U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Ccdc88c coiled-coil domain containing 88C [ Rattus norvegicus (Norway rat) ]

    Gene ID: 362770, updated on 27-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Ccdc88cprovided by RGD
    Official Full Name
    coiled-coil domain containing 88Cprovided by RGD
    Primary source
    RGD:1307429
    See related
    EnsemblRapid:ENSRNOG00000004482 AllianceGenome:RGD:1307429
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1307429
    Summary
    Predicted to enable several functions, including G-protein alpha-subunit binding activity; PDZ domain binding activity; and dynein light intermediate chain binding activity. Predicted to be involved in several processes, including apical constriction; negative regulation of canonical Wnt signaling pathway; and protein destabilization. Predicted to act upstream of or within with a positive effect on positive regulation of JNK cascade. Predicted to act upstream of or within several processes, including mucociliary clearance; negative regulation of microtubule depolymerization; and respiratory basal cell differentiation. Predicted to be located in cell junction. Predicted to be active in apical junction complex; centrosome; and cytoplasm. Human ortholog(s) of this gene implicated in hydrocephalus and spinocerebellar ataxia type 40. Orthologous to human CCDC88C (coiled-coil domain containing 88C). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 103.6), Spleen (RPKM 67.2) and 8 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Ccdc88c in Genome Data Viewer
    Location:
    6q32
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 6 NC_086024.1 (125899337..126019162, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 6 NC_051341.1 (120169752..120289459, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (124905811..125028011, complement)

    Chromosome 6 - NC_086024.1Genomic Context describing neighboring genes Neighboring gene D-glutamate cyclase Neighboring gene uncharacterized LOC120103602 Neighboring gene G protein-coupled receptor 68 Neighboring gene protein phosphatase 4, regulatory subunit 3A Neighboring gene ribosomal protein S3, pseudogene 6

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. A novel missense mutation in CCDC88C activates the JNK pathway and causes a dominant form of spinocerebellar ataxia. Tsoi H, et al. J Med Genet, 2014 Sep. PMID 25062847, Free PMC Article
    2. GPCR-independent activation of G proteins promotes apical cell constriction in vivo. Marivin A, et al. J Cell Biol, 2019 May 6. PMID 30948426, Free PMC Article
    3. Identification and characterization of a novel Dvl-binding protein that suppresses Wnt signalling pathway. Oshita A, et al. Genes Cells, 2003 Dec. PMID 14750955
    4. Daple is a novel non-receptor GEF required for trimeric G protein activation in Wnt signaling. Aznar N, et al. Elife, 2015 Jun 30. PMID 26126266, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables G-protein alpha-subunit binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables PDZ domain binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables dynein light intermediate chain binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables frizzled binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables guanyl-nucleotide exchange factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables microtubule binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables microtubule binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein dimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within Wnt signaling pathway, planar cell polarity pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in apical constriction ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cilium movement ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cilium organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    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
    		  
    acts_upstream_of_or_within microtubule bundle formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within mucociliary clearance ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of canonical Wnt signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of microtubule depolymerization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in non-canonical Wnt signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within_positive_effect positive regulation of JNK cascade ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein destabilization ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within respiratory basal cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in small GTPase-mediated signal transduction ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in apical junction complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell junction ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in centrosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    coiled-coil domain containing 88C; protein Daple

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001432084.1 → NP_001419013.1  coiled-coil domain containing 88C

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000006

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086024.1 Reference GRCr8

      Range
      125899337..126019162 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_343096.9 → XP_343097.4  protein Daple isoform X1

      Related
      ENSRNOP00000081834.1, ENSRNOT00000099776.2
      Conserved Domains (6) summary
      pfam05483
      Location:625 → 1286
      SCP-1; Synaptonemal complex protein 1 (SCP-1)
      pfam05622
      Location:17 → 562
      HOOK; HOOK protein
      pfam09755
      Location:440 → 791
      DUF2046; Uncharacterized conserved protein H4 (DUF2046)
      pfam16034
      Location:477 → 633
      JAKMIP_CC3; JAKMIP CC3 domain
      cl23720
      Location:737 → 841
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
      cl24005
      Location:661 → 739
      DUF2570; Protein of unknown function (DUF2570)

    2. XM_039113347.2 → XP_038969275.1  protein Daple isoform X2

      UniProtKB/TrEMBL
      A6JEI3, D4A9W1
      Related
      ENSRNOP00000005908.6, ENSRNOT00000005908.10
      Conserved Domains (3) summary
      PHA03247
      Location:1327 → 1917
      PHA03247; large tegument protein UL36; Provisional
      COG1196
      Location:519 → 1304
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cl41774
      Location:29 → 79
      HkD_SF; Hook domain-containing proteins superfamily

    3. XM_017594496.3 → XP_017449985.1  protein Daple isoform X3

      UniProtKB/TrEMBL
      A6JEI3

    RNA

    1. XR_005506202.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools