Ccs (copper chaperone for superoxide dismutase)

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Gene: Ccs (copper chaperone for superoxide dismutase) Rattus norvegicus

Analyze

Symbol:

Ccs

Name:

copper chaperone for superoxide dismutase

RGD ID:

620403

Description:

Exhibits enzyme binding activity. Predicted to be involved in positive regulation of oxidoreductase activity and removal of superoxide radicals. Predicted to localize to cytoplasm; extracellular space; and nucleus. Human ortholog(s) of this gene implicated in amyotrophic lateral sclerosis. Orthologous to human CCS (copper chaperone for superoxide dismutase); PARTICIPATES IN amyotrophic lateral sclerosis pathway; INTERACTS WITH (+)-schisandrin B; 1,2,4-trimethylbenzene; 1,2-dimethylhydrazine.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

superoxide dismutase copper chaperone

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	202,113,792 - 202,134,931 (-)	NCBI
Rnor_6.0 Ensembl	1	220,075,247 - 220,096,404 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	220,075,251 - 220,096,319 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	227,006,248 - 227,027,316 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	207,429,928 - 207,450,996 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	1	199,654,295 - 199,675,363 (-)	NCBI		Celera
Cytogenetic Map	1	q43	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

amyotrophic lateral sclerosis (ISO)

Chronic Hepatitis (ISO)

neurodegenerative disease (ISO)

nutritional deficiency disease (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

(S)-nicotine (ISO)

1,2,4-trimethylbenzene (EXP)

1,2-dimethylhydrazine (EXP,ISO)

2,2,2-tetramine (EXP)

2,3',4,4',5-Pentachlorobiphenyl (ISO)

2,3,2-tetramine (EXP,ISO)

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

2,3,7,8-Tetrachlorodibenzofuran (ISO)

2,4-dibromophenyl 2,4,5-tribromophenyl ether (EXP)

3,3',4,4',5-pentachlorobiphenyl (ISO)

acrylamide (EXP)

ammonium chloride (EXP)

bisphenol A (EXP,ISO)

cadmium dichloride (ISO)

cerium trichloride (ISO)

cisplatin (ISO)

clobetasol (ISO)

clofibrate (ISO)

clofibric acid (EXP)

cobalt dichloride (ISO)

copper atom (EXP,ISO)

copper(0) (EXP,ISO)

copper(II) chloride (ISO)

copper(II) sulfate (EXP,ISO)

crocidolite asbestos (ISO)

cyclosporin A (ISO)

cypermethrin (ISO)

diethyldithiocarbamic acid (EXP)

dioxygen (ISO)

enzyme inhibitor (ISO)

ethanol (ISO)

etoposide (ISO)

ferroheme b (ISO)

folic acid (ISO)

heme b (ISO)

hydrogen peroxide (ISO)

lactacystin (EXP,ISO)

lead diacetate (ISO)

lipopolysaccharide (ISO)

lutein (ISO)

methyl methanesulfonate (ISO)

N,N-diethyl-m-toluamide (EXP)

N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal (EXP)

N-nitrosodiethylamine (EXP)

nefazodone (EXP)

nicotine (ISO)

obeticholic acid (ISO)

oxaliplatin (ISO)

paracetamol (ISO)

paraquat (ISO)

permethrin (EXP)

pirinixic acid (ISO)

Pyridostigmine bromide (EXP)

silver atom (ISO)

silver(0) (ISO)

streptozocin (EXP)

tert-butyl hydroperoxide (ISO)

testosterone enanthate (ISO)

tetrachloromethane (EXP,ISO)

tetraethylenepentamine (ISO)

tetrathiomolybdate(2-) (EXP)

trichostatin A (ISO)

Tris(1-aziridinyl)phosphine oxide (ISO)

valproic acid (ISO)

vancomycin (ISO)

vitamin E (ISO)

zinc atom (EXP,ISO)

zinc(0) (EXP,ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

metal ion transport (IEA)

obsolete oxidation-reduction process (IEA)

positive regulation of oxidoreductase activity (IEA,ISO)

removal of superoxide radicals (IBA,IEA)

Cellular Component

cytoplasm (IEA,ISO)

extracellular space (IBA)

nucleus (IEA,ISO)

Molecular Function

copper ion binding (IBA,IEA,ISO)

enzyme binding (IDA)

metal ion binding (IEA)

protein binding (ISO)

superoxide dismutase activity (IBA,IEA)

superoxide dismutase copper chaperone activity (TAS)

Molecular Pathway Annotations Click to see Annotation Detail View

amyotrophic lateral sclerosis pathway (IEA)

References

References - curated


1.	Bertinato J and L'Abbe MR, J Biol Chem 2003 Sep 12;278(37):35071-8. Epub 2003 Jun 27.
2.	Bertinato J, etal., J Nutr 2003 Jan;133(1):28-31.
3.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4.	GOA data from the GO Consortium
5.	Hiromura M, etal., Biochem Biophys Res Commun. 2000 Aug 28;275(2):394-400.
6.	KEGG
7.	MGD data from the GO Consortium
8.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
9.	Pipeline to import KEGG annotations from KEGG into RGD
10.	RGD automated data pipeline
11.	RGD automated import pipeline for gene-chemical interactions
12.	West EC and Prohaska JR, Exp Biol Med (Maywood) 2004 Sep;229(8):756-64.
13.	Williams JR, etal., Neurobiol Dis. 2016 May;89:1-9. doi: 10.1016/j.nbd.2016.01.020. Epub 2016 Jan 27.

Additional References at PubMed

PMID:9726962	PMID:12477932	PMID:12968068	PMID:15722349	PMID:25468996

Genomics

Comparative Map Data

Ccs
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	202,113,792 - 202,134,931 (-)	NCBI
Rnor_6.0 Ensembl	1	220,075,247 - 220,096,404 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	220,075,251 - 220,096,319 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	227,006,248 - 227,027,316 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	207,429,928 - 207,450,996 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	1	199,654,295 - 199,675,363 (-)	NCBI		Celera
Cytogenetic Map	1	q43	NCBI

CCS
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	11	66,593,153 - 66,606,019 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	11	66,593,162 - 66,606,019 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	11	66,360,656 - 66,373,490 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
GRCh37	11	66,360,630 - 66,373,490 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	11	66,117,266 - 66,130,066 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	11	66,117,265 - 66,130,065	NCBI
Celera	11	63,692,424 - 63,699,333 (+)	NCBI
Cytogenetic Map	11	q13.2	NCBI
HuRef	11	62,688,333 - 62,701,716 (+)	NCBI		HuRef
CHM1_1	11	66,244,421 - 66,257,221 (+)	NCBI		CHM1_1

Ccs
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	19	4,875,394 - 4,889,384 (-)	NCBI	GRCm39		mm39
GRCm38	19	4,825,366 - 4,839,356 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	19	4,825,366 - 4,839,332 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	19	4,825,366 - 4,839,322 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	19	4,825,373 - 4,839,289 (-)	NCBI			mm8
Celera	19	4,696,420 - 4,710,377 (-)	NCBI		Celera
Cytogenetic Map	19	A	NCBI
cM Map	19	4.11	NCBI

Ccs
(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_004955422	18,758,580 - 18,772,757 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955422	18,761,703 - 18,772,762 (-)	NCBI	ChiLan1.0	ChiLan1.0

CCS
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	11	65,273,744 - 65,287,406 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	11	65,273,744 - 65,287,406 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	11	61,949,928 - 61,963,519 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

CCS
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	18	50,748,041 - 50,759,191 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	18	50,748,039 - 50,759,270 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Ccs
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936599	2,992,740 - 3,005,230 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CCS
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	5,819,471 - 5,836,064 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	5,819,471 - 5,833,263 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	4,867,363 - 4,875,306 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3
Pig Cytomap	2	p17-p14	NCBI

CCS
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	1	7,670,137 - 7,686,389 (-)	NCBI
ChlSab1.1 Ensembl	1	7,667,873 - 7,686,428 (-)	Ensembl

Ccs
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624767	19,803,945 - 19,815,590 (-)	NCBI

Position Markers

PMC16025P1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	220,095,876 - 220,096,268	NCBI	Rnor6.0
Rnor_5.0	1	227,026,873 - 227,027,265	UniSTS	Rnor5.0
Rnor_5.0	1	226,961,214 - 226,961,606	UniSTS	Rnor5.0
RGSC_v3.4	1	207,450,553 - 207,450,945	UniSTS	RGSC3.4
Celera	1	199,674,920 - 199,675,312	UniSTS
Cytogenetic Map	1	q43	UniSTS

RH129746

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	220,075,283 - 220,075,484	NCBI	Rnor6.0
Rnor_5.0	1	227,006,280 - 227,006,481	UniSTS	Rnor5.0
Rnor_5.0	1	226,940,166 - 226,940,367	UniSTS	Rnor5.0
RGSC_v3.4	1	207,429,960 - 207,430,161	UniSTS	RGSC3.4
Celera	1	199,654,327 - 199,654,528	UniSTS
RH 3.4 Map	1	1555.9	UniSTS
Cytogenetic Map	1	q43	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2292218	Kidm35	Kidney mass QTL 35			kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	217372257	244992610	Rat
619613	Bp77	Blood pressure QTL 77		0.01	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	175447029	220447029	Rat
619613	Bp77	Blood pressure QTL 77		0.01	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	175447029	220447029	Rat
631214	Bw61	Body weight QTL61	3.4	0.0001	intramuscular adipose amount (VT:0010044)	intramuscular fat area (CMO:0001162)	1	193220385	238220385	Rat
2302375	Bw83	Body weight QTL 83	4.87	0.0002	body mass (VT:0001259)	body weight (CMO:0000012)	1	215711860	260711860	Rat
2302378	Insul11	Insulin level QTL 11	3.25		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	156446196	274977688	Rat
70163	Bw20	Body weight QTL 20	5.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	189514504	234514504	Rat
724531	Uae5	Urinary albumin excretion QTL 5	4		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	1	161321152	273792054	Rat
724559	Pancm1	Pancreatic morphology QTL 1	7.1		islet of Langerhans morphology trait (VT:0005215)	pancreatic islet damage composite score (CMO:0001156)	1	198585664	236763415	Rat
724562	Rends1	Renal damage susceptibility QTL 1		0.05	kidney glomerulus integrity trait (VT:0010546)	index of glomerular damage (CMO:0001135)	1	137787261	236763528	Rat
737828	Hcas3	Hepatocarcinoma susceptibility QTL 3	4.9		liver integrity trait (VT:0010547)	liver tumorous lesion volume to total liver volume ratio (CMO:0001082)	1	156446196	243311614	Rat
1298084	Thym4	Thymus enlargement QTL 4	10.68		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	215828102	260828102	Rat
631658	Cm7	Cardiac mass QTL 7	5.32	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	1	216324817	261324817	Rat
737977	Bp160	Blood pressure QTL 160		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	197963658	242963658	Rat
1331790	Bp201	Blood pressure QTL 201	3.127		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	216213318	245529710	Rat
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	167394665	278228889	Rat
1582206	Kidm33	Kidney mass QTL 33	6.9		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	205603081	244401301	Rat
731168	Bp154	Blood pressure QTL 154	3.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	100131562	236763528	Rat
738032	Hcas5	Hepatocarcinoma susceptibility QTL 5	3.12		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	191825895	279986079	Rat
1302787	Stl25	Serum triglyceride level QTL 25	2.7	0.0073	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	1	197187728	230420772	Rat
1641926	Teswt2	Testicular weight QTL 2	2.82		testis mass (VT:1000644)	both testes wet weight (CMO:0000175)	1	215711860	258765521	Rat
1598853	Memor3	Memory QTL 3	4.5		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	1	153834077	232297227	Rat
2300161	Bmd43	Bone mineral density QTL 43	8.4	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	189170900	234170900	Rat
2300174	Bmd42	Bone mineral density QTL 42	8.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	bone mineral density (CMO:0001226)	1	189170900	234170900	Rat
2300187	Bmd41	Bone mineral density QTL 41	8.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	189170900	234170900	Rat
2293654	Bss30	Bone structure and strength QTL 30	32.65	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	1	189170900	234170900	Rat
2293673	Bss27	Bone structure and strength QTL 27	18.63	0.0001	femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	1	189170900	234170900	Rat
2293677	Bss41	Bone structure and strength QTL 41	9.38	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra cross-sectional area (CMO:0001689)	1	189170900	234170900	Rat
2293689	Bss47	Bone structure and strength QTL 47	7.25	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	1	189170900	234170900	Rat
2293693	Bss22	Bone structure and strength QTL 22	33.52	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	1	189170900	234170900	Rat
631838	Niddm36	Non-insulin dependent diabetes mellitus QTL 36		0.01	insulin secretion trait (VT:0003564)	calculated pancreatic islet insulin release measurement (CMO:0001217)	1	205195290	250195290	Rat
634312	Bp143	Blood pressure QTL 143	3	0.0002	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	198446729	240017341	Rat
634313	Niddm43	Non-insulin dependent diabetes mellitus QTL 43			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	217054291	281795785	Rat
634321	Hc1	Hypercalciuria QTL 1	2.91		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	193968438	261264776	Rat
634338	Hcar4	Hepatocarcinoma resistance QTL 4	4.6		liver integrity trait (VT:0010547)	liver tumorous lesion number to liver area ratio (CMO:0001210)	1	210960636	236763528	Rat
1357335	Bw39	Body weight QTL 39	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	1	215828102	260828102	Rat
1600363	Hc6	Hypercalciuria QTL 6	2.7		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	195598053	265002735	Rat
1600374	Mcs17	Mammary carcinoma susceptibility QTL 17	3		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	1	215684498	260684498	Rat
1600380	Niddm70	Non-insulin dependent diabetes mellitus QTL 70	3.1	0.0008	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	1	194554354	239554354	Rat
1600388	Niddm67	Non-insulin dependent diabetes mellitus QTL 67	5.84	0.000004	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	213476630	278978026	Rat
1600395	Niddm69	Non-insulin dependent diabetes mellitus QTL 69	4.14	0.0002	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	1	213476630	278978026	Rat
1600396	Niddm68	Non-insulin dependent diabetes mellitus QTL 68	4.97	0.0003	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	213476630	278978026	Rat
1578759	Uae30	Urinary albumin excretion QTL 30	3.3	0.003	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	161321256	273791893	Rat
1578763	Kidm29	Kidney mass QTL 29	3.3	0.0001	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	1	196395041	282763074	Rat
1578778	Pur4	Proteinuria QTL 4	3.3	0.003	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	1	161321256	273791893	Rat
1578780	Cm52	Cardiac mass QTL 52	3.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	1	82788437	239853971	Rat
1300145	Rf7	Renal function QTL 7	2.96		urine creatinine amount (VT:0010540)	urine creatinine level (CMO:0000125)	1	201146802	241482368	Rat
1354606	Bp246	Blood pressure QTL 246	3.6		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	108986301	238830534	Rat
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1354624	Cm35	Cardiac mass QTL35	5.7		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	192639698	278228889	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	161784169	278228889	Rat
1354652	Kidm20	Kidney mass QTL 20	4.3		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	192639698	278228889	Rat
1354653	Despr9	Despair related QTL 9		0.00019	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	1	185390068	230390068	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	161784169	278228889	Rat
1359018	Hrtrt20	Heart rate QTL 20	3.08		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	201358068	221983732	Rat
1558658	Bw59	Body weight QTL 59	3.5	0.0003	body mass (VT:0001259)	body weight (CMO:0000012)	1	196738546	241738546	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	163796316	282763074	Rat
1358191	Ept10	Estrogen-induced pituitary tumorigenesis QTL 10	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	1	210360774	264802828	Rat
2292220	Bp306	Blood pressure QTL 306	3.47	0.00087	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	174905700	264802994	Rat
2292222	Bp307	Blood pressure QTL 307	3.06	0.0014	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	174905700	233490237	Rat
2293083	Iddm25	Insulin dependent diabetes mellitus QTL 25	4.18		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	198655722	244992610	Rat
2312420	Pur17	Proteinuria QTL 17	7.1	0.0001	urine protein amount (VT:0005160)	urine total protein excretion rate (CMO:0000756)	1	167394665	238830534	Rat
2312564	Glom18	Glomerulus QTL 18	2.4	0.003	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	1	201358068	252480016	Rat
2314011	Gluco56	Glucose level QTL 56			blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	217776868	220128172	Rat
1358886	Bp260	Blood pressure QTL 260	3.67		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	161784422	246226103	Rat
1358898	Bp255	Blood pressure QTL 255	3.6		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	208517798	266948272	Rat
1549830	Bss1	Bone structure and strength QTL 1	4.8		femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	1	190282646	235282646	Rat
1358292	Cm37	Cardiac mass QTL 37	6.2	0.00000081	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	1	216324817	261324817	Rat
1358294	Bw37	Body weight QTL 37	5	0.000011	body mass (VT:0001259)	body weight (CMO:0000012)	1	188850303	233850303	Rat
61341	Bp26	Blood pressure QTL 26			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	137787261	236763528	Rat
61347	Bp197	Blood pressure QTL 197	4.2		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	1	175462885	220462885	Rat
61376	Bp42	Blood pressure QTL 42	23.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	215828102	260828102	Rat
6903303	Scl34	Serum cholesterol QTL 34	2.5	0.0033	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	197187728	238220385	Rat
8655655	Arrd2	Age-related retinal degeneration QTL 2	7.79		retinal layer morphology trait (VT:0003727)	percentage of study population developing retinopathy during a period of time (CMO:0002453)	1	202571665	264802994	Rat
7794788	Mcs32	Mammary carcinoma susceptibility QTL 32	2.61		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	1	122614824	262664716	Rat
7771612	Cm80	Cardiac mass QTL 80	8.4		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	1	144634295	241482368	Rat
7421630	Bp362	Blood pressure QTL 362		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	125875758	262433692	Rat
8552891	Epfw5	Epididymal fat weight QTL 5	4.4		epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	1	210652654	255652654	Rat
8655855	Arrd3	Age-related retinal degeneration QTL 3	3.07		lens clarity trait (VT:0001304)	cataract incidence/prevalence measurement (CMO:0001585)	1	202571665	264802994	Rat
10059590	Kidm44	Kidney mass QTL 44	3.42	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	210990171	255990171	Rat
10059600	Bp378	Blood pressure QTL 378	3.08	0.05	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	194872362	239872362	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	216
Count of miRNA genes:	102
Interacting mature miRNAs:	103
Transcripts:	ENSRNOT00000026670, ENSRNOT00000064728, ENSRNOT00000073983
Prediction methods:	Microtar, Miranda, Rnahybrid
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.

