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    CCDC28B coiled-coil domain containing 28B [ Homo sapiens (human) ]

    Gene ID: 79140, updated on 28-Oct-2024

    Summary

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    Official Symbol
    CCDC28Bprovided by HGNC
    Official Full Name
    coiled-coil domain containing 28Bprovided by HGNC
    Primary source
    HGNC:HGNC:28163
    See related
    Ensembl:ENSG00000160050 MIM:610162; AllianceGenome:HGNC:28163
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    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]
    Expression
    Broad expression in testis (RPKM 4.7), lymph node (RPKM 2.1) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CCDC28B in Genome Data Viewer
    Location:
    1p35.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (32196011..32205387)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (32058497..32063289)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (32666196..32670988)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene transmembrane protein 39B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32557367-32557892 Neighboring gene microRNA 5585 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32573351-32573869 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32573870-32574387 Neighboring gene Sharpr-MPRA regulatory region 5670 Neighboring gene karyopherin subunit alpha 6 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32644454-32645213 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32645214-32645972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 671 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 670 Neighboring gene taxilin alpha Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32664855-32665413 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32665414-32665971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 672 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr1:32666522-32667041 and GRCh37_chr1:32667042-32667562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32670259-32670760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 675 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:32681346-32682545 Neighboring gene doublecortin domain containing 2B Neighboring gene IQ motif containing C Neighboring gene transmembrane protein 234

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. A CVID-associated variant in the ciliogenesis protein CCDC28B disrupts immune synapse assembly. Capitani N, et al. Cell Death Differ, 2022 Jan. PMID 34294890, Free PMC Article
    2. The Bardet-Biedl syndrome-related protein CCDC28B modulates mTORC2 function and interacts with SIN1 to control cilia length independently of the mTOR complex. Cardenas-Rodriguez M, et al. Hum Mol Genet, 2013 Oct 15. PMID 23727834, Free PMC Article
    3. Kinesin 1 regulates cilia length through an interaction with the Bardet-Biedl syndrome related protein CCDC28B. Novas R, et al. Sci Rep, 2018 Feb 14. PMID 29445114, Free PMC Article
    4. BBS7 and TTC8 (BBS8) mutations play a minor role in the mutational load of Bardet-Biedl syndrome in a multiethnic population. Bin J, et al. Hum Mutat, 2009 Jul. PMID 19402160
    5. Characterization of CCDC28B reveals its role in ciliogenesis and provides insight to understand its modifier effect on Bardet-Biedl syndrome. Cardenas-Rodriguez M, et al. Hum Genet, 2013 Jan. PMID 23015189

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A CVID-associated variant in the ciliogenesis protein CCDC28B disrupts immune synapse assembly.
      Title: A CVID-associated variant in the ciliogenesis protein CCDC28B disrupts immune synapse assembly.
    2. these studies demonstrate that kinesin 1 regulates ciliogenesis through CCDC28B
      Title: Kinesin 1 regulates cilia length through an interaction with the Bardet-Biedl syndrome related protein CCDC28B.
    3. Findings implicate CCDC28B in the regulation of mTORC2, and uncover a novel function of SIN1 regulating cilia length that is likely independent of mTOR signaling.
      Title: The Bardet-Biedl syndrome-related protein CCDC28B modulates mTORC2 function and interacts with SIN1 to control cilia length independently of the mTOR complex.
    4. reports CCDC28B as a novel protein involved in the process of ciliogenesis whilst providing functional insight into the cellular basis of its modifier effect in Bardet-Biedl syndrome.
      Title: Characterization of CCDC28B reveals its role in ciliogenesis and provides insight to understand its modifier effect on Bardet-Biedl syndrome.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: BBS7 and TTC8 (BBS8) mutations play a minor role in the mutational load of Bardet-Biedl syndrome in a multiethnic population.
    6. identification of a novel locus, MGC1203, that contributes epistatic alleles to Bardet-Biedl syndrome, a pleiotropic, oligogenic disorder; MGC1203 encodes a pericentriolar protein that interacts and colocalizes with the BBS proteins
      Title: Dissection of epistasis in oligogenic Bardet-Biedl syndrome.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Bardet-Biedl syndrome 1
    MedGen: C2936862 OMIM: 209900 GeneReviews: Bardet-Biedl Syndrome Overview
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Clone Names

    • MGC1203, MGC16441

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in centrosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    coiled-coil domain-containing protein 28B

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_012178.1 RefSeqGene

      Range
      4995..9787
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001301011.2 → NP_001287940.1  coiled-coil domain-containing protein 28B isoform 1

      See identical proteins and their annotated locations for NP_001287940.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK291904, BC002462
      Consensus CDS
      CCDS72749.1
      UniProtKB/Swiss-Prot
      Q9BUN5
      Related
      ENSP00000413017.2, ENST00000421922.6
      Conserved Domains (1) summary
      pfam13270
      Location:86 → 183
      DUF4061; Domain of unknown function (DUF4061)

    2. NM_024296.5 → NP_077272.2  coiled-coil domain-containing protein 28B isoform 2

      See identical proteins and their annotated locations for NP_077272.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate segment in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AK291904, BC022848
      Consensus CDS
      CCDS354.2
      UniProtKB/Swiss-Prot
      A8K789, Q8TBV8, Q9BUN5
      Related
      ENSP00000362704.5, ENST00000373602.10
      Conserved Domains (1) summary
      pfam13270
      Location:86 → 184
      DUF4061; Domain of unknown function (DUF4061)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      32196011..32205387
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047430215.1 → XP_047286171.1  coiled-coil domain-containing protein 28B isoform X1

    2. XM_047430217.1 → XP_047286173.1  coiled-coil domain-containing protein 28B isoform X2

      UniProtKB/Swiss-Prot
      A8K789, Q8TBV8, Q9BUN5

    3. XM_017002308.3 → XP_016857797.1  coiled-coil domain-containing protein 28B isoform X3

      UniProtKB/TrEMBL
      A0A7P0TB33, E9PM81
      Related
      ENSP00000506476.1, ENST00000681230.1
      Conserved Domains (1) summary
      pfam13270
      Location:86 → 110
      DUF4061; Domain of unknown function (DUF4061)

    4. XM_011542113.4 → XP_011540415.1  coiled-coil domain-containing protein 28B isoform X1

      See identical proteins and their annotated locations for XP_011540415.1

      UniProtKB/Swiss-Prot
      Q9BUN5
      Conserved Domains (1) summary
      pfam13270
      Location:86 → 183
      DUF4061; Domain of unknown function (DUF4061)

    5. XM_017002307.2 → XP_016857796.1  coiled-coil domain-containing protein 28B isoform X2

      UniProtKB/Swiss-Prot
      A8K789, Q8TBV8, Q9BUN5
      Conserved Domains (1) summary
      pfam13270
      Location:86 → 184
      DUF4061; Domain of unknown function (DUF4061)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      32058497..32063289
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338690.1 → XP_054194665.1  coiled-coil domain-containing protein 28B isoform X3

      UniProtKB/TrEMBL
      A0A7P0TB33

    2. XM_054338687.1 → XP_054194662.1  coiled-coil domain-containing protein 28B isoform X1

    3. XM_054338688.1 → XP_054194663.1  coiled-coil domain-containing protein 28B isoform X1

    4. XM_054338689.1 → XP_054194664.1  coiled-coil domain-containing protein 28B isoform X2

      UniProtKB/Swiss-Prot
      A8K789, Q8TBV8, Q9BUN5
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BUN5.2 GenPept UniProtKB/Swiss-Prot:Q9BUN5

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