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CCDC66 Gene

protein-coding   GIFtS: 45
GCID: GC03P056567

Coiled-Coil Domain Containing 66

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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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Coiled-Coil Domain Containing 661 2
Coiled-Coil Domain-Containing Protein 662

External Ids:    HGNC: 277091   Entrez Gene: 2853312   Ensembl: ENSG000001803767   UniProtKB: A2RUB63   
ORGUL members:         

Export aliases for CCDC66 gene to outside databases


(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 CCDC66 Gene:
CCDC66 (coiled-coil domain containing 66) is a protein-coding 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_000003.11  NT_022517.19  NC_018914.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CCDC66 gene promoter:
         Nkx3-1 v4   Pbx1a   FOXJ2 (long isoform)   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   FOXJ2   POU3F2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCDC66 promoter sequence
   Search Chromatin IP Primers for CCDC66

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CCDC66


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

Entrez Gene cytogenetic band: 3p14.3   Ensembl cytogenetic band:  3p14.3   HGNC cytogenetic band: 3p14.3

CCDC66 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC66 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P056567:  view genomic region     (about GC identifiers)

Start:
56,591,184 bp from pter      End:
56,655,864 bp from pter
Size:
64,681 bases      Orientation:
plus 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: CCD66_HUMAN, A2RUB6 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 66  
Size: 948 amino acids; 109411 Da
Sequence caution: Sequence=AAH47509.1; Type=Erroneous initiation; Sequence=AAI32828.2; Type=Erroneous initiation;
Sequence=BAC04607.1; Type=Frameshift; Positions=214;
Secondary accessions: B3KWL8 Q4VC34 Q8N949
Alternative splicing: 4 isoforms:  A2RUB6-1   A2RUB6-2   A2RUB6-3   A2RUB6-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CCDC66: NX_A2RUB6

Explore proteomics data for CCDC66 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See CCDC66 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001012524.4  NP_001135419.1  

    ENSEMBL proteins: 
     ENSP00000401451   ENSP00000390652   ENSP00000378167   ENSP00000326050   ENSP00000394704  
     ENSP00000420192   ENSP00000410510   ENSP00000343840   ENSP00000404320   ENSP00000444919  

    CCDC66 Human Recombinant Protein Products:

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    Novus Biologicals CCDC66 Lysate
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    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for CCDC66

     
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    antibodies-online peptides for CCDC66

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    antibodies-online antibodies for CCDC66 (11 products) 

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    Cloud-Clone Corp. ELISAs for CCDC66
    Cloud-Clone Corp. CLIAs for CCDC66
    Search eBioscience for ELISAs for CCDC66 
    antibodies-online kits for CCDC66 (16 products) 


    (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: A2RUB6


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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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    Phenotypes:
         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Ccdc66):
     nervous system  vision/eye 

    Find genes that share phenotypes with CCDC66           About GenesLikeMe

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for CCDC66

    miRNA
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    Predesigned siRNA for gene silencing in human, mouse, rat CCDC66

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    GenScript: all cDNA clones in your preferred vector (see all 2): CCDC66 (NM_001012506)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CCDC66
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CCDC66

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC66


    (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 COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2
    cytoskeleton1

    (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 CCDC66
    Interactions:

        Search GeneGlobe Interaction Network for CCDC66

    1 Interacting protein for CCDC66 (A2RUB62) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    --Q9WMX22MINT-7048087
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0046548retinal rod cell development IEA--
    GO:0060060post-embryonic retina morphogenesis in camera-type eye IEA--

    Find genes that share ontologies with CCDC66           About GenesLikeMe



    (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 CCDC66 (CCD66)



    (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 CCDC66 gene (2 alternative transcripts): 
    NM_001012506.4  NM_001141947.1  

    Unigene Cluster for CCDC66:

    Coiled-coil domain containing 66
    Hs.476399  [show with all ESTs]
    Unigene Representative Sequence: AL833326
    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 24):
    ENST00000422222 ENST00000439445 ENST00000460838 ENST00000394672(uc003dhz.3 uc003dhy.3 uc003dhu.3)
    ENST00000326595 ENST00000459746 ENST00000472582 ENST00000434467(uc003dhv.2 uc003dhw.2)
    ENST00000471681(uc003dhx.3) ENST00000422788 ENST00000341455 ENST00000442522
    ENST00000469966 ENST00000484623 ENST00000487739 ENST00000473322 ENST00000482673
    ENST00000494672
    miRNA
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    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat CCDC66
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    GenScript: all cDNA clones in your preferred vector (see all 2): CCDC66 (NM_001012506)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CCDC66
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for CCDC66
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CCDC66
      QuantiTect SYBR Green Assays in human, mouse, rat CCDC66
      QuantiFast Probe-based Assays in human, mouse, rat CCDC66

    Additional mRNA sequence: 

    AK095688.1 AL832692.1 AL833326.1 BC047509.1 BC132827.1 HQ234308.1 HQ234309.1 NR_024460.1 

    Selected DOTS entries (see all 28):

    DT.412714  DT.91651676  DT.75157125  DT.101981057  DT.91651675  DT.97791476  DT.102834204  DT.120846057 
    DT.120846058  DT.120846123  DT.91690391  DT.95313922  DT.99942715  DT.120846075  DT.92457877  DT.100036213 
    DT.100783704  DT.102834203  DT.120846143  DT.120846220  DT.120846226  DT.91971157  DT.120846049  DT.220846 

