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

Gene ID: 57003, updated on 20-Dec-2019

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
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
Expression
Ubiquitous expression in colon (RPKM 44.7), duodenum (RPKM 34.8) and 25 other tissues See more
Orthologs

Genomic context

See CCDC47 in Genome Data Viewer
Location:
17q23.3
Exon count:
14
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (63745255..63773597, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (61822610..61851088, 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

Bibliography

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

General protein information

Preferred Names
coiled-coil domain-containing protein 47
Names
Calumin

NCBI Reference Sequences (RefSeq)

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  coiled-coil domain-containing protein 47 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
    Related
    ENSP00000225726.5, ENST00000225726.10
    Conserved Domains (2) summary
    pfam07946
    Location:135467
    DUF1682; Protein of unknown function (DUF1682)
    cl27146
    Location:18115
    Sigma70_r3; Sigma-70 region 3

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_005257527.2XP_005257584.1  coiled-coil domain-containing protein 47 isoform X1

    See identical proteins and their annotated locations for XP_005257584.1

    UniProtKB/Swiss-Prot
    Q96A33
    Related
    ENSP00000384888.3, ENST00000403162.7
    Conserved Domains (2) summary
    pfam07946
    Location:135467
    DUF1682; Protein of unknown function (DUF1682)
    cl27146
    Location:18115
    Sigma70_r3; Sigma-70 region 3
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