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

CCDC65 Gene

protein-coding   GIFtS: 41
GCID: GC12P049297

Coiled-Coil Domain Containing 65

  See related diseases
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 651 2
Testis Development Protein NYD-SP282 3
NYD-SP282
Coiled-Coil Domain-Containing Protein 652

External Ids:    HGNC: 299371   Entrez Gene: 854782   Ensembl: ENSG000001395377   OMIM: 6110885   UniProtKB: Q8IXS23   

Export aliases for CCDC65 gene to outside databases

Previous GC identifers: GC12P047585 GC12P046329


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

Entrez Gene summary for CCDC65 Gene:
CCDC65 is a sperm tail protein that is posttranslationally modified during sperm capacitation (Zheng et al., 2006
(PubMed 17089017)).(supplied by OMIM, Mar 2008)

GeneCards Summary for CCDC65 Gene: 
CCDC65 (coiled-coil domain containing 65) is a protein-coding gene. Diseases associated with CCDC65 include clear cell sarcoma, and sarcoma.




(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_000012.11  NT_029419.12  NC_018923.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CCDC65 gene promoter:
         c-Fos   PPAR-gamma1   AP-1   HSF2   ATF-2   HSF1 (long)   c-Jun   MIF-1   AP-4   PPAR-gamma2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCDC65 promoter sequence
   Search SABiosciences Chromatin IP Primers for CCDC65

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CCDC65


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

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

CCDC65 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC65 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P049297:  view genomic region     (about GC identifiers)

Start:
49,297,893 bp from pter      End:
49,325,623 bp from pter
Size:
27,731 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: CCD65_HUMAN, Q8IXS2 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 65  
Size: 484 amino acids; 57297 Da
Sequence caution: Sequence=BAC05324.1; Type=Erroneous initiation;
Secondary accessions: A6NJG5 B2RBE2 Q8N7G4 Q8NA91 Q96JA0
Alternative splicing: 2 isoforms:  Q8IXS2-1   Q8IXS2-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CCDC65: NX_Q8IXS2

Explore proteomics data for CCDC65 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8IXS2

  • CCDC65 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CCDC65 Protein Expression
    REFSEQ proteins: NP_149115.2  
    ENSEMBL proteins: 
     ENSP00000266984   ENSP00000446569   ENSP00000447157   ENSP00000312706  

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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: Q8IXS2


    (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 CCDC65:
     Increased S DNA content, incre 

    Animal Models:
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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 CCDC65

    (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 CCDC65 (CCD65)

    Search CenterWatch for drugs/clinical trials and news about CCDC65 / CCD65

    (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,
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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 CCDC65 gene: 
    NM_033124.4  

    Unigene Cluster for CCDC65:

    Coiled-coil domain containing 65
    Hs.512805  [show with all ESTs]
    Unigene Representative Sequence: NM_033124
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000266984 ENST00000552942 ENST00000547861 ENST00000320516(uc001rso.3)
    ENST00000552188
    miRNA
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    SwitchGear 3'UTR luciferase reporter plasmidCCDC65 3' UTR sequence
    Inhib. RNA
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CCDC65

    Additional mRNA sequence: 

    AF382188.1 AK093051.1 AK098529.1 AK302082.1 AK314623.1 BC039317.1 

    7 DOTS entries:

    DT.100774160  DT.97812076  DT.121151626  DT.95298694  DT.91993736  DT.91983112  DT.100774159 

    6 AceView cDNA sequences:

    BC039317 AK093051 AX747886 NM_033124 AF382188 AK098529 

    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

    CCDC65 expression in normal human tissues (normalized intensities)      CCDC65 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGTTTAAAA
    CCDC65 Expression
    About this image


    CCDC65 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/3 selected tissues (see all 3) fully expand
     
     Brain (Nervous System)    fully expand to see all 2 entries
             Choroid Plexus
             brain/hindbrain/4th ventricle   
     
     Pancreas (Endocrine System)
             Posterior foregut-like cells ( A scalable, suspension protocol for derivation of...
     
