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

Gene ID: 78317, updated on 12-May-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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See Ccdc88b in Genome Data Viewer
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)
  • Chemically induced (ENU) (1)  1 citation
  • Endonuclease-mediated (2) 

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

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Chemical Information
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