Ccdc47 (coiled-coil domain containing 47)

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Gene: Ccdc47 (coiled-coil domain containing 47) Rattus norvegicus

Analyze

Symbol:

Ccdc47

Name:

coiled-coil domain containing 47

RGD ID:

1308813

Description:

Predicted to have calcium ion binding activity. Predicted to be involved in several processes, including ER overload response; endoplasmic reticulum calcium ion homeostasis; and ubiquitin-dependent ERAD pathway. Predicted to localize to rough endoplasmic reticulum. Orthologous to human CCDC47 (coiled-coil domain containing 47); INTERACTS WITH acrylamide; bisphenol A; flutamide.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

coiled-coil domain-containing protein 47; LOC303606; RGD1308813; similar to adipocyte-specific protein 4

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

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):	CCDC47 (coiled-coil domain containing 47)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Ccdc47 (coiled-coil domain containing 47)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Ccdc47 (coiled-coil domain containing 47)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CCDC47 (coiled-coil domain containing 47)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CCDC47 (coiled-coil domain containing 47)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Ccdc47 (coiled-coil domain containing 47)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CCDC47 (coiled-coil domain containing 47)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	CCDC47 (coiled-coil domain containing 47)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Ccdc47 (coiled-coil domain containing 47)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Ccdc47 (coiled-coil domain containing 47)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Homo sapiens (human):	CCDC47 (coiled-coil domain containing 47)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	ccdc47 (coiled-coil domain containing 47)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	CG17593	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Saccharomyces cerevisiae (baker's yeast):	YNR021W	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	ccdc-47	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

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	10	91,130,303 - 91,148,829 (-)	NCBI
Rnor_6.0 Ensembl	10	94,388,430 - 94,406,949 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	10	94,388,425 - 94,406,949 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	10	94,139,727 - 94,158,251 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	95,593,531 - 95,612,057 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	95,607,905 - 95,626,427 (-)	NCBI
Celera	10	89,806,277 - 89,824,762 (-)	NCBI		Celera
Cytogenetic Map	10	q32.1	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Trichohepatoneurodevelopmental Syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

3,4-methylenedioxymethamphetamine (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-sulfonyldiphenol (ISO)

acrylamide (EXP)

aflatoxin B2 (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenous acid (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bisphenol A (EXP)

bisphenol F (ISO)

carbon nanotube (ISO)

clofibrate (ISO)

cobalt dichloride (ISO)

coumestrol (ISO)

crocidolite asbestos (ISO)

dexamethasone (ISO)

diarsenic trioxide (ISO)

ethanol (ISO)

flutamide (EXP)

hydralazine (ISO)

indometacin (ISO)

MeIQx (ISO)

methapyrilene (EXP)

N-methyl-4-phenylpyridinium (ISO)

nefazodone (EXP)

paracetamol (ISO)

pentachlorophenol (ISO)

phenobarbital (ISO)

pirinixic acid (ISO)

propiconazole (ISO)

sodium fluoride (ISO)

tetrachloromethane (ISO)

valdecoxib (EXP)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

calcium ion homeostasis (ISO)

endoplasmic reticulum calcium ion homeostasis (ISO,ISS)

endoplasmic reticulum organization (ISO)

ER overload response (ISO)

ERAD pathway (ISO,ISS)

post-embryonic development (ISO)

ubiquitin-dependent ERAD pathway (ISO)

Cellular Component

endoplasmic reticulum (IBA,ISO)

integral component of membrane (IEA)

rough endoplasmic reticulum (ISO)

rough endoplasmic reticulum membrane (IEA)

Molecular Function

calcium ion binding (IBA,ISO)

protein binding (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	MGD data from the GO Consortium
3.	RGD automated data pipeline
4.	RGD automated import pipeline for gene-chemical interactions
5.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Additional References at PubMed

PMID:15489334	PMID:16210410	PMID:17204322	PMID:19946888	PMID:22658674	PMID:25009997	PMID:30401460

Genomics

Comparative Map Data

Ccdc47
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	10	91,130,303 - 91,148,829 (-)	NCBI
Rnor_6.0 Ensembl	10	94,388,430 - 94,406,949 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	10	94,388,425 - 94,406,949 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	10	94,139,727 - 94,158,251 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	95,593,531 - 95,612,057 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	95,607,905 - 95,626,427 (-)	NCBI
Celera	10	89,806,277 - 89,824,762 (-)	NCBI		Celera
Cytogenetic Map	10	q32.1	NCBI

