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... See more...

Aliases for C1D Gene

Aliases for C1D Gene

  • C1D Nuclear Receptor Corepressor 2 3 5
  • Small Unique Nuclear Receptor Co-Repressor 2 3
  • Nuclear Nucleic Acid-Binding Protein C1D 3 4
  • C1D Nuclear Receptor Co-Repressor 2 3
  • HC1D 3 4
  • Small Unique Nuclear Receptor Corepressor 3
  • Nuclear DNA-Binding Protein 3
  • C1D DNA-Binding Protein 3
  • SUN-CoR 3
  • SUNCOR 3
  • Rrp47 3
  • LRP1 3

External Ids for C1D Gene

Previous GeneCards Identifiers for C1D Gene

  • GC02M068402
  • GC02M068227
  • GC02M068243
  • GC02M068180
  • GC02M068125
  • GC02M068006

Summaries for C1D Gene

Entrez Gene Summary for C1D Gene

  • 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]

GeneCards Summary for C1D Gene

C1D (C1D Nuclear Receptor Corepressor) is a Protein Coding gene. Diseases associated with C1D include Primary Ciliary Dyskinesia. Among its related pathways are rRNA processing in the nucleus and cytosol and Gene Expression. Gene Ontology (GO) annotations related to this gene include RNA binding and nuclear receptor binding.

UniProtKB/Swiss-Prot Summary for C1D Gene

  • Plays a role in the recruitment of the RNA exosome complex to pre-rRNA to mediate the 3'-5' end processing of the 5.8S rRNA; this function may include MPHOSPH6. Can activate PRKDC not only in the presence of linear DNA but also in the presence of supercoiled DNA. Can induce apoptosis in a p53/TP53 dependent manner. May regulate the TRAX/TSN complex formation. Potentiates transcriptional repression by NR1D1 and THRB (By similarity).

Gene Wiki entry for C1D Gene

Additional gene information for C1D Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for C1D Gene

Genomics for C1D Gene

GeneHancer (GH) Regulatory Elements for C1D Gene

Promoters and enhancers for C1D Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J068060 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 500.3 +48.3 48314 3.5 ZBTB40 ZNF217 EP300 TCF12 SIN3A POLR2G SP1 PHF8 ZFX ZNF639 lnc-PNO1-5 C1D lnc-WDR92-1 lnc-C1D-5 L13712-017
GH02J068196 Enhancer 0.6 ENCODE dbSUPER 10.9 -85.5 -85509 0.8 CTCF RAD21 SMC3 ZNF654 ZBTB33 WDR92 PPP3R1 PNO1 C1D ENSG00000273275 LOC102724389 ENSG00000273398
GH02J068179 Promoter/Enhancer 0.6 EPDnew Ensembl 10.9 -68.9 -68932 0.2 RBM22 ENSG00000273275 piR-37229 piR-47287 PPP3R1 WDR92 PNO1 C1D CNRIP1 LOC102724389 ENSG00000273398
GH02J068176 Enhancer 0.6 Ensembl dbSUPER 10.9 -66.0 -65952 1.8 POLR2A POLR2H RBM22 SUPT5H piR-37229 C1D CNRIP1 PPP3R1 NONHSAG028060.2 PNO1 ENSG00000273398
GH02J068361 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 2.8 -255.3 -255258 8.5 RXRA ZNF217 EP300 CTCF ZSCAN5C TCF12 SIN3A MYC USF1 SP1 PLEK ENSG00000203395 FBXO48 APLF ARHGAP25 C1D PPP3R1 LOC101927723 lnc-PLEK-1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around C1D on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for C1D

Top Transcription factor binding sites by QIAGEN in the C1D gene promoter:
  • AP-4
  • Bach2
  • LCR-F1
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • STAT1
  • STAT1alpha
  • STAT1beta
  • STAT3

Genomic Locations for C1D Gene

Genomic Locations for C1D Gene
chr2:68,041,130-68,110,948
(GRCh38/hg38)
Size:
69,819 bases
Orientation:
Minus strand
chr2:68,268,262-68,338,080
(GRCh37/hg19)
Size:
69,819 bases
Orientation:
Minus strand

