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Aliases for CLIP3 Gene

Aliases for CLIP3 Gene

  • CAP-Gly Domain Containing Linker Protein 3 2 3 5
  • Cytoplasmic Linker Protein 170-Related 59 KDa Protein 3 4
  • CLIP-170-Related 59 KDa Protein 3 4
  • Restin-Like 1 2 3
  • CLIPR-59 3 4
  • CLIPR59 3 4
  • CLIP-170-Related 2
  • RSNL1 3

External Ids for CLIP3 Gene

Previous GeneCards Identifiers for CLIP3 Gene

  • GC19M041198
  • GC19M036505
  • GC19M033011
  • GC19M036015
  • GC19M036689

Summaries for CLIP3 Gene

Entrez Gene Summary for CLIP3 Gene

  • 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]

GeneCards Summary for CLIP3 Gene

CLIP3 (CAP-Gly Domain Containing Linker Protein 3) is a Protein Coding gene. Among its related pathways are Signaling by GPCR and TNF signaling (REACTOME). GO annotations related to this gene include microtubule binding and ganglioside binding. An important paralog of this gene is CLIP4.

UniProtKB/Swiss-Prot for CLIP3 Gene

  • Functions as a cytoplasmic linker protein. Involved in TGN-endosome dynamics. May modulate the cellular compartmentalization of AKT kinase family and promote its cell membrane localization, thereby playing a role in glucose transport in adipocytes.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLIP3 Gene

Genomics for CLIP3 Gene

Regulatory Elements for CLIP3 Gene

Promoters for CLIP3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around CLIP3 on UCSC Golden Path with GeneCards custom track

Genomic Location for CLIP3 Gene

Chromosome:
19
Start:
36,014,660 bp from pter
End:
36,033,343 bp from pter
Size:
18,684 bases
Orientation:
Minus strand

Genomic View for CLIP3 Gene

Genes around CLIP3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLIP3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLIP3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLIP3 Gene

Proteins for CLIP3 Gene

  • Protein details for CLIP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96DZ5-CLIP3_HUMAN
    Recommended name:
    CAP-Gly domain-containing linker protein 3
    Protein Accession:
    Q96DZ5
    Secondary Accessions:
    • A8K0E4
    • Q8WWL1
    • Q96C99
    • Q9UFT7

    Protein attributes for CLIP3 Gene

    Size:
    547 amino acids
    Molecular mass:
    59560 Da
    Quaternary structure:
    • Homodimer. Interacts with AKT1 and AKT2; when AKT1 and AKT2 are phosphorylated and activated, affinity is higher for AKT2.
    Miscellaneous:
    • The N-terminal half is dispensable for proper Golgi targeting, whereas the GoLD region is required.

    Three dimensional structures from OCA and Proteopedia for CLIP3 Gene

neXtProt entry for CLIP3 Gene

Proteomics data for CLIP3 Gene at MOPED

Post-translational modifications for CLIP3 Gene

  • Palmitoylation by ZDHHC17 regulates association with the plasma membrane.
  • Ubiquitination at Lys 520
  • Modification sites at PhosphoSitePlus

Other Protein References for CLIP3 Gene

No data available for DME Specific Peptides for CLIP3 Gene

Domains & Families for CLIP3 Gene

Gene Families for CLIP3 Gene

Protein Domains for CLIP3 Gene

Graphical View of Domain Structure for InterPro Entry

Q96DZ5

UniProtKB/Swiss-Prot:

CLIP3_HUMAN :
  • Microtubule association is inhibited by the ANK repeats and the Golgi localization region (GoLD).
  • Contains 3 ANK repeats.
Domain:
  • Microtubule association is inhibited by the ANK repeats and the Golgi localization region (GoLD).
  • Contains 2 CAP-Gly domains.
Similarity:
  • Contains 3 ANK repeats.
genes like me logo Genes that share domains with CLIP3: view

Function for CLIP3 Gene

Molecular function for CLIP3 Gene

UniProtKB/Swiss-Prot Function:
Functions as a cytoplasmic linker protein. Involved in TGN-endosome dynamics. May modulate the cellular compartmentalization of AKT kinase family and promote its cell membrane localization, thereby playing a role in glucose transport in adipocytes.
genes like me logo Genes that share phenotypes with CLIP3: view

Animal Models for CLIP3 Gene

MGI Knock Outs for CLIP3:

Animal Model Products

miRNA for CLIP3 Gene

miRTarBase miRNAs that target CLIP3

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CLIP3 Gene

Localization for CLIP3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLIP3 Gene

Cell membrane; Lipid-anchor. Cytoplasm. Golgi apparatus, Golgi stack. Note=Localized to Golgi stacks as well as on tubulovesicular elements juxtaposed to Golgi cisternae.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CLIP3 Gene COMPARTMENTS Subcellular localization image for CLIP3 gene
Compartment Confidence
cytosol 5
endosome 5
golgi apparatus 5
plasma membrane 5
nucleus 2
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for CLIP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005795 Golgi stack IEA --
GO:0005886 plasma membrane IMP 15262990
GO:0031901 early endosome membrane IDA 11854307
GO:0045121 membrane raft IDA 15262990
genes like me logo Genes that share ontologies with CLIP3: view

Pathways & Interactions for CLIP3 Gene

genes like me logo Genes that share pathways with CLIP3: view

Pathways by source for CLIP3 Gene

Gene Ontology (GO) - Biological Process for CLIP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010803 regulation of tumor necrosis factor-mediated signaling pathway TAS --
GO:0010828 positive regulation of glucose transport ISS --
GO:0031115 negative regulation of microtubule polymerization IMP 15262990
GO:0045444 fat cell differentiation ISS --
GO:0045807 positive regulation of endocytosis IMP 11854307
genes like me logo Genes that share ontologies with CLIP3: view

No data available for SIGNOR curated interactions for CLIP3 Gene

Drugs & Compounds for CLIP3 Gene

No Compound Related Data Available

Transcripts for CLIP3 Gene

Unigene Clusters for CLIP3 Gene

CAP-GLY domain containing linker protein 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for CLIP3 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b
SP1:
SP2: - - - - - - -
SP3: - - - - - - -

Relevant External Links for CLIP3 Gene

GeneLoc Exon Structure for
CLIP3
ECgene alternative splicing isoforms for
CLIP3

Expression for CLIP3 Gene

mRNA expression in normal human tissues for CLIP3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLIP3 Gene

This gene is overexpressed in Brain - Cortex (x4.3).

Protein differential expression in normal tissues from HIPED for CLIP3 Gene

This gene is overexpressed in Fetal Brain (47.0) and Spinal cord (19.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for CLIP3 Gene



SOURCE GeneReport for Unigene cluster for CLIP3 Gene Hs.466539

genes like me logo Genes that share expression patterns with CLIP3: view

Protein tissue co-expression partners for CLIP3 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for CLIP3 Gene

Orthologs for CLIP3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CLIP3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLIP3 36
  • 100 (a)
OneToOne
CLIP3 35
  • 98.07 (n)
  • 97.54 (a)
cow
(Bos Taurus)
Mammalia CLIP3 35
  • 91.71 (n)
  • 98.17 (a)
CLIP3 36
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CLIP3 36
  • 99 (a)
OneToOne
CLIP3 35
  • 91.53 (n)
  • 98.54 (a)
mouse
(Mus musculus)
Mammalia Clip3 16
Clip3 35
  • 89.34 (n)
  • 98.54 (a)
Clip3 36
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CLIP3 36
  • 93 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CLIP3 36
  • 78 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLIP3 36
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia clip3 35
  • 71.86 (n)
  • 82.07 (a)
zebrafish
(Danio rerio)
Actinopterygii clip3 35
  • 72.09 (n)
  • 80.23 (a)
clip3 36
  • 78 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NIP100 36
  • 4 (a)
OneToMany
Species with no ortholog for CLIP3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CLIP3 Gene

ENSEMBL:
Gene Tree for CLIP3 (if available)
TreeFam:
Gene Tree for CLIP3 (if available)

Paralogs for CLIP3 Gene

Paralogs for CLIP3 Gene

(2) SIMAP similar genes for CLIP3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with CLIP3: view

Variants for CLIP3 Gene

Sequence variations from dbSNP and Humsavar for CLIP3 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
VAR_027962 -

Structural Variations from Database of Genomic Variants (DGV) for CLIP3 Gene

Variant ID Type Subtype PubMed ID
nsv911638 CNV Loss 21882294
dgv51n68 CNV Loss 17160897
nsv911641 CNV Loss 21882294
esv1000212 CNV Deletion 20482838
nsv833815 CNV Loss 17160897

Variation tolerance for CLIP3 Gene

Residual Variation Intolerance Score: 18.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.58; 12.58% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLIP3 Gene

HapMap Linkage Disequilibrium report
CLIP3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLIP3 Gene

Disorders for CLIP3 Gene

Relevant External Links for CLIP3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CLIP3

No disorders were found for CLIP3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CLIP3 Gene

Publications for CLIP3 Gene

  1. CLIPR-59, a new trans-Golgi/TGN cytoplasmic linker protein belonging to the CLIP-170 family. (PMID: 11854307) Perez F. … Goud B. (J. Cell Biol. 2002) 2 3 4 67
  2. ClipR-59 interacts with Akt and regulates Akt cellular compartmentalization. (PMID: 19139280) Ding J. … Du K. (Mol. Cell. Biol. 2009) 3 23
  3. CLIPR-59 is a lipid raft-associated protein containing a cytoskeleton-associated protein glycine-rich domain (CAP-Gly) that perturbs microtubule dynamics. (PMID: 15262990) Lallemand-Breitenbach V. … Perez F. (J. Biol. Chem. 2004) 3 23
  4. Spy1 induces de-ubiquitinating of RIP1 arrest and confers glioblastoma's resistance to tumor necrosis factor (TNF-I+)-induced apoptosis through suppressing the association of CLIPR-59 and CYLD. (PMID: 26017671) Ding Z. … Shen A. (Cell Cycle 2015) 3
  5. DHHC17 palmitoylates ClipR-59 and modulates ClipR-59 association with the plasma membrane. (PMID: 24001771) Ren W. … Du K. (Mol. Cell. Biol. 2013) 3

Products for CLIP3 Gene

Sources for CLIP3 Gene

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