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C1D C1D nuclear receptor corepressor [ Homo sapiens (human) ]

Gene ID: 10438, updated on 3-Nov-2024

Summary

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Official Symbol
C1Dprovided by HGNC
Official Full Name
C1D nuclear receptor corepressorprovided by HGNC
Primary source
HGNC:HGNC:29911
See related
Ensembl:ENSG00000197223 MIM:606997; AllianceGenome:HGNC:29911
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LRP1; hC1D; Rrp47; SUNCOR; SUN-CoR
Summary
The protein encoded by this gene is a DNA binding and apoptosis-inducing protein and is localized in the nucleus. It is also a Rac3-interacting protein which acts as a corepressor for the thyroid hormone receptor. This protein is thought to regulate TRAX/Translin complex formation. Alternate splicing results in multiple transcript variants that encode the same protein. Multiple pseudogenes of this gene are found on chromosome 10.[provided by RefSeq, Jun 2010]
Expression
Ubiquitous expression in bone marrow (RPKM 17.9), adrenal (RPKM 15.5) and 25 other tissues See more
Orthologs
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Genomic context

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See C1D in Genome Data Viewer
Location:
2p14
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (68041130..68063004, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (68051683..68073563, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (68268262..68290136, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:68035929-68037128 Neighboring gene long intergenic non-protein coding RNA 1812 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:68146782-68147981 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:68222082-68222296 Neighboring gene FBXL12 pseudogene 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:68289704-68290903 Neighboring gene uncharacterized LOC105374789 Neighboring gene small integral membrane protein 30-like

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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Related articles in PubMed

  1. Identification of a novel Rac3-interacting protein C1D. Haataja L, et al. Int J Mol Med, 1998 Apr. PMID 9852280
  2. Induction of apoptosis by overexpression of the DNA-binding and DNA-PK-activating protein C1D. Rothbarth K, et al. J Cell Sci, 1999 Jul. PMID 10362552
  3. Proteasome-mediated degradation antagonizes critical levels of the apoptosis-inducing C1D protein. Rothbarth K, et al. Cancer Cell Int, 2002 Sep 2. PMID 12379155, Free PMC Article
  4. C1D is a major autoantibody target in patients with the polymyositis-scleroderma overlap syndrome. Schilders G, et al. Arthritis Rheum, 2007 Jul. PMID 17599775
  5. Promoter of the gene encoding the 16 kDa DNA-binding and apoptosis-inducing C1D protein. Rothbarth K, et al. Biochim Biophys Acta, 2001 Apr 16. PMID 11311939

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Data confirm that C1D is not directly involved in repair of UV-damaged DNA; C1D appears to protects cells from oxidative stress (induced by UV irradiation or hydrogen peroxide oxidation) by regulating expression of DNA repair/transcription enzymes such as APEX1 or DDIT3. (C1D = nuclear receptor corepressor C1D; APEX1 = apurinic/apyrimidinic endodeoxyribonuclease-1; DDIT3 = DNA damage inducible transcript-3)
    Title: C1D is not directly involved in the repair of UV-damaged DNA but protects cells from oxidative stress by regulating gene expressions in human cell lines.
  2. C1D is associated with the DNA repair complex and may promote repair of ultraviolet irradiation-induced DNA damage.
    Title: XPB induces C1D expression to counteract UV-induced apoptosis.
  3. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
    Title: Polymorphisms in innate immunity genes and risk of childhood leukemia.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Risk of meningioma and common variation in genes related to innate immunity.
  5. Anti-C1D autoantibodies were observed in patients with polymyositis-scleroderma overlap syndrome.
    Title: C1D is a major autoantibody target in patients with the polymyositis-scleroderma overlap syndrome.
  6. Results are consistent with a role for the exosome-associated protein C1D in the recruitment of the exosome to pre-rRNA to mediate the 3' end processing of the 5.8S rRNA.
    Title: C1D and hMtr4p associate with the human exosome subunit PM/Scl-100 and are involved in pre-rRNA processing.
  7. TRAX enhances the DNA binding capacity of Translin, that binds to recombination regions in some malignancies. C1D interacts with TRAX following g-irradiation and prevents formation of TRAX/Translin complex, thereby inhibits any unwanted recombination.
    Title: DNA damage-dependent interaction of the nuclear matrix protein C1D with Translin-associated factor X (TRAX).
  8. The C1D protein interacts with the catalytic subunit of DNA-PK and is a very effective substrate for DNA-PK in vitro. Moreover, C1D directs the activation of DNA-PK in a manner that does not require DNA termini, suggesting a role for C1D in DNA repair.
    Title: DNA end-independent activation of DNA-PK mediated via association with the DNA-binding protein C1D.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Vif vif HIV-1 Vif modulates the expression of C1D nuclear receptor corepressor (C1D) in Vif-expression T cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC12261, MGC14659

