Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CCDC3 Gene

Aliases for CCDC3 Gene

  • Coiled-Coil Domain Containing 3 2 3 5
  • Favine 2 3 4
  • Fat/Vessel-Derived Secretory Protein 3 4
  • Coiled-Coil Domain-Containing Protein 3 3

External Ids for CCDC3 Gene

Previous GeneCards Identifiers for CCDC3 Gene

  • GC10M012943
  • GC10M012978
  • GC10M012938

Summaries for CCDC3 Gene

GeneCards Summary for CCDC3 Gene

CCDC3 (Coiled-Coil Domain Containing 3) is a Protein Coding gene.

UniProtKB/Swiss-Prot for CCDC3 Gene

  • Negatively regulates TNF-alpha-induced pro-inflammatory response in endothelial cells (ECs) via inhibition of TNF-alpha-induced NF-kappaB activation in ECs (PubMed:25193116). Positively regulates lipid accumulation in adipose cells (By similarity).

Gene Wiki entry for CCDC3 Gene

Additional gene information for CCDC3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CCDC3 Gene

Genomics for CCDC3 Gene

GeneHancer (GH) Regulatory Elements for CCDC3 Gene

Promoters and enhancers for CCDC3 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
GH10J013098 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE 650.7 -1.3 -1319 4.4 FOXA2 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 KLF13 SP3 CCDC3 OPTN BTBD7P1 ENSG00000239665 PRPF18 SNRPGP5
GH10J013001 Promoter 1.4 EPDnew Ensembl 660.1 +98.0 97973 0.8 ZBTB8A BMI1 ZIC2 ZNF2 ZNF335 GLIS2 POLR2A ZBTB48 GLIS1 CTBP2 CCDC3 OPTN RPL5P25 RNA5SP300
GH10J013160 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 9.9 -61.9 -61863 2.1 PKNOX1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 E2F8 GC10M013159 MCM10 RPL36AP36 BTBD7P1 ENSG00000228302 CCDC3 OPTN PRPF18 GC10P013202
GH10J012958 Enhancer 1 Ensembl ENCODE dbSUPER 19 +139.2 139211 3.7 FOXA2 NFIA RXRA MAX NR2F2 SP1 JUND POLR2A HNF4A CCDC3 OPTN RNA5SP300 LOC105376418 RPL5P25
GH10J012705 Enhancer 1.4 FANTOM5 Ensembl ENCODE 10.7 +391.1 391095 6.3 PKNOX1 SIN3A FEZF1 IRF4 YY1 ZNF213 ZNF143 FOS ATF7 RUNX3 CAMK1D CCDC3 OPTN ENSG00000239665 GC10P012703 MIR548Q
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CCDC3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CCDC3 gene promoter:

Genomic Locations for CCDC3 Gene

Genomic Locations for CCDC3 Gene
chr10:12,896,625-13,099,773
(GRCh38/hg38)
Size:
203,149 bases
Orientation:
Minus strand
chr10:12,938,625-13,141,652
(GRCh37/hg19)

Genomic View for CCDC3 Gene

Genes around CCDC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CCDC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CCDC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CCDC3 Gene

Proteins for CCDC3 Gene

  • Protein details for CCDC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BQI4-CCDC3_HUMAN
    Recommended name:
    Coiled-coil domain-containing protein 3
    Protein Accession:
    Q9BQI4
    Secondary Accessions:
    • Q5VYV8
    • Q5VYV9

    Protein attributes for CCDC3 Gene

    Size:
    270 amino acids
    Molecular mass:
    30731 Da
    Quaternary structure:
    • Homodimer.

    Alternative splice isoforms for CCDC3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CCDC3 Gene

Post-translational modifications for CCDC3 Gene

  • Glycosylation at Asn100
  • Modification sites at PhosphoSitePlus

Other Protein References for CCDC3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CCDC3 Gene

Domains & Families for CCDC3 Gene

Gene Families for CCDC3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for CCDC3 Gene

ProtoNet:

Suggested Antigen Peptide Sequences for CCDC3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CCDC3: view

No data available for UniProtKB/Swiss-Prot for CCDC3 Gene

Function for CCDC3 Gene

Molecular function for CCDC3 Gene

UniProtKB/Swiss-Prot Function:
Negatively regulates TNF-alpha-induced pro-inflammatory response in endothelial cells (ECs) via inhibition of TNF-alpha-induced NF-kappaB activation in ECs (PubMed:25193116). Positively regulates lipid accumulation in adipose cells (By similarity).
UniProtKB/Swiss-Prot Induction:
Up-regulated by pioglitazone and down-regulated by TNF in HUVEC.

Phenotypes From GWAS Catalog for CCDC3 Gene

genes like me logo Genes that share phenotypes with CCDC3: view

Animal Models for CCDC3 Gene

MGI Knock Outs for CCDC3:

Animal Model Products

miRNA for CCDC3 Gene

miRTarBase miRNAs that target CCDC3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CCDC3 Gene

Localization for CCDC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CCDC3 Gene

Secreted.

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 CCDC3 gene
Compartment Confidence
extracellular 4
endoplasmic reticulum 4
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CCDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005783 endoplasmic reticulum IDA --
genes like me logo Genes that share ontologies with CCDC3: view

Pathways & Interactions for CCDC3 Gene

SuperPathways for CCDC3 Gene

No Data Available

Interacting Proteins for CCDC3 Gene

Gene Ontology (GO) - Biological Process for CCDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010804 negative regulation of tumor necrosis factor-mediated signaling pathway IMP 25193116
GO:0045600 positive regulation of fat cell differentiation IEA --
GO:0046889 positive regulation of lipid biosynthetic process IEA --
genes like me logo Genes that share ontologies with CCDC3: view

No data available for Pathways by source and SIGNOR curated interactions for CCDC3 Gene

Drugs & Compounds for CCDC3 Gene

No Compound Related Data Available

Transcripts for CCDC3 Gene

mRNA/cDNA for CCDC3 Gene

(136) Selected AceView cDNA sequences:
(9) Additional mRNA sequences :
(2) REFSEQ mRNAs :
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CCDC3 Gene

Coiled-coil domain containing 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CCDC3 Gene

No ASD Table

Relevant External Links for CCDC3 Gene

GeneLoc Exon Structure for
CCDC3
ECgene alternative splicing isoforms for
CCDC3

Expression for CCDC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CCDC3 Gene

mRNA differential expression in normal tissues according to GTEx for CCDC3 Gene

This gene is overexpressed in Artery - Coronary (x9.3), Artery - Tibial (x6.0), and Artery - Aorta (x5.0).

Protein differential expression in normal tissues from HIPED for CCDC3 Gene

This gene is overexpressed in Gallbladder (68.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CCDC3 Gene



Protein tissue co-expression partners for CCDC3 Gene

NURSA nuclear receptor signaling pathways regulating expression of CCDC3 Gene:

CCDC3

SOURCE GeneReport for Unigene cluster for CCDC3 Gene:

Hs.498720

mRNA Expression by UniProt/SwissProt for CCDC3 Gene:

Q9BQI4-CCDC3_HUMAN
Tissue specificity: Expressed in umbilical vein endothelial cells (HUVEC), and at lower levels in aortic smooth muscle cells (HASMC).

Evidence on tissue expression from TISSUES for CCDC3 Gene

  • Spleen(4.5)
  • Nervous system(4.4)
  • Kidney(2.3)
  • Lung(2.3)
  • Muscle(2.3)
  • Heart(2.2)
genes like me logo Genes that share expression patterns with CCDC3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CCDC3 Gene

Orthologs for CCDC3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CCDC3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CCDC3 34 33
  • 98.64 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CCDC3 34 33
  • 90.34 (n)
OneToMany
-- 34
  • 76 (a)
OneToMany
-- 34
  • 75 (a)
OneToMany
-- 34
  • 71 (a)
OneToMany
dog
(Canis familiaris)
Mammalia CCDC3 34 33
  • 89.63 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Ccdc3 16 34 33
  • 88.37 (n)
rat
(Rattus norvegicus)
Mammalia Ccdc3 33
  • 87.71 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CCDC3 34
  • 76 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CCDC3 34
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves CCDC3 34 33
  • 77.55 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CCDC3 34
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ccdc3 33
  • 71.37 (n)
Str.19636 33
zebrafish
(Danio rerio)
Actinopterygii ccdc3 34 33
  • 68.68 (n)
OneToOne
Species where no ortholog for CCDC3 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 CCDC3 Gene

ENSEMBL:
Gene Tree for CCDC3 (if available)
TreeFam:
Gene Tree for CCDC3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CCDC3: view image

