Human Gene COPS2 (ENST00000388901.10_12) from GENCODE V47lift37
  Description: COP9 signalosome subunit 2, transcript variant 1 (from RefSeq NM_004236.4)
Gencode Transcript: ENST00000388901.10_12
Gencode Gene: ENSG00000166200.15_14
Transcript (Including UTRs)
   Position: hg19 chr15:49,414,924-49,447,796 Size: 32,873 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr15:49,420,147-49,447,775 Size: 27,629 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:49,414,924-49,447,796)mRNA (may differ from genome)Protein (443 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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-  Comments and Description Text from UniProtKB
  ID: CSN2_HUMAN
DESCRIPTION: RecName: Full=COP9 signalosome complex subunit 2; Short=SGN2; Short=Signalosome subunit 2; AltName: Full=Alien homolog; AltName: Full=JAB1-containing signalosome subunit 2; AltName: Full=Thyroid receptor-interacting protein 15; Short=TR-interacting protein 15; Short=TRIP-15;
FUNCTION: Essential 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/ICSBP, 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. Involved in early stage of neuronal differentiation via its interaction with NIF3L1.
SUBUNIT: Interacts with NIF3L1 (By similarity). 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 COPS1, COPS4, COPS5 COPS6 and COPS7 (COPS7A or COPS7B). Interacts with CUL1 and CUL2. Specifically interacts with the ligand binding domain of the thyroid receptor (TR). Does not require the presence of thyroid hormone for its interaction. Interacts with IRF8/ICSBP1 and with nuclear receptors NR2F1 and NR0B1.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
PTM: Phosphorylated by CK2 and PKD kinases.
SIMILARITY: Belongs to the CSN2 family.
SIMILARITY: Contains 1 PCI domain.
SEQUENCE CAUTION: Sequence=AAD30269.1; Type=Frameshift; Positions=304;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: COPS2
Diseases sorted by gene-association score: persistent hyperplastic primary vitreous (7)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 22.29 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 704.38 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR 0.00210.000 Picture PostScript Text
3' UTR -1243.605223-0.238 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
IPR019280 - COP9_signalosome_subunit_CSN8
IPR013143 - PAM
IPR000717 - PCI_dom
IPR011990 - TPR-like_helical
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF01399 - PCI domain

SCOP Domains:
48371 - ARM repeat
81901 - HCP-like
48452 - TPR-like
46785 - "Winged helix" DNA-binding domain

ModBase Predicted Comparative 3D Structure on P61201
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003714 transcription corepressor activity
GO:0004871 signal transducer activity
GO:0005515 protein binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0000338 protein deneddylation
GO:0000715 nucleotide-excision repair, DNA damage recognition
GO:0006283 transcription-coupled nucleotide-excision repair
GO:0006366 transcription from RNA polymerase II promoter
GO:0007165 signal transduction
GO:0008283 cell proliferation
GO:0022008 neurogenesis
GO:0030182 neuron differentiation
GO:0035914 skeletal muscle cell differentiation
GO:0043687 post-translational protein modification
GO:0045892 negative regulation of transcription, DNA-templated
GO:1903507 negative regulation of nucleic acid-templated transcription

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


-  Descriptions from all associated GenBank mRNAs
  JD560771 - Sequence 541795 from Patent EP1572962.
JD415672 - Sequence 396696 from Patent EP1572962.
JD242603 - Sequence 223627 from Patent EP1572962.
JD441000 - Sequence 422024 from Patent EP1572962.
BX648602 - Homo sapiens mRNA; cDNA DKFZp686E05213 (from clone DKFZp686E05213).
AK222590 - Homo sapiens mRNA for COP9 constitutive photomorphogenic homolog subunit 2 variant, clone: CAS05019.
AF084260 - Homo sapiens signalosome subunit 2 (SGN2) mRNA, complete cds.
AF120268 - Homo sapiens ALIEN (ALIEN) mRNA, complete cds.
AF100762 - Homo sapiens thyroid receptor interactor trip15 mRNA, complete cds.
AF212227 - Homo sapiens TRIP15-ISO mRNA, complete cds.
AB209799 - Homo sapiens mRNA for COP9 constitutive photomorphogenic homolog subunit 2 variant protein.
JD232234 - Sequence 213258 from Patent EP1572962.
JD301459 - Sequence 282483 from Patent EP1572962.
JD564850 - Sequence 545874 from Patent EP1572962.
BC012629 - Homo sapiens COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis), mRNA (cDNA clone MGC:13684 IMAGE:4245220), complete cds.
AK295598 - Homo sapiens cDNA FLJ52928 complete cds, highly similar to COP9 signalosome complex subunit 2.
JD313118 - Sequence 294142 from Patent EP1572962.
JD285928 - Sequence 266952 from Patent EP1572962.
JD313375 - Sequence 294399 from Patent EP1572962.
JD359807 - Sequence 340831 from Patent EP1572962.
JD267300 - Sequence 248324 from Patent EP1572962.
JD469584 - Sequence 450608 from Patent EP1572962.
JD160525 - Sequence 141549 from Patent EP1572962.
CR542063 - Homo sapiens full open reading frame cDNA clone RZPDo834F0336D for gene TRIP15, thyroid receptor interacting protein 15; complete cds, incl. stopcodon.
AK312643 - Homo sapiens cDNA, FLJ93029, highly similar to Homo sapiens COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis) (COPS2), mRNA.
KJ892742 - Synthetic construct Homo sapiens clone ccsbBroadEn_02136 COPS2 gene, encodes complete protein.
EU446744 - Synthetic construct Homo sapiens clone IMAGE:100070086; IMAGE:100011953; FLH257482.01L COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis) (COPS2) gene, encodes complete protein.
EU831466 - Synthetic construct Homo sapiens clone HAIB:100066495; DKFZo008F0817 COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis) protein (COPS2) gene, encodes complete protein.
EU831553 - Synthetic construct Homo sapiens clone HAIB:100066582; DKFZo004F0818 COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis) protein (COPS2) gene, encodes complete protein.
AB462991 - Synthetic construct DNA, clone: pF1KB5316, Homo sapiens COPS2 gene for COP9 constitutive photomorphogenic homolog subunit 2, without stop codon, in Flexi system.
CU680378 - Synthetic construct Homo sapiens gateway clone IMAGE:100018298 5' read COPS2 mRNA.
L40388 - Homo sapiens thyroid receptor interactor (TRIP15) mRNA, 5' end of cds.
JD138529 - Sequence 119553 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_vdrPathway - Control of Gene Expression by Vitamin D Receptor

Reactome (by CSHL, EBI, and GO)

Protein P61201 (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: CSN2, CSN2_HUMAN, ENST00000388901.1, ENST00000388901.2, ENST00000388901.3, ENST00000388901.4, ENST00000388901.5, ENST00000388901.6, ENST00000388901.7, ENST00000388901.8, ENST00000388901.9, NM_004236, O88950, P61201, Q15647, Q6FGP4, Q9BY54, Q9R249, Q9UNI2, Q9UNQ5, TRIP15, uc318tat.1, uc318tat.2
UCSC ID: ENST00000388901.10_12
RefSeq Accession: NM_004236.4
Protein: P61201 (aka CSN2_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.