CCDC47
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	17	63,745,255 - 63,776,351 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	17	63,745,255 - 63,773,597 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	17	61,822,615 - 61,850,957 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	59,176,342 - 59,204,668 (-)	NCBI	NCBI36		hg18	NCBI36
Celera	17	56,210,730 - 56,239,209 (-)	NCBI
Cytogenetic Map	17	q23.3	NCBI
HuRef	17	57,190,690 - 57,219,079 (-)	NCBI		HuRef
CHM1_1	17	61,887,006 - 61,915,427 (-)	NCBI		CHM1_1

Ccdc47
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	106,090,086 - 106,107,349 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	11	106,088,234 - 106,107,170 (-)	Ensembl
GRCm38	11	106,199,260 - 106,216,523 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	106,197,408 - 106,216,344 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	106,060,668 - 106,077,681 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	11	106,016,556 - 106,032,393 (-)	NCBI			mm8
Celera	11	117,929,788 - 117,946,801 (-)	NCBI		Celera
Cytogenetic Map	11	E1	NCBI

Ccdc47
(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_004955478	8,053,057 - 8,074,820 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955478	8,053,057 - 8,074,530 (+)	NCBI	ChiLan1.0	ChiLan1.0

CCDC47
(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	17	62,970,109 - 62,998,465 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	17	62,970,109 - 62,998,465 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	17	57,825,328 - 57,853,626 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

CCDC47
(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	9	11,717,163 - 11,736,890 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	9	11,715,793 - 11,737,055 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Ccdc47
(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_004936541	4,389,428 - 4,418,414 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CCDC47
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	12	15,165,405 - 15,204,719 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	12	15,165,268 - 15,186,141 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	12	15,155,169 - 15,174,513 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CCDC47
(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	16	57,517,759 - 57,545,495 (+)	NCBI
ChlSab1.1 Ensembl	16	57,525,512 - 57,547,798 (+)	Ensembl

Ccdc47
(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_004624849	1,237,364 - 1,282,588 (-)	NCBI

