2 Gene

Genomics for CALCOCO2 Gene

GeneHancer (GH) Regulatory Elements for CALCOCO2 Gene

Promoters and enhancers for CALCOCO2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CALCOCO2 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CALCOCO2

Top Transcription factor binding sites by QIAGEN in the CALCOCO2 gene promoter:
  • FOXI1
  • GATA-1
  • GATA-2
  • GATA-3
  • HFH-3
  • Sp1
  • USF-1
  • USF-1:USF-2
  • USF1
  • USF2

Genomic Locations for CALCOCO2 Gene

Genomic Locations for CALCOCO2 Gene
chr17:48,830,988-48,866,522
(GRCh38/hg38)
Size:
35,535 bases
Orientation:
Plus strand
chr17:46,908,350-46,943,884
(GRCh37/hg19)
Size:
35,535 bases
Orientation:
Plus strand

Genomic View for CALCOCO2 Gene

Genes around CALCOCO2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CALCOCO2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CALCOCO2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CALCOCO2 Gene

Proteins for CALCOCO2 Gene

  • Protein details for CALCOCO2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13137-CACO2_HUMAN
    Recommended name:
    Calcium-binding and coiled-coil domain-containing protein 2
    Protein Accession:
    Q13137
    Secondary Accessions:
    • B2RBT0
    • B4DDC4
    • B4DDT4
    • B4DP36
    • B4E0C0
    • E7ENK0
    • E7ETP5
    • E9PBE5
    • Q53FQ5
    • Q53HB5
    • Q6IBN9
    • Q9BTF7

    Protein attributes for CALCOCO2 Gene

    Size:
    446 amino acids
    Molecular mass:
    52254 Da
    Quaternary structure:
    • Dimer (PubMed:23511477). Part of a complex consisting of CALCOCO2, TAX1BP1 and MYO6 (PubMed:17635994). Interacts with GEMIN4 (PubMed:12869526). Interacts with ATG8 family members MAP1LC3A, MAP1LC3B, GABARAP, GABARAPL1 and GABARAPL2 (PubMed:25771791). Interacts with ATG8 family member MAP1LC3C (PubMed:23022382). Interacts with LGALS8 (PubMed:22246324, PubMed:25771791, PubMed:23511477, PubMed:23386746).

    Three dimensional structures from OCA and Proteopedia for CALCOCO2 Gene

    Alternative splice isoforms for CALCOCO2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CALCOCO2 Gene

Post-translational modifications for CALCOCO2 Gene

  • Ubiquitination at Lys299, Lys312, Lys339, and Lys395
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CALCOCO2 Gene

Domains & Families for CALCOCO2 Gene

Gene Families for CALCOCO2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for CALCOCO2 Gene

Blocks:
  • Coiled-coil transcriptional coactivator-like
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CALCOCO2 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ55141, highly similar to Homo sapiens nuclear domain 10 protein (NDP52), mRNA (B4DP36_HUMAN)
  • Nuclear dot protein 52 (CACO2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q13137

UniProtKB/Swiss-Prot:

CACO2_HUMAN :
  • The MYO6-binding domain is required for autophagy-mediated degradation of infecting bacteria such as Salmonella typhimurium, but not for bacteria targeting to autophagosomes.
  • Belongs to the CALCOCO family.
Domain:
  • The MYO6-binding domain is required for autophagy-mediated degradation of infecting bacteria such as Salmonella typhimurium, but not for bacteria targeting to autophagosomes.
  • The CLIR (LC3C-interacting region) motif is required for interaction with MAP1LC3C, but dispensable for CALCOCO2-mediated autophagosome maturation.
  • The LIR-like motif is required for interaction with MAP1LC3A, MAP1LC3B and GABARAPL2, as well as for CALCOCO2-mediated autophagosome maturation.
  • The LGALS8-binding domain is essential for the recruitment to cytosol-exposed infecting bacteria.
Family:
  • Belongs to the CALCOCO family.
genes like me logo Genes that share domains with CALCOCO2: view

