U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 67163, updated on 2-Nov-2024

    Summary

    Go to the top of the page Help
    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; ERAD pathway; and calcium ion homeostasis. Located in rough endoplasmic reticulum. Is expressed in several structures, including cerebellum external granule cell layer; liver; neural retina; submandibular gland primordium; and yolk sac. Orthologous to human CCDC47 (coiled-coil domain containing 47). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in placenta adult (RPKM 20.3), CNS E11.5 (RPKM 18.4) and 28 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Ccdc47 in Genome Data Viewer
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Mouse ENCODE transcriptome data 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

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

    Alleles

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

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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 protein folding chaperone ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables ribosome binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ribosome binding ISS
    Inferred from Sequence or Structural Similarity
    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
    		  
    involved_in endoplasmic reticulum calcium ion homeostasis ISS
    Inferred from Sequence or Structural Similarity
    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
    		  
    involved_in multi-pass transmembrane protein insertion into ER membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within post-embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein folding IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein insertion into ER membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein insertion into ER membrane ISS
    Inferred from Sequence or Structural Similarity
    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 endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of multi-pass translocon complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of multi-pass translocon complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of protein folding chaperone complex IEA
    Inferred from Electronic Annotation
    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 
    located_in rough endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    PAT complex subunit CCDC47
    Names
    adipocyte-specific protein 4
    coiled-coil domain-containing protein 47

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools