Cops4 (COP9 signalosome subunit 4)

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

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	COPS4 (COP9 signalosome subunit 4)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Cops4 (COP9 signalosome subunit 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Cops4 (COP9 signalosome subunit 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	COPS4 (COP9 signalosome subunit 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	COPS4 (COP9 signalosome subunit 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Cops4 (COP9 signalosome subunit 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	COPS4 (COP9 signalosome subunit 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	COPS4 (COP9 signalosome subunit 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Cops4 (COP9 signalosome subunit 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	STYXL2 (serine/threonine/tyrosine interacting like 2)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	COPS4 (COP9 signalosome subunit 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Cops4 (COP9 signalosome subunit 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	cops4 (COP9 constitutive photomorphogenic homolog subunit 4 (Arabidopsis))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	CSN4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	csn-4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

NCBI Annotation Information:

Annotation category: suggests misassembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	14	9,382,897 - 9,413,216 (-)	NCBI		GRCr8
mRatBN7.2	14	9,078,579 - 9,108,788 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	9,078,576 - 9,108,887 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	14	9,050,203 - 9,080,480 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	14	10,350,063 - 10,380,340 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	14	9,046,679 - 9,076,956 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	14	10,718,863 - 10,749,134 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	10,718,844 - 10,749,120 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	14	10,666,118 - 10,696,489 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	14	10,329,870 - 10,360,081 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	14	10,329,870 - 10,360,081 (-)	NCBI
Celera	14	9,187,509 - 9,217,727 (-)	NCBI		Celera
Cytogenetic Map	14	p22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

chromosome 4q21 deletion syndrome (ISO)

genetic disease (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2-methylcholine (ISO)

5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole (EXP)

6-propyl-2-thiouracil (EXP)

acrolein (ISO)

all-trans-retinoic acid (ISO)

alpha-pinene (ISO)

amiodarone (EXP)

antirheumatic drug (ISO)

arsenite(3-) (ISO)

benzatropine (ISO)

benzbromarone (EXP)

benzo[a]pyrene (ISO)

Benzo[k]fluoranthene (ISO)

bisphenol A (EXP,ISO)

Bisphenol B (ISO)

bisphenol F (ISO)

cadmium atom (ISO)

clofibrate (EXP)

copper(II) sulfate (ISO)

dibutyl phthalate (EXP,ISO)

dicrotophos (ISO)

doxorubicin (ISO)

ethanol (ISO)

finasteride (EXP)

flutamide (EXP)

folic acid (ISO)

gentamycin (EXP)

haloperidol (ISO)

hyaluronic acid (EXP)

hydralazine (ISO)

hydrogen peroxide (EXP)

ivermectin (ISO)

L-ethionine (EXP)

leflunomide (EXP)

nefazodone (EXP)

omeprazole (EXP)

ozone (ISO)

paracetamol (EXP,ISO)

perfluorododecanoic acid (EXP)

pirinixic acid (EXP)

quercetin (ISO)

SB 431542 (ISO)

sodium arsenite (EXP,ISO)

thapsigargin (ISO)

thioacetamide (EXP)

triptonide (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

protein deneddylation (IEA,ISO,ISS)

Cellular Component

cell junction (ISO)

COP9 signalosome (IBA,IEA,ISO)

cytoplasm (ISO)

cytosol (IEA)

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	14	9,382,897 - 9,413,216 (-)	NCBI		GRCr8
mRatBN7.2	14	9,078,579 - 9,108,788 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	9,078,576 - 9,108,887 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	14	9,050,203 - 9,080,480 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	14	10,350,063 - 10,380,340 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	14	9,046,679 - 9,076,956 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	14	10,718,863 - 10,749,134 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	10,718,844 - 10,749,120 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	14	10,666,118 - 10,696,489 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	14	10,329,870 - 10,360,081 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	14	10,329,870 - 10,360,081 (-)	NCBI
Celera	14	9,187,509 - 9,217,727 (-)	NCBI		Celera
Cytogenetic Map	14	p22	NCBI

COPS4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	4	83,035,183 - 83,075,818 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	4	83,034,447 - 83,075,818 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	4	83,956,336 - 83,996,971 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	4	84,175,263 - 84,215,995 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	4	84,313,417 - 84,354,149	NCBI
Celera	4	81,246,788 - 81,287,480 (+)	NCBI		Celera
Cytogenetic Map	4	q21.22	NCBI
HuRef	4	79,696,991 - 79,738,024 (+)	NCBI		HuRef
CHM1_1	4	83,932,721 - 83,973,422 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	4	86,364,418 - 86,405,022 (+)	NCBI		T2T-CHM13v2.0

Cops4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	100,666,223 - 100,695,668 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	100,666,175 - 100,695,669 (+)	Ensembl		GRCm39 Ensembl
GRCm38	5	100,518,295 - 100,547,802 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	100,518,309 - 100,547,803 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	100,947,328 - 100,976,821 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	5	100,758,758 - 100,788,078 (+)	NCBI		MGSCv36	mm8
Celera	5	97,844,415 - 97,873,735 (+)	NCBI		Celera
Cytogenetic Map	5	E4	NCBI
cM Map	5	48.49	NCBI

Cops4
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955474	6,539,313 - 6,582,551 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955474	6,540,022 - 6,581,881 (-)	NCBI	ChiLan1.0	ChiLan1.0

COPS4
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	3	46,997,314 - 47,039,384 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	4	47,186,479 - 47,228,019 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	4	41,129,731 - 41,171,150 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	4	46,980,585 - 47,022,117 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	4	46,980,585 - 47,022,117 (-)	Ensembl	panpan1.1		panPan2

COPS4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	32	6,957,189 - 6,997,573 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	32	6,957,390 - 6,997,180 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	32	34,887,844 - 34,928,232 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	32	6,978,409 - 7,018,953 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	32	6,873,174 - 7,018,945 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	32	7,049,431 - 7,089,809 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	32	6,917,989 - 6,958,354 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	32	33,003,236 - 33,048,104 (-)	NCBI		UU_Cfam_GSD_1.0

Cops4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405285	5,349,474 - 5,383,444 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936738	1,511,301 - 1,545,439 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936738	1,511,301 - 1,545,274 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

COPS4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	8	135,280,506 - 135,314,460 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	8	135,280,475 - 135,314,393 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	8	144,575,339 - 144,609,232 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

COPS4
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	7	31,426,600 - 31,466,590 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	7	31,427,121 - 31,466,721 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666037	10,005,130 - 10,045,121 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Cops4
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624900	89,940 - 131,300 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624900	90,154 - 127,299 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Cops4
288 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.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2300159	Bmd61	Bone mineral density QTL 61	5.3	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	14	1	26541967	Rat
2300183	Bmd60	Bone mineral density QTL 60	5.7	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	14	1	26541967	Rat
619619	Rf4	Renal disease susceptibility QTL 4	4.1	0.002	urine total protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	14	1	32754612	Rat
634352	Apr6	Acute phase response QTL 6	3.7		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	14	1	41131407	Rat
71115	Niddm15	Non-insulin dependent diabetes mellitus QTL 15	4.8		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	14	1217606	11030812	Rat
70204	Niddm20	Non-insulin dependent diabetes mellitus QTL 20	5.1	0.000008	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	14	1217606	16960180	Rat
724541	Niddm53	Non-insulin dependent diabetes mellitus QTL 53		0.001	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	14	3813074	9088978	Rat
2293089	Iddm31	Insulin dependent diabetes mellitus QTL 31	4.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	14	3813074	18274691	Rat
2293089	Iddm31	Insulin dependent diabetes mellitus QTL 31	4.7		blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	14	3813074	18274691	Rat
1300114	Srn2	Serum renin concentration QTL 2	3.27		blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	14	3813074	21217635	Rat
70195	Mcs8	Mammary carcinoma susceptibility QTL 8	4.28		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	14	3813074	24531477	Rat
1331740	Bw26	Body weight QTL 26	3.028		body mass (VT:0001259)	body weight (CMO:0000012)	14	3813074	30767156	Rat
1581500	Renag1	Renal agenesis QTL 1			kidney development trait (VT:0000527)	percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)	14	8170668	68298175	Rat
1358296	Ael3	Aortic elastin QTL 3	3.7	0.00051	aorta elastin amount (VT:0003905)	aortic elastin	14	8267090	53267090	Rat
2302045	Pia39	Pristane induced arthritis QTL 39	4.9	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G2a level (CMO:0002116)	14	8267090	53267090	Rat
731183	Pia20	Pristane induced arthritis QTL 20	3.55		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	14	9088978	39057237	Rat

Markers in Region

D14Rat3

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	9,088,809 - 9,088,978 (+)	MAPPER	mRatBN7.2
mRatBN7.2	1	242,824,821 - 242,824,860 (+)	MAPPER	mRatBN7.2
mRatBN7.2	1	242,824,825 - 242,824,866 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	10,729,098 - 10,729,268	NCBI	Rnor6.0
Rnor_5.0	14	10,676,485 - 10,676,655	UniSTS	Rnor5.0
RGSC_v3.4	14	10,339,971 - 10,340,377	RGD	RGSC3.4
RGSC_v3.4	14	10,340,102 - 10,340,272	UniSTS	RGSC3.4
RGSC_v3.1	14	10,340,102 - 10,340,272	RGD
Celera	14	9,197,754 - 9,197,924	UniSTS
RH 3.4 Map	14	152.08	UniSTS
RH 3.4 Map	14	152.08	RGD
RH 2.0 Map	14	162.0	RGD
SHRSP x BN Map	14	4.62	RGD
Cytogenetic Map	14	p22	UniSTS

RH143839

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	9,108,022 - 9,108,175 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	10,748,312 - 10,748,464	NCBI	Rnor6.0
Rnor_5.0	14	10,695,699 - 10,695,851	UniSTS	Rnor5.0
RGSC_v3.4	14	10,359,316 - 10,359,468	UniSTS	RGSC3.4
Celera	14	9,216,962 - 9,217,114	UniSTS
RH 3.4 Map	14	131.09	UniSTS
Cytogenetic Map	14	p22	UniSTS

BI274688

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	14	7,518,601 - 7,518,772	NCBI	Rnor6.0
Rnor_6.0	14	10,718,992 - 10,719,163	NCBI	Rnor6.0
Rnor_5.0	14	7,496,400 - 7,496,571	UniSTS	Rnor5.0
Rnor_5.0	14	10,666,247 - 10,666,418	UniSTS	Rnor5.0
RGSC_v3.4	14	10,329,995 - 10,330,166	UniSTS	RGSC3.4
Celera	14	9,187,634 - 9,187,805	UniSTS
RH 3.4 Map	14	130.59	UniSTS
Cytogenetic Map	14	p22	UniSTS

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

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001004275	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006250667	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006250668	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063273328	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063273329	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063273330	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC099384	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC079384	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474022	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000014	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000003046 ⟹ ENSRNOP00000003046

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	14	9,078,576 - 9,108,887 (-)	Ensembl
Rnor_6.0 Ensembl	14	10,718,844 - 10,749,120 (-)	Ensembl

RefSeq Acc Id:

NM_001004275 ⟹ NP_001004275

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	14	9,382,897 - 9,413,107 (-)	NCBI
mRatBN7.2	14	9,078,579 - 9,108,788 (-)	NCBI
Rnor_6.0	14	10,718,867 - 10,749,077 (-)	NCBI
Rnor_5.0	14	10,666,118 - 10,696,489 (-)	NCBI
RGSC_v3.4	14	10,329,870 - 10,360,081 (-)	RGD
Celera	14	9,187,509 - 9,217,727 (-)	RGD

Sequence:

show sequence

GCGAGAGGTCCCGCAGCCGTGGCTGAGCTGGAAGAAAGATGGCGGCTGCCGTGCGACAGGATTT
GGCCCAGCTCATGAATTCAAGCGGCTCTCACAAAGATCTGGCGGGCAAATATCGTCAGATTCTG
GAAAAAGCCATTCAGTTATCTGGGACAGAACAACTAGAAGCATTGAAAGCTTTTGTGGAAGCGA
TGGTGAACGAGAACGTCAGCCTTGTGATCTCACGGCAACTGCTAACAGATTTCTGCACACACCT
CCCCAACCTGCCAGACAGCACAGCCAAGGAGGTCTACCATTTCACCTTGGAGAAGGTCCAGCCT
CGGGTCATCTCCTTTGAGGAGCAGGTGGCTTCCATACGACAGCGTCTTGCATCTATTTATGAGA
AGGAAGAAGACTGGAGAAACGCAGCCCAAGTGTTGGTGGGGATTCCTCTGGAGACAGGACAAAA
ACAGTACAACGTAGACTATAAGCTGGAGACCTACCTGAAGATCGCGAGGCTATACTTGGAGGAT
GACGACCCTGTCCAGGCTGAGGCTTACATAAACCGAGCTTCCTTACTTCAGAATGAATCCACAA
ACGAACAGTTACAGATACACTATAAGGTTTGCTATGCACGTGTCCTTGACTACAGAAGGAAGTT
CATTGAAGCCGCCCAAAGGTACAATGAGCTCTCTTACAAGACAATAGTGCACGAAAGTGAGAGA
CTGGAGGCCTTGAAGCACGCACTGCACTGCACCATCCTAGCGTCGGCAGGACAGCAGCGCTCTC
GGATGCTGGCTACCCTTTTTAAGGATGAAAGGTGCCAGCAACTGGCTGCTTATGGGATCCTGGA
GAAAATGTACCTAGACAGGATCATCAGAGGGAACCAGCTTCAAGAATTTGCTGCAATGCTGATG
CCTCACCAAAAAGCAACCACAGCTGATGGTTCCAGCATCTTGGACAGAGCTGTTATTGAGCATA
ATTTGTTGTCAGCAAGCAAATTATATAACAACATCACCTTTGAGGAACTCGGAGCTCTTTTAGA
GATCCCTGCAGCTAAGGCAGAAAAGATAGCATCTCAGATGATAACAGAAGGACGCATGAACGGA
TTTATTGACCAGATCGATGGGATAGTTCATTTTGAAACACGAGAAGCCCTGCCGACGTGGGACA
AGCAGATCCAATCACTTTGTTTCCAAGTAAATAACCTCCTGGAGAAGATTAGTCAGACAGCCCC
CGAGTGGACAGCGCAAGCCATGGAGGCGCAGATGGCCCAGTGAGTCCTGGAGCTCCGTGCACAC
TGCGTCTTTGCACTTTGTGCGGATCGATTCACTGCCCTCACAGCATTTGCATCGTGACCATAGA
CATCTCAGTCCTTTTTTGCCAGCTCCCACGTGAGGACGACGCAGGAGCAAGCAGTGCAGCCTTG
AAGCAGTAGCTCCCGTGCCGCCTGGGTCTATGTTGAGCTGACTCGGGTGTCTTGAAAGCTTGTT
CTTTAAGTGAGCAAGCGAGCGAGCTGGGTAGTCGTGTAAAACTTCAGTGCTTTGTGCCTCTCCA
GATGTGGTTACTCTAATAAACGGAGCGATGAACCAGAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_063273328 ⟹ XP_063129398

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	14	9,382,897 - 9,413,175 (-)	NCBI

RefSeq Acc Id:

XM_063273329 ⟹ XP_063129399

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	14	9,382,897 - 9,413,216 (-)	NCBI

RefSeq Acc Id:

XM_063273330 ⟹ XP_063129400

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	14	9,382,897 - 9,413,144 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001004275	(Get FASTA)	NCBI Sequence Viewer
	XP_063129398	(Get FASTA)	NCBI Sequence Viewer
	XP_063129399	(Get FASTA)	NCBI Sequence Viewer
	XP_063129400	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH79384	(Get FASTA)	NCBI Sequence Viewer
	EDL99563	(Get FASTA)	NCBI Sequence Viewer
	EDL99564	(Get FASTA)	NCBI Sequence Viewer
	EDL99565	(Get FASTA)	NCBI Sequence Viewer
	EDL99566	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000003046
	ENSRNOP00000003046.4
	ENSRNOP00055007731
	ENSRNOP00060013727
	ENSRNOP00065015697
GenBank Protein	Q68FS2	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_001004275 ⟸ NM_001004275

- UniProtKB:

Q68FS2 (UniProtKB/Swiss-Prot), A6K5Z4 (UniProtKB/TrEMBL), A0A8L2Q0P3 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MAAAVRQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGTEQLEALKAFVEAMVNENVSLVISRQ
LLTDFCTHLPNLPDSTAKEVYHFTLEKVQPRVISFEEQVASIRQRLASIYEKEEDWRNAAQVLV
GIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTNEQLQIHYKVCYA
RVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASAGQQRSRMLATLFKDERCQ
QLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADGSSILDRAVIEHNLLSASKLYNNIT
FEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFETREALPTWDKQIQSLCFQVNNL
LEKISQTAPEWTAQAMEAQMAQ

hide sequence

RefSeq Acc Id:

ENSRNOP00000003046 ⟸ ENSRNOT00000003046

RefSeq Acc Id:	XP_063129399 ⟸ XM_063273329
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_063129398 ⟸ XM_063273328
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_063129400 ⟸ XM_063273330
- Peptide Label:	isoform X3

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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	14	10,749,048 - 10,749,108	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1302952	AgrOrtholog
BioCyc Gene	G2FUF-16406	BioCyc
Ensembl Genes	ENSRNOG00000023650	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOG00055006176	UniProtKB/Swiss-Prot
	ENSRNOG00060010449	UniProtKB/Swiss-Prot
	ENSRNOG00065012569	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000003046	ENTREZGENE
	ENSRNOT00000003046.7	UniProtKB/TrEMBL
	ENSRNOT00055010006	UniProtKB/Swiss-Prot
	ENSRNOT00060017665	UniProtKB/Swiss-Prot
	ENSRNOT00065020434	UniProtKB/Swiss-Prot
Gene3D-CATH	1.10.10.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7111425	IMAGE-MGC_LOAD
InterPro	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, UniProtKB/TrEMBL
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
RatGTEx	ENSRNOG00000023650	RatGTEx
	ENSRNOG00055006176	RatGTEx
	ENSRNOG00060010449	RatGTEx
	ENSRNOG00065012569	RatGTEx
SMART	PINT	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF46785	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A8L2Q0P3	ENTREZGENE, UniProtKB/TrEMBL
	A6K5Z3_RAT	UniProtKB/TrEMBL
	A6K5Z4	ENTREZGENE, UniProtKB/TrEMBL
	A6K5Z5_RAT	UniProtKB/TrEMBL
	A6K5Z6_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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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