Position Markers

RH133734

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	10	94,394,621 - 94,394,815	NCBI	Rnor6.0
Rnor_5.0	10	94,145,923 - 94,146,117	UniSTS	Rnor5.0
RGSC_v3.4	10	95,599,728 - 95,599,922	UniSTS	RGSC3.4
Celera	10	89,812,432 - 89,812,626	UniSTS
RH 3.4 Map	10	981.3	UniSTS
Cytogenetic Map	10	q32.1	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
61427	Cia16	Collagen induced arthritis QTL 16	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	6429075	99492409	Rat
2303118	Mamtr7	Mammary tumor resistance QTL 7		0.003	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	9841807	108540162	Rat
631268	Cia21	Collagen induced arthritis QTL 21	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	14827894	107857673	Rat
2316949	Gluco60	Glucose level QTL 60	3.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	14827894	110992275	Rat
1554317	Bmd4	Bone mineral density QTL 4	9.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	20170031	102897474	Rat
1331791	Cm31	Cardiac mass QTL 31	3.84606		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	23861015	112626471	Rat
631267	Cia20	Collagen induced arthritis QTL 20	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61325	Aia5	Adjuvant induced arthritis QTL 5		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61354	Pia10	Pristane induced arthritis QTL 10		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
1298069	Bp168	Blood pressure QTL 168	5.5		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	10	27237530	101482600	Rat
631542	Bp82	Blood pressure QTL 82	6.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	27237530	102427718	Rat
631552	Vetf2	Vascular elastic tissue fragility QTL 2	4.5	0.0002	aorta elastic tissue integrity trait (VT:0010556)	artery internal elastic lamina non-tumorous lesion count (CMO:0001913)	10	36185929	95845311	Rat
1576308	Schws1	Schwannoma susceptibility QTL 1		0.0041	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	10	41260363	106105607	Rat
631269	Cia22	Collagen induced arthritis QTL 22	8.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	41260363	107857673	Rat
631270	Cia23	Collagen induced arthritis QTL 23	3.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	41260363	107857673	Rat
1298078	Stresp5	Stress response QTL 5	2.99	0.00025	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	43289657	108540162	Rat
2300218	Hpcl2	Hepatic cholesterol level QTL 2			liver cholesterol amount (VT:0010498)	liver cholesterol level (CMO:0001597)	10	46593021	98939209	Rat
631547	Bp87	Blood pressure QTL 87	4.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	50638337	95638337	Rat
1549846	Scl47	Serum cholesterol level QTL 47	3.6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	10	53104718	98104718	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	53621375	112626471	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	53621375	112626471	Rat
631530	Tls3	T-lymphoma susceptibility QTL 3	0	0.0001	thymus integrity trait (VT:0010555)	percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)	10	53625815	98939209	Rat
631535	Cm51	Cardiac mass QTL 51	3		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	10	53637485	94807701	Rat
1359017	Hrtrt21	Heart rate QTL 21	2.4		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	10	55224855	100224855	Rat
70171	Cari1	Carrageenan-induced inflammation QTL 1	4.9	0.0005	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	10	55678976	112626471	Rat
70164	Bw21	Body weight QTL 21	4.36	0.00005	body mass (VT:0001259)	body weight (CMO:0000012)	10	55679084	102427604	Rat
1354608	Cm33	Cardiac mass QTL 33	2.8		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	10	56698730	101698730	Rat
1549831	Bss6	Bone structure and strength QTL 6	4		lumbar vertebra strength trait (VT:0010574)	vertebra ultimate force (CMO:0001678)	10	60450007	105450007	Rat
2312662	Slep8	Serum leptin concentration QTL 8		0.05	blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	10	60875260	105875260	Rat
2312668	Scl65	Serum cholesterol level QTL 65		0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	10	60875260	105875260	Rat
2312672	Insul15	Insulin level QTL 15		0.01	blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	10	60875260	105875260	Rat
2293698	Bss43	Bone structure and strength QTL 43	5.33	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra cross-sectional area (CMO:0001689)	10	62096293	107096293	Rat
2306970	Anxrr22	Anxiety related response QTL 22	5.95		fear/anxiety-related behavior trait (VT:1000241)	number of periods of voluntary immobility (CMO:0001045)	10	64648175	101691360	Rat
1558643	Cm44	Cardiac mass QTL 44	4.8	0.0000368	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	64648175	102149713	Rat
6893336	Cm75	Cardiac mass QTL 75	0.1	0.87	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	10	64648175	102149713	Rat
61449	Ciaa2	CIA Autoantibody QTL 2	7.1		blood autoantibody amount (VT:0003725)	calculated serum anti-type 2 collagen antibody titer (CMO:0001279)	10	65590122	110590122	Rat
2313103	Bss80	Bone structure and strength QTL 80	2	0.0001	tibia strength trait (VT:1000284)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	10	65992275	110992275	Rat
2313105	Bss79	Bone structure and strength QTL 79	1.8	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	10	65992275	110992275	Rat
7387312	Bw125	Body weight QTL 125	3	0.0047	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight (CMO:0000356)	10	67880046	112626471	Rat
1581559	Eae18	Experimental allergic encephalomyelitis QTL 18		0.00002	nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	10	67988218	110992091	Rat
1357344	Bp249	Blood pressure QTL 249		0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	69123603	101482600	Rat