Genomic View for C1D Gene

Genes around C1D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
C1D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for C1D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for C1D Gene

Proteins for C1D Gene

  • Protein details for C1D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13901-C1D_HUMAN
    Recommended name:
    Nuclear nucleic acid-binding protein C1D
    Protein Accession:
    Q13901
    Secondary Accessions:
    • A8K336
    • D6W5F8
    • Q05D64

    Protein attributes for C1D Gene

    Size:
    141 amino acids
    Molecular mass:
    16019 Da
    Quaternary structure:
    • Monomer and homodimer. Interacts with NR1D1, THRA, THRB, NCOR1 and NCOR2 (By similarity). Interacts with EXOSC10; the interaction probably mediates the association with the nuclear form of the RNA exosome. The homodimeric form interacts with TSNAX following gamma-radiation. Interacts with RAC3.

neXtProt entry for C1D Gene

Post-translational modifications for C1D Gene

Other Protein References for C1D Gene

No data available for DME Specific Peptides for C1D Gene

Domains & Families for C1D Gene

Gene Families for C1D Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for C1D Gene

Suggested Antigen Peptide Sequences for C1D Gene

GenScript: Design optimal peptide antigens:
  • Nuclear nucleic acid-binding protein C1D (C1D_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q13901

UniProtKB/Swiss-Prot:

C1D_HUMAN :
  • Belongs to the C1D family.
Family:
  • Belongs to the C1D family.
genes like me logo Genes that share domains with C1D: view

Function for C1D Gene

Molecular function for C1D Gene

UniProtKB/Swiss-Prot Function:
Plays a role in the recruitment of the RNA exosome complex to pre-rRNA to mediate the 3'-5' end processing of the 5.8S rRNA; this function may include MPHOSPH6. Can activate PRKDC not only in the presence of linear DNA but also in the presence of supercoiled DNA. Can induce apoptosis in a p53/TP53 dependent manner. May regulate the TRAX/TSN complex formation. Potentiates transcriptional repression by NR1D1 and THRB (By similarity).
UniProtKB/Swiss-Prot Induction:
By gamma-radiation.

Phenotypes From GWAS Catalog for C1D Gene

Gene Ontology (GO) - Molecular Function for C1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA,TAS --
GO:0003714 transcription corepressor activity IEA --
GO:0003723 RNA binding IDA,IEA 17412707
GO:0005515 protein binding IPI 17412707
GO:0016922 nuclear receptor binding IEA --
genes like me logo Genes that share ontologies with C1D: view
genes like me logo Genes that share phenotypes with C1D: view

Animal Model Products

CRISPR Products

miRNA for C1D Gene

miRTarBase miRNAs that target C1D

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for C1D Gene

Localization for C1D Gene

Subcellular locations from UniProtKB/Swiss-Prot for C1D Gene

Nucleus. Cytoplasm. Nucleus, nucleolus. Note=EXOSC10 is required for nucleolar localization (PubMed:17412707). Colocalizes with TSNAX in the nucleus (PubMed:11801738). {ECO:0000269 PubMed:11801738, ECO:0000269 PubMed:17412707}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for C1D gene
Compartment Confidence
nucleus 5
cytosol 3
extracellular 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for C1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000176 nuclear exosome (RNase complex) TAS 17412707
GO:0005634 nucleus TAS 9469821
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IEA,IDA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with C1D: view

Pathways & Interactions for C1D Gene

genes like me logo Genes that share pathways with C1D: view

Pathways by source for C1D Gene

SIGNOR curated interactions for C1D Gene

Activates:

Gene Ontology (GO) - Biological Process for C1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000460 maturation of 5.8S rRNA IMP 17412707
GO:0006364 rRNA processing TAS --
GO:0006915 apoptotic process IEA --
GO:0045892 negative regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with C1D: view

Drugs & Compounds for C1D Gene

(4) Drugs for C1D Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for C1D Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with C1D: view

Transcripts for C1D Gene

mRNA/cDNA for C1D Gene

4 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for C1D Gene

No ASD Table

Relevant External Links for C1D Gene

GeneLoc Exon Structure for
C1D

Expression for C1D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for C1D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for C1D Gene

This gene is overexpressed in Lung (38.7) and Pancreas (18.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for C1D Gene



Protein tissue co-expression partners for C1D Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for C1D

SOURCE GeneReport for Unigene cluster for C1D Gene:

Hs.602900

mRNA Expression by UniProt/SwissProt for C1D Gene:

Q13901-C1D_HUMAN
Tissue specificity: Ubiquitous. Expressed at very high levels in the hippocampus, medulla oblongata, mammary gland, thyroid and salivary gland. Expressed at high levels in the fetal; lung, liver and kidney. Expressed at low levels in skeletal muscle, appendix, heart, lung and colon.

