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COPS4 COP9 signalosome subunit 4 [ Homo sapiens (human) ]

Gene ID: 51138, updated on 2-Nov-2024

Summary

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Official Symbol
COPS4provided by HGNC
Official Full Name
COP9 signalosome subunit 4provided by HGNC
Primary source
HGNC:HGNC:16702
See related
Ensembl:ENSG00000138663 MIM:616008; AllianceGenome:HGNC:16702
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
CSN4; SGN4
Summary
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]
Expression
Ubiquitous expression in testis (RPKM 26.4), brain (RPKM 21.8) and 25 other tissues See more
Orthologs
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Genomic context

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See COPS4 in Genome Data Viewer
Location:
4q21.22
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (83035183..83075818)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (86364418..86405022)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (83956336..83996971)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:83821853-83822372 Neighboring gene THAP9 antisense RNA 1 Neighboring gene THAP domain containing 9 Neighboring gene lin-54 DREAM MuvB core complex component Neighboring gene ReSE screen-validated silencer GRCh37_chr4:83887737-83887940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15537 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:83933797-83934682 Neighboring gene RNA, U6 small nuclear 615, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21670 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21671 Neighboring gene Sharpr-MPRA regulatory region 7954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21673 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:83956719-83957224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21677 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21678 Neighboring gene placenta associated 8 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:84042619-84042813 Neighboring gene uncharacterized LOC124900167 Neighboring gene Sharpr-MPRA regulatory region 10366 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:84091705-84092904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21680 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:84102258-84102833 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:84115858-84116088 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21681

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. [Effects of CSN4 knockdown on proliferation and apoptosis of breast cancer MDA-MB-231 cells]. Yu TL, et al. Yi Chuan, 2019 Apr 20. PMID 30992253
  2. COP9 signalosome revisited: a novel mediator of protein degradation. Schwechheimer C, et al. Trends Cell Biol, 2001 Oct. PMID 11567875
  3. Aberrant expression of signaling-related proteins 14-3-3 gamma and RACK1 in fetal Down syndrome brain (trisomy 21). Peyrl A, et al. Electrophoresis, 2002 Jan. PMID 11824616
  4. Intracellular IL-1 receptor antagonist type 1 inhibits IL-1-induced cytokine production in keratinocytes through binding to the third component of the COP9 signalosome. Banda NK, et al. J Immunol, 2005 Mar 15. PMID 15749898
  5. Interaction between interferon consensus sequence-binding protein and COP9/signalosome subunit CSN2 (Trip15). A possible link between interferon regulatory factor signaling and the COP9/signalosome. Cohen H, et al. J Biol Chem, 2000 Dec 15. PMID 10991940

See all (161) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CSN4 modulates the proliferation and apoptosis of breast cancer cells by regulating the expression of CDK6 and Caspase3 genes and thereby tumorigenesis
    Title: [Effects of CSN4 knockdown on proliferation and apoptosis of breast cancer MDA-MB-231 cells].
  2. CSN4 silencing decreases CSN5 protein levels and suggest that the CSN4 effects on sGCA1 and p53 proteins are mediated by CSN5.
    Title: COP9 subunits 4 and 5 target soluble guanylyl cyclase α1 and p53 in prostate cancer cells.
  3. Identified is a novel-binding partner of torsin A, the subunit 4 (CSN4) of CSN signalosome.
    Title: CSN complex controls the stability of selected synaptic proteins via a torsinA-dependent process.
  4. Level in fetal Down syndrome brain found to be comparable to that of controls.
    Title: Aberrant expression of signaling-related proteins 14-3-3 gamma and RACK1 in fetal Down syndrome brain (trisomy 21).
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See Variation Viewer (GRCh37.p13)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Vpr vpr HIV-1 Vpr is identified to have a physical interaction with COP9 constitutive photomorphogenic homolog subunit 4 (COPS4; CSN4) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC10899, MGC15160

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables deNEDDylase activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in protein deneddylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein deneddylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein neddylation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of protein neddylation NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of COP9 signalosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of COP9 signalosome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of COP9 signalosome IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of COP9 signalosome ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cell junction IDA
Inferred from Direct Assay
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in nuclear speck IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus HDA PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in synaptic vesicle IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
COP9 signalosome complex subunit 4
Names
COP9 constitutive photomorphogenic homolog subunit 4
COP9 constitutive photomorphogenic-like protein subunit 4
JAB1-containing signalosome subunit 4
signalosome subunit 4
testis tissue sperm-binding protein Li 42a

NCBI Reference Sequences (RefSeq)

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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_001258006.2 → NP_001244935.1  COP9 signalosome complex subunit 4 isoform 2

    See identical proteins and their annotated locations for NP_001244935.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate coding exon compared to variant 1, that causes a frameshift. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AK094238, BC009292
    Consensus CDS
    CCDS58909.1
    UniProtKB/TrEMBL
    B3KM48, Q53FV3
    Related
    ENSP00000425976.1, ENST00000509093.5
    Conserved Domains (1) summary
    COG5071
    Location:71 → 337
    RPN5; 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

  2. NM_001330727.2 → NP_001317656.1  COP9 signalosome complex subunit 4 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) includes an alternate penultimate exon, compared to variant 1, resulting in a novel 3' coding region and longer 3' UTR. The resulting isoform (3) has a longer and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AK001148, BC004302, BC009292, KU178634
    Consensus CDS
    CCDS82935.1
    UniProtKB/TrEMBL
    B3KM48, D6RAX7, Q53FV3
    Related
    ENSP00000424655.1, ENST00000511653.1
    Conserved Domains (2) summary
    COG5071
    Location:71 → 374
    RPN5; 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
    pfam01399
    Location:264 → 362
    PCI; PCI domain

  3. NM_016129.3 → NP_057213.2  COP9 signalosome complex subunit 4 isoform 1

    See identical proteins and their annotated locations for NP_057213.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform (1).
    Source sequence(s)
    AK001148, BC004302, BC009292
    Consensus CDS
    CCDS3600.1
    UniProtKB/Swiss-Prot
    B3KN88, B3KST5, Q561W7, Q9BT78, Q9NW31, Q9Y677
    UniProtKB/TrEMBL
    A0A0S2Z5H7, B3KM48, Q53FV3
    Related
    ENSP00000264389.2, ENST00000264389.7
    Conserved Domains (3) summary
    COG5071
    Location:71 → 377
    RPN5; 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
    pfam18420
    Location:365 → 406
    CSN4_RPN5_eIF3a; CSN4/RPN5/eIF3a helix turn helix domain
    pfam01399
    Location:264 → 362
    PCI; PCI domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    83035183..83075818
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    86364418..86405022
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BT78.1 GenPept UniProtKB/Swiss-Prot:Q9BT78

Gene LinkOut

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