Cops4 (COP9 signalosome subunit 4) - Rat Genome Database

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Gene: Cops4 (COP9 signalosome subunit 4) Rattus norvegicus
Analyze
Symbol: Cops4
Name: COP9 signalosome subunit 4
RGD ID: 1302952
Description: Predicted to be involved in protein deneddylation. Located in synaptic vesicle. Orthologous to human COPS4 (COP9 signalosome subunit 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: COP9 (constitutive photomorphogenic) homolog, subunit 4; COP9 (constitutive photomorphogenic) homolog, subunit 4 (Arabidopsis thaliana); COP9 constitutive photomorphogenic homolog subunit 4; COP9 constitutive photomorphogenic homolog subunit 4 (Arabidopsis); COP9 signalosome complex subunit 4; JAB1-containing signalosome subunit 4; MGC94896; SGN4; signalosome subunit 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
NCBI Annotation Information: Annotation category: suggests misassembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2149,078,579 - 9,108,788 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl149,078,576 - 9,108,887 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx149,050,203 - 9,080,480 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01410,350,063 - 10,380,340 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0149,046,679 - 9,076,956 (-)NCBIRnor_WKY
Rnor_6.01410,718,863 - 10,749,134 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1410,718,844 - 10,749,120 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01410,666,118 - 10,696,489 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41410,329,870 - 10,360,081 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11410,329,870 - 10,360,081 (-)NCBI
Celera149,187,509 - 9,217,727 (-)NCBICelera
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cell junction  (ISO)
COP9 signalosome  (IBA,IEA,ISO)
cytoplasm  (ISO)
nuclear speck  (IEA,ISO)
nucleus  (ISO)
synaptic vesicle  (IDA,IEA,ISO)

Molecular Function
protein binding  (IPI,ISO)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. CSN complex controls the stability of selected synaptic proteins via a torsinA-dependent process. Granata A, etal., EMBO J. 2011 Jan 5;30(1):181-93. doi: 10.1038/emboj.2010.285. Epub 2010 Nov 19.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
7. The COP9 complex is conserved between plants and mammals and is related to the 26S proteasome regulatory complex. Wei N, etal., Curr Biol 1998 Jul 30-Aug 13;8(16):919-22.
Additional References at PubMed
PMID:15489334   PMID:18850735   PMID:19141280   PMID:21630459   PMID:23376485   PMID:32357304  


Genomics

Comparative Map Data
Cops4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2149,078,579 - 9,108,788 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl149,078,576 - 9,108,887 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx149,050,203 - 9,080,480 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01410,350,063 - 10,380,340 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0149,046,679 - 9,076,956 (-)NCBIRnor_WKY
Rnor_6.01410,718,863 - 10,749,134 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1410,718,844 - 10,749,120 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01410,666,118 - 10,696,489 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41410,329,870 - 10,360,081 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11410,329,870 - 10,360,081 (-)NCBI
Celera149,187,509 - 9,217,727 (-)NCBICelera
Cytogenetic Map14p22NCBI
COPS4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38483,035,183 - 83,075,818 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl483,034,447 - 83,075,818 (+)EnsemblGRCh38hg38GRCh38
GRCh37483,956,336 - 83,996,971 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36484,175,263 - 84,215,995 (+)NCBINCBI36Build 36hg18NCBI36
Build 34484,313,417 - 84,354,149NCBI
Celera481,246,788 - 81,287,480 (+)NCBICelera
Cytogenetic Map4q21.22NCBI
HuRef479,696,991 - 79,738,024 (+)NCBIHuRef
CHM1_1483,932,721 - 83,973,422 (+)NCBICHM1_1
T2T-CHM13v2.0486,364,418 - 86,405,022 (+)NCBIT2T-CHM13v2.0
Cops4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395100,666,135 - 100,695,668 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5100,666,175 - 100,695,669 (+)EnsemblGRCm39 Ensembl
GRCm385100,518,295 - 100,547,802 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5100,518,309 - 100,547,803 (+)EnsemblGRCm38mm10GRCm38
MGSCv375100,947,328 - 100,976,821 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365100,758,758 - 100,788,078 (+)NCBIMGSCv36mm8
Celera597,844,415 - 97,873,735 (+)NCBICelera
Cytogenetic Map5E4NCBI
cM Map548.49NCBI
Cops4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554746,539,313 - 6,582,551 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554746,540,022 - 6,581,881 (-)NCBIChiLan1.0ChiLan1.0
COPS4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1446,980,585 - 47,022,117 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl446,980,585 - 47,022,117 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0441,129,731 - 41,171,150 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
COPS4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1326,957,189 - 6,997,573 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl326,957,390 - 6,997,180 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3234,887,844 - 34,928,232 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0326,978,409 - 7,018,953 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl326,873,174 - 7,018,945 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1327,049,431 - 7,089,809 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0326,917,989 - 6,958,354 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03233,003,236 - 33,048,104 (-)NCBIUU_Cfam_GSD_1.0
Cops4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244052855,349,474 - 5,383,444 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367381,511,301 - 1,545,439 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049367381,511,301 - 1,545,274 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COPS4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8135,280,506 - 135,314,460 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18135,280,475 - 135,314,393 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28144,575,339 - 144,609,232 (-)NCBISscrofa10.2Sscrofa10.2susScr3
COPS4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1731,426,600 - 31,466,590 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl731,427,121 - 31,466,721 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603710,005,130 - 10,045,121 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cops4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462490089,940 - 131,300 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462490090,154 - 127,299 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cops4
276 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:204
Count of miRNA genes:139
Interacting mature miRNAs:160
Transcripts:ENSRNOT00000003046
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
71115Niddm15Non-insulin dependent diabetes mellitus QTL 154.8blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14121760611030812Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14121760616960180Rat
724541Niddm53Non-insulin dependent diabetes mellitus QTL 530.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1438130749088978Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)14381307418274691Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14381307418274691Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat

Markers in Region
D14Rat3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2149,088,809 - 9,088,978 (+)MAPPERmRatBN7.2
mRatBN7.21242,824,821 - 242,824,860 (+)MAPPERmRatBN7.2
mRatBN7.21242,824,825 - 242,824,866 (+)MAPPERmRatBN7.2
Rnor_6.01410,729,098 - 10,729,268NCBIRnor6.0
Rnor_5.01410,676,485 - 10,676,655UniSTSRnor5.0
RGSC_v3.41410,339,971 - 10,340,377RGDRGSC3.4
RGSC_v3.41410,340,102 - 10,340,272UniSTSRGSC3.4
RGSC_v3.11410,340,102 - 10,340,272RGD
Celera149,197,754 - 9,197,924UniSTS
RH 3.4 Map14152.08UniSTS
RH 3.4 Map14152.08RGD
RH 2.0 Map14162.0RGD
SHRSP x BN Map144.62RGD
Cytogenetic Map14p22UniSTS
RH143839  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2149,108,022 - 9,108,175 (+)MAPPERmRatBN7.2
Rnor_6.01410,748,312 - 10,748,464NCBIRnor6.0
Rnor_5.01410,695,699 - 10,695,851UniSTSRnor5.0
RGSC_v3.41410,359,316 - 10,359,468UniSTSRGSC3.4
Celera149,216,962 - 9,217,114UniSTS
RH 3.4 Map14131.09UniSTS
Cytogenetic Map14p22UniSTS
BI274688  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0147,518,601 - 7,518,772NCBIRnor6.0
Rnor_6.01410,718,992 - 10,719,163NCBIRnor6.0
Rnor_5.0147,496,400 - 7,496,571UniSTSRnor5.0
Rnor_5.01410,666,247 - 10,666,418UniSTSRnor5.0
RGSC_v3.41410,329,995 - 10,330,166UniSTSRGSC3.4
Celera149,187,634 - 9,187,805UniSTS
RH 3.4 Map14130.59UniSTS
Cytogenetic Map14p22UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003046   ⟹   ENSRNOP00000003046
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl149,078,576 - 9,108,887 (-)Ensembl
Rnor_6.0 Ensembl1410,718,844 - 10,749,120 (-)Ensembl
RefSeq Acc Id: NM_001004275   ⟹   NP_001004275
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2149,078,579 - 9,108,788 (-)NCBI
Rnor_6.01410,718,867 - 10,749,077 (-)NCBI
Rnor_5.01410,666,118 - 10,696,489 (-)NCBI
RGSC_v3.41410,329,870 - 10,360,081 (-)RGD
Celera149,187,509 - 9,217,727 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001004275   ⟸   NM_001004275
- UniProtKB: Q68FS2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003046   ⟸   ENSRNOT00000003046
Protein Domains
PCI

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q68FS2-F1-model_v2 AlphaFold Q68FS2 1-406 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13699195
Promoter ID:EPDNEW_R9719
Type:initiation region
Name:Cops4_1
Description:COP9 signalosome subunit 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01410,749,048 - 10,749,108EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1302952 AgrOrtholog
BioCyc Gene G2FUF-16406 BioCyc
Ensembl Genes ENSRNOG00000023650 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003046 ENTREZGENE
  ENSRNOP00000003046.4 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003046 ENTREZGENE
  ENSRNOT00000003046.7 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7111425 IMAGE-MGC_LOAD
InterPro CSN4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CSN4_HTH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PCI_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PSMD12/CSN4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:360915 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94896 IMAGE-MGC_LOAD
NCBI Gene 360915 ENTREZGENE
PANTHER PTHR10855 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10855:SF2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CSN4_RPN5_eIF3a UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PCI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cops4 PhenoGen
PROSITE PCI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PINT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2Q0P3_RAT UniProtKB/TrEMBL
  CSN4_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-20 Cops4  COP9 signalosome subunit 4  Cops4  COP9 constitutive photomorphogenic homolog subunit 4 (Arabidopsis)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-23 Cops4  COP9 constitutive photomorphogenic homolog subunit 4 (Arabidopsis)  Cops4  COP9 (constitutive photomorphogenic) homolog, subunit 4 (Arabidopsis thaliana)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Cops4  COP9 (constitutive photomorphogenic) homolog, subunit 4 (Arabidopsis thaliana)    COP9 signalosome subunit 4  Name updated 1299863 APPROVED
2005-02-14 Cops4  COP9 signalosome subunit 4      Symbol and Name status set to provisional 70820 PROVISIONAL