Paralogs for CCDC3 Gene

No data available for Paralogs for CCDC3 Gene

Variants for CCDC3 Gene

Sequence variations from dbSNP and Humsavar for CCDC3 Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
rs1000549349 uncertain-significance, Amyotrophic Lateral Sclerosis, Recessive, Primary open angle glaucoma 13,100,194(-) G/T upstream_transcript_variant
rs11548142 benign, Amyotrophic Lateral Sclerosis, Recessive, Primary open angle glaucoma 13,100,251(-) G/A/C upstream_transcript_variant
rs2580915 likely-benign, Amyotrophic Lateral Sclerosis, Recessive, Primary open angle glaucoma 13,100,211(-) C/G upstream_transcript_variant
rs3814657 benign, Primary open angle glaucoma, Amyotrophic Lateral Sclerosis, Recessive 13,100,087(-) G/A/T upstream_transcript_variant
rs552494483 likely-benign, Amyotrophic Lateral Sclerosis, Recessive, Primary open angle glaucoma 13,100,192(-) C/A upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for CCDC3 Gene

Variant ID Type Subtype PubMed ID
dgv176e212 CNV loss 25503493
dgv367n106 OTHER inversion 24896259
dgv957n54 CNV loss 21841781
dgv958n54 CNV loss 21841781
dgv959n54 CNV loss 21841781
esv1638252 OTHER inversion 17803354
esv1974400 CNV deletion 18987734
esv24014 CNV loss 19812545
esv2439266 OTHER inversion 19546169
esv2661464 CNV deletion 23128226
esv2668184 CNV deletion 23128226
esv2677992 CNV deletion 23128226
esv2733295 CNV deletion 23290073
esv2733306 CNV deletion 23290073
esv2759733 CNV loss 17122850
esv2762844 CNV loss 21179565
esv2762845 CNV loss 21179565
esv2764257 CNV loss 21179565
esv2863457 CNV insertion 24192839
esv3302488 CNV tandem duplication 20981092
esv3352556 CNV duplication 20981092
esv3386766 OTHER inversion 20981092
esv3545918 CNV deletion 23714750
esv3578643 CNV loss 25503493
esv3622390 CNV loss 21293372
esv3622392 CNV loss 21293372
esv3622393 CNV loss 21293372
esv3622394 CNV loss 21293372
esv3622395 CNV loss 21293372
esv3622397 CNV loss 21293372
esv3622398 OTHER inversion 21293372
esv3622399 CNV loss 21293372
esv3766 OTHER inversion 18987735
esv8188 OTHER inversion 19470904
nsv1035341 CNV loss 25217958
nsv1045253 CNV loss 25217958
nsv1051704 CNV loss 25217958
nsv1053098 CNV gain 25217958
nsv1074181 CNV deletion 25765185
nsv1125330 OTHER inversion 24896259
nsv1127089 CNV deletion 24896259
nsv442570 CNV loss 18776908
nsv473053 CNV novel sequence insertion 20440878
nsv473780 CNV novel sequence insertion 20440878
nsv514543 CNV loss 21397061
nsv516198 CNV loss 19592680
nsv521491 CNV gain 19592680
nsv549979 CNV loss 21841781
nsv5831 CNV insertion 18451855
nsv818747 CNV loss 17921354
nsv818748 CNV loss 17921354
nsv8604 CNV loss 18304495
nsv947739 CNV duplication 23825009
nsv971901 CNV duplication 23825009

Variation tolerance for CCDC3 Gene

Residual Variation Intolerance Score: 51.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.78; 47.30% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CCDC3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CCDC3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CCDC3 Gene

Disorders for CCDC3 Gene

Additional Disease Information for CCDC3

No disorders were found for CCDC3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CCDC3 Gene

Publications for CCDC3 Gene

  1. Identification of a new secretory factor, CCDC3/Favine, in adipocytes and endothelial cells. (PMID: 20043878) Kobayashi S … Shimomura I (Biochemical and biophysical research communications 2010) 2 3 4 58
  2. Coiled-coil domain containing 3 (CCDC3) represses tumor necrosis factor-α/nuclear factor κB-induced endothelial inflammation. (PMID: 25193116) Azad AK … Fu Y (Cellular signalling 2014) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 3 4 58

Products for CCDC3 Gene

Sources for CCDC3 Gene

Content
Loading form....