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

Gene ID: 25999, updated on 17-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
109.20190607 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (36014660..36032873, 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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