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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
  • CAP-Gly Domain-Containing Linker Protein 3 3
  • CLIP-170-Related 2
  • RSNL1 3

External Ids for CLIP3 Gene

Previous GeneCards Identifiers for CLIP3 Gene

  • GC19M041198
  • GC19M036505
  • GC19M033011
  • GC19M036015
  • GC19M036689
  • GC19M036688
  • GC19M036812
  • GC19M037408
  • GC19M037738
  • GC19M038033

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). Gene Ontology (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.

Additional gene information for CLIP3 Gene

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

Genomics for CLIP3 Gene

GeneHancer (GH) Regulatory Elements for CLIP3 Gene

Promoters and enhancers for CLIP3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19I036032 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 550.8 +0.7 663 1.2 MXI1 POLR2A NRF1 ZBTB33 CLIP3 WDR62 THAP8 TBCB GC19M038860 LOC101927572
GH19I035508 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE 32.1 +523.5 523478 2.5 SMAD1 MLX ARID4B SIN3A ZNF2 ZBTB7B IRF4 SLC30A9 ZNF143 KLF13 DMKN ZFP82 CLIP3 ARHGAP33 TMEM147-AS1 LINC00665 ZNF566 PROSER3 KMT2B ZNF599
GH19I035897 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 20.8 +129.3 129285 13 CLOCK FEZF1 IRF4 YY1 ZNF213 ZNF143 ZNF548 SP3 NFYC ZFP41 NFKBID TYROBP HCST ENSG00000280194 ZNF567 ZNF566 ZNF790 ZNF529 TMEM147-AS1 ZNF260
GH19I035246 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 20.7 +784.7 784718 3.4 CLOCK MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 ZNF416 ZNF143 LSR RBM42 KMT2B ZNF599 TMEM147-AS1 HAUS5 ZNF792 ZNF30 ZNF302 KIAA0355
GH19I035266 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 20.7 +764.9 764882 4.2 HDGF PKNOX1 SMAD1 ARID4B SIN3A ZNF2 IRF4 YY1 POLR2B ZNF766 USF2 ZNF599 HAUS5 TMEM147-AS1 KMT2B PROSER3 ZNF146 ZNF792 ZNF565 RBM42
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CLIP3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLIP3 gene promoter:

Genomic Locations for CLIP3 Gene

Genomic Locations for CLIP3 Gene
chr19:36,014,660-36,033,343
(GRCh38/hg38)
Size:
18,684 bases
Orientation:
Minus strand
chr19:36,505,562-36,524,245
(GRCh37/hg19)

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 (PubMed:19139280). Interacts with ZDHHC13 (via ANK repeats) (PubMed:26198635). Interacts with ZDHHC17 (via ANK repeats) (PubMed:26198635, PubMed:28882895).
    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

Post-translational modifications for CLIP3 Gene

  • Palmitoylation by ZDHHC17 regulates association with the plasma membrane.
  • Ubiquitination at posLast=520520

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

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

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).
Domain:
  • Microtubule association is inhibited by the ANK repeats and the Golgi localization region (GoLD).
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.

Phenotypes From GWAS Catalog for CLIP3 Gene

Gene Ontology (GO) - Molecular Function for CLIP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 26198635
GO:0008017 microtubule binding IMP 20052288
GO:0035594 ganglioside binding IDA 20052288
genes like me logo Genes that share ontologies with CLIP3: view
genes like me logo Genes that share phenotypes with CLIP3: view

Animal Models for CLIP3 Gene

MGI Knock Outs for CLIP3:

miRNA for CLIP3 Gene

miRTarBase miRNAs that target CLIP3

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLIP3 gene
Compartment Confidence
plasma membrane 5
cytosol 5
golgi apparatus 5
endosome 5
nucleus 2
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for CLIP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005794 Golgi apparatus IEA --
GO:0005795 Golgi stack IEA --
GO:0005802 trans-Golgi network ISS --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with CLIP3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLIP3 Gene

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:0001934 positive regulation of protein phosphorylation ISS --
GO:0010803 regulation of tumor necrosis factor-mediated signaling pathway TAS --
GO:0010828 positive regulation of glucose transport ISS --
GO:0018230 peptidyl-L-cysteine S-palmitoylation IMP 15262990
GO:0031115 negative regulation of microtubule polymerization IMP 15262990
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:

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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



Protein tissue co-expression partners for CLIP3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CLIP3 Gene:

CLIP3

SOURCE GeneReport for Unigene cluster for CLIP3 Gene:

Hs.466539

Evidence on tissue expression from TISSUES for CLIP3 Gene

  • Nervous system(5)
  • Skin(4)
genes like me logo Genes that share expression patterns with CLIP3: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33 34
  • 98.07 (n)
oppossum
(Monodelphis domestica)
Mammalia CLIP3 34
  • 93 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CLIP3 33 34
  • 91.71 (n)
dog
(Canis familiaris)
Mammalia CLIP3 33 34
  • 91.53 (n)
mouse
(Mus musculus)
Mammalia Clip3 33 16 34
  • 89.34 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CLIP3 34
  • 78 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLIP3 34
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia clip3 33
  • 71.86 (n)
zebrafish
(Danio rerio)
Actinopterygii clip3 33 34
  • 72.09 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NIP100 34
  • 4 (a)
OneToMany
Species where no ortholog for CLIP3 was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs1000028536 -- 36,032,921(-) G/T upstream_transcript_variant
rs1000105680 -- 36,029,821(-) T/C intron_variant
rs1000210396 -- 36,026,492(-) C/T intron_variant
rs1000496667 -- 36,028,111(-) C/T intron_variant
rs1000582183 -- 36,029,431(-) A/G intron_variant

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

Variant ID Type Subtype PubMed ID
nsv833815 CNV loss 17160897
esv3644244 CNV gain 21293372
esv1000212 CNV deletion 20482838
dgv51n68 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)

Additional Variant Information for CLIP3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLIP3

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

Disorders for CLIP3 Gene

Additional Disease Information for 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 interacts with Akt and regulates Akt cellular compartmentalization. (PMID: 19139280) Ding J … Du K (Molecular and cellular biology 2009) 3 4 22 58
  2. CLIPR-59, a new trans-Golgi/TGN cytoplasmic linker protein belonging to the CLIP-170 family. (PMID: 11854307) Perez F … Goud B (The Journal of cell biology 2002) 2 3 4 58
  3. Identification of a Novel Sequence Motif Recognized by the Ankyrin Repeat Domain of zDHHC17/13 S-Acyltransferases. (PMID: 26198635) Lemonidis K … Chamberlain LH (The Journal of biological chemistry 2015) 3 4 58
  4. DHHC17 palmitoylates ClipR-59 and modulates ClipR-59 association with the plasma membrane. (PMID: 24001771) Ren W … Du K (Molecular and cellular biology 2013) 3 4 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for CLIP3 Gene

Sources for CLIP3 Gene

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