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    CLIP3 CAP-Gly domain containing linker protein 3 [ Homo sapiens (human) ]

    Gene ID: 25999, updated on 15-Jun-2019

    Summary

    Official Symbol
    CLIP3provided by HGNC
    Official Full Name
    CAP-Gly domain containing linker protein 3provided by HGNC
    Primary source
    HGNC:HGNC:24314
    See related
    Ensembl:ENSG00000105270 MIM:607382
    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
    Also known as
    RSNL1; CLIPR59; CLIPR-59
    Summary
    This gene encodes a member of the cytoplasmic linker protein 170 family. Members of this protein family contain a cytoskeleton-associated protein glycine-rich domain and mediate the interaction of microtubules with cellular organelles. The encoded protein plays a role in T cell apoptosis by facilitating the association of tubulin and the lipid raft ganglioside GD3. The encoded protein also functions as a scaffold protein mediating membrane localization of phosphorylated protein kinase B. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Dec 2010]
    Expression
    Biased expression in brain (RPKM 97.6), endometrium (RPKM 19.6) and 9 other tissues See more
    Orthologs

    Genomic context

    See CLIP3 in Genome Data Viewer
    Location:
    19q13.12
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (36014660..36032895, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (36505562..36523797, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene spectrin repeat containing nuclear envelope family member 4 Neighboring gene uncharacterized LOC101927572 Neighboring gene alkB homolog 6 Neighboring gene THAP domain containing 8 Neighboring gene RNY5 pseudogene 10 Neighboring gene WD repeat domain 62

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of CAP-GLY domain containing linker protein 3 (CLIP3) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    • Death Receptor Signalling, organism-specific biosystem (from REACTOME)
      Death Receptor Signalling, organism-specific biosystemThe death receptors, all cell-surface receptors, begin the process of caspase activation. The common feature of these type 1 transmembrane proteins is the "death-domain" a conserved cytoplasmic motif...
    • Regulation of TNFR1 signaling, organism-specific biosystem (from REACTOME)
      Regulation of TNFR1 signaling, organism-specific biosystemTumor necrosis factor-alpha (TNFalpha) is an inflammatory cytokine, that activates either cell survival (e.g.,inflammation, proliferation) or cell death upon association with TNF receptor 1 (TNFR1). ...
    • Signal Transduction, organism-specific biosystem (from REACTOME)
      Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
    • TNF signaling, organism-specific biosystem (from REACTOME)
      TNF signaling, organism-specific biosystemThe inflammatory cytokine tumor necrosis factor alpha (TNF-alpha) is expressed in immune and nonimmune cell types including macrophages, T cells, mast cells, granulocytes, natural killer (NK) cells, ...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ33413, DKFZp586N1922

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    ganglioside binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    microtubule binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    microtubule binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    chaperone-mediated protein transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    fat cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    membrane biogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of microtubule polymerization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    peptidyl-L-cysteine S-palmitoylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of glucose transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of protein localization to plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of protein phosphorylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of tumor necrosis factor-mediated signaling pathway TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    Golgi stack IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    early endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    membrane raft IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    recycling endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    trans-Golgi network ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    trans-Golgi network membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    trans-Golgi network membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 

    General protein information

    Preferred Names
    CAP-Gly domain-containing linker protein 3
    Names
    CLIP-170-related 59 kDa protein
    cytoplasmic linker protein 170-related 59 kDa protein
    restin-like 1

    NCBI Reference Sequences (RefSeq)

    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_001199570.2NP_001186499.1  CAP-Gly domain-containing linker protein 3

      See identical proteins and their annotated locations for NP_001186499.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AK289509, AL117468
      Consensus CDS
      CCDS12486.1
      UniProtKB/Swiss-Prot
      Q96DZ5
      Related
      ENSP00000466832.1, ENST00000593074.5
      Conserved Domains (3) summary
      cd00204
      Location:112234
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      sd00045
      Location:120157
      ANK; ANK repeat [structural motif]
      pfam01302
      Location:418482
      CAP_GLY; CAP-Gly domain
    2. NM_015526.3NP_056341.1  CAP-Gly domain-containing linker protein 3

      See identical proteins and their annotated locations for NP_056341.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AJ427922, AL117468
      Consensus CDS
      CCDS12486.1
      UniProtKB/Swiss-Prot
      Q96DZ5
      Related
      ENSP00000353732.3, ENST00000360535.9
      Conserved Domains (3) summary
      cd00204
      Location:112234
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      sd00045
      Location:120157
      ANK; ANK repeat [structural motif]
      pfam01302
      Location:418482
      CAP_GLY; CAP-Gly domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

      Range
      36014660..36032873 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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