     Testis (Reproductive System)

    See CCDC65 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CCDC65

    SOURCE GeneReport for Unigene cluster: Hs.512805

    UniProtKB/Swiss-Prot: CCD65_HUMAN, Q8IXS2
    Tissue specificity: Highly expressed in adult testis, in spermatocytes and spermatids. Also observed in
    spermatogonia. Not detected in Leydig cells, nor in fetal testis (at protein level)

        SABiosciences Custom PCR Arrays for CCDC65
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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC65

    (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 animals.

    Orthologs for CCDC65 gene from 5/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ccdc651 , 5 coiled-coil domain containing 651, 5 81.65(n)1
    83.01(a)1
      15 (54.65 cM)5
    1058331  NM_153518.11  NP_705738.11 
     987082275 
    chicken
    (Gallus gallus)
    Aves LOC1008573461 coiled-coil domain-containing protein 65-like 56.21(n)
    46.19(a)
      100857346  XM_003643485.1  XP_003643533.1 
    lizard
    (Anolis carolinensis)
    Reptilia CCDC656
    Uncharacterized protein
    61(a)
    1 ↔ 1
    2(94181178-94192131)
    zebrafish
    (Danio rerio)
    Actinopterygii ccdc651 coiled-coil domain containing 65 52.73(n)
    42.92(a)
      368824  NM_001002603.1  NP_001002603.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG302591 CG30259 43.25(n)
    27.62(a)
      37606  NM_137864.2  NP_611708.2 


    ENSEMBL Gene Tree for CCDC65 (if available)
    TreeFam Gene Tree for CCDC65 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CCDC65 gene

    CCDC65 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for CCDC65
    PGOHUM00000245543


    (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

    10/453 SNPs in CCDC65 are shown (see all 453)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1122947891,2
    C--46334217(+) CCAGGATTAT   
      TATT
    /-
    ATTAT
    1 -- int11Minor allele frequency- -:0.50CSA 2
    rs74890361,2
    C,F,A--49295949(+) aaaaaG/Agagag 1 -- us2k1 trp32Minor allele frequency- A:0.40NA EA 240
    rs1812487081,2
    --49295982(+) AGAGAC/GAAAGA 1 -- us2k10--------
    rs1861305531,2
    --49296026(+) TAATCG/TACTTT 1 -- us2k10--------
    rs44336141,2
    C,F,H--49296056(-) tatccG/Agaaaa 1 -- us2k110Minor allele frequency- A:0.31EA NS NA CSA WA 660
    rs1493219161,2
    --49296128(+) TAGGGG/TTTTTT 1 -- us2k10--------
    rs1917221681,2
    --49296143(+) CCGAAC/TATGGT 1 -- us2k10--------
    rs1821813541,2
    --49296178(+) TTTGGA/GAGGCC 1 -- us2k10--------
    rs1445671351,2
    C--49296398(+) TGACAA/GAGTGA 1 -- us2k10--------
    rs1876107241,2
    C--49296522(+) TTGACC/TTCTGG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for CCDC65 (49297893 - 49325623 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for CCDC65:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv832404CNV Gain17160897

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    (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
    OMIM gene information: 611088    OMIM disorders: --

    2 diseases for CCDC65:    About MalaCards
    clear cell sarcoma    sarcoma

    1 disease from the University of Copenhagen DISEASES database for CCDC65:
    Clear cell sarcoma

    CCDC65 for disorders           About GeneDecksing


    Export disorders for CCDC65 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 CCDC65 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with CCDC65)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and characterization of a novel sperm tail protein, NYD- SP28. (PubMed id 17089017)1, 2, 3 Zheng Y.... Sha J.-H. (2006)
    2. Building blocks of the nexin-dynein regulatory complex in Chlamydomonas flagella. (PubMed id 21700706)1, 3 Lin J....Nicastro D. (2011)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    5. The finished DNA sequence of human chromosome 12. (PubMed id 16541075)2 Scherer S.E.... Gibbs R.A. (2006)
    6. 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)
    7. 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. (2002)
    8. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (1996)

    (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: 85478 HGNC: 29937 AceView: NYD-SP28 Ensembl:ENSG00000139537 euGenes: HUgn85478
    ECgene: CCDC65 H-InvDB: CCDC65

    (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 CCDC65 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 CCDC65 gene:
    Search GeneIP for patents involving CCDC65

    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
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    (GIFtS: 73)
    transforming growth factor, beta 1
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