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

CCDC28B Gene

protein-coding   GIFtS: 48
GCID: GC01P032666

Coiled-Coil Domain Containing 28B

  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 28B1 2
RP4-622L5.52
Coiled-Coil Domain-Containing Protein 28B2

External Ids:    HGNC: 281631   Entrez Gene: 791402   Ensembl: ENSG000001600507   OMIM: 6101625   UniProtKB: Q9BUN53   

Export aliases for CCDC28B gene to outside databases

Previous GC identifers: GC01P032336 GC01P032438 GC01P030782


(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 CCDC28B Gene:
The product of this gene localizes to centrosomes and basal bodies. It interacts and colocalizes with several
proteins associated with Bardet-Biedl syndrome (BBS). (provided by RefSeq, Jul 2008)

GeneCards Summary for CCDC28B Gene: 
CCDC28B (coiled-coil domain containing 28B) is a protein-coding gene. Diseases associated with CCDC28B include bardet-biedl syndrome 1, and congenital nystagmus. GO annotations related to this gene include protein binding. An important paralog of this gene is CCDC28A.

UniProtKB/Swiss-Prot: CC28B_HUMAN, Q9BUN5
Function: Involved in ciliogenesis

Gene Wiki entry for CCDC28B 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_000001.10  NC_018912.2  NT_032977.9  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CCDC28B gene promoter:
         NF-1   HSF1 (long)   E47   Pax-3   POU2F1   POU2F1a   STAT3   Hand1   HSF1short   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCDC28B promoter sequence
   Search SABiosciences Chromatin IP Primers for CCDC28B

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CCDC28B


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

Entrez Gene cytogenetic band: 1p36.11-p34.2   Ensembl cytogenetic band:  1p35.1   HGNC cytogenetic band: 1p36.11-p34.2

CCDC28B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC28B gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P032666:  view genomic region     (about GC identifiers)

Start:
32,665,987 bp from pter      End:
32,670,991 bp from pter
Size:
5,005 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: CC28B_HUMAN, Q9BUN5 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 28B  
Size: 200 amino acids; 22037 Da
Subunit: Interacts with BBS1, BBS2, BBS4, BBS5, BBS6, BBS7 AND BBS8
Subcellular location: Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Note=It localizes near
centrosomes and basal bodies
Sequence caution: Sequence=CAI22057.1; Type=Erroneous gene model prediction;
Secondary accessions: A8K789 Q8TBV8
Alternative splicing: 2 isoforms:  Q9BUN5-1   Q9BUN5-3   

Explore the universe of human proteins at neXtProt for CCDC28B: NX_Q9BUN5

Explore proteomics data for CCDC28B at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9BUN5

  • CCDC28B Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CCDC28B Protein Expression
    REFSEQ proteins: NP_077272.2  
    ENSEMBL proteins: 
     ENSP00000362704   ENSP00000435036   ENSP00000413017   ENSP00000431257  

    Human Recombinant Protein Products for CCDC28B: 
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    Cloud-Clone Corp. Proteins for CCDC28B 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--
    GO:0005813centrosome IDA16327777

    CCDC28B for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR025271 DUF4061

    Graphical View of Domain Structure for InterPro Entry Q9BUN5

    ProtoNet protein and cluster: Q9BUN5


    CCDC28B for domains           About GeneDecksing


    (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

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CC28B_HUMAN, Q9BUN5
    Function: Involved in ciliogenesis

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI16327777
         
    CCDC28B for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for CCDC28B 
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CCDC28B 
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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 CCDC28B

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0042384cilium assembly IMP--

    CCDC28B for ontologies           About GeneDecksing



    (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 CCDC28B (CC28B)

    Search CenterWatch for drugs/clinical trials and news about CCDC28B / CC28B

    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    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 CCDC28B gene: 
    NM_024296.3  

    Unigene Cluster for CCDC28B:

    Coiled-coil domain containing 28B
    Hs.534482  [show with all ESTs]
    Unigene Representative Sequence: AK126027
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000373602(uc001bul.1) ENST00000469003 ENST00000421922(uc021okt.1)
    ENST00000461819 ENST00000483009
    miRNA
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    8/10 QIAGEN miScript miRNA Assays for microRNAs that regulate CCDC28B (see all 10):
    hsa-miR-224 hsa-miR-27a hsa-miR-29a hsa-miR-29c hsa-miR-128 hsa-miR-3681* hsa-miR-29b-1* hsa-miR-637
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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    Additional mRNA sequence: 

    AK092702.1 AK126027.1 AK225113.1 AK291904.1 BC022848.2 

    5 DOTS entries:

    DT.215092  DT.100748653  DT.86840926  DT.91919747  DT.99935076 

    24/332 AceView cDNA sequences (see all 332):

    NM_024296 CA417053 AW083209 AI815547 BF478216 AA281337 BM697068 BC080578 
    AW294086 BC029686 BQ054155 AI807746 AK096161 AI394288 BQ057342 BE513525 
    BU726101 AI419038 BM053066 BM471221 BG169290 AI816489 AI146364 CN480364 

    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

    CCDC28B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTGGCTCAGC
    CCDC28B Expression
    About this image


    See CCDC28B Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CCDC28B

    SOURCE GeneReport for Unigene cluster: Hs.534482
        SABiosciences Custom PCR Arrays for CCDC28B
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CCDC28B

