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

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: human all
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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_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.

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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

RH126129 (e-PCR)
- UniSTS:162841

G38043 (e-PCR)
- UniSTS:105031

G38044 (e-PCR)
- UniSTS:105032

Ndp52l1 (e-PCR)
- UniSTS:254300

RH126911 (e-PCR)
- UniSTS:208740

NoName (e-PCR)
- UniSTS:237461

NoName (e-PCR)
- UniSTS:492984

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

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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)

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

NC_000077.7 Reference GRCm39 C57BL/6J

Range

95990195..96015362 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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.
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.