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

Summary

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

Location:: 11; 11 E1

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
109	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_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

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.
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.
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.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

C88307 (e-PCR)
- UniSTS:160336

NoName (e-PCR)
- UniSTS:491465

D17S1437E (e-PCR)
- UniSTS:150475

Homology

Homologs of the Ccdc47 gene: The Ccdc47 gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 492 organisms have orthologs with human gene Ccdc47
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables calcium ion binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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
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
acts_upstream_of_or_within ubiquitin-dependent ERAD pathway	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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; coiled-coil domain-containing protein 47

Names: adipocyte-specific protein 4

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_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

Q920S6, Q9D024

UniProtKB/TrEMBL

A0A8C6I491, 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: Mus musculus Annotation Release 109 details...

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

106090086..106107349 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030246238.1 → XP_030102098.1 coiled-coil domain-containing protein 47 isoform X1

Conserved Domains (1) summary

pfam07946
Location:1 → 326

DUF1682; Protein of unknown function (DUF1682)