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	57	41	19	41		3	74	35	41	11
Low		8					8	8					8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053425	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039092800	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC126581	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF255305	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC158586	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473953	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	EU340033	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000045	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000073983 ⟹ ENSRNOP00000065189

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	220,075,247 - 220,096,404 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000091787 ⟹ ENSRNOP00000074464

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	220,075,290 - 220,096,319 (-)	Ensembl

RefSeq Acc Id:

NM_053425 ⟹ NP_445877

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	202,113,792 - 202,134,862 (-)	NCBI
Rnor_6.0	1	220,075,251 - 220,096,319 (-)	NCBI
Rnor_5.0	1	227,006,248 - 227,027,316 (-)	NCBI
RGSC_v3.4	1	207,429,928 - 207,450,996 (-)	RGD
Celera	1	199,654,295 - 199,675,363 (-)	RGD

Sequence:

show sequence

GGTCTCTGGACCCTACCGGTTGTGTGGCCCAAGCGGGTGACTGCAGCCAGGATGGCTTCGAAGT
CGGGGGACGGTGGAACTATGTGTGCGTTGGAGTTTACAGTACAGATGAGTTGTCAGAGCTGCGT
GGACGCTGTGCACAAGACCCTGAAAGGGGCGGCGGGTGTCCAGAATGTGGAAGTTCAGTTGGAG
AACCAGATGGTGTTGGTGCAGACCACTTTGCCCAGCCAGGAGGTGCAAGCGCTCCTGGAAAGCA
CAGGGAGGCAGGCTGTACTCAAGGGCATGGGCAGCAGCCAACTAAAGAATCTGGGAGCAGCAGT
GGCCATTATGGAGGGCAGTGGCACCGTACAGGGGGTGGTCCGCTTCCTACAGCTGTCCTCTGAG
CTCTGCCTGATTGAGGGAACCATCGACGGCCTGGAGCCTGGGCTGCATGGGCTTCATGTCCATC
AGTATGGGGACCTTACCAAGGACTGCAGCAGCTGTGGGGACCATTTTAACCCTGATGGAGCATC
TCATGGGGGTCCTCAGGACACTGATCGGCACCGGGGAGATCTGGGCAATGTTCACGCTGAAGCT
AGTGGCCGAGCTACCTTCCGGATAGAGGATAAACAGCTGAAGGTGTGGGATGTGATTGGCCGCA
GTCTGGTTGTTGATGAGGGAGAAGATGACCTGGGCCGGGGAGGCCATCCCTTATCCAAGGTCAC
AGGGAATTCTGGGAAGAGGTTGGCCTGTGGCATCATTGCACGCTCTGCTGGCCTTTTCCAGAAT
CCCAAGCAGATCTGCTCCTGTGATGGGCTCACTATCTGGGAGGAGCGAGGCCGGCCCATTGCTG
GCCAAGGCCGAAAGGACTCAGCCCAACCCCCTGCTCACCTCTGAACAGAGCCTCCTGTCAGGTT
ATTCAGTCCTCCTAGCTGAACATCTTCCTGCAGAGGGAGCCTCAAGCCCTTGCTTGTATAGGCC
TAAAGGGCAGATAGGCATTGTTGTATCCTGAGCAAATTAAATTGTTACTCTCATATGGC

hide sequence

RefSeq Acc Id:

XM_039092800 ⟹ XP_038948728

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	202,114,186 - 202,134,931 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_445877	(Get FASTA)	NCBI Sequence Viewer
	XP_038948728	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAF65572	(Get FASTA)	NCBI Sequence Viewer
	AAI58587	(Get FASTA)	NCBI Sequence Viewer
	ACA50926	(Get FASTA)	NCBI Sequence Viewer
	EDM12425	(Get FASTA)	NCBI Sequence Viewer
	EDM12426	(Get FASTA)	NCBI Sequence Viewer
	EDM12427	(Get FASTA)	NCBI Sequence Viewer
	EDM12428	(Get FASTA)	NCBI Sequence Viewer
	Q9JK72	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_445877 ⟸ NM_053425

- UniProtKB:

Q9JK72 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MASKSGDGGTMCALEFTVQMSCQSCVDAVHKTLKGAAGVQNVEVQLENQMVLVQTTLPSQEVQA
LLESTGRQAVLKGMGSSQLKNLGAAVAIMEGSGTVQGVVRFLQLSSELCLIEGTIDGLEPGLHG
LHVHQYGDLTKDCSSCGDHFNPDGASHGGPQDTDRHRGDLGNVHAEASGRATFRIEDKQLKVWD
VIGRSLVVDEGEDDLGRGGHPLSKVTGNSGKRLACGIIARSAGLFQNPKQICSCDGLTIWEERG
RPIAGQGRKDSAQPPAHL

hide sequence

RefSeq Acc Id:

ENSRNOP00000065189 ⟸ ENSRNOT00000073983

RefSeq Acc Id:

ENSRNOP00000074464 ⟸ ENSRNOT00000091787

RefSeq Acc Id:	XP_038948728 ⟸ XM_039092800
- Peptide Label:	isoform X1

Protein Domains

HMA Sod_Cu

Transcriptome

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

Promoters

RGD ID:

13690638

Promoter ID:

EPDNEW_R1156

Type:

initiation region

Name:

Ccs_1

Description:

copper chaperone for superoxide dismutase

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	1	220,096,329 - 220,096,389	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620403	AgrOrtholog
Ensembl Genes	ENSRNOG00000047816	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000065189	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOP00000074464	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000073983	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOT00000091787	UniProtKB/TrEMBL
Gene3D-CATH	2.60.40.200	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:9099085	IMAGE-MGC_LOAD
InterPro	HMA_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HMA_dom_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SOD-like_Cu/Zn_dom_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SOD_Cu/Zn_/chaperone	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SOD_Cu/Zn_BS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SOD_Cu_Zn_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:84485	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:187351	IMAGE-MGC_LOAD
NCBI Gene	84485	ENTREZGENE
PANTHER	PTHR10003	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	HMA	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Sod_Cu	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Ccs	PhenoGen
PRINTS	CUZNDISMTASE	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	HMA_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SOD_CU_ZN_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF49329	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF55008	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A0G2JSZ9_RAT	UniProtKB/TrEMBL
	B9TSW3_RAT	UniProtKB/TrEMBL
	CCS_RAT	UniProtKB/Swiss-Prot
	E9PSS2_RAT	UniProtKB/TrEMBL
	Q9JK72	ENTREZGENE
UniProt Secondary	B0BMW1	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2004-09-10	Ccs	copper chaperone for superoxide dismutase			Symbol and Name status set to approved	1299863	APPROVED
2002-08-07	Ccs	copper chaperone for superoxide dismutase			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_disease	increased protein levels may be a marker for assessing copper deficiency	634854
gene_regulation	Ccs degradation via the 26 S proteosome is regulated by copper	737850

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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)