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CCDC93 Gene

protein-coding   GIFtS: 48
GCID: GC02M118673

Coiled-Coil Domain Containing 93

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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 931 2
Coiled-Coil Domain-Containing Protein 932

External Ids:    HGNC: 256111   Entrez Gene: 545202   Ensembl: ENSG000001256337   UniProtKB: Q567U63   

Export aliases for CCDC93 gene to outside databases

Previous GC identifers: GC02M118389 GC02M111000


(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 CCDC93 Gene:
CCDC93 (coiled-coil domain containing 93) is a protein-coding gene.

Gene Wiki entry for CCDC93 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_000002.11  NT_005403.18  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CCDC93 gene promoter:
         GR   TBP   ATF-2   FOXO3   LUN-1   FOXO3b   POU2F1a   FOXO3a   GR-alpha   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCDC93 promoter sequence
   Search Chromatin IP Primers for CCDC93

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CCDC93


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

Entrez Gene cytogenetic band: 2q14.1   Ensembl cytogenetic band:  2q14.1   HGNC cytogenetic band: 2q14.1

CCDC93 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC93 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M118673:  view genomic region     (about GC identifiers)

Start:
118,673,054 bp from pter      End:
118,771,739 bp from pter
Size:
98,686 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: CCD93_HUMAN, Q567U6 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 93  
Size: 631 amino acids; 73198 Da
Sequence caution: Sequence=BAB15188.1; Type=Erroneous initiation; Sequence=BAE06075.1; Type=Erroneous initiation;
Secondary accessions: A8K3V7 Q4LE78 Q53TJ2 Q8TBX5 Q9H6R5 Q9NV15

Explore the universe of human proteins at neXtProt for CCDC93: NX_Q567U6

Explore proteomics data for CCDC93 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys601
  • Modification sites at PhosphoSitePlus

  • See CCDC93 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_061917.3  
    ENSEMBL proteins: 
     ENSP00000365477   ENSP00000324135   ENSP00000392989  

    CCDC93 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for CCDC93

     
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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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    1 InterPro protein domain:
     IPR019159 DUF2037

    Graphical View of Domain Structure for InterPro Entry Q567U6

    ProtoNet protein and cluster: Q567U6

    UniProtKB/Swiss-Prot: CCD93_HUMAN, Q567U6
    Similarity: Belongs to the CCDC93 family


    Find genes that share domains with CCDC93           About GenesLikeMe


    (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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    Phenotypes:
         3 GenomeRNAi human phenotypes for CCDC93:
     G0/1 arrest  Increased G1 DNA content  Increased gamma-H2AX phosphory 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CCDC93
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CCDC93
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    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate CCDC93 (see all 25):
    hsa-miR-1178 hsa-miR-148b* hsa-let-7d hsa-miR-1260b hsa-let-7c hsa-miR-374c hsa-miR-548m hsa-let-7g
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for CCDC93
    Predesigned siRNA for gene silencing in human, mouse, rat CCDC93

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    Clone
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    OriGene ORF clones in mouse, rat for CCDC93
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: CCDC93 (NM_019044)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CCDC93
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CCDC93

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC93


    (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
    mitochondrion1

    (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 CCDC93
    Interactions:

        Search GeneGlobe Interaction Network for CCDC93

    STRING Interaction Network Preview (showing 5 interactants - click image to see more details)

    Selected Interacting proteins for CCDC93 (Q567U63 ENSP000003654774) via UniProtKB, MINT, STRING, and/or I2D (see all 7)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    EXOC1Q9NV703, ENSP000003265144I2D: score=1 STRING: ENSP00000326514
    TRAF3IP1Q8TDR03, ENSP000003624244I2D: score=2 STRING: ENSP00000362424
    EXOC7Q9UPT53I2D: score=2 
    SLC2A4P146723I2D: score=1 
    CCDC22ENSP000003654014STRING: ENSP00000365401
    About this table

    (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 CCDC93 (CCD93)



    (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 CCDC93 gene: 
    NM_019044.4  

    Unigene Cluster for CCDC93:

    Coiled-coil domain containing 93
    Hs.107845  [show with all ESTs]
    Unigene Representative Sequence: NM_019044
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000376300(uc002tlj.3 uc010fld.2) ENST00000319432 ENST00000437999
    ENST00000474546 ENST00000470650 ENST00000466171 ENST00000488908 ENST00000460781
    ENST00000474006
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate CCDC93 (see all 25):
    hsa-miR-1178 hsa-miR-148b* hsa-let-7d hsa-miR-1260b hsa-let-7c hsa-miR-374c hsa-miR-548m hsa-let-7g
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for CCDC93
    Predesigned siRNA for gene silencing in human, mouse, rat CCDC93
    Clone
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    OriGene clones in human, mouse for CCDC93 (see all 7)
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    GenScript: all cDNA clones in your preferred vector: CCDC93 (NM_019044)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CCDC93
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CCDC93
    Primer
    Products:
        
    OriGene qSTAR qPCR primer pairs in human, mouse for CCDC93
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CCDC93
      QuantiTect SYBR Green Assays in human, mouse, rat CCDC93
      QuantiFast Probe-based Assays in human, mouse, rat CCDC93

    Additional mRNA sequence: 

    AB209993.1 AF070582.1 AK001858.1 AK025611.1 AK057926.1 AK124683.1 AK290722.1 AK309040.1 
    AL050001.1 AY726577.1 BC005078.1 BC012052.1 BC028609.1 BC080559.1 BC093018.1 

    8 DOTS entries:

    DT.308353  DT.91718236  DT.433878  DT.40119324  DT.104336  DT.91690521  DT.100857480  DT.213560 

    Selected AceView cDNA sequences (see all 232):

    BM833479 BM972138 CA306714 AA749394 CD515305 BQ446970 AA865961 BQ651270 
    BU621185 AA703071 AA720610 AA621959 AI433397 CR590543 BQ641752 AI818957 
    AK001858 CB529798 BX472657 BM992889 BM831328 AI580313 BU619050 BU685956 

    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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    CCDC93 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAATGGTTCT
    CCDC93 Expression
    About this image


    CCDC93 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Neural Tube (Nervous System)
             Diencephalon
    CCDC93 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CCDC93 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.107845
        Custom PCR Arrays for CCDC93
    Primer
    Products:
    OriGene qSTAR qPCR primer pairs in human, mouse for CCDC93
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CCDC93
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    QuantiFast Probe-based Assays in human, mouse, rat CCDC93
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC93

    (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 eukaryotes.

    Orthologs for CCDC93 gene from Selected species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ccdc931 , 5 coiled-coil domain containing 931, 5 86.8(n)1
    92.05(a)1
      1 (52.97 cM)5
    708291  NM_001025156.21  NP_001020327.11 
     1214310495 
    chicken
    (Gallus gallus)
    Aves CCDC931 coiled-coil domain containing 93 75.27(n)
    80.84(a)
      424277  NM_001031262.1  NP_001026433.1 
    lizard
    (Anolis carolinensis)
    Reptilia CCDC936
    coiled-coil domain containing 93
    78(a)
    1 ↔ 1
    1(82191136-82238841)
    African clawed frog
    (Xenopus laevis)
    Amphibia CD361732.12   -- 74.83(n)    CD361732.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BQ078420.12   -- 79.41(n)    BQ078420.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta fidipidine1 fidipidine 51.27(n)
    42.21(a)
      36808  NM_079036.4  NP_523760.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT4G325601 AT4G32560 46.13(n)
    32.1(a)
      829391  NM_001036694.2  NP_001031771.1 


    ENSEMBL Gene Tree for CCDC93 (if available)
    TreeFam Gene Tree for CCDC93 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CCDC93 gene

    Find genes that share paralogs with CCDC93           About GenesLikeMe


    2 Pseudogenes.org Pseudogenes for CCDC93
    PGOHUM00000245134 PGOHUM00000241132


    (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 CCDC93 (see all 2140)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0354994
    A colorectal cancer sample4--see VAR_0354992 H R mis40--------
    rs723126141,2
    C--111068361(+) ATATA-/AACTGCTCA
    AAAT
    /ATATAT
    TATAT
    2 -- int1 cds10--------
    rs1167187141,2
    --118672592(+) CCCCTC/GACTGG 1 -- int10--------
    rs1391938431,2
    C--118672633(+) ACACAC/TGGCCA 1 -- int10--------
    rs728343731,2
    C,F--118672643(+) ACCTCG/AGAGCT 1 -- int11Minor allele frequency- A:0.09NA 120
    rs21135911,2
    C,H--118672719(+) GGTTTC/TTACAC 1 -- int16Minor allele frequency- T:0.00NS EA NA 598
    rs1431031981,2
    C--118672722(+) TTCTAC/TACAAG 1 -- int10--------
    rs762522711,2
    C--118672786(+) GGTATA/GCCTAT 1 -- int10--------
    rs1437841961,2
    --118672811(+) AAGTCA/GGAGGA 1 -- int10--------
    rs1481349351,2
    C--118672868(+) AGCCCA/GTCTGT 1 -- int10--------

    HapMap Linkage Disequilibrium report for CCDC93 (118673054 - 118771739 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for CCDC93:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2177498CNV Deletion18987734
    nsv515493CNV Loss19592680

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CCDC93
    DNA2.0 Custom Variant and Variant Library Synthesis for CCDC93

    (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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      --

    (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 CCDC93 gene, integrated from 10 sources (see all 21):
    (articles sorted by number of sources associating them with CCDC93)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)1, 2 Hillier L.W.... Wilson R.K. (Nature 2005)
    2. 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)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    5. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    6. The proteomic analysis of endogenous FAT10 substrates identifies p62/SQSTM1 as a substrate of FAT10ylation. (PubMed id 22797925)1 Aichem A....Groettrup M. (J. Cell. Sci. 2012)
    7. Recruitment of the endosomal WASH complex is mediated by the extended 'tail' of Fam21 binding to the retromer protein Vps35. (PubMed id 22070227)1 Harbour M.E....Seaman M.N. (Biochem. J. 2012)
    8. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    9. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    10. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)

    (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: 54520 HGNC: 25611 AceView: FLJ10996 Ensembl:ENSG00000125633 euGenes: HUgn54520
    ECgene: CCDC93 H-InvDB: CCDC93

    (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 CCDC93 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 CCDC93 gene:
    Search GeneIP for patents involving CCDC93

    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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