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    CALCOCO2 calcium binding and coiled-coil domain 2 [ Homo sapiens (human) ]

    Gene ID: 10241, updated on 6-Nov-2024

    Summary

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    Official Symbol
    CALCOCO2provided by HGNC
    Official Full Name
    calcium binding and coiled-coil domain 2provided by HGNC
    Primary source
    HGNC:HGNC:29912
    See related
    Ensembl:ENSG00000136436 MIM:604587; AllianceGenome:HGNC:29912
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NDP52
    Summary
    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]
    Expression
    Ubiquitous expression in fat (RPKM 39.0), testis (RPKM 32.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CALCOCO2 in Genome Data Viewer
    Location:
    17q21.32
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (48831035..48865245)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (49694621..49728978)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (46908397..46942607)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 125, pseudogene Neighboring gene tubulin tyrosine ligase like 6 Neighboring gene uncharacterized LOC105371813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8659 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46908401-46909282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12340 Neighboring gene uncharacterized LOC105371814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12341 Neighboring gene small nucleolar RNA SNORA68 Neighboring gene SUMO2 pseudogene 17

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. NDP52 SUMOylation contributes to low-dose X-rays-induced cardiac hypertrophy through PINK1/Parkin-mediated mitophagy via MUL1/SUMO2 signalling. Gao A, et al. J Cell Physiol, 2024 Jan. PMID 37942585
    2. Structural and biochemical advances on the recruitment of the autophagy-initiating ULK and TBK1 complexes by autophagy receptor NDP52. Fu T, et al. Sci Adv, 2021 Aug. PMID 34389544, Free PMC Article
    3. Novel Insights into NDP52 Autophagy Receptor Functioning. Viret C, et al. Trends Cell Biol, 2018 Apr. PMID 29395717
    4. Influenza virus protein PB1-F2 interacts with CALCOCO2 (NDP52) to modulate innate immune response. Leymarie O, et al. J Gen Virol, 2017 Jun. PMID 28613140
    5. A variant in the nuclear dot protein 52kDa gene increases the risk for spontaneous bacterial peritonitis in patients with alcoholic liver cirrhosis. Lutz P, et al. Dig Liver Dis, 2016 Jan. PMID 26493630

    See all (131) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Vangl2 suppresses NF-kappaB signaling and ameliorates sepsis by targeting p65 for NDP52-mediated autophagic degradation.
      Title: Vangl2 suppresses NF-κB signaling and ameliorates sepsis by targeting p65 for NDP52-mediated autophagic degradation.
    2. CALCOCO2/NDP52 associates with RAB9 to initiate an antiviral response to hepatitis B virus infection through a lysosomal degradation pathway.
      Title: CALCOCO2/NDP52 associates with RAB9 to initiate an antiviral response to hepatitis B virus infection through a lysosomal degradation pathway.
    3. NDP52 SUMOylation contributes to low-dose X-rays-induced cardiac hypertrophy through PINK1/Parkin-mediated mitophagy via MUL1/SUMO2 signalling.
      Title: NDP52 SUMOylation contributes to low-dose X-rays-induced cardiac hypertrophy through PINK1/Parkin-mediated mitophagy via MUL1/SUMO2 signalling.
    4. Crotonylated BEX2 interacts with NDP52 and enhances mitophagy to modulate chemotherapeutic agent-induced apoptosis in non-small-cell lung cancer cells.
      Title: Crotonylated BEX2 interacts with NDP52 and enhances mitophagy to modulate chemotherapeutic agent-induced apoptosis in non-small-cell lung cancer cells.
    5. NDP52 acts as a redox sensor in PINK1/Parkin-mediated mitophagy.
      Title: NDP52 acts as a redox sensor in PINK1/Parkin-mediated mitophagy.
    6. Baicalein Activates Parkin-Dependent Mitophagy through NDP52 and OPTN.
      Title: Baicalein Activates Parkin-Dependent Mitophagy through NDP52 and OPTN.
    7. Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy.
      Title: Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy.
    8. Crosstalk Between NDP52 and LUBAC in Innate Immune Responses, Cell Death, and Xenophagy.
      Title: Crosstalk Between NDP52 and LUBAC in Innate Immune Responses, Cell Death, and Xenophagy.
    9. The autophagy adaptor NDP52 and the FIP200 coiled-coil allosterically activate ULK1 complex membrane recruitment.
      Title: The autophagy adaptor NDP52 and the FIP200 coiled-coil allosterically activate ULK1 complex membrane recruitment.
    10. The CALCOCO2, but not SQSTM1, suppresses the antiviral type I interferon signaling by promoting autophagy-mediated degradation of the mitochondrial antiviral signaling (MAVS) protein.
      Title: CALCOCO2/NDP52 and SQSTM1/p62 differentially regulate coxsackievirus B3 propagation.
    Submit: New GeneRIF Correction See all GeneRIFs (40)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC17318

