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CCDC47 coiled-coil domain containing 47 [ Homo sapiens (human) ]

Gene ID: 57003, updated on 8-Jan-2023

Summary

Official Symbol
CCDC47provided by HGNC
Official Full Name
coiled-coil domain containing 47provided by HGNC
Primary source
HGNC:HGNC:24856
See related
Ensembl:ENSG00000108588 MIM:618260; AllianceGenome:HGNC:24856
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
THNS; GK001; MSTP041
Summary
Enables protein folding chaperone and ribosome binding activity. Involved in ERAD pathway; endoplasmic reticulum calcium ion homeostasis; and protein insertion into ER membrane. Located in endoplasmic reticulum. Is integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in colon (RPKM 44.7), duodenum (RPKM 34.8) and 25 other tissues See more
Orthologs
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Genomic context

See CCDC47 in Genome Data Viewer
Location:
17q23.3
Exon count:
13
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (63745255..63773597, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (64616174..64644489, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (61822615..61850957, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC729683 Neighboring gene LIM domain containing 2 Neighboring gene STE20 related adaptor alpha Neighboring gene DEAD-box helicase 42 Neighboring gene FtsJ RNA 2'-O-methyltransferase 3 Neighboring gene proteasome 26S subunit, ATPase 5

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpr vpr HIV-1 Vpr is identified to have a physical interaction with coiled-coil domain containing 47 (CCDC47) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein folding chaperone IDA
Inferred from Direct Assay
more info
PubMed 
enables ribosome binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in ER overload response IEA
Inferred from Electronic Annotation
more info
 
involved_in ERAD pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in endoplasmic reticulum calcium ion homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in osteoblast differentiation HDA PubMed 
involved_in post-embryonic development IEA
Inferred from Electronic Annotation
more info
 
involved_in protein folding IEA
Inferred from Electronic Annotation
more info
 
involved_in protein insertion into ER membrane IDA
Inferred from Direct Assay
more info
PubMed 
involved_in ubiquitin-dependent ERAD pathway IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
part_of chaperone complex IPI
Inferred from Physical Interaction
more info
PubMed 
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
 
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in membrane HDA PubMed 
located_in rough endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
PAT complex subunit CCDC47
Names
Calumin
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_020198.3NP_064583.2  PAT complex subunit CCDC47 precursor

    See identical proteins and their annotated locations for NP_064583.2

    Status: VALIDATED

    Source sequence(s)
    AF226054, AK027844, BC001300, DB222124
    Consensus CDS
    CCDS11643.1
    UniProtKB/Swiss-Prot
    Q96A33, Q9NRG3
    Related
    ENSP00000225726.5, ENST00000225726.10
    Conserved Domains (2) summary
    PRK05901
    Location:18115
    PRK05901; RNA polymerase sigma factor; Provisional
    pfam07946
    Location:135467
    DUF1682; Protein of unknown function (DUF1682)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    63745255..63773597 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005257527.3XP_005257584.1  PAT complex subunit CCDC47 isoform X1

    See identical proteins and their annotated locations for XP_005257584.1

    UniProtKB/Swiss-Prot
    Q96A33, Q9NRG3
    Conserved Domains (2) summary
    PRK05901
    Location:18115
    PRK05901; RNA polymerase sigma factor; Provisional
    pfam07946
    Location:135467
    DUF1682; Protein of unknown function (DUF1682)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    64616174..64644489 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)