Human Gene COP1 (uc001gku.1)
  Description: Homo sapiens ring finger and WD repeat domain 2, E3 ubiquitin protein ligase (COP1), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:175,913,967-176,176,370 Size: 262,404 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr1:175,914,289-176,176,114 Size: 261,826 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:175,913,967-176,176,370)mRNA (may differ from genome)Protein (731 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
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H-INVHPRDLynxMGIneXtProtOMIM
PubMedReactomeTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RFWD2_HUMAN
DESCRIPTION: RecName: Full=E3 ubiquitin-protein ligase RFWD2; EC=6.3.2.-; AltName: Full=Constitutive photomorphogenesis protein 1 homolog; Short=hCOP1; AltName: Full=RING finger and WD repeat domain protein 2; AltName: Full=RING finger protein 200;
FUNCTION: E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin- conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Involved in JUN ubiquitination and degradation. Directly involved in p53 (TP53) ubiquitination and degradation, thereby abolishing p53-dependent transcription and apoptosis. Ubiquitinates p53 independently of MDM2 or RCHY1. Probably mediates E3 ubiquitin ligase activity by functioning as the essential RING domain subunit of larger E3 complexes. In contrast, it does not constitute the catalytic RING subunit in the DCX DET1-COP1 complex that negatively regulates JUN, the ubiquitin ligase activity being mediated by RBX1. Involved in 14-3-3 protein sigma/SFN ubiquitination and proteasomal degradation, leading to AKT activation and promotion of cell survival.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Homodimer. Homodimerization is mediated by the coiled coil domain. Component of the DCX DET1-COP1 ubiquitin ligase complex at least composed of RBX1, DET1, DDB1, CUL4A and COP1. Isoform 2 does not interact with CUL4A but still binds to RBX1, suggesting that the interaction may be mediated by another cullin protein. Isoform 1 and isoform 2 interact with CUL5 but not with CUL1, CUL2 not CUL3. Interacts with bZIP transcription factors JUN, JUNB and JUND but not with FOS, ATF2 nor XBP1. Interacts with p53 (TP53). Interacts with COPS6; this interaction stabilizes RFWD2 through reducing its auto-ubiquitination and decelerating its turnover rate. Interacts with SFN; this interaction leads to SFN degradation. Isoform 4 forms heterodimers with isoform 1, preventing its association with DET1.
INTERACTION: Q7L5N1:COPS6; NbExp=3; IntAct=EBI-1176214, EBI-486838; P31947:SFN; NbExp=5; IntAct=EBI-1176214, EBI-476295;
SUBCELLULAR LOCATION: Nucleus speckle. Cytoplasm. Note=In the nucleus, it forms nuclear speckles.
TISSUE SPECIFICITY: Ubiquitously expressed at low level. Expressed at higher level in testis, placenta, skeletal muscle and heart.
INDUCTION: By p53/TP53.
DOMAIN: The RING finger domain, in addition to its role in ubiquitination, functions as a structural scaffold to bring two clusters of positive-charged residues within spatial proximity to mimic a bipartite nuclear localization signal (NLS) (By similarity).
SIMILARITY: Belongs to the COP1 family.
SIMILARITY: Contains 1 RING-type zinc finger.
SIMILARITY: Contains 7 WD repeats.

-  Primer design for this transcript
 

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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.
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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


+  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: 19.85 RPKM in Testis
Total median expression: 474.03 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 -138.13256-0.540 Picture PostScript Text
3' UTR -71.50322-0.222 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
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR019775 - WD40_repeat_CS
IPR017986 - WD40_repeat_dom
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD
IPR017907 - Znf_RING_CS

Pfam Domains:
PF00097 - Zinc finger, C3HC4 type (RING finger)
PF00400 - WD domain, G-beta repeat
PF13445 - RING-type zinc-finger
PF13639 - Ring finger domain
PF13920 - Zinc finger, C3HC4 type (RING finger)
PF13923 - Zinc finger, C3HC4 type (RING finger)
PF14634 - zinc-RING finger domain

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Prolyl oligopeptidase, N-terminal domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - Dipeptidyl peptidase IV/CD26, N-terminal domain
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on Q8NHY2
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-  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 BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0046872 metal ion binding
GO:0061630 ubiquitin protein ligase activity

Biological Process:
GO:0010212 response to ionizing radiation
GO:0016567 protein ubiquitination
GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0043687 post-translational protein modification

Cellular Component:
GO:0000139 Golgi membrane
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016607 nuclear speck
GO:0031464 Cul4A-RING E3 ubiquitin ligase complex


