Dnaja4 (DnaJ heat shock protein family (Hsp40) member A4)

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Gene: Dnaja4 (DnaJ heat shock protein family (Hsp40) member A4) Rattus norvegicus

Analyze

Symbol:

Dnaja4

Name:

DnaJ heat shock protein family (Hsp40) member A4

RGD ID:

1310035

Description:

Predicted to have chaperone binding activity and unfolded protein binding activity. Predicted to be involved in several processes, including negative regulation of endothelial cell migration; negative regulation of inclusion body assembly; and protein refolding. Predicted to localize to cytosol and membrane. Orthologous to human DNAJA4 (DnaJ heat shock protein family (Hsp40) member A4); INTERACTS WITH 1-naphthyl isothiocyanate; 2,4-dinitrotoluene; 2,6-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

DnaJ (Hsp40) homolog, subfamily A, member 4; dnaJ homolog subfamily A member 4; LOC300721

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	8	55,085,246 - 55,102,715 (+)	NCBI
Rnor_6.0 Ensembl	8	59,278,262 - 59,294,003 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	8	59,278,262 - 59,294,003 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	8	57,859,314 - 57,875,055 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	8	58,250,793 - 58,266,534 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	8	58,269,846 - 58,285,588 (+)	NCBI
Celera	8	54,573,032 - 54,588,773 (+)	NCBI		Celera
Cytogenetic Map	8	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1-dichloroethene (ISO)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17beta-estradiol (ISO)

1H-pyrazole (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

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

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

2-hydroxypropanoic acid (ISO)

3,3',5,5'-tetrabromobisphenol A (ISO)

3,4-methylenedioxymethamphetamine (ISO)

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

4,4'-diaminodiphenylmethane (ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

5-aza-2'-deoxycytidine (ISO)

6-propyl-2-thiouracil (EXP)

acrylamide (EXP)

aflatoxin B1 (ISO)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cadmium atom (ISO)

cadmium dichloride (EXP)

carbon nanotube (ISO)

chloropicrin (ISO)

chloroprene (ISO)

copper atom (ISO)

copper(0) (ISO)

CU-O LINKAGE (ISO)

decabromodiphenyl ether (EXP)

dexamethasone (ISO)

diarsenic trioxide (ISO)

dioxygen (ISO)

disulfiram (ISO)

diuron (EXP)

doxorubicin (ISO)

ethanol (ISO)

folic acid (ISO)

formaldehyde (ISO)

indometacin (ISO)

methamphetamine (EXP)

methylisothiazolinone (ISO)

methylmercury chloride (ISO)

nickel sulfate (ISO)

organoselenium compound (ISO)

oxaliplatin (EXP)

paracetamol (EXP,ISO)

phenobarbital (ISO)

pirinixic acid (ISO)

potassium dichromate (ISO)

propiconazole (ISO)

rac-lactic acid (ISO)

silicon dioxide (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenite (ISO)

sodium fluoride (ISO)

sunitinib (ISO)

tetraphene (ISO)

titanium dioxide (ISO)

topotecan (EXP)

triclosan (ISO)

tris(2-butoxyethyl) phosphate (ISO)

valproic acid (EXP,ISO)

vinclozolin (EXP)

zinc atom (ISO)

zinc oxide (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

negative regulation of endothelial cell migration (ISO)

negative regulation of inclusion body assembly (ISO)

positive regulation of gene expression (ISO)

protein refolding (ISO)

response to heat (IEA)

Cellular Component

cytosol (IBA,ISO)

membrane (ISO)

Molecular Function

ATP binding (IEA)

chaperone binding (ISO)

heat shock protein binding (IEA)

metal ion binding (IEA)

protein binding (ISO)

unfolded 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.	Lee KJ, etal., Cell Stress Chaperones. 2004 Mar;9(1):58-68.
3.	RGD automated data pipeline
4.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932	PMID:21231916	PMID:23142051

Genomics

Comparative Map Data

Dnaja4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	8	55,085,246 - 55,102,715 (+)	NCBI
Rnor_6.0 Ensembl	8	59,278,262 - 59,294,003 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	8	59,278,262 - 59,294,003 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	8	57,859,314 - 57,875,055 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	8	58,250,793 - 58,266,534 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	8	58,269,846 - 58,285,588 (+)	NCBI
Celera	8	54,573,032 - 54,588,773 (+)	NCBI		Celera
Cytogenetic Map	8	q24	NCBI

DNAJA4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	15	78,264,086 - 78,282,196 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	15	78,264,145 - 78,282,191 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	15	78,556,487 - 78,574,533 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	15	76,343,551 - 76,361,591 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	15	76,343,550 - 76,361,591	NCBI
Celera	15	55,492,988 - 55,511,050 (+)	NCBI
Cytogenetic Map	15	q25.1	NCBI
HuRef	15	55,314,570 - 55,332,634 (+)	NCBI		HuRef
CHM1_1	15	78,674,451 - 78,692,505 (+)	NCBI		CHM1_1

Dnaja4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	9	54,606,132 - 54,623,601 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	9	54,606,157 - 54,623,599 (+)	Ensembl
GRCm38	9	54,698,848 - 54,716,317 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	9	54,698,873 - 54,716,315 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	9	54,547,366 - 54,564,119 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	9	54,497,696 - 54,514,449 (+)	NCBI			mm8
Celera	9	51,950,424 - 51,960,699 (+)	NCBI		Celera
Cytogenetic Map	9	A5.3	NCBI

Dnaja4
(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_004955450	757,485 - 771,033 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955450	757,485 - 771,033 (+)	NCBI	ChiLan1.0	ChiLan1.0

DNAJA4
(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	15	76,158,155 - 76,176,089 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	15	76,158,155 - 76,176,089 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	15	57,193,545 - 57,211,518 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

DNAJA4
(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	3	58,342,874 - 58,401,276 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	3	58,390,379 - 58,402,497 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Dnaja4
(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_004936471	36,724,689 - 36,741,029 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

DNAJA4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	47,656,541 - 47,675,383 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	7	47,660,361 - 47,674,890 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	53,214,362 - 53,228,899 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

DNAJA4
(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	26	5,054,934 - 5,072,510 (-)	NCBI
ChlSab1.1 Ensembl	26	5,056,668 - 5,072,459 (-)	Ensembl

Dnaja4
(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_004624894	2,593,341 - 2,606,516 (-)	NCBI

Position Markers

BF396771

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	8	59,284,539 - 59,284,773	NCBI	Rnor6.0
Rnor_5.0	8	57,865,591 - 57,865,825	UniSTS	Rnor5.0
RGSC_v3.4	8	58,257,070 - 58,257,304	UniSTS	RGSC3.4
Celera	8	54,579,309 - 54,579,543	UniSTS
RH 3.4 Map	8	608.5	UniSTS
Cytogenetic Map	8	q24	UniSTS

AA799570

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	8	59,294,183 - 59,294,330	NCBI	Rnor6.0
Rnor_6.0	1	29,706,112 - 29,706,259	NCBI	Rnor6.0
Rnor_5.0	8	57,875,235 - 57,875,382	UniSTS	Rnor5.0
Rnor_5.0	1	31,140,954 - 31,141,101	UniSTS	Rnor5.0
RGSC_v3.4	8	58,266,714 - 58,266,861	UniSTS	RGSC3.4
RGSC_v3.4	1	28,059,551 - 28,059,698	UniSTS	RGSC3.4
Celera	1	26,005,927 - 26,006,074	UniSTS
Celera	8	54,588,953 - 54,589,100	UniSTS
RH 3.4 Map	8	611.5	UniSTS
Cytogenetic Map	1	p11	UniSTS
Cytogenetic Map	8	q24	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
2316950	Scl66	Serum cholesterol level QTL 66	4.1		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	8	33558764	113580387	Rat
737824	Hcar10	Hepatocarcinoma resistance QTL 10	2.9		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	8	44219197	89542960	Rat
1298065	Scl16	Serum cholesterol level QTL 16	3.8		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	8	35041414	80041414	Rat
1298079	Activ2	Activity QTL 2	9.5	0.000001	voluntary movement trait (VT:0003491)	rearing measurement (CMO:0001515)	8	45712344	90712344	Rat
631648	Stl5	Serum triglyceride level QTL 5	4	0.0003	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	8	29867983	59908353	Rat
631650	Stl6	Serum triglyceride level QTL 6	4	0.0019	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	8	10938911	120496129	Rat
631664	Hcar3	Hepatocarcinoma resistance QTL 3	2.9	0.0005	liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	8	58425510	106526740	Rat
4889938	Bss89	Bone structure and strength QTL 89	3.8		tibia size trait (VT:0100001)	tibia cortical bone volume (CMO:0001725)	8	54065044	89058369	Rat
5684973	Bss100	Bone structure and strength QTL 100	4.7		tibia area (VT:1000281)	tibia area measurement (CMO:0001382)	8	54065044	89058369	Rat
731182	Uae24	Urinary albumin excretion QTL 24	6.4		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	21813070	100873963	Rat
631271	Lecl1	Lens clarity QTL 1		0.001	lens clarity trait (VT:0001304)	age of onset/diagnosis of cataract (CMO:0001584)	8	21464919	91140553	Rat
8662823	Vetf5	Vascular elastic tissue fragility QTL 5	1.9		artery integrity trait (VT:0010639)	patent ductus arteriosus score (CMO:0002566)	8	30918112	107206309	Rat
1300146	Rf17	Renal function QTL 17	2.9		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	8	30918112	75918112	Rat
1300150	Cm3	Cardiac mass QTL 3	3.97		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	58425679	59716199	Rat
1331744	Bp217	Blood pressure QTL 217	3.398		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	33558660	62857995	Rat
1331769	Rf39	Renal function QTL 39	3.871		urine output (VT:0003620)	timed urine volume (CMO:0000260)	8	45712344	80003418	Rat
1331838	Niddm61	Non-insulin dependent diabetes mellitus QTL 61	3.53	0.0004	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	8	39230130	106506973	Rat
1300177	Cm2	Cardiac mass QTL 2	3.65		heart mass (VT:0007028)	heart weight (CMO:0000017)	8	59234112	108068306	Rat
1549908	Neudeg1	Neurodegradation QTL 1	5.5	0	nervous system integrity trait (VT:0010566)	logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)	8	32888352	101374135	Rat
1558646	Swd5	Spike wave discharge measurement QTL 5	3.45	0.00036	brain electrophysiology trait (VT:0010557)	brain spike-and-wave discharge frequency (CMO:0001742)	8	17666555	62666555	Rat
1554321	Bmd3	Bone mineral density QTL 3	7.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	8	44458129	118087517	Rat
1358896	Bp262	Blood pressure QTL 262	2.89		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	29867983	106526740	Rat
1358906	Bp253	Blood pressure QTL 253	4	0.0004	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	44219197	100873963	Rat
1359033	Bp273	Blood pressure QTL 273			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	33558660	65717592	Rat
1582254	Kidm31	Kidney mass QTL 31	3		kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	8	58425510	91990535	Rat
1581557	Eae16	Experimental allergic encephalomyelitis QTL 16	3.8		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	8	9531047	119211942	Rat
1578755	Pur5	Proteinuria QTL 5	3.3	0.0001	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	8	33558660	109028082	Rat
1578765	Klgr1	Kidney lesion grade QTL 1	3.3	0.0001	kidney morphology trait (VT:0002135)	organ lesion measurement (CMO:0000677)	8	33558660	109028082	Rat
1578769	Uae31	Urinary albumin excretion QTL 31	3.3	0.001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	33558660	109028082	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	50529480	128036471	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	8	50529480	128036471	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	8	50529480	128036471	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	50529480	128036471	Rat
631216	Stl9	Serum triglyceride level QTL 9	4.71	0.0001	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	8	45712475	75971259	Rat
70161	Bp62	Blood pressure QTL 62	2.9	0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	46588437	96998640	Rat
724514	Uae15	Urinary albumin excretion QTL 15	2.9		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	32201981	75971421	Rat
2303564	Gluco43	Glucose level QTL 43	3		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	8	30144800	75144800	Rat
2303570	Gluco48	Glucose level QTL 48	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	8	55659105	100659105	Rat
61373	Mcs4	Mammary carcinoma susceptibility QTL 4	1.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	8	20717592	65717592	Rat
11556286	Cm81	Cardiac mass QTL 81		0.01	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	33558660	65717592	Rat
631842	Inf1	Infertility severity QTL 1	4.1	0.001	seminal gland mass (VT:0010524)	seminal vesicle wet weight (CMO:0001603)	8	27841496	72841496	Rat
12879882	Am8	Aortic mass QTL 8		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	8	47200750	106394378	Rat
12879879	Cm99	Cardiac mass QTL 99		0.001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	47200750	106394378	Rat
1358912	Bw51	Body weight QTL 51	2.95		body mass (VT:0001259)	body weight (CMO:0000012)	8	55435004	115812386	Rat
1582222	Epfw2	Epididymal fat weight QTL 2	3.2	0.0005	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	8	35925594	80925594	Rat
61464	Niddm11	Non-insulin dependent diabetes mellitus QTL 11	3.1	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	8	39958022	84958022	Rat
12879881	Cm101	Cardiac mass QTL 101		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	8	47200750	106394378	Rat
1582243	Bw66	Body weight QTL 66	3.4	0.0048	body mass (VT:0001259)	body weight (CMO:0000012)	8	58425510	91990535	Rat
2303572	Insul13	Insulin level QTL 13	2		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	8	30144800	75144800	Rat
2293697	Bmd39	Bone mineral density QTL 39			femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	8	58230766	106394378	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	33558660	65717592	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	8	33558660	65717592	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	33558660	65717592	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	8	33558660	65717592	Rat
61358	Bp39	Blood pressure QTL 39	2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	39927901	84927901	Rat
1358907	Cm40	Cardiac mass QTL 40	1.89		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	29867983	106526740	Rat
2313067	Bss77	Bone structure and strength QTL 77	3.1	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	8	33558660	89058369	Rat
12879883	Kidm65	Kidney mass QTL 65		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	8	47200750	106394378	Rat
2313086	Bss60	Bone structure and strength QTL 60	4.1	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	8	54065044	89058369	Rat
2313088	Bss75	Bone structure and strength QTL 75	3.1	0.0001	body length (VT:0001256)	body length, nose to rump (CMO:0000079)	8	33558660	89058369	Rat
2313057	Bss76	Bone structure and strength QTL 76	3	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	8	33558660	89058369	Rat
1358892	Kidm26	Kidney mass QTL 26	3.69		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	8	29867983	106526740	Rat
12879880	Cm100	Cardiac mass QTL 100		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	8	47200750	106394378	Rat
12879878	Bw183	Body weight QTL 183		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	8	47200750	106394378	Rat
1331837	Bw23	Body weight QTL 23	4.19	0.00007	body mass (VT:0001259)	body weight (CMO:0000012)	8	50529563	106506973	Rat
2313046	Bss78	Bone structure and strength QTL 78	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	8	33558660	89058369	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	47
Count of miRNA genes:	44
Interacting mature miRNAs:	46
Transcripts:	ENSRNOT00000017053
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