    Selected AceView cDNA sequences (see all 116):

    AI889889 BM679742 AA887479 AA936319 BU619724 AW080083 BM768393 BF056073 
    AI217101 AI208381 CD370868 AI352142 AA045176 CN480548 BM755589 AI654269 
    AW003305 BQ432590 CF994722 AL599229 CD517287 AI648495 BG564345 BU674751 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for CCDC66 (see all 9)    About this scheme

    ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b · 7c · 7d ^ 8 ^ 9 ^ 10 ^ 11 ^ 12
    SP1:                                      -                 -     -                                                                           
    SP2:                                      -                       -           -     -                                                         
    SP3:                                      -                 -     -           -     -                                                         
    SP4:                                                  -     -     -           -     -                                                         
    SP5:                                                                                                                                          


    ECgene alternative splicing isoforms for CCDC66

    (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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    CCDC66 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTGAAAAATA
    CCDC66 Expression
    About this image

    CCDC66 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CCDC66 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.476399
        Custom PCR Arrays for CCDC66
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC66

    (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 CCDC66 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ccdc661 , 5 coiled-coil domain containing 661, 5 79.48(n)1
    70.14(a)1
      14 (16.51 cM)5
    3202341  NM_177111.31  NP_796085.31 
     274824125 
    chicken
    (Gallus gallus)
    Aves CCDC661 coiled-coil domain containing 66 64.91(n)
    54.13(a)
      415997  XM_414339.4  XP_414339.4 
    lizard
    (Anolis carolinensis)
    Reptilia CCDC666
    coiled-coil domain containing 66
    47(a)
    1 ↔ 1
    2(162584943-162647277)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia ccdc661 coiled-coil domain-containing protein 66 52.62(n)
    47.46(a)
      733901  XM_004914177.1  XP_004914234.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC7966281 coiled-coil domain-containing protein 66-like 51.93(n)
    40.22(a)
      796628  XM_001336957.5  XP_001336993.4 


    ENSEMBL Gene Tree for CCDC66 (if available)
    TreeFam Gene Tree for CCDC66 (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 CCDC66 (see all 1488)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1395259441,2
    C--56589192(+) GGCTCC/TACAGG 3 -- us2k10--------
    rs1920286121,2
    --56589227(+) GTCTCA/GCCATG 3 -- us2k10--------
    rs1499010341,2
    --56589249(+) GGTCTC/TGAACT 3 -- us2k10--------
    rs1848475121,2
    --56589250(+) GTCTCA/GAACTC 3 -- us2k10--------
    rs1893214231,2
    --56589297(+) AGTGCC/TGCAAT 3 -- us2k10--------
    rs750963281,2
    --56589354(+) ATATTA/GCTTAT 3 -- us2k10--------
    rs1923235981,2
    --56589413(+) AATTAA/CGCAGA 3 -- us2k10--------
    rs1127075691,2
    C,F--56589454(+) GCTCAC/TGCCTA 3 -- us2k11Minor allele frequency- T:0.50CSA 2
    rs1430503981,2
    --56589490(+) GGTGGA/GAGGAC 3 -- us2k10--------
    rs1843920551,2
    --56589533(+) GCAACA/GTAAAC 3 -- us2k10--------

    HapMap Linkage Disequilibrium report for CCDC66 (56591184 - 56655864 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for CCDC66 (see all 19):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2621307CNV Deletion19546169
    esv2671315CNV Deletion23128226
    esv2725303CNV Deletion23290073
    esv2659644CNV Deletion23128226
    esv2555353CNV Deletion19546169
    esv1141708CNV Deletion17803354
    esv2725304CNV Deletion23290073
    esv1966969CNV Deletion18987734
    esv2678954CNV Deletion23128226
    nsv435762CNV Deletion17901297

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CCDC66
    DNA2.0 Custom Variant and Variant Library Synthesis for CCDC66

    (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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    1 disease from the University of Copenhagen DISEASES database for CCDC66:
    Night blindness

    Find genes that share disorders with CCDC66           About GenesLikeMe

    Genetic Association Database (GAD): CCDC66
    Human Genome Epidemiology (HuGE) Navigator: CCDC66 (1 document)

    Export disorders for CCDC66 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 CCDC66 gene, integrated from 10 sources (see all 13):
    (articles sorted by number of sources associating them with CCDC66)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2, 3 Ota T.... Sugano S. (Nat. Genet. 2004)
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    3. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    4. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
    5. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    6. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (Proc. Natl. Acad. Sci. U.S.A. 2008)
    7. Genome-wide association with bone mass and geometry in the Framingham Heart Study. (PubMed id 17903296)4 Kiel D.P....Karasik D. (BMC Med. Genet. 2007)
    8. Large-scale identification of human genes implicated in epidermal barrier function. (PubMed id 17562024)1 Toulza E.... Guerrin M. (Genome Biol. 2007)
    9. The DNA sequence, annotation and analysis of human chromosome 3. (PubMed id 16641997)2 Muzny D.M....Gibbs R.A. (Nature 2006)
    10. 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)

    (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: 285331 HGNC: 27709 AceView: LOC285331 Ensembl:ENSG00000180376 euGenes: HUgn285331
    ECgene: CCDC66 H-InvDB: CCDC66

    (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 CCDC66 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 CCDC66 gene:
    Search GeneIP for patents involving CCDC66

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



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