-  Descriptions from all associated GenBank mRNAs
  BC039723 - Homo sapiens ring finger and WD repeat domain 2, mRNA (cDNA clone IMAGE:5244448).
BC094728 - Homo sapiens ring finger and WD repeat domain 2, mRNA (cDNA clone MGC:104553 IMAGE:5271629), complete cds.
LP895183 - Sequence 47 from Patent EP3253886.
AF527539 - Homo sapiens putative ubiquitin ligase COP1 (COP1) mRNA, complete cds.
AF508940 - Homo sapiens constitutive photomorphogenic protein mRNA, complete cds.
AY509921 - Homo sapiens constitutive photomorphogenic protein isoform d24 mRNA, complete cds.
AK314750 - Homo sapiens cDNA, FLJ95614, Homo sapiens constitutive photomorphogenic protein (COP1), mRNA.
KJ894546 - Synthetic construct Homo sapiens clone ccsbBroadEn_03940 RFWD2 gene, encodes complete protein.
KJ534928 - Homo sapiens clone RFWD2_iso-A_adult-A01 ring finger and WD repeat domain 2 isoform A (RFWD2) mRNA, partial cds, alternatively spliced.
KJ534929 - Homo sapiens clone RFWD2_iso-F_adult-A02 ring finger and WD repeat domain 2 isoform F (RFWD2) mRNA, partial cds, alternatively spliced.
KJ534930 - Homo sapiens clone RFWD2_iso-C_adult-A07 ring finger and WD repeat domain 2 isoform C (RFWD2) mRNA, partial cds, alternatively spliced.
KJ534931 - Homo sapiens clone RFWD2_iso-D_adult-A09 ring finger and WD repeat domain 2 isoform D (RFWD2) mRNA, partial cds, alternatively spliced.
KJ534932 - Homo sapiens clone RFWD2_iso-B_adult-A13 ring finger and WD repeat domain 2 isoform B (RFWD2) mRNA, partial cds, alternatively spliced.
KJ534933 - Homo sapiens clone RFWD2_iso-H_fetal-F11 ring finger and WD repeat domain 2 isoform H (RFWD2) mRNA, partial cds, alternatively spliced.
KJ534992 - Homo sapiens clone RFWD2_iso-I_fetal-F08 ring finger and WD repeat domain 2 isoform I (RFWD2) mRNA, complete cds, alternatively spliced.
KJ535061 - Homo sapiens clone RFWD2_iso-G_adult-A14 ring finger and WD repeat domain 2 isoform G (RFWD2) mRNA, complete cds, alternatively spliced.
KJ535076 - Homo sapiens clone RFWD2_iso-E_fetal-F15 ring finger and WD repeat domain 2 isoform E (RFWD2) mRNA, complete cds, alternatively spliced.
BC020845 - Homo sapiens ring finger and WD repeat domain 2, mRNA (cDNA clone IMAGE:4718123), partial cds.
BX537932 - Homo sapiens mRNA; cDNA DKFZp686E19279 (from clone DKFZp686E19279).
AK025789 - Homo sapiens cDNA: FLJ22136 fis, clone HEP20890.
AK001278 - Homo sapiens cDNA FLJ10416 fis, clone NT2RP1000111, highly similar to RING finger and WD repeat domain protein 2 (EC 6.3.2.-).
LF365533 - JP 2014500723-A/173036: Polycomb-Associated Non-Coding RNAs.
MA601110 - JP 2018138019-A/173036: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04115 - p53 signaling pathway
hsa04120 - Ubiquitin mediated proteolysis

Reactome (by CSHL, EBI, and GO)

Protein Q8NHY2 (Reactome details) participates in the following event(s):

R-HSA-264444 Autoubiquitination of phospho-COP1(Ser-387 )
R-HSA-264418 Translocation of COP1 from the nucleus to the cytoplasm
R-HSA-264435 Dissociation of the COP1-p53 complex
R-HSA-349444 Phosphorylation of COP1 at Ser-387 by ATM
R-HSA-8955245 CAND1 binds CRL4 E3 ubiquitin ligase in the nucleus
R-HSA-8955285 COMMDs displace CAND1 from CRL4 E3 ubiquitin ligase complex
R-HSA-8952639 NEDD8:AcM-UBE2M binds CRL4 E3 ubiquitin ligase complex
R-HSA-8956045 COP9 signalosome deneddylates nuclear CRL4 E3 ubiquitin ligase complex
R-HSA-8952638 AcM-UBE2M transfers NEDD8 to CRL4 E3 ubiquitin ligase complex
R-HSA-349425 Autodegradation of the E3 ubiquitin ligase COP1
R-HSA-69541 Stabilization of p53
R-HSA-69563 p53-Dependent G1 DNA Damage Response
R-HSA-8951664 Neddylation
R-HSA-69580 p53-Dependent G1/S DNA damage checkpoint
R-HSA-597592 Post-translational protein modification
R-HSA-69615 G1/S DNA Damage Checkpoints
R-HSA-392499 Metabolism of proteins
R-HSA-69620 Cell Cycle Checkpoints
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: NM_022457, NP_071902, Q504W6, Q6H103, Q8NHY2, Q9H6L7, RFWD2, RFWD2_HUMAN, RNF200
UCSC ID: uc001gku.1
RefSeq Accession: NM_022457
Protein: Q8NHY2 (aka RFWD2_HUMAN)
CCDS: CCDS30944.1, CCDS44279.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_022457.5
exon count: 20CDS single in 3' UTR: no RNA size: 2801
ORF size: 2196CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4583.00frame shift in genome: no % Coverage: 99.04
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
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.