Dnajb9 (DnaJ heat shock protein family (Hsp40) member B9)

	Submit Data \| Help \| Video Tutorials \| News \| Publications \| Download \| REST API \| Citing RGD \| Contact
	Search RGD Grant Resources Citing RGD About Us Contact Us Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper VCMap Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease Find Models new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive Pathways Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
	Advanced Search (OLGA)

Gene: Dnajb9 (DnaJ heat shock protein family (Hsp40) member B9) Rattus norvegicus

Analyze

Symbol:

Dnajb9

Name:

DnaJ heat shock protein family (Hsp40) member B9

RGD ID:

3070

Description:

Predicted to enable Hsp70 protein binding activity; chaperone binding activity; and misfolded protein binding activity. Predicted to be involved in several processes, including negative regulation of IRE1-mediated unfolded protein response; positive regulation of immunoglobulin production; and ubiquitin-dependent ERAD pathway. Located in cytoplasm and nucleolus. Orthologous to human DNAJB9 (DnaJ heat shock protein family (Hsp40) member B9); INTERACTS WITH (+)-schisandrin B; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

DnaJ (Hsp40) homolog subfamily B member 9; DnaJ (Hsp40) homolog, subfamily B, member 9; dnaJ homolog subfamily B member 9; dnaJ homolog, subfamily b, member 9; endoplasmic reticulum DNA J domain-containing protein 4; ER-resident protein ERdj4; ERdj4; mdg-1; Mdg1; Microvascular endothelial differentiation gene 1

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	6	61,270,385 - 61,276,795 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	6	61,269,913 - 61,275,063 (-)	Ensembl
Rnor_6.0	6	64,165,913 - 64,170,122 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	64,165,913 - 64,170,151 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	73,754,560 - 73,770,497 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	63,583,033 - 63,587,247 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	6	63,586,159 - 63,590,373 (-)	NCBI
Celera	6	60,267,249 - 60,271,433 (-)	NCBI		Celera
Cytogenetic Map	6	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Chemical and Drug Induced Liver Injury (ISO)

cholestasis (ISO)

pleomorphic xanthoastrocytoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

(-)-epigallocatechin 3-gallate (ISO)

(S)-nicotine (ISO)

1,2-dimethylhydrazine (ISO)

1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (ISO)

1-naphthyl isothiocyanate (ISO)

17beta-estradiol (ISO)

17beta-hydroxy-5alpha-androstan-3-one (ISO)

1H-pyrazole (ISO)

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

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

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

2,4-diaminotoluene (ISO)

2,6-dinitrotoluene (EXP)

2-amino-2-deoxy-D-glucopyranose (ISO)

2-hydroxypropanoic acid (ISO)

3,3',4,4'-tetrachlorobiphenyl (ISO)

3,4-dichloroaniline (ISO)

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

3H-1,2-dithiole-3-thione (EXP,ISO)

4,4'-sulfonyldiphenol (ISO)

4-phenylbutyric acid (ISO)

8-Br-cAMP (ISO)

acetamide (EXP)

aflatoxin B1 (ISO)

aldehydo-D-glucosamine (ISO)

all-trans-retinoic acid (ISO)

amiodarone (ISO)

ammonium chloride (EXP)

Aroclor 1254 (ISO)

arsenous acid (ISO)

atazanavir sulfate (ISO)

avobenzone (ISO)

azoxystrobin (EXP)

benzene (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

beta-D-glucosamine (ISO)

bicalutamide (ISO)

bis(2-ethylhexyl) phthalate (EXP,ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cadmium atom (ISO)

cadmium dichloride (EXP,ISO)

caffeine (ISO)

cannabidiol (ISO)

carbamazepine (ISO)

carbaryl (ISO)

carbon nanotube (ISO)

chenodeoxycholic acid (ISO)

chloroacetaldehyde (ISO)

chloropicrin (ISO)

chlorpyrifos (EXP)

cidofovir anhydrous (ISO)

ciguatoxin CTX1B (ISO)

cisplatin (ISO)

clodronic acid (ISO)

clofibrate (ISO)

cobalt dichloride (EXP,ISO)

copper atom (ISO)

copper(0) (ISO)

copper(II) sulfate (ISO)

coumarin (EXP)

coumestrol (ISO)

crocidolite asbestos (ISO)

CU-O LINKAGE (ISO)

curcumin (ISO)

cyclosporin A (EXP,ISO)

deguelin (ISO)

deoxycholic acid (ISO)

dexamethasone (ISO)

diarsenic trioxide (ISO)

dibutyl phthalate (ISO)

dichloromethane (ISO)

diclofenac (ISO)

dicrotophos (ISO)

dieldrin (EXP)

dimethyl sulfoxide (EXP)

dinophysistoxin 1 (ISO)

dioxygen (ISO)

dorsomorphin (ISO)

doxorubicin (EXP)

elesclomol (ISO)

endosulfan (EXP)

