This gene encodes one of eight subunits composing COP9 signalosome, a highly conserved protein complex that functions as an important regulator in multiple signaling pathways. The structure and function of COP9 signalosome is similar to that of the 19S regulatory particle of 26S proteasome. COP9 signalosome has been shown to interact with SCF-type E3 ubiquitin ligases and act a... See more...

Aliases for COPS4 Gene

Aliases for COPS4 Gene

  • COP9 Signalosome Subunit 4 2 3 5
  • CSN4 2 3 4
  • JAB1-Containing Signalosome Subunit 4 3 4
  • COP9 Signalosome Complex Subunit 4 3 4
  • Signalosome Subunit 4 3 4
  • SGN4 3 4
  • COP9 (Constitutive Photomorphogenic, Arabidopsis, Homolog) Subunit 4 2
  • COP9 Constitutive Photomorphogenic Homolog Subunit 4 (Arabidopsis) 2
  • COP9 Constitutive Photomorphogenic-Like Protein Subunit 4 3
  • COP9 Constitutive Photomorphogenic Homolog Subunit 4 3
  • Testis Tissue Sperm-Binding Protein Li 42a 3
  • COPS4 5

External Ids for COPS4 Gene

Previous GeneCards Identifiers for COPS4 Gene

  • GC04P083880
  • GC04P084249
  • GC04P084348
  • GC04P084414
  • GC04P084313
  • GC04P083955
  • GC04P079696

Summaries for COPS4 Gene

Entrez Gene Summary for COPS4 Gene

  • This gene encodes one of eight subunits composing COP9 signalosome, a highly conserved protein complex that functions as an important regulator in multiple signaling pathways. The structure and function of COP9 signalosome is similar to that of the 19S regulatory particle of 26S proteasome. COP9 signalosome has been shown to interact with SCF-type E3 ubiquitin ligases and act as a positive regulator of E3 ubiquitin ligases. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

GeneCards Summary for COPS4 Gene

COPS4 (COP9 Signalosome Subunit 4) is a Protein Coding gene. Diseases associated with COPS4 include Xeroderma Pigmentosum, Complementation Group E and Retinitis Pigmentosa 32. Among its related pathways are Clathrin-mediated endocytosis and Transcription-Coupled Nucleotide Excision Repair (TC-NER). An important paralog of this gene is PSMD12.

UniProtKB/Swiss-Prot Summary for COPS4 Gene

  • Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. Also involved in the deneddylation of non-cullin subunits such as STON2. The complex is also involved in phosphorylation of p53/TP53, c-jun/JUN, IkappaBalpha/NFKBIA, ITPK1, IRF8/ICSBP and SNAPIN, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.

Gene Wiki entry for COPS4 Gene

Additional gene information for COPS4 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for COPS4 Gene

Genomics for COPS4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for COPS4 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
GH04J083033 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 600.7 +1.2 1156 4 SP1 HNRNPL CREB1 GATAD2A CTCF PRDM10 ZNF629 REST TFE3 SIX5 COPS4 HELQ HNRNPD THAP9-AS1 ABRAXAS1 HNRNPDL SEC31A RF00017-4349 PLAC8
GH04J083107 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 0.2 +77.5 77451 9.3 HNRNPL CREB1 CTCF TEAD4 PRDM10 REST POLR2A BACH1 TARDBP FOXA1 PLAC8 HELQ THAP9 LIN54 COQ2 HPSE lnc-LIN54-3 lnc-COPS4-1 COPS4
GH04J083019 Enhancer 0.8 ENCODE 0.4 -14.2 -14177 0.7 LEF1 PKNOX1 DPF2 HDAC1 SOX6 TCF12 EP300 ZNF766 HMBOX1 RUNX3 THAP9-AS1 LIN54 COPS4 piR-34822-248
GH04J083074 Enhancer 1.1 Ensembl ENCODE dbSUPER 0.3 +40.7 40653 2.6 CTCF FOXA1 ZNF143 PKNOX1 REST RAD21 TRIM22 ARID3A HMBOX1 JUND ENSG00000286035 lnc-PLAC8-1 COPS4 PLAC8
GH04J083022 Enhancer 0.7 FANTOM5 Ensembl 0.4 -11.3 -11346 2.2 CEBPB BCOR ZNF146 KDM1A ZMYM3 ZNF280D THAP9-AS1 THAP9 HPSE PLAC8 COQ2 HELQ piR-34822-248 COPS4 LIN54
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COPS4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for COPS4

