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    Ccdc88b coiled-coil domain containing 88B [ Mus musculus (house mouse) ]

    Gene ID: 78317, updated on 30-Apr-2024

    Summary

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    Official Symbol
    Ccdc88bprovided by MGI
    Official Full Name
    coiled-coil domain containing 88Bprovided by MGI
    Primary source
    MGI:MGI:1925567
    See related
    Ensembl:ENSMUSG00000047810 AllianceGenome:MGI:1925567
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Ccdc88; 2610041P08Rik
    Summary
    Predicted to enable dynein light intermediate chain binding activity and microtubule binding activity. Involved in defense response to protozoan; positive regulation of T cell proliferation; and positive regulation of cytokine production. Located in membrane. Orthologous to human CCDC88B (coiled-coil domain containing 88B). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in thymus adult (RPKM 28.3), spleen adult (RPKM 15.0) and 8 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    19 A; 19 5.08 cM
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (6821991..6835586, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (6844623..6858222, complement)

    Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene high mobility group box 1, pseudogene 4 Neighboring gene STARR-seq mESC enhancer starr_45439 Neighboring gene STARR-seq mESC enhancer starr_45441 Neighboring gene ribosomal protein S6 kinase, polypeptide 4 Neighboring gene microRNA 5046 Neighboring gene CapStarr-seq enhancer MGSCv37_chr19:6946569-6946770 Neighboring gene predicted gene, 54051 Neighboring gene tRNA methyltransferase 11-2 Neighboring gene peroxiredoxin 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. CCDC88B is required for mobility and inflammatory functions of dendritic cells. Olivier JF, et al. J Leukoc Biol, 2020 Dec. PMID 32480428
    2. CCDC88B is required for pathogenesis of inflammatory bowel disease. Fodil N, et al. Nat Commun, 2017 Oct 13. PMID 29030607, Free PMC Article
    3. CCDC88B is a novel regulator of maturation and effector functions of T cells during pathological inflammation. Kennedy JM, et al. J Exp Med, 2014 Dec 15. PMID 25403443, Free PMC Article
    4. Antisense transcription in the mammalian transcriptome. Katayama S, et al. Science, 2005 Sep 2. PMID 16141073
    5. High-efficiency full-length cDNA cloning. Carninci P, et al. Methods Enzymol, 1999. PMID 10349636

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CCDC88B interacts with RASAL3 and ARHGEF2 and regulates dendritic cell function in neuroinflammation and colitis.
      Title: CCDC88B interacts with RASAL3 and ARHGEF2 and regulates dendritic cell function in neuroinflammation and colitis.
    2. CCDC88B is required for mobility and inflammatory functions of dendritic cells.
      Title: CCDC88B is required for mobility and inflammatory functions of dendritic cells.
    3. A critical function of CCDC88B in colonic inflammation
      Title: CCDC88B is required for pathogenesis of inflammatory bowel disease.
    4. These results identify CCDC88B as a novel and important regulator of T cell function.
      Title: CCDC88B is a novel regulator of maturation and effector functions of T cells during pathological inflammation.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Chemically induced (ENU) (1)  1 citation

    General gene information

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    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables dynein light intermediate chain binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables microtubule binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cytoplasmic microtubule organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cytoskeleton-dependent intracellular transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in defense response to protozoan IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of T cell activation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of T cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of cytokine production IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in centrosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    coiled-coil domain-containing protein 88B
    Names
    coiled-coil domain containing 88
    gipie
    hkRP3
    hook-related protein 3

    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.

    mRNA and Protein(s)

    1. NM_001081291.1 → NP_001074760.1  coiled-coil domain-containing protein 88B

      See identical proteins and their annotated locations for NP_001074760.1

      Status: PROVISIONAL

      Source sequence(s)
      AC120557
      Consensus CDS
      CCDS37900.1
      UniProtKB/Swiss-Prot
      B2RX63, Q4QRL3
      UniProtKB/TrEMBL
      B2RXR1
      Related
      ENSMUSP00000109067.2, ENSMUST00000113440.2
      Conserved Domains (2) summary
      TIGR02168
      Location:202 → 960
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cl11433
      Location:261 → 320
      DivIC; Septum formation initiator

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000085.7 Reference GRCm39 C57BL/6J

      Range
      6821991..6835586 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036161731.1 → XP_036017624.1  coiled-coil domain-containing protein 88B isoform X2

      UniProtKB/TrEMBL
      B2RXR1
      Conserved Domains (2) summary
      TIGR02168
      Location:201 → 959
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd22230
      Location:10 → 183
      HkD_Gipie; Hook domain found in Gipie (GRP78-interacting protein induced by ER stress) and similar proteins

    2. XM_011247402.4 → XP_011245704.1  coiled-coil domain-containing protein 88B isoform X1

      UniProtKB/TrEMBL
      B2RXR1
      Conserved Domains (1) summary
      TIGR02168
      Location:202 → 960
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    3. XM_006527464.5 → XP_006527527.1  coiled-coil domain-containing protein 88B isoform X3

      UniProtKB/TrEMBL
      A0A494BB08
      Related
      ENSMUSP00000158268.2, ENSMUST00000236028.2
      Conserved Domains (1) summary
      TIGR02168
      Location:428 → 997
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    RNA

    1. XR_003952826.2 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_198008.1: Suppressed sequence

      Description
      NM_198008.1: This RefSeq was permanently suppressed because it contains the wrong CDS.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q4QRL3.2 GenPept UniProtKB/Swiss-Prot:Q4QRL3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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