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

Gene ID: 51138, updated on 9-Dec-2018

Summary

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
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

Genomic context

See COPS4 in Genome Data Viewer
Location:
4q21.22
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 4 NC_000004.12 (83035086..83075818)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (83956239..83996971)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene THAP9 antisense RNA 1 Neighboring gene THAP domain containing 9 Neighboring gene lin-54 DREAM MuvB core complex component Neighboring gene RNA, U6 small nuclear 615, pseudogene Neighboring gene placenta specific 8 Neighboring gene coenzyme Q2, polyprenyltransferase Neighboring gene aminomethyltransferase pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

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 BioSystems

  • Cargo recognition for clathrin-mediated endocytosis, organism-specific biosystem (from REACTOME)
    Cargo recognition for clathrin-mediated endocytosis, organism-specific biosystemRecruitment of plasma membrane-localized cargo into clathrin-coated endocytic vesicles is mediated by interaction with a variety of clathrin-interacting proteins collectively called CLASPs (clathrin-...
  • Clathrin-mediated endocytosis, organism-specific biosystem (from REACTOME)
    Clathrin-mediated endocytosis, organism-specific biosystemClathrin-mediated endocytosis (CME) is one of a number of process that control the uptake of material from the plasma membrane, and leads to the formation of clathrin-coated vesicles (Pearse et al, 1...
  • DNA Damage Recognition in GG-NER, organism-specific biosystem (from REACTOME)
    DNA Damage Recognition in GG-NER, organism-specific biosystemIn global genome nucleotide excision repair (GG-NER), the DNA damage is recognized by two protein complexes. The first complex consists of XPC, RAD23A or RAD23B, and CETN2. This complex probes the DN...
  • DNA Repair, organism-specific biosystem (from REACTOME)
    DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
  • Formation of TC-NER Pre-Incision Complex, organism-specific biosystem (from REACTOME)
    Formation of TC-NER Pre-Incision Complex, organism-specific biosystemFormation of TC-NER pre-incision complex is initiated when the RNA polymerase II (RNA Pol II) complex stalls at a DNA damage site. The stalling is caused by misincorporation of a ribonucleotide oppos...
  • Global Genome Nucleotide Excision Repair (GG-NER), organism-specific biosystem (from REACTOME)
    Global Genome Nucleotide Excision Repair (GG-NER), organism-specific biosystemThe DNA damage in GG-NER is recognized by the joint action of two protein complexes. The first complex is composed of XPC, RAD23A or RAD23B and CETN2. The second complex, known as the UV-DDB complex,...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Nucleotide Excision Repair, organism-specific biosystem (from REACTOME)
    Nucleotide Excision Repair, organism-specific biosystemNucleotide excision repair (NER) was first described in the model organism E. coli in the early 1960s as a process whereby bulky base damage is enzymatically removed from DNA, facilitating the recove...
  • Transcription-Coupled Nucleotide Excision Repair (TC-NER), organism-specific biosystem (from REACTOME)
    Transcription-Coupled Nucleotide Excision Repair (TC-NER), organism-specific biosystemDNA damage in transcribed strands of active genes is repaired through a specialized nucleotide excision repair (NER) pathway known as transcription-coupled nucleotide excision repair (TC-NER). TC-NER...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC10899, MGC15160

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to NEDD8-specific protease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
NEDD8-specific protease activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
nucleotide-excision repair, DNA damage recognition TAS
Traceable Author Statement
more info
 
post-translational protein modification TAS
Traceable Author Statement
more info
 
protein deneddylation IDA
Inferred from Direct Assay
more info
PubMed 
protein deneddylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription-coupled nucleotide-excision repair TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
COP9 signalosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
COP9 signalosome IDA
Inferred from Direct Assay
more info
PubMed 
cell junction IDA
Inferred from Direct Assay
more info
 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
nuclear speck IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus HDA PubMed 
synaptic vesicle IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

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_001258006.1NP_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/Swiss-Prot
    Q9BT78
    Related
    ENSP00000425976.1, ENST00000509093.5
    Conserved Domains (1) summary
    COG5071
    Location:71337
    RPN5; 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
  2. NM_001330727.1NP_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, CD690475, KU178634
    Consensus CDS
    CCDS82935.1
    UniProtKB/Swiss-Prot
    Q9BT78
    UniProtKB/TrEMBL
    B3KM48, D6RAX7
    Related
    ENSP00000424655.1, ENST00000511653.1
    Conserved Domains (2) summary
    COG5071
    Location:71374
    RPN5; 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
    pfam01399
    Location:264362
    PCI; PCI domain
  3. NM_016129.3NP_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
    Q9BT78
    UniProtKB/TrEMBL
    A0A0S2Z5H7, B3KM48
    Related
    ENSP00000264389.2, ENST00000264389.6
    Conserved Domains (2) summary
    COG5071
    Location:71377
    RPN5; 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
    pfam01399
    Location:264362
    PCI; PCI domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p12 Primary Assembly

    Range
    83035086..83075818
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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