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of autophagosome maturation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of autophagosome maturation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to type II interferon IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in viral process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in xenophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in xenophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in PML body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in PML body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in autophagosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in autophagosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in autophagosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasmic vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in membrane HDA PubMed 
    located_in nucleus TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    calcium-binding and coiled-coil domain-containing protein 2
    Names
    antigen nuclear dot 52 kDa protein
    nuclear domain 10 protein 52
    nuclear domain 10 protein NDP52
    nuclear dot protein 52

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001261390.2 → NP_001248319.1  calcium-binding and coiled-coil domain-containing protein 2 isoform 1

      See identical proteins and their annotated locations for NP_001248319.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC068531, AK298177, AL042638
      Consensus CDS
      CCDS58559.1
      UniProtKB/Swiss-Prot
      Q13137
      Related
      ENSP00000398523.2, ENST00000448105.7
      Conserved Domains (3) summary
      pfam06273
      Location:150 → 211
      eIF-4B; Plant specific eukaryotic initiation factor 4B
      cl19219
      Location:189 → 269
      DUF342; Protein of unknown function (DUF342)
      cl24005
      Location:253 → 334
      DUF2570; Protein of unknown function (DUF2570)

    2. NM_001261391.2 → NP_001248320.1  calcium-binding and coiled-coil domain-containing protein 2 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon and includes an alternate exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC068531, AK293329
      Consensus CDS
      CCDS58558.1
      UniProtKB/Swiss-Prot
      Q13137
      Related
      ENSP00000424352.1, ENST00000509507.5
      Conserved Domains (3) summary
      pfam06273
      Location:147 → 208
      eIF-4B; Plant specific eukaryotic initiation factor 4B
      cl23720
      Location:164 → 259
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
      cl24005
      Location:250 → 331
      DUF2570; Protein of unknown function (DUF2570)

    3. NM_001261393.2 → NP_001248322.1  calcium-binding and coiled-coil domain-containing protein 2 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two exons in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
      Source sequence(s)
      AC068531, AK303313
      Consensus CDS
      CCDS58560.1
      UniProtKB/Swiss-Prot
      Q13137
      Related
      ENSP00000406974.2, ENST00000416445.6
      Conserved Domains (3) summary
      pfam04871
      Location:139 → 211
      Uso1_p115_C; Uso1 / p115 like vesicle tethering protein, C terminal region
      pfam07888
      Location:22 → 301
      CALCOCO1; Calcium binding and coiled-coil domain (CALCOCO1) like
      cl24005
      Location:187 → 268
      DUF2570; Protein of unknown function (DUF2570)

    4. NM_001261395.2 → NP_001248324.1  calcium-binding and coiled-coil domain-containing protein 2 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks two consecutive internal exons and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (5) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC068531, AK293137, BE315542
      Consensus CDS
      CCDS58561.1
      UniProtKB/Swiss-Prot
      Q13137
      Related
      ENSP00000423437.1, ENST00000508679.5
      Conserved Domains (3) summary
      pfam06273
      Location:54 → 115
      eIF-4B; Plant specific eukaryotic initiation factor 4B
      cl19219
      Location:93 → 173
      DUF342; Protein of unknown function (DUF342)
      cl24005
      Location:157 → 238
      DUF2570; Protein of unknown function (DUF2570)

    5. NM_005831.5 → NP_005822.1  calcium-binding and coiled-coil domain-containing protein 2 isoform 3

      See identical proteins and their annotated locations for NP_005822.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an exon in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AC068531, U22897
      Consensus CDS
      CCDS11538.1
      UniProtKB/Swiss-Prot
      B2RBT0, B4DDC4, B4DDT4, B4DP36, B4E0C0, E7ENK0, E7ETP5, E9PBE5, Q13137, Q53FQ5, Q53HB5, Q6IBN9, Q9BTF7
      Related
      ENSP00000258947.3, ENST00000258947.8
      Conserved Domains (1) summary
      cl25732
      Location:22 → 316
      SMC_N; RecF/RecN/SMC N terminal domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      48831035..48865245
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435100.1 → XP_047291056.1  calcium-binding and coiled-coil domain-containing protein 2 isoform X1

    2. XM_047435099.1 → XP_047291055.1  calcium-binding and coiled-coil domain-containing protein 2 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      49694621..49728978
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314673.1 → XP_054170648.1  calcium-binding and coiled-coil domain-containing protein 2 isoform X1

    2. XM_054314672.1 → XP_054170647.1  calcium-binding and coiled-coil domain-containing protein 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q13137.1 GenPept UniProtKB/Swiss-Prot:Q13137

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools