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CCDC84 Gene

protein-coding   GIFtS: 40
GCID: GC11P118868

Coiled-Coil Domain Containing 84

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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): antisense

Quality score for the ORGUL clustered with this gene is 3

Aliases
Coiled-Coil Domain Containing 841 2
Coiled-Coil Domain-Containing Protein 842

External Ids:    HGNC: 304601   Entrez Gene: 3386572   Ensembl: ENSG000001861667   UniProtKB: Q86UT83   
ORGUL members:         

Export aliases for CCDC84 gene to outside databases

Previous GC identifers: GC11P118377 GC11P114808


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for CCDC84 Gene:
This gene encodes a protein thought to contain a coiled coil motif. No function has been determined for the
encoded protein. A pseudogene of this gene is located on chromosome 20. Alternate splicing results in multiple
transcript variants. (provided by RefSeq, Aug 2013)

GeneCards Summary for CCDC84 Gene:
CCDC84 (coiled-coil domain containing 84) 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_000011.9  NT_033899.9  NC_018922.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CCDC84 gene promoter:
         E2F-3a   E2F-4   E2F-5   RP58   AML1a   E2F-2   Roaz   HEN1   E2F-1   E2F   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCDC84 promoter sequence
   Search Chromatin IP Primers for CCDC84

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CCDC84


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

Entrez Gene cytogenetic band: 11q23.3   Ensembl cytogenetic band:  11q23.3   HGNC cytogenetic band: 11q23.3

CCDC84 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC84 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P118868:  view genomic region     (about GC identifiers)

Start:
118,868,852 bp from pter      End:
118,886,501 bp from pter
Size:
17,650 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., 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: CCD84_HUMAN, Q86UT8 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 84  
Size: 332 amino acids; 37974 Da

Explore the universe of human proteins at neXtProt for CCDC84: NX_Q86UT8

Explore proteomics data for CCDC84 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See CCDC84 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_940891.1  
    ENSEMBL proteins: 
     ENSP00000334767   ENSP00000436340   ENSP00000431889  

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    Search eBioscience for ELISAs for CCDC84 


    (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:
     IPR028015 CCDC84

    Graphical View of Domain Structure for InterPro Entry Q86UT8

    ProtoNet protein and cluster: Q86UT8


    Find genes that share domains with CCDC84           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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    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CCDC84
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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 COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2
    mitochondrion2
    extracellular1
    peroxisome1

    (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 CCDC84
    Interactions:

        Search GeneGlobe Interaction Network for CCDC84

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for CCDC84 (ENSP000003347674) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    WDR26ENSP000002950244STRING: ENSP00000295024
    PPP2R1BENSP000003113444STRING: ENSP00000311344
    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 CCDC84 (CCD84)



    (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 CCDC84 gene: 
    NM_198489.2  

    Unigene Cluster for CCDC84:

    Coiled-coil domain containing 84
    Hs.534613  [show with all ESTs]
    Unigene Representative Sequence: BC144208
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000334418(uc001pul.3 uc010ryk.2 uc010ryl.2) ENST00000524670
    ENST00000526463(uc010rym.2) ENST00000532132 ENST00000534656 ENST00000580556
    ENST00000528088 ENST00000583842 ENST00000527356 ENST00000533787
    miRNA
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CCDC84
    Primer
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    Additional mRNA sequence: 

    AB094093.1 BC126469.1 BC126471.1 BC144208.1 BC144209.1 BC144210.1 

    17 DOTS entries:

    DT.95272257  DT.87016238  DT.100795737  DT.91747087  DT.120718661  DT.91804642  DT.95232829  DT.100795734 
    DT.120718651  DT.301568  DT.100036000  DT.91747085  DT.100795736  DT.99940039  DT.92383658  DT.120718579 
    DT.91861985 

    Selected AceView cDNA sequences (see all 116):

    CB216913 BM729072 BQ007036 CD171823 BM709425 AA779404 BF109076 AI678463 
    BG149789 BX281470 AI270685 CB241703 CA438335 AI887619 NM_198489 BM972124 
    CB321979 BU733404 AB094093 BQ006160 AI696295 BE796421 AI559322 BM684305 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for CCDC84    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10
    SP1:                          -     -                                             
    SP2:                                                                              
    SP3:                                                                              
    SP4:                                                                              


    ECgene alternative splicing isoforms for CCDC84

    (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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    CCDC84 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGGCTAAAAG
    CCDC84 Expression
    About this image

    CCDC84 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CCDC84 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.534613
        Custom PCR Arrays for CCDC84
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC84

    (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 CCDC84 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ccdc841 , 5 coiled-coil domain containing 841, 5 85.14(n)1
    85.84(a)1
      9 (24.84 cM)5
    3820731  NM_201372.31  NP_958760.21 
     444101605 
    chicken
    (Gallus gallus)
    Aves CCDC841 coiled-coil domain containing 84 60.42(n)
    49.82(a)
      419787  XM_417924.4  XP_417924.4 
    lizard
    (Anolis carolinensis)
    Reptilia CCDC846
    coiled-coil domain containing 84
    54(a)
    1 ↔ 1
    GL344273.1(2127-12550)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.306842 Xenopus laevis transcribed sequence with weak similarity more 74(n)    48062170 
    zebrafish
    (Danio rerio)
    Actinopterygii ccdc841 coiled-coil domain containing 84 56.16(n)
    47.27(a)
      767736  NM_001076705.1  NP_001070173.1 


    ENSEMBL Gene Tree for CCDC84 (if available)
    TreeFam Gene Tree for CCDC84 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CCDC84 gene

    Find genes that share paralogs with CCDC84           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for CCDC84
    PGOHUM00000247446


    (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 CCDC84 (see all 410)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1913601341,2
    --118866949(+) AGATGC/TTGAGT 1 -- us2k10--------
    rs1430291631,2
    --118866978(+) AATTCC/TGATGC 1 -- us2k10--------
    rs1831755411,2
    --118867069(+) GTTGAA/GGCAGA 1 -- us2k10--------
    rs750489151,2
    C,F--118867116(+) ATGAGG/AGAAGC 1 -- us2k11Minor allele frequency- A:0.02NA 120
    rs749463211,2
    C,F--118867288(+) GATCCC/TGCATC 1 -- us2k11Minor allele frequency- T:0.09WA 118
    rs1482136271,2
    --118867364(+) TTTGAA/GACGGA 1 -- us2k10--------
    rs1412139851,2
    --118867510(+) GGCTAA/GTTTTT 1 -- us2k10--------
    rs1881068571,2
    --118867636(+) ACCACA/GACAGG 1 -- us2k10--------
    rs1930848081,2
    --118867652(+) ACCCCA/GAGTTT 1 -- us2k10--------
    rs49386171,2
    C,F,A,H--118867695(+) atgtgC/Tgttac 1 -- us2k114Minor allele frequency- T:0.09NS EA NA CSA WA 806

    HapMap Linkage Disequilibrium report for CCDC84 (118868852 - 118886501 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for CCDC84: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CCDC84
    DNA2.0 Custom Variant and Variant Library Synthesis for CCDC84

    (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 CCDC84 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with CCDC84)
        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. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    3. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)
    4. (PubMed id )2 

    (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: 338657 HGNC: 30460 AceView: DLNB14 Ensembl:ENSG00000186166 euGenes: HUgn338657
    ECgene: CCDC84 H-InvDB: CCDC84

    (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 CCDC84 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 CCDC84 gene:
    Search GeneIP for patents involving CCDC84

    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)
    About This Section

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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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