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CCDC3 Gene

protein-coding   GIFtS: 44
GCID: GC10M012938

Coiled-Coil Domain Containing 3

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Coiled-Coil Domain Containing 31 2
Fat/Vessel-Derived Secretory Protein2 3
Coiled-Coil Domain-Containing Protein 32
favine2
Favine3
CCDC345

External Ids:    HGNC: 238131   Entrez Gene: 836432   Ensembl: ENSG000001514687   OMIM: 6123245   UniProtKB: Q9BQI43   

Export aliases for CCDC3 gene to outside databases

Previous GC identifers: GC10M012943 GC10M012978


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for CCDC3 Gene:
CCDC3 (coiled-coil domain containing 3) is a protein-coding gene.

Gene Wiki entry for CCDC3 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000010.10  NC_018921.2  NT_008705.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the CCDC3 gene promoter:
         AML1a   NCX/Ncx   MyoD   STAT5A   YY1   AREB6   Pax-3   POU2F1   POU2F1a   En-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCDC3 promoter sequence
   Search Chromatin IP Primers for CCDC3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CCDC3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 10p13   Ensembl cytogenetic band:  10p13   HGNC cytogenetic band: 10p14

CCDC3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC3 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10M012938:  view genomic region     (about GC identifiers)

Start:
12,938,625 bp from pter      End:
13,141,652 bp from pter
Size:
203,028 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CCDC3_HUMAN, Q9BQI4 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 3 precursor  
Size: 270 amino acids; 30731 Da
Subunit: Homodimer (By similarity)
Secondary accessions: Q5VYV8

Explore the universe of human proteins at neXtProt for CCDC3: NX_Q9BQI4

Explore proteomics data for CCDC3 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn100
  • Modification sites at PhosphoSitePlus

  • See CCDC3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001269587.1  NP_113643.1  

    ENSEMBL proteins: 
     ENSP00000368102   ENSP00000368116  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    ProtoNet protein and cluster: Q9BQI4


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CCDC3_HUMAN, Q9BQI4
    Induction: Up-regulated by pioglitazone and down-regulated by TNF in HUVEC

    Animal Models:

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    hsa-mir-124-3p (MIRT022206)

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    hsa-miR-623 hsa-miR-3173-3p hsa-miR-100* hsa-miR-3938 hsa-miR-3660 hsa-miR-589* hsa-miR-151-3p hsa-miR-298
    SwitchGear 3'UTR luciferase reporter plasmidCCDC3 3' UTR sequence
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    CCDC3_HUMAN, Q9BQI4: Secreted (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endoplasmic reticulum4
    extracellular3
    cytosol1
    mitochondrion1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--
    GO:0005783endoplasmic reticulum IDA--

    Find genes that share ontologies with CCDC3           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for CCDC3
    Interactions:

        Search GeneGlobe Interaction Network for CCDC3

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for CCDC3



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for CCDC3 gene (2 alternative transcripts): 
    NM_001282658.1  NM_031455.3  

    Unigene Cluster for CCDC3:

    Coiled-coil domain containing 3
    Hs.498720  [show with all ESTs]
    Unigene Representative Sequence: AK095792
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000378825(uc001ilq.1) ENST00000378839(uc009xjb.1 uc001ilr.2 uc009xjc.1 uc009xjd.1)

    miRNA
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    8 qRT-PCR Assays for microRNAs that regulate CCDC3:
    hsa-miR-623 hsa-miR-3173-3p hsa-miR-100* hsa-miR-3938 hsa-miR-3660 hsa-miR-589* hsa-miR-151-3p hsa-miR-298
    SwitchGear 3'UTR luciferase reporter plasmidCCDC3 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat CCDC3
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CCDC3
    Primer
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    Additional mRNA sequence: 

    AF190154.1 AK024578.1 AK095792.1 AK123393.1 AK124195.1 AK307203.1 AK307304.1 AL136562.1 
    BC051334.1 

    5 DOTS entries:

    DT.452185  DT.101979320  DT.100751472  DT.95157924  DT.121250123 

    Selected AceView cDNA sequences (see all 136):

    AI921755 AI924580 BE549983 T47013 AI690473 BM712203 AA045504 BM705580 
    AA058939 R67634 BF725141 AI804926 AI702223 CR618046 AW439377 BU726400 
    AW662224 AI582141 BF725142 AI369042 AI669775 BF594160 AI619787 AA709346 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    CCDC3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAAGCTACAC
    CCDC3 Expression
    About this image


    CCDC3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 6) fully expand
     
     Brain (Nervous System)    fully expand to see all 8 entries
             Thalamus
     
     Neural Tube (Nervous System)    fully expand to see all 5 entries
             Late Floor Plate Cells Mesencephalic Floor Plate
             Mesencephalic Floor Plate
     