    (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 CCDC28B gene from 6/12 species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ccdc28b1 , 5 coiled coil domain containing 28B1, 5 88.83(n)1
    96.5(a)1
      4 (63.26 cM)5
    662641  NM_025455.21  NP_079731.21 
     1296192745 
    chicken
    (Gallus gallus)
    Aves CCDC28B1 coiled-coil domain containing 28B 73.26(n)
    70.35(a)
      419647  XM_003642571.1  XP_003642619.1 
    lizard
    (Anolis carolinensis)
    Reptilia CCDC28B6
    Uncharacterized protein
    69(a)
    1 ↔ 1
    GL343706.1(134179-143788)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.97392 Xenopus laevis transcribed sequence with weak similarity more 80.19(n)    CA973705.1 
    zebrafish
    (Danio rerio)
    Actinopterygii ccdc28b1 coiled-coil domain containing 28B 66.11(n)
    66.67(a)
      559814  NM_001145573.1  NP_001139045.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG108746
    --
    17(a)
    1 → many
    2L(2189913-2192371)


    ENSEMBL Gene Tree for CCDC28B (if available)
    TreeFam Gene Tree for CCDC28B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CCDC28B gene
    CCDC28A2  
    1 SIMAP similar gene for CCDC28B using alignment to 3 protein entries:     CC28B_HUMAN (see all proteins):
    CCDC28A

    CCDC28B for paralogs           About GeneDecksing



    (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

    10/158 SNPs in CCDC28B are shown (see all 158)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1850596961,2
    --32743705(+) GGGGGC/TGAGGC 1 -- us2k10--------
    rs1909331321,2
    --32743727(+) TCTGGA/GTACCA 1 -- us2k10--------
    rs1387679331,2
    --32743790(+) TTCAAC/TAGGAA 1 -- us2k10--------
    rs1830825841,2
    --32743840(+) AGGCAC/TAGGCC 1 -- us2k10--------
    rs793870041,2
    C,F--32743886(+) CACTGC/GTATTT 1 -- us2k11Minor allele frequency- G:0.07EA 120
    rs1418888151,2
    --32743957(+) CTCTAA/GTTGTA 1 -- us2k10--------
    rs1874615091,2
    --32743997(+) TTCAGA/TTTTTA 1 -- us2k10--------
    rs1903761601,2
    --32744175(+) CCAGGA/CCTCCA 1 -- us2k10--------
    rs168349261,2
    C,F,H--32744202(+) CAATGA/GCTGTG 1 -- us2k125Minor allele frequency- G:0.18NA NS EA WA CSA 2467
    rs1444262781,2
    C--32744305(+) GGTGT-/GGGGGG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for CCDC28B (32665987 - 32670991 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for CCDC28B: --

    Human Gene Mutation Database (HGMD): CCDC28B
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing CCDC28B
    DNA2.0 Custom Variant and Variant Library Synthesis for CCDC28B

    (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: 610162    OMIM disorders: --

    UniProtKB/Swiss-Prot: CC28B_HUMAN, Q9BUN5
  • Note=Phenotypic expression of Bardet-Biedl syndrome (BBS) can be modulated by genetic variations in
    CCDC28B (PubMed:16327777). Ciliary dysfunction leads to a broad spectrum of disorders, collectively termed
    ciliopathies. Overlapping clinical features include retinal degeneration, renal cystic disease, skeletal
    abnormalities, fibrosis of various organ, and a complex range of anatomical and functional defects of the central
    and peripheral nervous system. The ciliopathy range of diseases includes Meckel-Gruber syndrome, Bardet-Biedl
    syndrome, Joubert syndrome, nephronophtisis, Senior-Loken syndrome, and Jeune asphyxiating thoracic dystrophy
    among others. Single-locus allelism is insufficient to explain the variable penetrance and expressivity of such
    disorders, leading to the suggestion that variations across multiple sites of the ciliary proteome influence the
    clinical outcome

  • 9 diseases for CCDC28B:    About MalaCards
    bardet-biedl syndrome 1    congenital nystagmus    retinal disease    bardet-biedl syndrome
    senior-loken syndrome    asphyxiating thoracic dystrophy    joubert syndrome    retinal degeneration
    retinitis

    2 diseases from the University of Copenhagen DISEASES database for CCDC28B:
    Bardet-Biedl syndrome     Congenital nystagmus

    CCDC28B for disorders           About GeneDecksing

    Genetic Association Database (GAD): CCDC28B
    Human Genome Epidemiology (HuGE) Navigator: CCDC28B (1 document)

    Export disorders for CCDC28B 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 CCDC28B gene, integrated from 9 sources (see all 15):
    (articles sorted by number of sources associating them with CCDC28B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Dissection of epistasis in oligogenic Bardet-Biedl syndrome. (PubMed id 16327777)1, 2, 3 Badano J.L....Katsanis N. (2006)
    2. Characterization of CCDC28B reveals its role in ciliogenesis and provides insight to understand its modifier effect on Bardet-Biedl syndrome. (PubMed id 23015189)1, 2 Cardenas-Rodriguez M.... Badano J.L. (2013)
    3. BBS7 and TTC8 (BBS8) mutations play a minor role in the mutational load of Bardet-Biedl syndrome in a multiethnic population. (PubMed id 19402160)1, 4 Bin J....HAcon E. (2009)
    4. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
    5. 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. (2004)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    7. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
    8. 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)
    9. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (2007)
    10. 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)

    (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: 79140 HGNC: 28163 AceView: MGC1203andDKFZp451J0118 Ensembl:ENSG00000160050 euGenes: HUgn79140
    ECgene: CCDC28B H-InvDB: CCDC28B

    (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 CCDC28B 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 CCDC28B gene:
    Search GeneIP for patents involving CCDC28B

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    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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