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	33	23	13	23	8	11	64	35	41	11	8
Low			24	18	6	18			10
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001025411	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039081075	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005487764	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC094775	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC082010	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC097438	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473975	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000198	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000017053 ⟹ ENSRNOP00000017053

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	8	59,278,262 - 59,294,003 (+)	Ensembl

RefSeq Acc Id:

NM_001025411 ⟹ NP_001020582

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	55,085,464 - 55,101,207 (+)	NCBI
Rnor_6.0	8	59,278,262 - 59,294,003 (+)	NCBI
Rnor_5.0	8	57,859,314 - 57,875,055 (+)	NCBI
RGSC_v3.4	8	58,250,793 - 58,266,534 (+)	RGD
Celera	8	54,573,032 - 54,588,773 (+)	RGD

Sequence:

show sequence

CCGGCGTCCAAACTAAGGCCACCTGAAGGCCGCCGTTCACATCTTCAAAGGCTAAGGGGGTCAC
CCAGCCTTCAAGATGCCTAGGGGGAACCAGCAACCACAGGATCTCGACACCACCGCAGAAGGCA
GCCATCCACTCCAACACCCTCAAAAATGCAACAATCCGAGGCAGACCCCAGAGCACACCCCCGC
AGTGACCGAACAGAAGGCGGCCACACCCCGAGGCAGAGGCCGGGTGGGGCCAGCACGCACGCTG
CCCTTCCAGTCCAAGCTCTCCTCCGCCCAGGGTTCGCGCACACGAGGCCCTCCTGCAAGCCAGC
GGATCTCAGAGCGGCCTAACCCCGGGGACCCACGCAAGGGCAAGGGGCCAGCCTCGGGGCGGCG
TGACAGCCGGCAGCGGCCAACCTCCACCACGAAGCCCGAATCCTCCACGCCGAAAACCCCCGCC
ACCGAGCATCCCAACATGGCCCGTGGCGGCAATCAGAACTGGAGCTCCGGGGAGTCGGACGGCC
AGCCAGAGGAGCAGACTTCCGAGGAGAACGGAGACAAGATGGTGAAGGAGACCCAGTACTATGA
CATCCTGGGGGTGAAGCCCAGCGCGTCCCCGGAGGAGATCAAGAAGGCCTATCGGAAGCTGGCG
CTCAAGTACCACCCAGACAAGAACCCGGATGAGGGCGAAAAGTTTAAACTTATATCCCAGGCAT
ATGAAGTACTTTCAGATCCAAAGAAAAGAGACATCTATGACCAAGGTGGAGAACAGGCAATTAA
AGAAGGGGGATCGGGTAGCCCCAGCTTCTCTTCACCCATGGATATCTTTGACATGTTTTTTGGT
GGTGGAGGGCGGATGACTAGAGAGAGAAGAGGCAAGAATGTTGTACACCAGCTGTCAGTAACTC
TGGAAGACTTATATAATGGAATCACTAAGAAACTGGCCCTCCAGAAAAATATAATTTGTGAGAA
ATGTGAAGGCATTGGTGGGAAGAAGGGATCCGTGGAGAAGTGCCCTCTGTGCAAGGGGCGGGGG
ATGCAGATCCATATCCAGCAGATCGGGCCGGGCATGGTGCAGCAGATCCAGACTGTGTGCATCG
AGTGCAAGGGCCAGGGCGAGCGTATCAACCCCAAGGACCGCTGTGAGGACTGCAGCGGTGCCAA
GGTTACCCGAGAGAAGAAGATTATCGAGGTACACGTGGATAAAGGTATGAAGGATGGGCAAAAG
ATACTGTTTCATGGAGAAGGAGATCAGGAGCCTGAGCTGGAACCTGGTGATGTCATAATTGTGC
TTGATCAGAAGGATCATAGTGTCTTTCAGAGACGAGGCCATGATTTGATCATGAAAATGAAAAT
TCAGCTCTCTGAAGCTCTTTGTGGCTTCAAGAAGACAATAAAAACGCTGGATGATCGAGTCCTC
ATCATTTCGTCTAAGTCAGGTGAGGTGATAAAGCATGGAGACCTCAAGTGTGTCCGCAATGAGG
GGATGCCCATCTACAAAGCCCCCCTGGAGAAGGGGATGCTTATCATACAGTTCTTAGTAGTCTT
CCCTGAAAAACAGTGGCTTTCTCTAGAGAAGCTTCCTCAGCTGGAGGCTCTGCTTCCCCCTCGG
CAGAAGGTGAGGATCACAGATGATATGGATCAGGTGGAGCTGAAGGAGTTCAACCCCAACGAGC
AGAGCTGGCGCCAGCACAGGGAGGCCTATGAGGAGGACGACGATGGGCCCCGCGCTGGCGTGCA
GTGCCAGACAGCATGATGGTGCGGTGTGGCATGGCCTGGTTGGACTAGCACATGATGAATGTAA
ACTTGGCACAATGAAAATGGCATCGCTTTAATAGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_039081075 ⟹ XP_038937003

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	55,085,407 - 55,097,728 (+)	NCBI

RefSeq Acc Id:

XR_005487764

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	55,085,246 - 55,102,715 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001020582	(Get FASTA)	NCBI Sequence Viewer
	XP_038937003	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH82010	(Get FASTA)	NCBI Sequence Viewer
	AAH97438	(Get FASTA)	NCBI Sequence Viewer
	EDL95548	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001020582 ⟸ NM_001025411

- UniProtKB:

Q4QR73 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MPRGNQQPQDLDTTAEGSHPLQHPQKCNNPRQTPEHTPAVTEQKAATPRGRGRVGPARTLPFQS
KLSSAQGSRTRGPPASQRISERPNPGDPRKGKGPASGRRDSRQRPTSTTKPESSTPKTPATEHP
NMARGGNQNWSSGESDGQPEEQTSEENGDKMVKETQYYDILGVKPSASPEEIKKAYRKLALKYH
PDKNPDEGEKFKLISQAYEVLSDPKKRDIYDQGGEQAIKEGGSGSPSFSSPMDIFDMFFGGGGR
MTRERRGKNVVHQLSVTLEDLYNGITKKLALQKNIICEKCEGIGGKKGSVEKCPLCKGRGMQIH
IQQIGPGMVQQIQTVCIECKGQGERINPKDRCEDCSGAKVTREKKIIEVHVDKGMKDGQKILFH
GEGDQEPELEPGDVIIVLDQKDHSVFQRRGHDLIMKMKIQLSEALCGFKKTIKTLDDRVLIISS
KSGEVIKHGDLKCVRNEGMPIYKAPLEKGMLIIQFLVVFPEKQWLSLEKLPQLEALLPPRQKVR
ITDDMDQVELKEFNPNEQSWRQHREAYEEDDDGPRAGVQCQTA

hide sequence

RefSeq Acc Id:

ENSRNOP00000017053 ⟸ ENSRNOT00000017053

RefSeq Acc Id:	XP_038937003 ⟸ XM_039081075
- Peptide Label:	isoform X1

Protein Domains

CR-type J

Transcriptome

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

Promoters

RGD ID:

13695983

Promoter ID:

EPDNEW_R6507

Type:

single initiation site

Name:

Dnaja4_1

Description:

DnaJ heat shock protein family member A4

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	8	59,278,252 - 59,278,312	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

Damaging Variants

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
8	59293841	59293842	A	C	snv	COP/CrCrl (MCW & UW)

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
8	58257981	58257982	T	A	snv	BN/NHsdMcwi (KNAW)
8	58266372	58266373	A	C	snv	SHRSP/Gcrc (MDC)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1310035	AgrOrtholog
Ensembl Genes	ENSRNOG00000012106	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000017053	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000017053	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	1.10.287.110	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7131770	IMAGE-MGC_LOAD
	IMAGE:7455678	IMAGE-MGC_LOAD
InterPro	DnaJ_bact	UniProtKB/TrEMBL
	DnaJ_C	UniProtKB/TrEMBL
	DnaJ_dom_sf	UniProtKB/TrEMBL
	DnaJ_N	UniProtKB/TrEMBL
	Heat_shock_DnaJ_CS	UniProtKB/TrEMBL
	HSP40/DnaJ_pept-bd	UniProtKB/TrEMBL
	HSP_DnaJ_Cys-rich_dom	UniProtKB/TrEMBL
	HSP_DnaJ_Cys-rich_dom_sf	UniProtKB/TrEMBL
KEGG Report	rno:300721	UniProtKB/TrEMBL
MGC_CLONE	MGC:114488	IMAGE-MGC_LOAD
	MGC:94264	IMAGE-MGC_LOAD
NCBI Gene	300721	ENTREZGENE
Pfam	DnaJ	UniProtKB/TrEMBL
	DnaJ_C	UniProtKB/TrEMBL
	DnaJ_CXXCXGXG	UniProtKB/TrEMBL
PhenoGen	Dnaja4	PhenoGen
PRINTS	DNAJPROTEIN	UniProtKB/TrEMBL
PROSITE	DNAJ_1	UniProtKB/TrEMBL
	DNAJ_2	UniProtKB/TrEMBL
	ZF_CR	UniProtKB/TrEMBL
SMART	DnaJ	UniProtKB/TrEMBL
Superfamily-SCOP	DnaJ_N	UniProtKB/TrEMBL
	HSP40_DnaJ_pep	UniProtKB/TrEMBL
	HSP_DnaJ_cys-rich	UniProtKB/TrEMBL
UniProt	Q4QR73	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-11-25	Dnaja4	DnaJ heat shock protein family (Hsp40) member A4	Dnaja4	DnaJ (Hsp40) homolog, subfamily A, member 4	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	Dnaja4	DnaJ (Hsp40) homolog, subfamily A, member 4	Dnaja4_predicted	DnaJ (Hsp40) homolog, subfamily A, member 4 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	Dnaja4_predicted	DnaJ (Hsp40) homolog, subfamily A, member 4 (predicted)			Symbol and Name status set to approved	70820	APPROVED

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

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

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

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