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables nuclear receptor binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription corepressor activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in maturation of 5.8S rRNA IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in maturation of 5.8S rRNA IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
part_of exosome (RNase complex) IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of nuclear exosome (RNase complex) TAS
Traceable Author Statement
more info
 PubMed 
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus TAS
Traceable Author Statement
more info
 PubMed 
part_of transcription repressor complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
nuclear nucleic acid-binding protein C1D
Names
C1D DNA-binding protein
C1D nuclear receptor co-repressor
nuclear DNA-binding protein
small unique nuclear receptor co-repressor
small unique nuclear receptor corepressor

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_001190263.2 → NP_001177192.1  nuclear nucleic acid-binding protein C1D

    See identical proteins and their annotated locations for NP_001177192.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC079112, AI004680, AK290451
    Consensus CDS
    CCDS1883.1
    UniProtKB/Swiss-Prot
    A8K336, D6W5F8, Q05D64, Q13901
    Related
    ENSP00000386779.1, ENST00000409302.1
    Conserved Domains (1) summary
    pfam04000
    Location:18 → 95
    Sas10_Utp3; Sas10/Utp3/C1D family

  2. NM_001190265.2 → NP_001177194.1  nuclear nucleic acid-binding protein C1D

    See identical proteins and their annotated locations for NP_001177194.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC079112, AI004680, DA900336
    Consensus CDS
    CCDS1883.1
    UniProtKB/Swiss-Prot
    A8K336, D6W5F8, Q05D64, Q13901
    Conserved Domains (1) summary
    pfam04000
    Location:18 → 95
    Sas10_Utp3; Sas10/Utp3/C1D family

  3. NM_006333.4 → NP_006324.1  nuclear nucleic acid-binding protein C1D

    See identical proteins and their annotated locations for NP_006324.1

    Status: REVIEWED

    Description
    Transcript Variant: This transcript represents variant (1). Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC079112, BC016284, BG505686, BM354091, CN342947
    Consensus CDS
    CCDS1883.1
    UniProtKB/Swiss-Prot
    A8K336, D6W5F8, Q05D64, Q13901
    Related
    ENSP00000348107.3, ENST00000355848.7
    Conserved Domains (1) summary
    pfam04000
    Location:18 → 95
    Sas10_Utp3; Sas10/Utp3/C1D family

  4. NM_173177.3 → NP_775269.1  nuclear nucleic acid-binding protein C1D

    See identical proteins and their annotated locations for NP_775269.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC079112, BC009589, BG505686, BM354091, CN342947
    Consensus CDS
    CCDS1883.1
    UniProtKB/Swiss-Prot
    A8K336, D6W5F8, Q05D64, Q13901
    Related
    ENSP00000386468.3, ENST00000410067.8
    Conserved Domains (1) summary
    pfam04000
    Location:18 → 95
    Sas10_Utp3; Sas10/Utp3/C1D family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    68041130..68063004 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    68051683..68073563 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13901.1 GenPept UniProtKB/Swiss-Prot:Q13901

Gene LinkOut

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