2317029	Aia19	Adjuvant induced arthritis QTL 19	2.98		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	10	69385595	112626471	Rat
2317039	Aia6	Adjuvant induced arthritis QTL 6	4.31		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	10	69385595	112626471	Rat
10450498	Bp384	Blood pressure QTL 384		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	70166960	112626471	Rat
1642980	Bp300	Blood pressure QTL 300			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	70800069	112626471	Rat
61396	Bp9	Blood pressure QTL 9	4.8	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	71692298	112626471	Rat
2300172	Bmd57	Bone mineral density QTL 57	9.8	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	10	73008136	112626471	Rat
2293646	Bss25	Bone structure and strength QTL 25	10.96	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	10	73008136	112626471	Rat
2293663	Bss33	Bone structure and strength QTL 33	9.34	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	10	73008136	112626471	Rat
6893366	Bw106	Body weight QTL 106	0.3	0.47	body mass (VT:0001259)	body weight (CMO:0000012)	10	73467158	112626471	Rat
2306793	Ean5	Experimental allergic neuritis QTL 5	4.7		nervous system integrity trait (VT:0010566)	IFNG-secreting splenocyte count (CMO:0002122)	10	75045391	97308358	Rat
70193	Mcs7	Mammary carcinoma susceptibility QTL 7	2.38		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	10	75544754	112626471	Rat
2298548	Neuinf7	Neuroinflammation QTL 7	3.4		nervous system integrity trait (VT:0010566)	spinal cord RT1-B protein level (CMO:0002132)	10	75544754	112626471	Rat
1358188	Ept9	Estrogen-induced pituitary tumorigenesis QTL 9	3.9		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	10	75983805	99492217	Rat
2292617	Ept18	Estrogen-induced pituitary tumorigenesis QTL 18	3.9		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	10	75983805	99492217	Rat
1579919	Bp281	Blood pressure QTL 281		0.01	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	77055741	98282519	Rat
10450495	Bp383	Blood pressure QTL 383		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	78970279	98282519	Rat
2292438	Bp311	Blood pressure QTL 311			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	78970279	112626471	Rat
1302404	Cia27	Collagen induced arthritis QTL 27	2.6	0.0045	joint integrity trait (VT:0010548)	experimental arthritis severity measurement (CMO:0001459)	10	79927661	112626471	Rat
4889492	Pancm2	Pancreatic morphology QTL 2	3.2		pancreatic beta cell morphology trait (VT:0005217)	ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)	10	80239190	112626471	Rat
1300107	Rf18	Renal function QTL 18	3.41		urine output (VT:0003620)	timed urine volume (CMO:0000260)	10	81515116	101758478	Rat
631555	Bp134	Blood pressure QTL 134		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	83389828	94488181	Rat
6893357	Bw102	Body weight QTL 102	0.5	0.36	body mass (VT:0001259)	body weight (CMO:0000012)	10	83389828	104994768	Rat
2303589	Bw87	Body weight QTL 87	2		body mass (VT:0001259)	body weight (CMO:0000012)	10	85079943	112626471	Rat
4889948	Bss91	Bone structure and strength QTL 91	4		tibia area (VT:1000281)	tibia midshaft total cross-sectional area (CMO:0001715)	10	85513822	95638337	Rat
2317754	Glom25	Glomerulus QTL 25	3.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	86566908	112626471	Rat
2301398	Kidm38	Kidney mass QTL 38		0.002	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	10	86962563	99303173	Rat
12880055	Am11	Aortic mass QTL 11		0.004	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	10	86962563	99303173	Rat
2306792	Ean4	Experimental allergic neuritis QTL 4	4		nervous system integrity trait (VT:0010566)	IFNG-secreting splenocyte count (CMO:0002122)	10	86977861	97308569	Rat
1600367	Mcs15	Mammary carcinoma susceptibility QTL 15	4.5		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	10	88544136	107545372	Rat
631538	Oia5	Oil induced arthritis QTL 5			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	90041957	112626471	Rat
2313856	Bp342	Blood pressure QTL 342	4.4	0.0001	life span trait (VT:0005372)	age at time of death (CMO:0001193)	10	90296897	99492409	Rat
61363	Oia3	Oil induced arthritis QTL 3		0.001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	90296897	112626471	Rat
70364	Bp72	Blood pressure QTL 72			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	91548145	99492409	Rat
634320	Niddm49	Non-insulin dependent diabetes mellitus QTL 49	4.41		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	10	91689348	112626471	Rat
1579915	Bp280	Blood pressure QTL 280		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	93662786	112626471	Rat
12880395	Cm109	Cardiac mass QTL 109		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	10	93662786	112626471	Rat
12880396	Am13	Aortic mass QTL 13		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	10	93662786	112626471	Rat
12880398	Kidm67	Kidney mass QTL 67		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	10	93662786	112626471	Rat
12880384	Cm107	Cardiac mass QTL 107		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)		93662786	112626471	Rat
12880385	Cm108	Cardiac mass QTL 108		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)		93662786	112626471	Rat
1300137	Bp186	Blood pressure QTL 186	3.57		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	10	93886117	110992275	Rat
724530	Bp149	Blood pressure QTL 149		0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	93886117	112626471	Rat
1558652	Bw57	Body weight QTL 57	4.2	0.0008	body mass (VT:0001259)	body weight (CMO:0000012)	10	94170766	112626471	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	191
Count of miRNA genes:	134
Interacting mature miRNAs:	162
Transcripts:	ENSRNOT00000012533
Prediction methods:	Miranda, 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.

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	40	11	8
Low											1
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001013974	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039086169	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC133055	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC085824	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473948	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000220	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000012533 ⟹ ENSRNOP00000012533

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	10	94,388,430 - 94,406,949 (-)	Ensembl

RefSeq Acc Id:

NM_001013974 ⟹ NP_001013996

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	91,130,303 - 91,148,829 (-)	NCBI
Rnor_6.0	10	94,388,425 - 94,406,949 (-)	NCBI
Rnor_5.0	10	94,139,727 - 94,158,251 (-)	NCBI
RGSC_v3.4	10	95,593,531 - 95,612,057 (-)	RGD
Celera	10	89,806,277 - 89,824,762 (-)	RGD

Sequence:

show sequence

TGAAGAGTAGGGTACCGTGACTGAGCTACCTGCTCTGGGCTGTTCAGTGACCTCGCGGCCCGCA
GATAAATCTTTGCGACCTGAAGGCAGAAACCAGACAAAGGCAGGCCGGGTGGAGGTGGTGGCCT
CAGGAGCCCCGGGTCCGGTGGTAGCCTCGGGTGCAGCTTATTTTTAAGGTGCAATGAAAGCCTT
CTGTGCTTTCTGTGTTGTTCTCTTGGTGTTTGGGAGTGTCTCTGAAGCCAAGTTTGATGATTTC
GAGGATGAGGAAGACATAGTAGAGTATGATGATAATGATTTTGCTGAGTTTGAGGACGTCGTGG
AAGATTCTGTTACGGAATCTCCTCAGCGAGTGATCAACACTGAAGATGACGAGGATGAGGCCAC
CGTGGAATTGGAAGGGCAGGATGAAGGCCAAGAAGGCGATTTCGAAGATGCAGATACCCAGGAG
GGAGATACAGAAAGTGAGCCATATGATGACGAAGAATTTGAGGGTTATGAAGACAAACCTGATA
CCTCTTCTAACAAAAATAAAGATCCAATAACAATTGTTGATGTTCCTGCACACCTCCAGAACAG
TTGGGAGAGTTATTACCTAGAAATTTTGATGGTGACCGGTCTGCTTGCCTATATCATGAACTAT
ATCATCGGGAAGAATAAAAACAGCCGACTTGCTCAGGCCTGGTTTAACTCTCATAGAGAGCTTT
TGGAGAGCAATTTTACCTTAGTGGGGGATGATGGGACTAACAAAGAAGCCACAAGCACAGGGAA
GTTGAACCAGGAGAATGAGCACATCTATAACCTGTGGTGTTCTGGCCGAGTGTGCTGTGAAGGC
ATGCTCATCCAGCTGAGGTTCCTGAAGAGACAAGACTTACTTAACGTCCTGGCCCGGATGATGA
GGCCAGTGAGTGATCAGGTGCAAATAAAAGTCACAATGAACGACGAGGACATGGATACATACGT
GTTCGCTGTCGGCACTCGCAAAGCTTTGCTGCGACTGCAGAAAGAGATGCAGGATCTGAGTGAG
TTTTGTAGTGATAAACCTAAGTCTGGAGCGAAGTATGGACTGCCAGACTCTTTGGCCATTCTGT
CAGAGATGGGAGAAGTCACAGAGGGGATGATGGATACAAAGATGGTTCACTTTCTTACACACTA
TGCTGATAAGATTGAATCTGTTCATTTTTCAGACCAGTTCTCTGGTCCAAAGATTATGCAAGAG
GAAGGGCAGCCTTTAAAGCTGCCTGACACCAAGAGGACACTACTGTTTACATTTAATGTGCCTG
GCTCAGGTAACACGTACCCAAAGGATATGGAGGCTTTGCTACCCCTGATGAACATGGTGATTTA
TTCTATCGATAAAGCCAAAAAGTTCCGCCTCAACAGAGAAGGCAAACAAAAAGCAGATAAGAAC
CGGGCACGCGTGGAAGAGAACTTTCTGAAGCTGACACATGTACAGAGACAGGAGGCTGCACAGT
CTCGGCGTGAGGAGAAGAAAAGAGCTGAGAAGGAGCGGATCATGAATGAGGAGGACCCTGAAAA
GCAGCGCAGGCTGGAGGAAGCGGCTTTGAGGAGAGAACAAAAGAAGTTGGAGAAGAAGCAAATG
AAAATGAAACAAATCAAAGTGAAAGCCATGTAAAGTGGTCCTACGGGCCTGTCCTCGATGCCGA
TGCCGGAAGCTGGAAGCGCTGTGTCTGCCGAGTCCTCACCTAACAGTCACGTGTTTCTGGTGAC
TCAGAGATCTTTATTTCACCCTCTCCTTTTGGTTTGGAGTTCTACAGAGGTTAGAGATACATTG
AAAGGGCTTTTTCAGCTATCTCCTTCCAGATAATCAAATTATTTTGGTTATTCTCTAAAAGGAA
TGGTATATAAGTATGTGTAGTTTTACAATGTTTAAATTATAATGTGAATCATTAGTGCTTTACT
TTGGTGTTTGAAGAACGATCATGAAATTTCTAGGTAGGTTGTTGCTTTTTGTTTAAACTGAGAG
TTGAAATTTCTATGGAGACTGACTCTAACCCAACACCCTAAGAATATCTATTGGAATTGCACAA
TAGCCATTGCTTGTTTTTCTGTGTCCACATTAAACTTGTGAAAAAAGTGGAATCTAGAACACTG
TATGTGATGACAAGGTCAGAGACTTAGAACGTAGTACAGCATATGTTTTGTGTGGGGGTGGTGC
TGATGGCAGTATGATAGGAAGAGATCCATAGGTGTTAGGATACTGTAAGTCCATGGAGGACTCT
CGAGGTAGGTAGTACAGGAGTGGTTTCTCATTGCCTGATACTATGAGCTAATGACACTGAGTGC
TGGATTTGAAGTAGTTATGTGCTTATTTTTTCTGAGCAAGAAATGCATGAATAAATGGACTGCG
TCAGCTAGCCGGATCAGCAGTCAGATGGCTGGTCTCTGTGAGGTCATAATGGGTTTCTTGCTTG
CTGCAGCCTGTGAGGTTTTCATGGAGGAGCTGATCTGTCTTATGAGTGCGCTTGTTCTCTGCCT
GCTTTTATATTGTCCACAAGGCCGGTATGTACTGTCTTGAAACACATAACCATTGATATGCACA
AATATGCTTTTAAAAAGTGAGCTTTTTTAAGTGATTCAGAATTTTGTCTGACTCGTGGGGCAGG
AGCGATGGTGGAGAGAGGCCCCTCTCTGTGCATAAGCATTGGCTTGTCGAGAGCTCTGCATTTT
ATAAATGCTTCCTACCGAGAAAGCATTTCTTAAGTCTCTGCTTGTACCAGGTAGTTCTTGCTGG
GGTGGGAAAGGGTTGTTTTGTGTTGGGAGTGGGTAGTGGGGTTTGGTTGACAATTTCTGTGTTC
TGATGCCGCAGTAACAGTGAGGTGTGGTGAAAGCTGTGTGCTGTTGCCTTGGGGATTACATGGG
GTTTTTCATGTGGCTTTGTCTAGGTTAATAGAAATTATGCACTGGGATATACAGGTGTAGTTAA
GTTATTAAAAATAACACAAGATTGAATCACTTTAAGGCCATATAATTTTAGACTTAACATTGTT
TTACAAATCTTAAAGTACATTTAGAGTCAAATTTTATGTGCTTAGTTATTGTTTAAGTAATATA
AGCTTTCTGAAAGTCCCATATATTGGACCGTGGCAGCTAATTTTGTAACTTAAGCATTCATATG
ACTACCTATGACATATTAAACTGATTGACAAAAATCTGAGACTGCGGCTTTGACTTTTTATAGT
TGTCCTACAAGAATATGTATACTGTTCTCTTATTAAAAACATTAAAAGGTTTTCCTTCAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_039086169 ⟹ XP_038942097

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	91,131,194 - 91,142,918 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001013996	(Get FASTA)	NCBI Sequence Viewer
	XP_038942097	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH85824	(Get FASTA)	NCBI Sequence Viewer
	EDM06368	(Get FASTA)	NCBI Sequence Viewer
	Q5U2X6	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001013996 ⟸ NM_001013974
- Peptide Label:	precursor
- UniProtKB:	Q5U2X6 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MKAFCAFCVVLLVFGSVSEAKFDDFEDEEDIVEYDDNDFAEFEDVVEDSVTESPQRVINTEDDE DEATVELEGQDEGQEGDFEDADTQEGDTESEPYDDEEFEGYEDKPDTSSNKNKDPITIVDVPAH LQNSWESYYLEILMVTGLLAYIMNYIIGKNKNSRLAQAWFNSHRELLESNFTLVGDDGTNKEAT STGKLNQENEHIYNLWCSGRVCCEGMLIQLRFLKRQDLLNVLARMMRPVSDQVQIKVTMNDEDM DTYVFAVGTRKALLRLQKEMQDLSEFCSDKPKSGAKYGLPDSLAILSEMGEVTEGMMDTKMVHF LTHYADKIESVHFSDQFSGPKIMQEEGQPLKLPDTKRTLLFTFNVPGSGNTYPKDMEALLPLMN MVIYSIDKAKKFRLNREGKQKADKNRARVEENFLKLTHVQRQEAAQSRREEKKRAEKERIMNEE DPEKQRRLEEAALRREQKKLEKKQMKMKQIKVKAM hide sequence

RefSeq Acc Id:

ENSRNOP00000012533 ⟸ ENSRNOT00000012533

RefSeq Acc Id:	XP_038942097 ⟸ XM_039086169
- Peptide Label:	isoform X1

Transcriptome

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

Promoters

RGD ID:

13697836

Promoter ID:

EPDNEW_R8361

Type:

initiation region

Name:

Ccdc47_1

Description:

coiled-coil domain containing 47

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	10	94,406,971 - 94,407,031	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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CSV

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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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CSV

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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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CSV

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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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CSV

TAB

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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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CSV

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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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CSV

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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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CSV

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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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CSV

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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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CSV

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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

Damaging Variants

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
10	94399044	94399045	C	T	snv	LEW/NCrlBR (RGD), F344/NCrl (RGD)

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
10	95604152	95604153	C	T	snv	ACI/EurMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1308813	AgrOrtholog
Ensembl Genes	ENSRNOG00000009006	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000012533	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000012533	ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7127239	IMAGE-MGC_LOAD
InterPro	DUF1682	UniProtKB/Swiss-Prot
KEGG Report	rno:303606	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:94138	IMAGE-MGC_LOAD
NCBI Gene	303606	ENTREZGENE
PANTHER	PTHR12883	UniProtKB/Swiss-Prot
Pfam	DUF1682	UniProtKB/Swiss-Prot
PhenoGen	Ccdc47	PhenoGen
UniProt	CCD47_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-09-08	Ccdc47	coiled-coil domain containing 47	RGD1308813	similar to adipocyte-specific protein 4	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	RGD1308813	similar to adipocyte-specific protein 4	RGD1308813_predicted	similar to adipocyte-specific protein 4 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-20	RGD1308813_predicted	similar to adipocyte-specific protein 4 (predicted)	LOC303606_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC303606_predicted	similar to adipocyte-specific protein 4 (predicted)			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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - OMIM