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Aliases for CCDC28B Gene

Aliases for CCDC28B Gene

  • Coiled-Coil Domain Containing 28B 2 3 5
  • Coiled-Coil Domain-Containing Protein 28B 3

External Ids for CCDC28B Gene

Previous GeneCards Identifiers for CCDC28B Gene

  • GC01P032336
  • GC01P032438
  • GC01P032666
  • GC01P030782

Summaries for CCDC28B Gene

Entrez Gene Summary for CCDC28B Gene

  • The product of this gene localizes to centrosomes and basal bodies. The protein colocalizes with several proteins associated with Bardet-Biedl syndrome (BBS) and participates in the regulation of cilia development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

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 Bardet-Biedl Syndrome. An important paralog of this gene is CCDC28A.

UniProtKB/Swiss-Prot for CCDC28B Gene

  • Involved in ciliogenesis. Regulates cilia length through its interaction with MAPKAP1/SIN1 but independently of mTORC2 complex. Modulates mTORC2 complex assembly and function, possibly enhances AKT1 phosphorylation. Does not seem to modulate assembly and function of mTORC1 complex.

Gene Wiki entry for CCDC28B Gene

Additional gene information for CCDC28B Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CCDC28B Gene

Genomics for CCDC28B Gene

GeneHancer (GH) Regulatory Elements for CCDC28B Gene

Promoters and enhancers for CCDC28B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J032197 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 -0.2 -196 5.3 HDGF PKNOX1 ATF1 SMAD1 ARID4B SIN3A ZNF2 ZNF48 YY1 SLC30A9 CCDC28B GC01M032200 KPNA6 MTMR9LP LRRC37A12P TXLNA
GH01J032196 Promoter 0.6 EPDnew 650.7 -4.1 -4075 0.1 POLR2A CCDC28B GC01M032200 TXLNA
GH01J032106 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.8 -92.2 -92235 3 HDGF FOXA2 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B KPNA6 TMEM39B SNRNP40 TXLNA TSSK3 KHDRBS1 RBBP4 ENSG00000229447 AK2 ENSG00000203325
GH01J032319 Enhancer 1.3 Ensembl ENCODE dbSUPER 10.7 +121.2 121216 4.7 HDGF FOXA2 MLX ARID4B SIN3A DMAP1 ZNF48 YY1 ZNF121 ATF7 LOC105378629 HDAC1 ENSG00000252450 TMEM234 EIF3I DCDC2B ENSG00000224066 IQCC CCDC28B MTMR9LP
GH01J032132 Enhancer 1.2 Ensembl ENCODE 11.3 -67.0 -66975 2.3 HDGF PKNOX1 ARNT NEUROD1 SIN3A ZNF766 CBX5 E2F8 ZNF548 FOS SNRNP40 TXLNA KPNA6 KHDRBS1 ENSG00000229447 IQCC TSSK3 EIF3I CCDC28B AK2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CCDC28B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CCDC28B gene promoter:
  • NF-1
  • POU2F1a
  • POU2F1
  • Hand1
  • E47
  • HSF1short
  • HSF1 (long)
  • Pax-3
  • STAT3

Genomic Locations for CCDC28B Gene

Genomic Locations for CCDC28B Gene
chr1:32,200,386-32,205,390
(GRCh38/hg38)
Size:
5,005 bases
Orientation:
Plus strand
chr1:32,665,987-32,670,991
(GRCh37/hg19)
Size:
5,005 bases
Orientation:
Plus strand

Genomic View for CCDC28B Gene

Genes around CCDC28B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CCDC28B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CCDC28B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CCDC28B Gene

Proteins for CCDC28B Gene

  • Protein details for CCDC28B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BUN5-CC28B_HUMAN
    Recommended name:
    Coiled-coil domain-containing protein 28B
    Protein Accession:
    Q9BUN5
    Secondary Accessions:
    • A8K789
    • Q8TBV8