Evidence on tissue expression from TISSUES for C1D Gene

  • Nervous system(4.6)
  • Bone marrow(4.2)
  • Lung(4.2)
genes like me logo Genes that share expression patterns with C1D: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for C1D Gene

Orthologs for C1D Gene

This gene was present in the common ancestor of chordates.

Orthologs for C1D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia C1D 31 30
  • 99.53 (n)
OneToOne
dog
(Canis familiaris)
Mammalia C1D 31 30
  • 94.09 (n)
OneToOne
cow
(Bos Taurus)
Mammalia C1D 31 30
  • 93.14 (n)
OneToOne
mouse
(Mus musculus)
Mammalia C1d 17 31 30
  • 87.38 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia C1D 31
  • 86 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia C1D 31
  • 81 (a)
OneToOne
chicken
(Gallus gallus)
Aves C1D 31 30
  • 79.79 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia C1D 31
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia c1d 30
  • 71.67 (n)
Str.6344 30
zebrafish
(Danio rerio)
Actinopterygii c1d 31 30
  • 65.22 (n)
OneToOne
wufc33g02 30
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 34 (a)
OneToOne
Species where no ortholog for C1D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for C1D Gene

ENSEMBL:
Gene Tree for C1D (if available)
TreeFam:
Gene Tree for C1D (if available)
Aminode:
Evolutionary constrained regions (ECRs) for C1D: view image

Paralogs for C1D Gene

Pseudogenes.org Pseudogenes for C1D Gene

genes like me logo Genes that share paralogs with C1D: view

No data available for Paralogs for C1D Gene

Variants for C1D Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for C1D Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs10444 - p.Ser127Pro

Additional dbSNP identifiers (rs#s) for C1D Gene

Structural Variations from Database of Genomic Variants (DGV) for C1D Gene

Variant ID Type Subtype PubMed ID
nsv525802 CNV loss 19592680
nsv834251 CNV loss 17160897

Variation tolerance for C1D Gene

Residual Variation Intolerance Score: 55.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.54; 72.09% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for C1D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
C1D

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for C1D Gene

Disorders for C1D Gene

MalaCards: The human disease database

(1) MalaCards diseases for C1D Gene - From: DISEASES

Disorder Aliases PubMed IDs
primary ciliary dyskinesia
  • pcd
- elite association - COSMIC cancer census association via MalaCards
Search C1D in MalaCards View complete list of genes associated with diseases

Additional Disease Information for C1D

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with C1D: view

No data available for UniProtKB/Swiss-Prot and Genatlas for C1D Gene

Publications for C1D Gene

  1. C1D and hMtr4p associate with the human exosome subunit PM/Scl-100 and are involved in pre-rRNA processing. (PMID: 17412707) Schilders G … Pruijn GJ (Nucleic acids research 2007) 2 3 4 54
  2. DNA damage-dependent interaction of the nuclear matrix protein C1D with Translin-associated factor X (TRAX). (PMID: 11801738) Erdemir T … Yavuzer U (Journal of cell science 2002) 2 3 4 54
  3. cDNA cloning, recombinant expression and characterization of polypetides with exceptional DNA affinity. (PMID: 9469821) Nehls P … Werner D (Nucleic acids research 1998) 2 3 4 54
  4. Risk of meningioma and common variation in genes related to innate immunity. (PMID: 20406964) Rajaraman P … Inskip PD (Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2010) 3 41 54
  5. Polymorphisms in innate immunity genes and risk of childhood leukemia. (PMID: 20438785) Han S … Kang D (Human immunology 2010) 3 41 54

Products for C1D Gene

Sources for C1D Gene