Function for CALCOCO2 Gene

Molecular function for CALCOCO2 Gene

UniProtKB/Swiss-Prot Function:
Xenophagy-specific receptor required for autophagy-mediated intracellular bacteria degradation. Acts as an effector protein of galectin-sensed membrane damage that restricts the proliferation of infecting pathogens such as Salmonella typhimurium upon entry into the cytosol by targeting LGALS8-associated bacteria for autophagy (PubMed:22246324). Initially orchestrates bacteria targeting to autophagosomes and subsequently ensures pathogen degradation by regulating pathogen-containing autophagosome maturation (PubMed:23022382, PubMed:25771791). Bacteria targeting to autophagosomes relies on its interaction with MAP1LC3A, MAP1LC3B and/or GABARAPL2, whereas regulation of pathogen-containing autophagosome maturation requires the interaction with MAP3LC3C (PubMed:23022382, PubMed:25771791). May play a role in ruffle formation and actin cytoskeleton organization and seems to negatively regulate constitutive secretion (PubMed:17635994).
UniProtKB/Swiss-Prot Induction:
Treatment with IFNB1/IFN-beta and IFNG/IFN-gamma show an increase in number and size of CALCOCO2-specific dots and partial redistribution to the cytoplasm (PubMed:7540613). IFNG/IFN-gamma increases gene expression only slightly and IFNB does not increase expression (PubMed:9230084).

Phenotypes From GWAS Catalog for CALCOCO2 Gene

Gene Ontology (GO) - Molecular Function for CALCOCO2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12869526
GO:0042803 protein homodimerization activity IPI 9230084
genes like me logo Genes that share ontologies with CALCOCO2: view
genes like me logo Genes that share phenotypes with CALCOCO2: view

Animal Model Products

CRISPR Products

miRNA for CALCOCO2 Gene

miRTarBase miRNAs that target CALCOCO2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CALCOCO2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CALCOCO2 Gene

Localization for CALCOCO2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CALCOCO2 Gene

Cytoplasm, perinuclear region. Cytoplasm, cytoskeleton. Cytoplasmic vesicle, autophagosome membrane; Peripheral membrane protein. Note=According to PubMed:7540613, localizes to nuclear dots. According to PubMed:9230084 and PubMed:12869526, it is not a nuclear dot-associated protein but localizes predominantly in the cytoplasm with a coarse-grained distribution preferentially close to the nucleus. {ECO:0000269 PubMed:12869526, ECO:0000269 PubMed:7540613, ECO:0000269 PubMed:9230084}.

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 CALCOCO2 gene
Compartment Confidence
nucleus 5
cytosol 5
cytoskeleton 4
lysosome 3
plasma membrane 2
extracellular 2
mitochondrion 2
peroxisome 2
endoplasmic reticulum 2
endosome 2
golgi apparatus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CALCOCO2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000421 autophagosome membrane IEA --
GO:0005634 nucleus TAS 7540613
GO:0005737 cytoplasm IDA,IEA 9230084
GO:0005776 autophagosome IDA 25771791
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with CALCOCO2: view

Pathways & Interactions for CALCOCO2 Gene

PathCards logo

SuperPathways for CALCOCO2 Gene

SuperPathway Contained pathways
1 Measles
2 Mitophagy - animal
3 Shigellosis
genes like me logo Genes that share pathways with CALCOCO2: view

Pathways by source for CALCOCO2 Gene

3 KEGG pathways for CALCOCO2 Gene

Gene Ontology (GO) - Biological Process for CALCOCO2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006914 autophagy IEA --
GO:0016032 viral process TAS 7540613
GO:0034341 response to interferon-gamma IDA 9230084
GO:0098792 xenophagy IMP 25771791
GO:1901098 positive regulation of autophagosome maturation IMP 25771791
genes like me logo Genes that share ontologies with CALCOCO2: view

No data available for SIGNOR curated interactions for CALCOCO2 Gene

Drugs & Compounds for CALCOCO2 Gene

No Compound Related Data Available

Transcripts for CALCOCO2 Gene

mRNA/cDNA for CALCOCO2 Gene

5 REFSEQ mRNAs :
19 NCBI additional mRNA sequence :
28 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 CALCOCO2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CALCOCO2 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c · 7d · 7e ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b · 11c · 11d ^ 12a · 12b ^
SP1: - - - - - - - - -
SP2: - - - -
SP3: - - - - - - - -
SP4: - - - -
SP5: - -
SP6: - -
SP7: - - - -
SP8: - -
SP9: -
SP10: -
SP11: - - - -

ExUns: 13 ^ 14a · 14b ^ 15
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for CALCOCO2 Gene

GeneLoc Exon Structure for
CALCOCO2

Expression for CALCOCO2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CALCOCO2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CALCOCO2 Gene

This gene is overexpressed in Testis (19.8) and Peripheral blood mononuclear cells (8.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CALCOCO2 Gene



Protein tissue co-expression partners for CALCOCO2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CALCOCO2

SOURCE GeneReport for Unigene cluster for CALCOCO2 Gene:

Hs.514920

mRNA Expression by UniProt/SwissProt for CALCOCO2 Gene:

Q13137-CACO2_HUMAN
Tissue specificity: Expressed in all tissues tested with highest expression in skeletal muscle and lowest in brain.