     Bone (Muscoskeletal System)    fully expand to see all 2 entries
             Chondrocyte-like cells
     
     Cartilage (Muscoskeletal System)    fully expand to see all 2 entries
             Chondrocyte-like cells
     
     Lung (Respiratory System)
             Basal Cells Trachea
    CCDC3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CCDC3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.498720

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

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for CCDC3 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ccdc31 , 5 coiled-coil domain containing 31, 5 88.37(n)1
    91.76(a)1
      2 (3.25 cM)5
    741861  NM_028804.11  NP_083080.11 
     51377765 
    chicken
    (Gallus gallus)
    Aves CCDC31 coiled-coil domain containing 3 77.55(n)
    82.85(a)
      769832  XM_003640333.1  XP_003640381.1 
    lizard
    (Anolis carolinensis)
    Reptilia CCDC36
    coiled-coil domain containing 3
    76(a)
    1 ↔ 1
    GL343349.1(81987-160634)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.196362 Transcribed sequence with moderate similarity to protein more 77.44(n)    BX781788.1 
    zebrafish
    (Danio rerio)
    Actinopterygii ccdc31 coiled-coil domain containing 3 68.68(n)
    68.95(a)
      560952  NM_001025510.1  NP_001020681.1 


    ENSEMBL Gene Tree for CCDC3 (if available)
    TreeFam Gene Tree for CCDC3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for CCDC3 (see all 2768)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1123462551,2
    C--12847251(+) ATGTGA/CGTTGA 1 -- int10--------
    rs803019861,2
    C,F--12847350(+) CATCAA/GGGTCG 1 -- int11Minor allele frequency- G:0.06EA 120
    rs735840541,2
    C,F--12847541(+) TGCAGG/CTGTGT 1 -- int11Minor allele frequency- C:0.01WA 118
    rs1875197881,2
    --12847663(+) CCCCCA/CAGAGG 1 -- int10--------
    rs2005560201,2
    --12847846(+) ACATT-/ACCCTT 1 -- ut310--------
    rs32321,2
    C,F,A,H--12847876(+) GGGGGC/TGCAAA 1 -- ut31 ese324Minor allele frequency- N:0.00EA MN NA NS WA 3478
    rs1406789821,2
    C--12848022(+) TTCTG-/TCCAGT 1 -- ut310--------
    rs1158934381,2
    C,F--12848049(+) TCCCCC/TGTGGA 1 -- ut311Minor allele frequency- T:0.02WA 118
    rs1914038531,2
    --12848050(+) CCCCCG/TTGGAC 1 -- ut310--------
    rs22800761,2
    C,F,A,H--12848083(-) CTTACG/ATTGCT 1 -- ut31 ese325Minor allele frequency- A:0.20EA NA NS 4036

    HapMap Linkage Disequilibrium report for CCDC3 (12938625 - 13141652 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for CCDC3:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2733295CNV Deletion23290073
    esv1974400CNV Deletion18987734
    esv2733306CNV Deletion23290073
    nsv5831CNV Insertion18451855
    nsv894884CNV Gain21882294
    nsv521491CNV Gain19592680
    esv259462OTHER Complex20981092

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 612324    OMIM disorders: --


    Find genes that share disorders with CCDC3           About GenesLikeMe

    Genetic Association Database (GAD): CCDC3

    Export disorders for CCDC3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for CCDC3 gene, integrated from 10 sources (see all 13):
    (articles sorted by number of sources associating them with CCDC3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    2. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2 Wiemann S.... Poustka A. (Genome Res. 2001)
    3. Hundreds of variants clustered in genomic loci and biological pathways affect human height. (PubMed id 20881960)1 Lango Allen H....Hirschhorn J.N. (Nature 2010)
    4. Identification of a new secretory factor, CCDC3/Favine, in adipocytes and endothelial cells. (PubMed id 20043878)2 Kobayashi S.... Shimomura I. (Biochem. Biophys. Res. Commun. 2010)
    5. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (BMC Med. Genet. 2007)
    6. The LIFEdb database in 2006. (PubMed id 16381901)1 Mehrle A....Wiemann S. (Nucleic Acids Res. 2006)
    7. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    9. The DNA sequence and comparative analysis of human chromosome 10. (PubMed id 15164054)2 Deloukas P.... Rogers J. (Nature 2004)
    10. From ORFeome to biology: a functional genomics pipeline. (PubMed id 15489336)1 Wiemann S....Poustka A. (Genome Res. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 83643 HGNC: 23813 AceView: CCDC3 Ensembl:ENSG00000151468 euGenes: HUgn83643
    ECgene: CCDC3 H-InvDB: CCDC3

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for CCDC3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CCDC3 gene:
    Search GeneIP for patents involving CCDC3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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