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    Calcoco2 calcium binding and coiled-coil domain 2 [ Mus musculus (house mouse) ]

    Gene ID: 76815, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Calcoco2provided by MGI
    Official Full Name
    calcium binding and coiled-coil domain 2provided by MGI
    Primary source
    MGI:MGI:1343177
    See related
    Ensembl:ENSMUSG00000006056 AllianceGenome:MGI:1343177
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Ndp52; Ndp52l1; 2410154J16Rik
    Summary
    Predicted to enable protein homodimerization activity. Predicted to be involved in positive regulation of autophagosome maturation; response to type II interferon; and xenophagy. Predicted to be located in cytosol; intracellular membrane-bounded organelle; and perinuclear region of cytoplasm. Predicted to be active in PML body and autophagosome. Orthologous to human CALCOCO2 (calcium binding and coiled-coil domain 2). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    human all
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    Genomic context

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    See Calcoco2 in Genome Data Viewer
    Location:
    11 D; 11 59.4 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (95990195..96015362, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (96098916..96124560, complement)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_30532 Neighboring gene ATP synthase membrane subunit c locus 1 Neighboring gene predicted gene, 22423 Neighboring gene STARR-seq mESC enhancer starr_30533 Neighboring gene STARR-positive B cell enhancer mm9_chr11:95988247-95988548 Neighboring gene STARR-seq mESC enhancer starr_30537 Neighboring gene STARR-seq mESC enhancer starr_30538 Neighboring gene STARR-seq mESC enhancer starr_30539 Neighboring gene tubulin tyrosine ligase-like family, member 6 Neighboring gene predicted gene, 30084 Neighboring gene STARR-seq mESC enhancer starr_30541 Neighboring gene homeobox B13

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. H2B homology region of major immediate-early protein 1 is essential for murine cytomegalovirus to disrupt nuclear domain 10, but is not important for viral replication in cell culture. Cosme-Cruz R, et al. J Gen Virol, 2011 Sep. PMID 21632568, Free PMC Article
    2. NDP52 associates with phosphorylated tau in brains of an Alzheimer disease mouse model. Kim S, et al. Biochem Biophys Res Commun, 2014 Nov 7. PMID 25450380
    3. Functional interaction of nuclear domain 10 and its components with cytomegalovirus after infections: cross-species host cells versus native cells. Cosme RC, et al. PLoS One, 2011 Apr 28. PMID 21552525, Free PMC Article
    4. NDP52 Protects Against Myocardial Infarction-Provoked Cardiac Anomalies Through Promoting Autophagosome-Lysosome Fusion via Recruiting TBK1 and RAB7. Sun M, et al. Antioxid Redox Signal, 2022 Jun. PMID 34382418
    5. Vangl2 suppresses NF-κB signaling and ameliorates sepsis by targeting p65 for NDP52-mediated autophagic degradation. Lu J, et al. Elife, 2024 Sep 13. PMID 39269442, Free PMC Article

    See all (24) 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. NDP52 Protects Against Myocardial Infarction-Provoked Cardiac Anomalies Through Promoting Autophagosome-Lysosome Fusion via Recruiting TBK1 and RAB7.
      Title: NDP52 Protects Against Myocardial Infarction-Provoked Cardiac Anomalies Through Promoting Autophagosome-Lysosome Fusion via Recruiting TBK1 and RAB7.
    3. expression and association of NDP52 with autophagy-regulated gene proteins including LC3, as well as phosphorylated tau and amyloid-beta in brains of an Alzheimer disease model
      Title: NDP52 associates with phosphorylated tau in brains of an Alzheimer disease mouse model.
    4. The authors conclude that the dispersion of ND10 by major immediate-early protein 1 (IE1) appears not to be important for murine cytomegalovirus replication in a mouse-cell culture.
      Title: H2B homology region of major immediate-early protein 1 is essential for murine cytomegalovirus to disrupt nuclear domain 10, but is not important for viral replication in cell culture.
    5. ND10 and ND10 components might be important defensive factors against the CMV cross-species infection
      Title: Functional interaction of nuclear domain 10 and its components with cytomegalovirus after infections: cross-species host cells versus native cells.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (1) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in response to type II interferon ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in xenophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in xenophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in xenophagy ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in PML body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in PML body ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in autophagosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in autophagosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in autophagosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasmic vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    calcium-binding and coiled-coil domain-containing protein 2
    Names
    nuclear domain 10 protein 52 like 1
    nuclear domain 10 protein NDP52

    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_001271018.2 → NP_001257947.1  calcium-binding and coiled-coil domain-containing protein 2

      See identical proteins and their annotated locations for NP_001257947.1

      Status: VALIDATED

      Source sequence(s)
      AL603682
      Consensus CDS
      CCDS59567.1
      UniProtKB/Swiss-Prot
      A2A6M5, Q3TK36, Q3TKZ6, Q3TL30, Q9CWE3
      Related
      ENSMUSP00000087407.5, ENSMUST00000068686.13
      Conserved Domains (1) summary
      pfam07888
      Location:17 → 188
      CALCOCO1; Calcium binding and coiled-coil domain (CALCOCO1) like

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      95990195..96015362 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006534460.5 → XP_006534523.1  calcium-binding and coiled-coil domain-containing protein 2 isoform X1

      Conserved Domains (1) summary
      pfam17751
      Location:31 → 133
      SKICH; SKICH domain

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001100177.1: Suppressed sequence

      Description
      NM_001100177.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

    2. NM_029755.3: Suppressed sequence

      Description
      NM_029755.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A2A6M5.1 GenPept UniProtKB/Swiss-Prot:A2A6M5

    Gene LinkOut

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

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