    Protein attributes for CCDC28B Gene

    Size:
    200 amino acids
    Molecular mass:
    22037 Da
    Quaternary structure:
    • Interacts with BBS1, BBS2, BBS4, BBS5, BBS6, BBS7 and TTC8/BBS8. Interacts with MAPKAP1/SIN1 isoform 1 and RICTOR.
    SequenceCaution:
    • Sequence=CAI22057.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for CCDC28B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CCDC28B Gene

Post-translational modifications for CCDC28B Gene

  • Ubiquitination at posLast=112112
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CCDC28B Gene

Domains & Families for CCDC28B Gene

Gene Families for CCDC28B Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for CCDC28B Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CCDC28B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CCDC28B: view

No data available for UniProtKB/Swiss-Prot for CCDC28B Gene

Function for CCDC28B Gene

Molecular function for CCDC28B Gene

UniProtKB/Swiss-Prot Function:
Involved in ciliogenesis. Regulates cilia length through its interaction with MAPKAP1/SIN1 but independently of mTORC2 complex. Modulates mTORC2 complex assembly and function, possibly enhances AKT1 phosphorylation. Does not seem to modulate assembly and function of mTORC1 complex.

Gene Ontology (GO) - Molecular Function for CCDC28B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16327777
genes like me logo Genes that share ontologies with CCDC28B: view
genes like me logo Genes that share phenotypes with CCDC28B: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CCDC28B Gene

Localization for CCDC28B Gene

Subcellular locations from UniProtKB/Swiss-Prot for CCDC28B Gene

Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Note=It localizes near centrosomes and basal bodies.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CCDC28B gene
Compartment Confidence
cytoskeleton 5
nucleus 3
cytosol 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for CCDC28B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005813 centrosome IDA 16327777
GO:0005815 microtubule organizing center IEA --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with CCDC28B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CCDC28B Gene

Pathways & Interactions for CCDC28B Gene

SuperPathways for CCDC28B Gene

No Data Available

Gene Ontology (GO) - Biological Process for CCDC28B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030030 cell projection organization IEA --
GO:0060271 cilium assembly IMP 23015189
genes like me logo Genes that share ontologies with CCDC28B: view

No data available for Pathways by source and SIGNOR curated interactions for CCDC28B Gene

Drugs & Compounds for CCDC28B Gene

No Compound Related Data Available

Transcripts for CCDC28B Gene

Unigene Clusters for CCDC28B Gene

Coiled-coil domain containing 28B:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CCDC28B Gene

No ASD Table

Relevant External Links for CCDC28B Gene

GeneLoc Exon Structure for
CCDC28B
ECgene alternative splicing isoforms for
CCDC28B

Expression for CCDC28B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CCDC28B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CCDC28B Gene

This gene is overexpressed in Muscle - Skeletal (x5.7).

Protein differential expression in normal tissues from HIPED for CCDC28B Gene

This gene is overexpressed in Platelet (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CCDC28B Gene



Protein tissue co-expression partners for CCDC28B Gene

NURSA nuclear receptor signaling pathways regulating expression of CCDC28B Gene:

CCDC28B

SOURCE GeneReport for Unigene cluster for CCDC28B Gene:

Hs.534482

Evidence on tissue expression from TISSUES for CCDC28B Gene

  • Muscle(4.2)
  • Lung(4.1)
genes like me logo Genes that share expression patterns with CCDC28B: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CCDC28B Gene

Orthologs for CCDC28B Gene

This gene was present in the common ancestor of animals.

