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CCDC13 Gene

protein-coding   GIFtS: 43
GCID: GC03M042735

Coiled-Coil Domain Containing 13

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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 131 2
Coiled-Coil Domain-Containing Protein 132
CCDC1375

External Ids:    HGNC: 263581   Entrez Gene: 1522062   Ensembl: ENSG000002446077   OMIM: 6142715   UniProtKB: Q8IYE13   
ORGUL members:         

Export aliases for CCDC13 gene to outside databases

Previous GC identifer: GC03M042725


(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 CCDC13 Gene:
CCDC13 (coiled-coil domain containing 13) 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 CCDC13 gene promoter:
         GR   Sox5   RFX1   GR-beta   FOXD3   Evi-1   SRY   HOXA5   GR-alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCDC13 promoter sequence
   Search Chromatin IP Primers for CCDC13

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CCDC13


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

Entrez Gene cytogenetic band: 3p22.1   Ensembl cytogenetic band:  3p22.1   HGNC cytogenetic band: 3p22.1

CCDC13 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC13 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M042735:  view genomic region     (about GC identifiers)

Start:
42,734,155 bp from pter      End:
42,814,745 bp from pter
Size:
80,591 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., 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, LSBio, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: CCD13_HUMAN, Q8IYE1 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 13  
Size: 715 amino acids; 80884 Da

Explore the universe of human proteins at neXtProt for CCDC13: NX_Q8IYE1

Explore proteomics data for CCDC13 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See CCDC13 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_653320.3  
    ENSEMBL proteins: 
     ENSP00000309836  

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    antibodies-online antibodies for CCDC13 (10 products) 

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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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    ProtoNet protein and cluster: Q8IYE1


    (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 CCDC13
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for CCDC13

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    hsa-mir-877-3p (MIRT037097), hsa-mir-155-5p (MIRT020508), hsa-mir-615-3p (MIRT040105)

    Block miRNA regulation of human, mouse, rat CCDC13 using miScript Target Protectors
    1 qRT-PCR Assays for microRNA that regulate CCDC13:
    hsa-miR-1289
    SwitchGear 3'UTR luciferase reporter plasmidCCDC13 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat CCDC13

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC13


    (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

    (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 CCDC13
    Interactions:

        Search GeneGlobe Interaction Network for CCDC13

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for CCDC13 (ENSP000003098364) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MUC12ENSP000003687554STRING: ENSP00000368755
    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 CCDC13 (CCD13)



    (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 CCDC13 gene: 
    NM_144719.3  

    Unigene Cluster for CCDC13:

    Coiled-coil domain containing 13
    Hs.604182  [show with all ESTs]
    Unigene Representative Sequence: NM_144719
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000479631 ENST00000496027 ENST00000310232(uc003cly.4) ENST00000466031
    ENST00000472921 ENST00000482100 ENST00000479576 ENST00000492806(uc003clz.2)
    ENST00000435327(uc011azq.1)
    miRNA
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    1 qRT-PCR Assays for microRNA that regulate CCDC13:
    hsa-miR-1289
    SwitchGear 3'UTR luciferase reporter plasmidCCDC13 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat CCDC13
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CCDC13
    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse / rat CCDC13
      QuantiTect SYBR Green Assays in human, mouse, rat CCDC13
      QuantiFast Probe-based Assays in human, mouse, rat CCDC13

    Additional mRNA sequence: 

    AK058196.1 AK302859.1 BC036050.1 

    7 DOTS entries:

    DT.100016115  DT.99941739  DT.40221861  DT.75141946  DT.110182  DT.99930936  DT.99932363 

    Selected AceView cDNA sequences (see all 115):

    BQ636656 BM671928 BX280806 BM710469 AA485602 AI866785 BM693454 F16581 
    CF552510 BU728280 BF724275 BM696113 BM664398 AB032999 AW104762 BM709726 
    AL138080 BM709407 BX279905 AI332809 AB042554 AI199105 BU733344 AK058196 

    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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    CCDC13 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCACTCAGCC
    CCDC13 Expression
    About this image

    CCDC13 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CCDC13 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.604182
        Custom PCR Arrays for CCDC13
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC13

    (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 animals.

    Orthologs for CCDC13 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ccdc131 , 5 coiled-coil domain containing 131, 5 80.84(n)1
    78.11(a)1
      9 (72.63 cM)5
    1005028611  NM_028384.11  NP_082660.11 
     1217976275 
    chicken
    (Gallus gallus)
    Aves CCDC131 coiled-coil domain containing 13 62.15(n)
    54.72(a)
      420392  XM_001232697.3  XP_001232698.2 
    lizard
    (Anolis carolinensis)
    Reptilia CCDC136
    coiled-coil domain containing 13
    49(a)
    1 ↔ 1
    6(2779775-2799748)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia ccdc131 coiled-coil domain containing 13 60.75(n)
    52.84(a)
      100489430  XM_002939312.2  XP_002939358.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5553451 uncharacterized LOC555345 54.29(n)
    46.63(a)
      555345  XM_005171105.1  XP_005171162.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG130326
    --
    20(a)
    1 ↔ 1
    3L(16667064-16669364)


    ENSEMBL Gene Tree for CCDC13 (if available)
    TreeFam Gene Tree for CCDC13 (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 CCDC13 (see all 1034)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1807858741,2
    --42749502(+) CATGGC/TGAGGG 1 -- int10--------
    rs1866947111,2
    --42749581(+) CACCTC/TGGCCC 1 -- int10--------
    rs1911766261,2
    --42749598(+) ACCAGC/TATCCA 1 -- int10--------
    rs1389586811,2
    C--42749647(+) CTGCT-/GCGCCTA 1 -- int10--------
    rs1838312621,2
    C--42749708(+) TGAACA/C/GGCAAG 1 -- int10--------
    rs1396435521,2
    --42749717(+) AGACCC/TTGGTT 1 -- int10--------
    rs1143091801,2
    F--42749870(+) ACTGGG/AAGCTG 1 -- int11Minor allele frequency- A:0.03WA 118
    rs1865866571,2
    C--42750001(+) TGGACA/GGCTAC 1 -- ut310--------
    rs1911107011,2
    --42750089(+) GGGCTC/TTTCTG 1 -- ut310--------
    rs1832577541,2
    C--42750243(+) CTGCTA/GTAACC 1 -- ut310--------

    HapMap Linkage Disequilibrium report for CCDC13 (42734155 - 42814745 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for CCDC13:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv3782CNV Insertion18451855

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CCDC13
    DNA2.0 Custom Variant and Variant Library Synthesis for CCDC13

    (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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    OMIM gene information: 614271    OMIM disorders: --


    Find genes that share disorders with CCDC13           About GenesLikeMe

    Genetic Association Database (GAD): CCDC13
    Human Genome Epidemiology (HuGE) Navigator: CCDC13 (1 document)

    Export disorders for CCDC13 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 CCDC13 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with CCDC13)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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)
    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. 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)
    4. Genome-wide association study of chronic periodontitis in a general German population. (PubMed id 24024966)1 Teumer A....Kocher T. (J. Clin. Periodontol. 2013)
    5. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PubMed id 23251661)1 Comuzzie A.G....Butte N.F. (PLoS ONE 2012)
    6. The DNA sequence, annotation and analysis of human chromosome 3. (PubMed id 16641997)2 Muzny D.M....Gibbs R.A. (Nature 2006)
    7. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)

    (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: 152206 HGNC: 26358 AceView: KIAA1173andFLJ25467 Ensembl:ENSG00000244607 euGenes: HUgn152206
    ECgene: CCDC13 H-InvDB: CCDC13

    (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 CCDC13 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 CCDC13 gene:
    Search GeneIP for patents involving CCDC13

    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, antibodies-online, 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 , 7 Oct 2014

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