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Ccdc47 coiled-coil domain containing 47 [ Mus musculus (house mouse) ]

Gene ID: 67163, updated on 5-Mar-2024

Summary

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Official Symbol
Ccdc47provided by MGI
Official Full Name
coiled-coil domain containing 47provided by MGI
Primary source
MGI:MGI:1914413
See related
Ensembl:ENSMUSG00000078622 AllianceGenome:MGI:1914413
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
asp4; calumin; 2610204L23Rik
Summary
Enables calcium ion binding activity. Acts upstream of or within several processes, including ER overload response; calcium ion homeostasis; and ubiquitin-dependent ERAD pathway. Located in rough endoplasmic reticulum. Is expressed in several structures, including alimentary system; cerebellum external granule cell layer; liver; neural retina; and yolk sac. Orthologous to human CCDC47 (coiled-coil domain containing 47). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in placenta adult (RPKM 20.3), CNS E11.5 (RPKM 18.4) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
11 E1; 11 68.89 cM
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (106090086..106107349, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (106199260..106216523, complement)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:106020710-106020950 Neighboring gene LIM domain containing 2 Neighboring gene predicted gene 10840 Neighboring gene STE20-related kinase adaptor alpha Neighboring gene STARR-positive B cell enhancer ABC_E7078 Neighboring gene STARR-positive B cell enhancer ABC_E739 Neighboring gene STARR-positive B cell enhancer ABC_E5285 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:106078089-106078198 Neighboring gene DEAD box helicase 42 Neighboring gene STARR-positive B cell enhancer ABC_E7080 Neighboring gene STARR-positive B cell enhancer ABC_E5286 Neighboring gene STARR-positive B cell enhancer ABC_E597 Neighboring gene FtsJ RNA 2'-O-methyltransferase 3 Neighboring gene protease (prosome, macropain) 26S subunit, ATPase 5 Neighboring gene predicted gene, 23645

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. Calumin, a Ca²⁺-binding protein on the endoplasmic reticulum, alters the ion permeability of Ca²⁺ release-activated Ca²⁺ (CRAC) channels. Konno M, et al. Biochem Biophys Res Commun, 2012 Jan 13. PMID 22197811
  2. Calumin, a novel Ca2+-binding transmembrane protein on the endoplasmic reticulum. Zhang M, et al. Cell Calcium, 2007 Jul. PMID 17204322
  3. Contribution of calumin to embryogenesis through participation in the endoplasmic reticulum-associated degradation activity. Yamamoto S, et al. Dev Biol, 2014 Sep 1. PMID 25009997
  4. Epilepsy- and intellectual disability-associated CYFIP2 interacts with both actin regulators and RNA-binding proteins in the neonatal mouse forebrain. Lee Y, et al. Biochem Biophys Res Commun, 2020 Aug 13. PMID 32560809
  5. Characterization of an exchangeable gene trap using pU-17 carrying a stop codon-beta geo cassette. Taniwaki T, et al. Dev Growth Differ, 2005 Apr. PMID 15840001

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. these findings suggested that calumin serves to maintain the yolk sac integrity through participation in the ERAD activity, contributing to embryonic development.
    Title: Contribution of calumin to embryogenesis through participation in the endoplasmic reticulum-associated degradation activity.
  2. These results reveal a novel mechanism for the regulation of Ca(2+) release-activated Ca(2+) channels by calumin.
    Title: Calumin, a Ca²⁺-binding protein on the endoplasmic reticulum, alters the ion permeability of Ca²⁺ release-activated Ca²⁺ (CRAC) channels.
  3. observations suggest that calumin plays an essential role in ER Ca2+ handling and is also implicated in signaling from the ER, which is closely associated with cell-fate decision
    Title: Calumin, a novel Ca2+-binding transmembrane protein on the endoplasmic reticulum.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (1)  1 citation
  • Endonuclease-mediated (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 calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables calcium ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein folding chaperone ISO
Inferred from Sequence Orthology
more info
  
enables ribosome binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within ER overload response IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within ERAD pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in ERAD pathway ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within calcium ion homeostasis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within embryo development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endoplasmic reticulum calcium ion homeostasis ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within endoplasmic reticulum organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in multi-pass transmembrane protein insertion into ER membrane ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within post-embryonic development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein insertion into ER membrane ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
is_active_in endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum ISO
Inferred from Sequence Orthology
more info
  
located_in endoplasmic reticulum membrane ISO
Inferred from Sequence Orthology
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
part_of multi-pass translocon complex ISO
Inferred from Sequence Orthology
more info
  
part_of protein folding chaperone complex ISO
Inferred from Sequence Orthology
more info
  
located_in rough endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
PAT complex subunit CCDC47
Names
adipocyte-specific protein 4
coiled-coil domain-containing protein 47

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_026009.2 → NP_080285.2  PAT complex subunit CCDC47 precursor

    See identical proteins and their annotated locations for NP_080285.2

    Status: VALIDATED

    Source sequence(s)
    AK011882, AK078812, AL596331, CJ157793
    Consensus CDS
    CCDS25551.1
    UniProtKB/Swiss-Prot
    B1AR94, Q3TSB5, Q3V1S7, Q8C5D9, Q920S6, Q9D024
    UniProtKB/TrEMBL
    Q0VBU4
    Related
    ENSMUSP00000002043.4, ENSMUST00000002043.10
    Conserved Domains (2) summary
    PRK05901
    Location:18 → 115
    PRK05901; RNA polymerase sigma factor; Provisional
    pfam07946
    Location:135 → 467
    DUF1682; Protein of unknown function (DUF1682)

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
    106090086..106107349 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030246238.1 → XP_030102098.1  PAT complex subunit CCDC47 isoform X1

    Conserved Domains (1) summary
    pfam07946
    Location:1 → 326
    DUF1682; Protein of unknown function (DUF1682)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9D024.2 GenPept UniProtKB/Swiss-Prot:Q9D024

Gene LinkOut

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

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