Top Transcription factor binding sites by QIAGEN in the COPS4 gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • MAZR
  • Nkx2-5
  • Nkx5-1
  • RP58

Genomic Locations for COPS4 Gene

Genomic Locations for COPS4 Gene
chr4:83,034,447-83,075,818
(GRCh38/hg38)
Size:
41,372 bases
Orientation:
Plus strand
chr4:83,955,600-83,996,971
(GRCh37/hg19)
Size:
41,372 bases
Orientation:
Plus strand

Genomic View for COPS4 Gene

Genes around COPS4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COPS4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COPS4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COPS4 Gene

Proteins for COPS4 Gene

  • Protein details for COPS4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BT78-CSN4_HUMAN
    Recommended name:
    COP9 signalosome complex subunit 4
    Protein Accession:
    Q9BT78
    Secondary Accessions:
    • B3KN88
    • B3KST5
    • Q561W7
    • Q9NW31
    • Q9Y677

    Protein attributes for COPS4 Gene

    Size:
    406 amino acids
    Molecular mass:
    46269 Da
    Quaternary structure:
    • Component of the CSN complex, composed of COPS1/GPS1, COPS2, COPS3, COPS4, COPS5, COPS6, COPS7 (COPS7A or COPS7B), COPS8 and COPS9 isoform 1 (PubMed:18850735, PubMed:26456823). In the complex, it probably interacts directly with COPS1, COPS2, COPS3, COPS5, COPS6, COPS7 (COPS7A or COPS7B) and COPS8 (PubMed:18850735). Interacts with TOR1A; the interaction is direct and associates TOR1A and SNAPIN with the CSN complex (PubMed:21102408). Interacts with STON2; controls STON2 neddylation levels (PubMed:21102408). Interacts with ERCC6 (PubMed:26030138).

    Three dimensional structures from OCA and Proteopedia for COPS4 Gene

    Alternative splice isoforms for COPS4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COPS4 Gene

Post-translational modifications for COPS4 Gene

  • Ubiquitination at Lys20, Lys227, Lys266, and Lys372
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for COPS4 Gene

Domains & Families for COPS4 Gene

Gene Families for COPS4 Gene

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

Protein Domains for COPS4 Gene

Suggested Antigen Peptide Sequences for COPS4 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ36919 fis, clone BRACE2003987, highly similar to COP9 signalosome complex subunit 4 (B3KST5_HUMAN)
  • JAB1-containing signalosome subunit 4 (CSN4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BT78

UniProtKB/Swiss-Prot:

CSN4_HUMAN :
  • Belongs to the CSN4 family.
Family:
  • Belongs to the CSN4 family.
genes like me logo Genes that share domains with COPS4: view

Function for COPS4 Gene

Molecular function for COPS4 Gene

UniProtKB/Swiss-Prot Function:
Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. Also involved in the deneddylation of non-cullin subunits such as STON2. The complex is also involved in phosphorylation of p53/TP53, c-jun/JUN, IkappaBalpha/NFKBIA, ITPK1, IRF8/ICSBP and SNAPIN, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.

Phenotypes From GWAS Catalog for COPS4 Gene

Gene Ontology (GO) - Molecular Function for COPS4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0019784 NEDD8-specific protease activity IBA,TAS --
genes like me logo Genes that share ontologies with COPS4: view
genes like me logo Genes that share phenotypes with COPS4: view

Animal Models for COPS4 Gene

MGI Knock Outs for COPS4:
  • Cops4 Cops4<tm1a(EUCOMM)Hmgu>

Animal Model Products

CRISPR Products

miRNA for COPS4 Gene

miRTarBase miRNAs that target COPS4

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COPS4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for COPS4 Gene

Localization for COPS4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COPS4 Gene

Cytoplasm. Nucleus. Cytoplasmic vesicle, secretory vesicle, synaptic vesicle.

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 COPS4 gene
Compartment Confidence
nucleus 5
cytosol 4
cytoskeleton 2
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
golgi apparatus 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for COPS4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,HDA 21630459
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0008021 synaptic vesicle IEA,IDA 21102408
genes like me logo Genes that share ontologies with COPS4: view

Pathways & Interactions for COPS4 Gene

genes like me logo Genes that share pathways with COPS4: view

Gene Ontology (GO) - Biological Process for COPS4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000338 protein deneddylation IMP 21102408
GO:0000715 nucleotide-excision repair, DNA damage recognition TAS --
GO:0006283 transcription-coupled nucleotide-excision repair TAS --
GO:0043687 post-translational protein modification TAS --
genes like me logo Genes that share ontologies with COPS4: view

No data available for SIGNOR curated interactions for COPS4 Gene

Drugs & Compounds for COPS4 Gene

No Compound Related Data Available

Transcripts for COPS4 Gene

mRNA/cDNA for COPS4 Gene

3 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COPS4

Alternative Splicing Database (ASD) splice patterns (SP) for COPS4 Gene

No ASD Table

Relevant External Links for COPS4 Gene

GeneLoc Exon Structure for
COPS4

Expression for COPS4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for COPS4 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for COPS4 Gene



Protein tissue co-expression partners for COPS4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for COPS4

SOURCE GeneReport for Unigene cluster for COPS4 Gene:

Hs.190384

Evidence on tissue expression from TISSUES for COPS4 Gene

  • Nervous system(4.8)
  • Muscle(4.4)
  • Liver(4.4)
  • Pancreas(4.2)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with COPS4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for COPS4 Gene

Orthologs for COPS4 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for COPS4 Gene

Organism Taxonomy Gene Similarity Type Details
Oppossum
(Monodelphis domestica)
Mammalia COPS4 31
  • 100 (a)
OneToOne
Chimpanzee
(Pan troglodytes)
Mammalia COPS4 30 31
  • 99.67 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 98 (a)
OneToMany
-- 31
  • 95 (a)
OneToMany
Dog
(Canis familiaris)
Mammalia COPS4 30 31
  • 95.48 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia COPS4 30 31
  • 95.4 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Cops4 30 17 31
  • 90.64 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Cops4 30
  • 88.92 (n)
Chicken
(Gallus gallus)
Aves COPS4 30 31
  • 84.07 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia COPS4 31
  • 94 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia cops4 30
  • 80.05 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.33935 30
Zebrafish
(Danio rerio)
Actinopterygii cops4 30 31
  • 78.65 (n)
OneToOne
wufc90c08 30
Fruit Fly
(Drosophila melanogaster)
Insecta CSN4 30 31 32
  • 64.38 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009834 30
  • 63.61 (n)
Worm
(Caenorhabditis elegans)
Secernentea csn-4 31
  • 36 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons COP8 30
  • 55.11 (n)
Rice
(Oryza sativa)
Liliopsida Os03g0197400 30
  • 55.77 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 68 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.2409 30
Species where no ortholog for COPS4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • 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)
  • 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)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for COPS4 Gene

ENSEMBL:
Gene Tree for COPS4 (if available)
TreeFam:
Gene Tree for COPS4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for COPS4: view image

Paralogs for COPS4 Gene

Paralogs for COPS4 Gene

genes like me logo Genes that share paralogs with COPS4: view

Variants for COPS4 Gene

Additional dbSNP identifiers (rs#s) for COPS4 Gene

Structural Variations from Database of Genomic Variants (DGV) for COPS4 Gene

Variant ID Type Subtype PubMed ID
esv2658715 CNV deletion 23128226
nsv1123813 CNV deletion 24896259
nsv478738 CNV novel sequence insertion 20440878
nsv829990 CNV gain 17160897

Variation tolerance for COPS4 Gene

Residual Variation Intolerance Score: 27.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.57; 12.30% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for COPS4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
COPS4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for COPS4 Gene

Disorders for COPS4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for COPS4 Gene - From: DISEASES and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search COPS4 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with COPS4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for COPS4 Gene

Publications for COPS4 Gene

  1. Identification of Novel Proteins Co-Purifying with Cockayne Syndrome Group B (CSB) Reveals Potential Roles for CSB in RNA Metabolism and Chromatin Dynamics. (PMID: 26030138) Nicolai S … Proietti-De-Santis L (PloS one 2015) 3 4
  2. CSN complex controls the stability of selected synaptic proteins via a torsinA-dependent process. (PMID: 21102408) Granata A … Warner TT (The EMBO journal 2011) 3 4
  3. Characterization of the human COP9 signalosome complex using affinity purification and mass spectrometry. (PMID: 18850735) Fang L … Huang L (Journal of proteome research 2008) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for COPS4 Gene

Sources for COPS4 Gene