Orthologs for CCDC28B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CCDC28B 34 33
  • 99.67 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CCDC28B 34
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CCDC28B 34 33
  • 92.83 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Ccdc28b 16 34 33
  • 88.83 (n)
rat
(Rattus norvegicus)
Mammalia Ccdc28b 33
  • 88.33 (n)
oppossum
(Monodelphis domestica)
Mammalia CCDC28B 34
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CCDC28B 34
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves CCDC28B 34 33
  • 71.91 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CCDC28B 34
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ccdc28b 33
  • 67.05 (n)
Str.1267 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.9739 33
zebrafish
(Danio rerio)
Actinopterygii ccdc28b 34 33
  • 62.96 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG10874 34
  • 18 (a)
OneToMany
Species where no ortholog for CCDC28B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CCDC28B Gene

ENSEMBL:
Gene Tree for CCDC28B (if available)
TreeFam:
Gene Tree for CCDC28B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CCDC28B: view image

Paralogs for CCDC28B Gene

Paralogs for CCDC28B Gene

(1) SIMAP similar genes for CCDC28B Gene using alignment to 3 proteins:

  • CC28B_HUMAN
  • E9PM03_HUMAN
  • E9PM81_HUMAN
genes like me logo Genes that share paralogs with CCDC28B: view

Variants for CCDC28B Gene

Sequence variations from dbSNP and Humsavar for CCDC28B Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs41263993 risk-factor, Bardet-Biedl syndrome 1, modifier of 32,204,044(+) C/T coding_sequence_variant, synonymous_variant
rs199647520 uncertain-significance, not specified 32,204,190(+) G/A coding_sequence_variant, intron_variant, synonymous_variant
rs200163249 uncertain-significance, not specified 32,203,995(+) G/A/T coding_sequence_variant, missense_variant
rs140234450 benign, not specified 32,204,317(+) G/A coding_sequence_variant, intron_variant, missense_variant
rs1000383939 -- 32,204,373(+) T/A coding_sequence_variant, intron_variant, synonymous_variant

Variation tolerance for CCDC28B Gene

Residual Variation Intolerance Score: 52.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.92; 59.43% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CCDC28B Gene

Human Gene Mutation Database (HGMD)
CCDC28B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CCDC28B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for CCDC28B Gene

Disorders for CCDC28B Gene

MalaCards: The human disease database

(5) MalaCards diseases for CCDC28B Gene - From: HGMD, OMIM, ClinVar, GTR, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
bardet-biedl syndrome 1
  • bbs1
bardet-biedl syndrome
  • biedl-bardet syndrome
bardet-biedl syndrome 16
  • bbs16
bardet-biedl syndrome 13
  • bbs13
pathologic nystagmus
  • nystagmus
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CC28B_HUMAN
  • Bardet-Biedl syndrome (BBS) [MIM:209900]: A syndrome characterized by usually severe pigmentary retinopathy, early-onset obesity, polydactyly, hypogenitalism, renal malformation and mental retardation. Secondary features include diabetes mellitus, hypertension and congenital heart disease. Bardet-Biedl syndrome inheritance is autosomal recessive, but three mutated alleles (two at one locus, and a third at a second locus) may be required for clinical manifestation of some forms of the disease. {ECO:0000269 PubMed:16327777}. Note=The gene represented in this entry acts as a disease modifier.

Additional Disease Information for CCDC28B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CCDC28B: view

No data available for Genatlas for CCDC28B Gene

Publications for CCDC28B Gene

  1. The Bardet-Biedl syndrome-related protein CCDC28B modulates mTORC2 function and interacts with SIN1 to control cilia length independently of the mTOR complex. (PMID: 23727834) Cardenas-Rodriguez M … Badano JL (Human molecular genetics 2013) 2 3 4 58
  2. Dissection of epistasis in oligogenic Bardet-Biedl syndrome. (PMID: 16327777) Badano JL … Katsanis N (Nature 2006) 2 3 4 58
  3. Characterization of CCDC28B reveals its role in ciliogenesis and provides insight to understand its modifier effect on Bardet-Biedl syndrome. (PMID: 23015189) Cardenas-Rodriguez M … Badano JL (Human genetics 2013) 3 4 58
  4. BBS7 and TTC8 (BBS8) mutations play a minor role in the mutational load of Bardet-Biedl syndrome in a multiethnic population. (PMID: 19402160) Bin J … Héon E (Human mutation 2009) 3 44 58
  5. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58

Products for CCDC28B Gene

Sources for CCDC28B Gene

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