Human Gene COPS6 (uc003usu.3) Description and Page Index
  Description: Homo sapiens COP9 signalosome subunit 6 (COPS6), mRNA.
RefSeq Summary (NM_006833): The protein encoded by this gene is one of the eight subunits of 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. This protein belongs to translation initiation factor 3 (eIF3) superfamily. It is involved in the regulation of cell cycle and likely to be a cellular cofactor for HIV-1 accessory gene product Vpr. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR5189658.127123.1, SRR3476690.539176.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000303904.8/ ENSP00000304102.3 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr7:99,686,583-99,689,822 Size: 3,240 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr7:99,686,614-99,689,412 Size: 2,799 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr7:99,686,583-99,689,822)mRNA (may differ from genome)Protein (327 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=COP9 signalosome complex subunit 6; Short=SGN6; Short=Signalosome subunit 6; AltName: Full=JAB1-containing signalosome subunit 6; AltName: Full=MOV34 homolog; AltName: Full=Vpr-interacting protein; Short=hVIP;
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. The complex is also involved in phosphorylation of p53/TP53, c-jun/JUN, IkappaBalpha/NFKBIA, ITPK1 and IRF8, 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. Has some glucocorticoid receptor- responsive activity. Stabilizes RFWD2/COP1 through reducing RFWD2 auto-ubiquitination and decelerating RFWD2 turnover rate, hence regulates the ubiquitination of RFWD2 targets.
SUBUNIT: Component of the CSN complex, composed of COPS1/GPS1, COPS2, COPS3, COPS4, COPS5, COP6, COPS7 (COPS7A or COPS7B) and COPS8. In the complex, it probably interacts directly with COPS2, COPS4, COPS5 and COPS7 (COPS7A or COPS7B). Interacts with the translation initiation factor EIF3S6. Interacts weakly with RBX1. Interacts with the HIV-1 protein Vpr. Directly interacts with RFWD2 and 14-3-3 protein sigma/SFN.
INTERACTION: Q9BX70:BTBD2; NbExp=2; IntAct=EBI-486838, EBI-710091; Q8NHY2:RFWD2; NbExp=3; IntAct=EBI-486838, EBI-1176214; P31947:SFN; NbExp=7; IntAct=EBI-486838, EBI-476295;
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=The interaction with HIV-1 Vpr protein possibly leads its translocation to a perinuclear region.
TISSUE SPECIFICITY: Widely expressed.
MISCELLANEOUS: Although strongly related to metalloprotease proteins, it lacks the JAMM motif that probably constitutes the catalytic center. Its function as protease is therefore unsure.
SIMILARITY: Belongs to the peptidase M67A family. CSN6 subfamily.
SIMILARITY: Contains 1 MPN (JAB/Mov34) domain.
SEQUENCE CAUTION: Sequence=AAD03469.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  MalaCards Disease Associations
  MalaCards Gene Search: COPS6
Diseases sorted by gene-association score: hiv-1 (6)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 65.58 RPKM in Pituitary
Total median expression: 2716.23 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -8.8031-0.284 Picture PostScript Text
3' UTR -128.90410-0.314 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000555 - JAB1_Mov34_MPN_PAD1
IPR024969 - Rpn11/EIF3F_C

Pfam Domains:
PF01398 - JAB1/Mov34/MPN/PAD-1 ubiquitin protease
PF13012 - Maintenance of mitochondrial structure and function

ModBase Predicted Comparative 3D Structure on Q7L5N1
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  Protein SequenceProtein SequenceProtein Sequence 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0000338 protein deneddylation
GO:0000715 nucleotide-excision repair, DNA damage recognition
GO:0006283 transcription-coupled nucleotide-excision repair
GO:0016032 viral process
GO:0043687 post-translational protein modification

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0008180 COP9 signalosome

-  Descriptions from all associated GenBank mRNAs
  LF384057 - JP 2014500723-A/191560: Polycomb-Associated Non-Coding RNAs.
AK312024 - Homo sapiens cDNA, FLJ92300, Homo sapiens COP9 subunit 6 (MOV34 homolog, 34 kD) (COPS6), mRNA.
AK295237 - Homo sapiens cDNA FLJ57370 complete cds, highly similar to COP9 signalosome complex subunit 6.
BC002520 - Homo sapiens COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis), mRNA (cDNA clone MGC:1263 IMAGE:3140042), complete cds.
KJ893191 - Synthetic construct Homo sapiens clone ccsbBroadEn_02585 COPS6 gene, encodes complete protein.
CU678014 - Synthetic construct Homo sapiens gateway clone IMAGE:100020670 5' read COPS6 mRNA.
LF359979 - JP 2014500723-A/167482: Polycomb-Associated Non-Coding RNAs.
JD482336 - Sequence 463360 from Patent EP1572962.
U70735 - Homo sapiens 34 kDa Mov34 homolog mRNA, complete cds.
DQ894927 - Synthetic construct Homo sapiens clone IMAGE:100009387; FLH181644.01L; RZPDo839F08135D COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis) (COPS6) gene, encodes complete protein.
DQ891943 - Synthetic construct clone IMAGE:100004573; FLH181648.01X; RZPDo839F08136D COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis) (COPS6) gene, encodes complete protein.
LF359980 - JP 2014500723-A/167483: Polycomb-Associated Non-Coding RNAs.
JD556082 - Sequence 537106 from Patent EP1572962.
MA619634 - JP 2018138019-A/191560: Polycomb-Associated Non-Coding RNAs.
MA595556 - JP 2018138019-A/167482: Polycomb-Associated Non-Coding RNAs.
MA595557 - JP 2018138019-A/167483: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q7L5N1 (Reactome details) participates in the following event(s):

R-HSA-8863721 NEDD8-STON binds TOR1 hexamer and COP9 complex
R-HSA-5691006 XPC:RAD23:CETN2 and UV-DDB bind distorted dsDNA site
R-HSA-6781833 ERCC8 (CSA) binds stalled RNA Pol II
R-HSA-8956040 COP9 signalosome deneddylates cytosolic CRL E3 ubiquitin ligase complexes
R-HSA-8956045 COP9 signalosome deneddylates nuclear CRL4 E3 ubiquitin ligase complex
R-HSA-8856825 Cargo recognition for clathrin-mediated endocytosis
R-HSA-5696394 DNA Damage Recognition in GG-NER
R-HSA-6781823 Formation of TC-NER Pre-Incision Complex
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-8951664 Neddylation
R-HSA-5696399 Global Genome Nucleotide Excision Repair (GG-NER)
R-HSA-6781827 Transcription-Coupled Nucleotide Excision Repair (TC-NER)
R-HSA-199991 Membrane Trafficking
R-HSA-597592 Post-translational protein modification
R-HSA-5696398 Nucleotide Excision Repair
R-HSA-5653656 Vesicle-mediated transport
R-HSA-392499 Metabolism of proteins
R-HSA-73894 DNA Repair

-  Other Names for This Gene
  Alternate Gene Symbols: A4D2A3, CSN6, CSN6_HUMAN, HVIP, NM_006833, NP_006824, O15387, Q7L5N1
UCSC ID: uc003usu.3
RefSeq Accession: NM_006833
Protein: Q7L5N1 (aka CSN6_HUMAN)
CCDS: CCDS5682.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_006833.4
exon count: 10CDS single in 3' UTR: no RNA size: 1441
ORF size: 984CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2165.00frame shift in genome: no % Coverage: 98.89
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.