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

    Gene ID: 51138, updated on 28-Oct-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
    mouse all
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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 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 variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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