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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CCDC54 Gene

protein-coding   GIFtS: 40
GCID: GC03P107096

Coiled-Coil Domain Containing 54

  Search for CCDC54
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Coiled-Coil Domain Containing 541 2     SP172
Sperm Protein 171 2     Coiled-Coil Domain-Containing Protein 542
Testis Development Protein NYD-SP172 3     Testes Development-Related NYD-SP172
NYD-SP172     

External Ids:    HGNC: 307031   Entrez Gene: 846922   Ensembl: ENSG000001384837   UniProtKB: Q8NEL03   

Export aliases for CCDC54 gene to outside databases

Previous GC identifers: GC03P108579 GC03P104470


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for CCDC54 Gene: 
CCDC54 (coiled-coil domain containing 54) 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000003.11  NC_018914.2  NT_005612.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CCDC54 gene promoter:
         TBP   CREB   HOXA9   HOXA9B   POU2F1   POU2F1a   Meis-1a   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCDC54 promoter sequence
   Search SABiosciences Chromatin IP Primers for CCDC54

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CCDC54


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

Entrez Gene cytogenetic band: 3q13.12   Ensembl cytogenetic band:  3q13.12   HGNC cytogenetic band: 3q13.12

CCDC54 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC54 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P107096:  view genomic region     (about GC identifiers)

Start:
107,096,188 bp from pter      End:
107,097,481 bp from pter
Size:
1,294 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: CCD54_HUMAN, Q8NEL0 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 54  
Size: 328 amino acids; 37886 Da
Secondary accessions: Q96A43

Explore the universe of human proteins at neXtProt for CCDC54: NX_Q8NEL0

Explore proteomics data for CCDC54 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8NEL0

  • CCDC54 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CCDC54 Protein Expression
    REFSEQ proteins: NP_115989.1  
    ENSEMBL proteins: 
     ENSP00000261058  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    ProtoNet protein and cluster: Q8NEL0


    (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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Phenotypes:
         1 GenomeRNAi human phenotype for CCDC54:
     Decreased Wnt reporter activit 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for CCDC54 
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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CCDC54

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for CCDC54 (CCD54)

    Search CenterWatch for drugs/clinical trials and news about CCDC54 / CCD54

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for CCDC54 gene: 
    NM_032600.2  

    Unigene Cluster for CCDC54:

    Coiled-coil domain containing 54
    Hs.164799  [show with all ESTs]
    Unigene Representative Sequence: NM_032600
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000261058(uc003dwi.1)
    miRNA
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CCDC54

    Additional mRNA sequence: 

    AF367469.1 AK058091.1 BC030780.2 

    1 DOTS entry:

    DT.40127832 

    24/29 AceView cDNA sequences (see all 29):

    BC030780 BP368864 BP369009 BP369313 AK058091 NM_032600 BP369705 BI462505 
    BP369615 BP369282 BI561115 AF367469 BP371393 BQ429566 BU561114 BF057148 
    BU854252 AI377758 BP369336 BP369765 BP369800 AI190903 BG720653 BG718966 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    CCDC54 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGGAAAATG
    CCDC54 Expression
    About this image


    See CCDC54 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CCDC54

    SOURCE GeneReport for Unigene cluster: Hs.164799
        SABiosciences Custom PCR Arrays for CCDC54
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC54

    (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)
    About This Section

    This gene was present in the common ancestor of human and mouse.

    Orthologs for CCDC54 gene from 1/7 species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ccdc541 , 5 coiled-coil domain containing 541, 5 76.52(n)1
    64.63(a)1
      16 (31.50 cM)5
    693391  NM_027046.31  NP_081322.11 
     505898595 


    ENSEMBL Gene Tree for CCDC54 (if available)
    TreeFam Gene Tree for CCDC54 (if available)

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

    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/121 SNPs in CCDC54 are shown (see all 121)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs48556041,2
    H--107094429(+) CAAATA/GCTGTT 1 -- us2k14Minor allele frequency- G:0.00NS EA 416
    rs1392823231,2
    --107094439(+) TATGTA/GGAAAA 1 -- us2k10--------
    rs1853104181,2
    --107094517(+) TGTGGA/GATGCT 1 -- us2k10--------
    rs7095631,2
    C,F,A,H--107094616(+) gcttaT/Catttg 1 -- us2k123Minor allele frequency- C:0.41NS EA NA WA CSA 2349
    rs1905161751,2
    --107094655(+) TGGTGG/TGTAAA 1 -- us2k10--------
    rs1435041741,2
    --107094656(+) GGTGGA/GTAAAA 1 -- us2k10--------
    rs1501044821,2
    --107094813(+) TCAACC/GCTTCA 1 -- us2k10--------
    rs1119340371,2
    F--107094913(+) AACGTC/ACATAA 1 -- us2k11Minor allele frequency- A:0.50CSA 2
    rs1142983131,2
    F--107095003(+) CATAGT/GTGGGC 1 -- us2k11Minor allele frequency- G:0.02NA 120
    rs1817099391,2
    --107095021(+) AAGCAC/TTTTTG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for CCDC54 (107096188 - 107097481 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for CCDC54:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv829653CNV Gain17160897

    SABiosciences Cancer Mutation PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for CCDC54

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    CCDC54 for disorders           About MalaCards

    CCDC54 for disorders           About GeneDecksing

    Genetic Association Database (GAD): CCDC54

    Export disorders for CCDC54 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)
    About This Section

    PubMed articles for CCDC54 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with CCDC54)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Association of sperm protein 17 with A-kinase anchoring protein 3 in flagella. (PubMed id 15257753)1, 3 Lea I.A....O'Rand M.G. (2004)
    2. 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. (2002)
    3. Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. (PubMed id 19690332)2 Mayya V.... Han D.K. (2009)
    4. Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study. (PubMed id 17903297)4 Seshadri S....Wolf P.A. (2007)
    5. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (2007)
    6. Cancer immunotherapy targeting Sp17: when should the laboratory findings be translated to the clinics? (PubMed id 16138340)1 Dadabayev A.R....Lim S.H. (2005)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
    9. Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1. (PubMed id )2 Aoki H.... Hino O. (2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 84692 HGNC: 30703 AceView: NYD-SP17 Ensembl:ENSG00000138483 euGenes: HUgn84692
    ECgene: CCDC54 H-InvDB: CCDC54

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for CCDC54 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for CCDC54 gene:
    Search GeneIP for patents involving CCDC54

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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    About This Section

     
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     Proteins for CCDC54
     Antibodies for CCDC54
     ELISAs for CCDC54
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     Search LifeMap BioReagents cell lines for CCDC54
     Gene Synthesis
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     Protein Production and Purification
     Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC54
     Browse SwitchGear 3'UTR luciferase reporter plasmids for CCDC54
     SwitchGear Promoter luciferase reporter plasmids for CCDC54
     Search ThermoFisher Antibodies for CCDC54
     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CCDC54
     inGenious Targeting Laboratory - Custom generated mouse model solutions for CCDC54
     inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for CCDC54
    Customized:
     lentivirus for stable overexpression of CCDC54
     lentivirus expression plasmids for stable overexpression of CCDC54
     adenovirus for overexpression of CCDC54
     LSBio Antibodies in human, mouse, rat for CCDC54
    Customized transgenic rodents for:
     Humanization
     Biomarker expression
     Off-target effect monitoring
     Translational medicine
     Tissue-specific gene expresssion
     Time-controlled gene expresssion
           
    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
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