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

Gene ID: 76815, updated on 5-Mar-2024

Summary

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 interferon-gamma; and xenophagy. Predicted to act upstream of or within autophagy. 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, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within autophagy IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of autophagosome maturation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in positive regulation of autophagosome maturation ISO
Inferred from Sequence Orthology
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
 
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 ISO
Inferred from Sequence Orthology
more info
 
located_in cytoplasm ISO
Inferred from Sequence Orthology
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 membrane IEA
Inferred from Electronic Annotation
more info
 
located_in perinuclear region of cytoplasm ISO
Inferred from Sequence Orthology
more info
 

General protein information

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_001271018.2NP_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:17188
    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_006534460.5XP_006534523.1  calcium-binding and coiled-coil domain-containing protein 2 isoform X1

    Conserved Domains (1) summary
    pfam17751
    Location:31133
    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.