Evidence on tissue expression from TISSUES for CALCOCO2 Gene

  • Nervous system(4.9)
  • Kidney(4.6)
  • Liver(4.5)
  • Skin(4.3)
  • Stomach(4.3)
  • Intestine(3.4)
  • Heart(2.7)
  • Blood(2.5)
  • Muscle(2.1)
  • Lung(2)
  • Spleen(2)
genes like me logo Genes that share expression patterns with CALCOCO2: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CALCOCO2 Gene

Orthologs for CALCOCO2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CALCOCO2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CALCOCO2 31 30
  • 99.48 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CALCOCO2 31 30
  • 89.16 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CALCOCO2 31 30
  • 88.94 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CALCOCO2 31
  • 78 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Calcoco2 30
  • 70.14 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CALCOCO2 31
  • 42 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Calcoco2 31
  • 40 (a)
OneToOne
chicken
(Gallus gallus)
Aves CALCOCO2 31 30
  • 62.12 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CALCOCO2 31
  • 42 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia calcoco2 30
  • 52.03 (n)
zebrafish
(Danio rerio)
Actinopterygii calcoco2 31 30
  • 47.95 (n)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.823 31
  • 17 (a)
OneToMany
Species where no ortholog for CALCOCO2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 (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)
  • worm (Caenorhabditis elegans)

Evolution for CALCOCO2 Gene

ENSEMBL:
Gene Tree for CALCOCO2 (if available)
TreeFam:
Gene Tree for CALCOCO2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CALCOCO2: view image

Paralogs for CALCOCO2 Gene

Paralogs for CALCOCO2 Gene

(71) SIMAP similar genes for CALCOCO2 Gene using alignment to 10 proteins:

  • CACO2_HUMAN
  • D6RBF9_HUMAN
  • D6RBI4_HUMAN
  • D6REB0_HUMAN
  • D6RF70_HUMAN
  • D6RJE7_HUMAN
  • H0Y9G3_HUMAN
  • H0YBP4_HUMAN
  • I3L493_HUMAN
  • I3L4E1_HUMAN
genes like me logo Genes that share paralogs with CALCOCO2: view

Variants for CALCOCO2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CALCOCO2 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
rs10278 - p.Pro389Ala
rs17849804 - p.Thr273Ala
rs2303015 - p.Val248Ala
rs2303016 - p.Gly227Arg
rs550510 - p.Gly140Glu

Additional dbSNP identifiers (rs#s) for CALCOCO2 Gene

Structural Variations from Database of Genomic Variants (DGV) for CALCOCO2 Gene

Variant ID Type Subtype PubMed ID
esv29639 CNV loss 19812545
nsv482969 CNV loss 15286789

Variation tolerance for CALCOCO2 Gene

Residual Variation Intolerance Score: 65.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.05; 92.14% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CALCOCO2 Gene

Human Gene Mutation Database (HGMD)
CALCOCO2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CALCOCO2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CALCOCO2 Gene

Disorders for CALCOCO2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for CALCOCO2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
influenza
  • flu
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CALCOCO2

genes like me logo Genes that share disorders with CALCOCO2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CALCOCO2 Gene

Publications for CALCOCO2 Gene

  1. Molecular characterization of NDP52, a novel protein of the nuclear domain 10, which is redistributed upon virus infection and interferon treatment. (PMID: 7540613) Korioth F … Frey J (The Journal of cell biology 1995) 2 3 4 54
  2. Autophagy receptor NDP52 regulates pathogen-containing autophagosome maturation. (PMID: 25771791) Verlhac P … Faure M (Cell host & microbe 2015) 3 4 54
  3. Molecular basis of ubiquitin recognition by the autophagy receptor CALCOCO2. (PMID: 26506893) Xie X … Pan L (Autophagy 2015) 2 3 54
  4. Structural basis for recognition of autophagic receptor NDP52 by the sugar receptor galectin-8. (PMID: 23511477) Kim BW … Song HK (Nature communications 2013) 3 4 54
  5. Sterical hindrance promotes selectivity of the autophagy cargo receptor NDP52 for the danger receptor galectin-8 in antibacterial autophagy. (PMID: 23386746) Li S … Randow F (Science signaling 2013) 3 4 54

Products for CALCOCO2 Gene

  • Biorbyt antibodies for CALCOCO2

Sources for CALCOCO2 Gene