Cops6 (COP9 signalosome subunit 6)

Gene: Cops6 (COP9 signalosome subunit 6) Rattus norvegicus

Analyze

Symbol:

Cops6

Name:

COP9 signalosome subunit 6

RGD ID:

1309919

Description:

Predicted to enable metallopeptidase activity. Predicted to be involved in protein deneddylation. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be part of COP9 signalosome. Orthologous to human COPS6 (COP9 signalosome subunit 6); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; ethanol.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

COP9 (constitutive photomorphogenic) homolog, subunit 6; COP9 (constitutive photomorphogenic) homolog, subunit 6 (Arabidopsis thaliana) ; COP9 constitutive photomorphogenic homolog subunit 6; COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis); COP9 signalosome complex subunit 6; LOC304343

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):	COPS6 (COP9 signalosome subunit 6)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Cops6 (COP9 signalosome subunit 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Cops6 (COP9 signalosome subunit 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	COPS6 (COP9 signalosome subunit 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	COPS6 (COP9 signalosome subunit 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Cops6 (COP9 signalosome subunit 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	COPS6 (COP9 signalosome subunit 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	COPS6 (COP9 signalosome subunit 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Cops6 (COP9 signalosome subunit 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	SUN1 (Sad1 and UNC84 domain containing 1)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	COPS6 (COP9 signalosome subunit 6)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Cops6 (COP9 signalosome subunit 6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	CSN6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	csn-6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	cops6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	12	22,152,688 - 22,155,527 (+)	NCBI		GRCr8
mRatBN7.2	12	17,038,979 - 17,041,818 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	12	17,038,979 - 17,046,371 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	12	17,862,350 - 17,865,183 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	12	18,486,094 - 18,488,927 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	12	17,539,500 - 17,542,333 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	12	19,303,387 - 19,306,226 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	12	19,303,387 - 19,306,226 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	12	21,361,017 - 21,363,856 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	17,604,017 - 17,606,856 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	12	17,587,845 - 17,596,347 (+)	NCBI
Celera	12	18,969,149 - 18,971,988 (+)	NCBI		Celera
Cytogenetic Map	12	q11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

human immunodeficiency virus infectious disease (ISO)

pleomorphic xanthoastrocytoma (ISO)

prostate cancer (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17alpha-ethynylestradiol (ISO)

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

antirheumatic drug (ISO)

aristolochic acid A (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

cadmium atom (ISO)

cadmium dichloride (ISO)

clofibrate (ISO)

cobalt dichloride (ISO)

copper(II) sulfate (ISO)

diarsenic trioxide (ISO)

dichloroacetic acid (ISO)

ethanol (EXP,ISO)

flutamide (EXP)

ivermectin (ISO)

methylmercury chloride (ISO)

paracetamol (ISO)

pirinixic acid (ISO)

SB 431542 (ISO)

tert-butyl hydroperoxide (ISO)

urethane (ISO)

valproic acid (ISO)

vinclozolin (EXP)

vitamin E (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

protein deneddylation (ISO)

Cellular Component

COP9 signalosome (IBA,ISO)

cytoplasm (ISO)

membrane (IEA)

nucleoplasm (IEA,ISO)

nucleus (ISO)

Molecular Function

metallopeptidase activity (IEA)

protein binding (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.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
3.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:9707402	PMID:18850735	PMID:19141280	PMID:23376485	PMID:30180991	PMID:32882218

Genomics

Comparative Map Data

Cops6
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	12	22,152,688 - 22,155,527 (+)	NCBI		GRCr8
mRatBN7.2	12	17,038,979 - 17,041,818 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	12	17,038,979 - 17,046,371 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	12	17,862,350 - 17,865,183 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	12	18,486,094 - 18,488,927 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	12	17,539,500 - 17,542,333 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	12	19,303,387 - 19,306,226 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	12	19,303,387 - 19,306,226 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	12	21,361,017 - 21,363,856 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	17,604,017 - 17,606,856 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	12	17,587,845 - 17,596,347 (+)	NCBI
Celera	12	18,969,149 - 18,971,988 (+)	NCBI		Celera
Cytogenetic Map	12	q11	NCBI

COPS6
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	7	100,088,969 - 100,092,187 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	7	100,088,969 - 100,092,187 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	7	99,686,592 - 99,689,810 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	99,524,519 - 99,527,759 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	7	99,331,233 - 99,334,471	NCBI
Celera	7	94,421,242 - 94,424,482 (+)	NCBI		Celera
Cytogenetic Map	7	q22.1	NCBI
HuRef	7	94,322,234 - 94,325,474 (+)	NCBI		HuRef
CHM1_1	7	99,616,742 - 99,619,982 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	7	101,328,815 - 101,332,033 (+)	NCBI		T2T-CHM13v2.0
CRA_TCAGchr7v2	7	99,046,703 - 99,049,943 (+)	NCBI

Cops6
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	138,159,364 - 138,162,246 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	138,159,333 - 138,162,908 (+)	Ensembl		GRCm39 Ensembl
GRCm38	5	138,161,102 - 138,163,984 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	138,161,071 - 138,164,646 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	138,602,330 - 138,605,212 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	5	138,390,890 - 138,393,772 (+)	NCBI		MGSCv36	mm8
Celera	5	135,140,434 - 135,143,316 (+)	NCBI		Celera
Cytogenetic Map	5	G2	NCBI
cM Map	5	76.97	NCBI

Cops6
(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_004955573	770,271 - 775,489 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955573	770,271 - 775,222 (-)	NCBI	ChiLan1.0	ChiLan1.0

COPS6
(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	6	118,008,389 - 118,011,377 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	7	166,273,021 - 166,276,006 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	7	92,124,166 - 92,127,165 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	7	105,557,778 - 105,560,998 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	7	105,557,778 - 105,560,998 (+)	Ensembl	panpan1.1		panPan2

COPS6
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	6	9,500,715 - 9,503,481 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	6	9,500,724 - 9,503,328 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
ROS_Cfam_1.0	6	9,437,718 - 9,440,669 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	6	9,437,717 - 9,440,346 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	6	9,287,044 - 9,289,721 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	6	9,267,344 - 9,270,300 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	6	9,446,955 - 9,449,633 (-)	NCBI		UU_Cfam_GSD_1.0

Cops6
(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_024409344	133,798,483 - 133,801,487 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936543	235,089 - 240,440 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936543	235,087 - 237,779 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

COPS6
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	7,982,892 - 8,005,633 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	8,002,702 - 8,005,545 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

COPS6
(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	28	12,986,194 - 12,989,189 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	28	12,986,346 - 12,989,174 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666070	3,283,730 - 3,286,718 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Cops6
(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_004624740	16,894,626 - 16,899,934 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624740	16,894,625 - 16,899,369 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Cops6
20 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	54
Count of miRNA genes:	49
Interacting mature miRNAs:	54
Transcripts:	ENSRNOT00000001820
Prediction methods:	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
2312418	Kidm41	Kidney mass QTL 41	3.7	0.0001	kidney mass (VT:0002707)	single kidney wet weight to body weight ratio (CMO:0000622)	12	1	19611090	Rat
10755457	Coatc14	Coat color QTL 14		0.01759	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	12	1	22591684	Rat
6893681	Bw109	Body weight QTL 109	2.3	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	12	1	23297788	Rat
1581516	Cm56	Cardiac mass QTL 56	4.2	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	12	1	29333307	Rat
1598855	Bp294	Blood pressure QTL 294	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	1	34851688	Rat
7411660	Foco28	Food consumption QTL 28	10.9	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	1	42110980	Rat
9590086	Insglur6	Insulin/glucose ratio QTL 6	18.97	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	12	1	42110980	Rat
8694179	Bw150	Body weight QTL 150	2.9	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	1	42110980	Rat
7411586	Foco5	Food consumption QTL 5	5.4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	1	42110980	Rat
7411595	Foco9	Food consumption QTL 9	4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	1	42110980	Rat
7411545	Bw128	Body weight QTL 128	5.2	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	1	42110980	Rat
9590147	Scort7	Serum corticosterone level QTL 7	13.61	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	12	1	42110980	Rat
2303575	Insul14	Insulin level QTL 14	4		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	12	1	42450532	Rat
737979	Pia22	Pristane induced arthritis QTL 22	53.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	1	44465750	Rat
634351	Apr5	Acute phase response QTL 5	6.7		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	12	1	44503507	Rat
2302042	Pia38	Pristane induced arthritis QTL 38	3.5	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	1	44503507	Rat
634350	Apr4	Acute phase response QTL 4	6		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	1172005	46172005	Rat
8552918	Pigfal7	Plasma insulin-like growth factor 1 level QTL 7			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	5564495	46669029	Rat
7411547	Bw129	Body weight QTL 129		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	5564495	46669029	Rat
7411597	Foco10	Food consumption QTL 10		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	5564495	46669029	Rat
7411641	Foco19	Food consumption QTL 19	27.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	5564495	46669029	Rat
8552964	Pigfal17	Plasma insulin-like growth factor 1 level QTL 17	3.5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	5564495	46669029	Rat
7411588	Foco6	Food consumption QTL 6		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	5564495	46669029	Rat
8552912	Pigfal6	Plasma insulin-like growth factor 1 level QTL 6	5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	5564498	46669029	Rat
10059594	Kidm46	Kidney mass QTL 46	3.79	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	12	6107579	46669029	Rat
1600391	Edcs2	Endometrial carcinoma susceptibility QTL2	3.5	0.01	uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	12	6833190	17870186	Rat
1302792	Scl21	Serum cholesterol level QTL 21	3.8	0.0011	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	12	7196730	46669029	Rat
2293086	Iddm30	Insulin dependent diabetes mellitus QTL 30	3.82		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	8449490	28302290	Rat
61331	Eau2	Experimental allergic uveoretinitis QTL 2		0.0005	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	12	8525423	28064601	Rat
1300157	Rf21	Renal function QTL 21	4.4		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	12	9318216	32103380	Rat
1549829	Scl48	Serum cholesterol level QTL 48	5		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	12	9603277	46669029	Rat
2293699	Bss49	Bone structure and strength QTL 49	5.61	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	12	10474137	46669029	Rat
2300186	Bmd59	Bone mineral density QTL 59	7.1	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	12	10474137	46669029	Rat
1331786	Kidm11	Kidney mass QTL 11	3.571		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	12	11073825	24234895	Rat
1331755	Bp219	Blood pressure QTL 219	3.041		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	11073825	28064557	Rat
1331761	Bp218	Blood pressure QTL 218	2.973		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	11073825	45055165	Rat
61404	Bw120	Body weight QTL 120	5.1		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	12	12351619	46669029	Rat
1641928	Alcrsp5	Alcohol response QTL 5			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	12	12812385	46669029	Rat
2303569	Gluco44	Glucose level QTL 44	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	12812385	46669029	Rat
7204484	Bp358	Blood pressure QTL 358		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	13008296	19212979	Rat
1549902	Bp269	Blood pressure QTL 269			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	13182736	46669029	Rat
1549912	Bp268	Blood pressure QTL 268			arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	13182736	46669029	Rat
2302060	Pia37	Pristane induced arthritis QTL 37	6.1	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	13198157	46669029	Rat
61416	Pia4	Pristane induced arthritis QTL 4	8.4		joint integrity trait (VT:0010548)	arthritic paw count (CMO:0001460)	12	13635523	30827399	Rat
61421	Cia12	Collagen induced arthritis QTL 12	4.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	13635523	35682913	Rat
61443	Btemp2	Thermal response to stress QTL 2	3.3	0.000094	body temperature trait (VT:0005535)	core body temperature (CMO:0001036)	12	15025183	20794014	Rat
631543	Bp83	Blood pressure QTL 83	5.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	15550826	38478808	Rat
2293684	Bmd26	Bone mineral density QTL 26	4.4	0.0002	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	12	15872653	32974238	Rat

Markers in Region

RH139725

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	12	17,041,890 - 17,042,094 (+)	MAPPER	mRatBN7.2
Rnor_6.0	12	19,306,299 - 19,306,502	NCBI	Rnor6.0
Rnor_5.0	12	21,363,929 - 21,364,132	UniSTS	Rnor5.0
RGSC_v3.4	12	17,606,929 - 17,607,132	UniSTS	RGSC3.4
Celera	12	18,972,061 - 18,972,264	UniSTS
RH 3.4 Map	12	254.4	UniSTS
Cytogenetic Map	12	q11	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	35	51	35	19	35	4	7	74	35	41	11	4
Low		8	6	6		6	4	4					4
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001107129	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH474107	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000012	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000001820 ⟹ ENSRNOP00000001820

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	12	17,038,979 - 17,041,818 (+)	Ensembl
Rnor_6.0 Ensembl	12	19,303,387 - 19,306,226 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000098915 ⟹ ENSRNOP00000077318

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	12	17,038,979 - 17,046,371 (+)	Ensembl

RefSeq Acc Id:

NM_001107129 ⟹ NP_001100599

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	12	22,152,688 - 22,155,527 (+)	NCBI
mRatBN7.2	12	17,038,979 - 17,041,818 (+)	NCBI
Rnor_6.0	12	19,303,387 - 19,306,226 (+)	NCBI
Rnor_5.0	12	21,361,017 - 21,363,856 (+)	NCBI
RGSC_v3.4	12	17,604,017 - 17,606,856 (+)	RGD
Celera	12	18,969,149 - 18,971,988 (+)	RGD

Sequence:

show sequence

AGATGGAAAGGGGCGGGCCGTGGCTGGCGGGCGCGGGGAAAATGGCGGCGGCGGCGGCGGCGGC
TGCGGCGGCGGCGGCGGCGGCGGCGAACGGGAGCGGAGGCAGCAGCGGCATGGAGGTGGATGCA
GCAGTCCCCAGCGTGATGGCCTCCGGAGTGACTGGGAGTGTTTCCGTCGCTCTTCATCCCCTTG
TCATCCTCAACATCTCAGACCATTGGATCCGCATGCGCTCCCAGGAGGGGCGGCCTATGCAGGT
GATTGGGGCTCTGATCGGGAAGCAGGAGGGGCGAAATATCGAAGTGATGAACTCCTTTGAGCTG
CTGTCTCACACCGTGGAAAAGAAGATTATCATTGACAAAGAATATTATTACACCAAGGAGGAGC
AGTTTAAACAGGTTTTCAAGGAGCTGGAGTTTTTGGGTTGGTATACCACAGGGGGGCCACCTGA
CCCCTCAGACATCCACGTCCATAAGCAGGTTTGCGAGATAATTGAGAGTCCTCTCTTTCTGAAG
TTGAACCCTATGACCAAGCACACAGATCTGCCTGTCAGCGTTTTTGAGTCTGTCATCGATATAA
TCAATGGAGAGGCCACAATGCTGTTTGCTGAACTCACTTACACTCTGGCCACTGAGGAAGCTGA
ACGTATCGGTGTAGACCATGTGGCCCGGATGACAGCTACAGGCAGTGGGGAGAACTCCACTGTG
GCTGAACACCTCATAGCTCAGCACAGCGCCATCAAGATGCTGCACAGCCGTGTGAAGCTCATTT
TAGAGTACGTCAAGGCCTCTGAAGCAGGAGAGGTTCCCTTCAACCATGAGATCCTGCGGGAGGC
CTATGCCCTATGCCACTGTCTTCCAGTTCTCAGCACTGACAAGTTCAAGACAGACTTTTATGAT
CAATGCAATGACGTGGGGCTTATGGCCTACCTCGGCACCATCACCAAAACGTGCAACACAATGA
ACCAGTTTGTGAACAAGTTCAACGTCCTGTATGACCGACAAGGCATCGGCAGGCGGATGCGGGG
ACTGTTTTTCTGATGAGGGCTCTTGGAAGGGATGCTGTATGGGGCTCAGACAACTGTGCCACGG
GACTGAGCACTTTCCCCTTAGAGAAACTCACTAATAAAGAACAGCCCCTTAGCAGCCCTTCCAG
TGGCTTTGTCCTCTCAGGCAC

hide sequence

Protein Sequences


Protein RefSeqs	NP_001100599	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL83891	(Get FASTA)	NCBI Sequence Viewer
	EDL83892	(Get FASTA)	NCBI Sequence Viewer
	EDL83893	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000001820
	ENSRNOP00000001820.4
	ENSRNOP00000077318.1

RefSeq Acc Id:

NP_001100599 ⟸ NM_001107129

- UniProtKB:

D3ZI16 (UniProtKB/TrEMBL), A6KSS5 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MERGGPWLAGAGKMAAAAAAAAAAAAAAANGSGGSSGMEVDAAVPSVMASGVTGSVSVALHPLV
ILNISDHWIRMRSQEGRPMQVIGALIGKQEGRNIEVMNSFELLSHTVEKKIIIDKEYYYTKEEQ
FKQVFKELEFLGWYTTGGPPDPSDIHVHKQVCEIIESPLFLKLNPMTKHTDLPVSVFESVIDII
NGEATMLFAELTYTLATEEAERIGVDHVARMTATGSGENSTVAEHLIAQHSAIKMLHSRVKLIL
EYVKASEAGEVPFNHEILREAYALCHCLPVLSTDKFKTDFYDQCNDVGLMAYLGTITKTCNTMN
QFVNKFNVLYDRQGIGRRMRGLFF

hide sequence

RefSeq Acc Id:

ENSRNOP00000001820 ⟸ ENSRNOT00000001820

RefSeq Acc Id:

ENSRNOP00000077318 ⟸ ENSRNOT00000098915

Protein Domains

MPN

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D3ZI16-F1-model_v2	AlphaFold	D3ZI16	1-344	view protein structure

Transcriptome

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

Promoters

RGD ID:

13698492

Promoter ID:

EPDNEW_R9017

Type:

multiple initiation site

Name:

Cops6_1

Description:

COP9 signalosome subunit 6

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	12	19,303,406 - 19,303,466	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1309919	AgrOrtholog
BioCyc Gene	G2FUF-19819	BioCyc
Ensembl Genes	ENSRNOG00000001346	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000001820	ENTREZGENE
	ENSRNOT00000001820.5	UniProtKB/TrEMBL
	ENSRNOT00000098915.1	UniProtKB/TrEMBL
Gene3D-CATH	Cytidine Deaminase, domain 2	UniProtKB/TrEMBL
InterPro	Mov34_MPN_PAD1	UniProtKB/TrEMBL
	MPN	UniProtKB/TrEMBL
	MPN_CSN6	UniProtKB/TrEMBL
	Rpn11/EIF3F_C	UniProtKB/TrEMBL
KEGG Report	rno:304343	UniProtKB/TrEMBL
NCBI Gene	304343	ENTREZGENE
PANTHER	COP9 SIGNALOSOME COMPLEX SUBUNIT 6	UniProtKB/TrEMBL
	EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT F-RELATED	UniProtKB/TrEMBL
Pfam	MitMem_reg	UniProtKB/TrEMBL
	Mov34	UniProtKB/TrEMBL
PhenoGen	Cops6	PhenoGen
PROSITE	MPN	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000001346	RatGTEx
SMART	JAB_MPN	UniProtKB/TrEMBL
UniProt	A0A8I5YBR2_RAT	UniProtKB/TrEMBL
	A6KSS5	ENTREZGENE, UniProtKB/TrEMBL
	D3ZI16	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2013-03-20	Cops6	COP9 signalosome subunit 6	Cops6	COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-10-23	Cops6	COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis)	Cops6	COP9 (constitutive photomorphogenic) homolog, subunit 6 (Arabidopsis thaliana)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Cops6	COP9 (constitutive photomorphogenic) homolog, subunit 6 (Arabidopsis thaliana)	Cops6_predicted	COP9 (constitutive photomorphogenic) homolog, subunit 6 (Arabidopsis thaliana) (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Cops6_predicted	COP9 (constitutive photomorphogenic) homolog, subunit 6 (Arabidopsis thaliana) (predicted)			Symbol and Name status set to approved	70820	APPROVED

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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