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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

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 CIViC summary , 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

Enhancers for CLIP3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19G036257 1 FANTOM5 Ensembl 8.9 -224.3 -224258 0.8 NRF1 PTTG1 ZNF274 POLR2A ZNF610 ZNF416 ZNF18 TRIM28 SETDB1 LINC00665 ZNF567 ZNF829 ZNF383 CLIP3 LOC100134317 COX7A1 APLP1 ZNF382 ZNF529
GH19G036229 0.5 FANTOM5 1.4 -196.2 -196209 0.4 ZNF274 ZNF140 TRIM28 LINC00665 APLP1 ZNF565 ZFP14 ZNF566 ARHGAP33 ZNF529 ZNF260 ZNF382 CLIP3
GH19G036035 0.9 ENCODE 0.7 -2.4 -2391 0.2 HDAC1 HDGF PKNOX1 ARNT ZBTB40 TCF12 GATA2 EGR1 ETV6 BCLAF1 WDR62 CLIP3 PIR59294
GH19G036041 1.1 Ensembl ENCODE 0.4 -8.6 -8555 1.8 ARID4B FEZF1 ZEB1 SCRT2 RCOR1 EGR2 ZNF362 SP5 CEBPB ZEB2 ZNF345 ZNF567 ZNF850 TBCB THAP8 WDR62 OVOL3 POLR2I ZNF829 TMEM147-AS1
GH19G036032 0.6 ENCODE 0.7 +0.7 664 1.2 ZNF263 CTCF MXI1 NRF1 REST EP300 ZNF560 POLR2A FOXP2 ZBTB33 WDR62 THAP8 TBCB CLIP3 GC19M038260
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLIP3 on UCSC Golden Path with GeneCards custom track

Promoters for CLIP3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000109103 643 1001 ZNF263 CTCF NRF1 REST EP300 ZNF560 POLR2A FOXP2 ZBTB33

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

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.

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:

Animal Model Products

CRISPR Products

miRNA for CLIP3 Gene

miRTarBase miRNAs that target CLIP3

Inhibitory RNA Products

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

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:

CRISPR Products

Inhibitory RNA Products

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

Primer Products

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 34 35
  • 98.07 (n)
oppossum
(Monodelphis domestica)
Mammalia CLIP3 35
  • 93 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CLIP3 34 35
  • 91.71 (n)
dog
(Canis familiaris)
Mammalia CLIP3 34 35
  • 91.53 (n)
mouse
(Mus musculus)
Mammalia Clip3 34 16 35
  • 89.34 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CLIP3 35
  • 78 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLIP3 35
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia clip3 34
  • 71.86 (n)
zebrafish
(Danio rerio)
Actinopterygii clip3 34 35
  • 72.09 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NIP100 35
  • 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 Sequence Context AA Info Type
rs1000028536 -- 36,032,921(+) CGGCG(G/T)GGGAG intron-variant, upstream-variant-2KB
rs1000105680 -- 36,029,821(+) TCCTC(C/T)TGGAG intron-variant
rs1000210396 -- 36,026,492(+) GATCA(C/T)CGTCC intron-variant
rs1000496667 -- 36,028,111(+) GCGGG(C/T)GGATC intron-variant
rs1000582183 -- 36,029,431(+) ACAGT(A/G)TACAT intron-variant

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

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

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

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 interacts with Akt and regulates Akt cellular compartmentalization. (PMID: 19139280) Ding J. … Du K. (Mol. Cell. Biol. 2009) 3 4 22 64
  2. 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 64
  3. Identification of a novel sequence motif recognized by the ankyrin repeat domain of zDHHC17/13 S-acyltransferases. (PMID: 26198635) Lemonidis K. … Chamberlain L.H. (J. Biol. Chem. 2015) 3 4 64
  4. DHHC17 palmitoylates ClipR-59 and modulates ClipR-59 association with the plasma membrane. (PMID: 24001771) Ren W. … Du K. (Mol. Cell. Biol. 2013) 3 4 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64

Products for CLIP3 Gene

Sources for CLIP3 Gene

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