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

Summary

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: mouse all
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Genomic context

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Polymorphisms in innate immunity genes and risk of childhood leukemia.
Observational study of gene-disease association. (HuGE Navigator)
Title: Risk of meningioma and common variation in genes related to innate immunity.
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.
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.
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).
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.

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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)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH40315 (e-PCR)
- UniSTS:85797

G23952 (e-PCR)
- UniSTS:2406

RH69539 (e-PCR)
- UniSTS:86905

PMC24996P1 (e-PCR)
- UniSTS:272278

RH69396 (e-PCR)
- UniSTS:70829

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)

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
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
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
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