Enterolactone (ISO)

ethyl methanesulfonate (ISO)

ethylbenzene (ISO)

fenofibrate (EXP)

flavonoids (EXP)

fluoranthene (ISO)

fluoxetine (EXP)

flutamide (EXP)

folic acid (ISO)

formaldehyde (ISO)

furan (EXP)

genistein (ISO)

gentamycin (EXP)

glafenine (EXP)

glycochenodeoxycholic acid (ISO)

glycocholic acid (ISO)

glycodeoxycholic acid (ISO)

glyphosate (EXP)

gold atom (ISO)

gold(0) (ISO)

hydroquinone O-beta-D-glucopyranoside (ISO)

ifosfamide (ISO)

imidacloprid (EXP)

indometacin (ISO)

isoflavones (ISO)

isoprenaline (ISO)

L-serine (ISO)

lead(0) (ISO)

lead(2+) (ISO)

lipopolysaccharide (ISO)

luteolin (ISO)

mercury dichloride (EXP)

metformin (EXP)

methotrexate (ISO)

methyl methanesulfonate (ISO)

methylmercury chloride (ISO)

methylparaben (ISO)

methylseleninic acid (ISO)

mifepristone (ISO)

N-acetyl-L-cysteine (ISO)

nefazodone (EXP,ISO)

nickel dichloride (ISO)

nicotine (ISO)

nimesulide (EXP)

o-xylene (ISO)

organoselenium compound (ISO)

paracetamol (ISO)

perfluorooctanoic acid (EXP)

phenobarbital (ISO)

phorbol 13-acetate 12-myristate (ISO)

picoxystrobin (ISO)

pirinixic acid (ISO)

pregnenolone 16alpha-carbonitrile (EXP)

progesterone (ISO)

propiconazole (ISO)

quinolin-8-ol (ISO)

rac-lactic acid (ISO)

raloxifene (ISO)

resveratrol (ISO)

rotenone (ISO)

SB 203580 (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

tartrazine (ISO)

tetrachloromethane (EXP,ISO)

thalidomide (ISO)

thapsigargin (ISO)

thiabendazole (EXP)

titanium dioxide (ISO)

toluene (ISO)

triadimefon (ISO)

Tributyltin oxide (EXP)

trichloroethene (ISO)

trichostatin A (ISO)

triptonide (ISO)

troglitazone (EXP)

tunicamycin (ISO)

urethane (ISO)

valproic acid (ISO)

zinc atom (ISO)

zinc(0) (ISO)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

B cell differentiation (ISO,ISS)

negative regulation of IRE1-mediated unfolded protein response (ISS)

positive regulation of immunoglobulin production (ISO,ISS)

response to endoplasmic reticulum stress (ISO,ISS)

response to unfolded protein (IEA)

ubiquitin-dependent ERAD pathway (ISO,ISS)

Cellular Component

cytoplasm (IDA)

endoplasmic reticulum (ISO,ISS)

endoplasmic reticulum lumen (ISO,ISS)

nucleolus (IDA)

Molecular Function

chaperone binding (ISO,ISS)

Hsp70 protein binding (ISO)

misfolded protein binding (ISO)

protein binding (ISO)

References

References - curated


1.	Berger BJ, etal., Exp Cell Res 2003 Oct 15;290(1):82-92.
2.	MGD data from the GO Consortium
3.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
4.	Prols F, etal., Exp Cell Res 2001 Sep 10;269(1):42-53.
5.	RGD automated data pipeline
6.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7.	RGD automated import pipeline for gene-chemical interactions
8.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
9.	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data

Additional References at PubMed

PMID:11836248	PMID:15489334	PMID:18400946	PMID:19199708	PMID:21231916	PMID:22267725	PMID:25222125

Genomics

Comparative Map Data

Dnajb9
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	6	61,270,385 - 61,276,795 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	6	61,269,913 - 61,275,063 (-)	Ensembl
Rnor_6.0	6	64,165,913 - 64,170,122 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	64,165,913 - 64,170,151 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	73,754,560 - 73,770,497 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	63,583,033 - 63,587,247 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	6	63,586,159 - 63,590,373 (-)	NCBI
Celera	6	60,267,249 - 60,271,433 (-)	NCBI		Celera
Cytogenetic Map	6	q21	NCBI

DNAJB9
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	7	108,569,867 - 108,574,850 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	7	108,569,874 - 108,574,850 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	7	108,210,318 - 108,215,294 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	107,997,592 - 108,002,530 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	7	107,804,306 - 107,809,245	NCBI
Celera	7	103,023,727 - 103,028,665 (+)	NCBI
Cytogenetic Map	7	q31.1	NCBI
HuRef	7	102,578,406 - 102,583,511 (+)	NCBI		HuRef
CHM1_1	7	108,143,475 - 108,148,580 (+)	NCBI		CHM1_1
CRA_TCAGchr7v2	7	107,577,403 - 107,582,508 (+)	NCBI

Dnajb9
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	44,252,680 - 44,256,851 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	12	44,252,342 - 44,257,109 (-)	Ensembl
GRCm38	12	44,205,897 - 44,210,068 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	44,205,559 - 44,210,326 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	12	45,306,884 - 45,311,055 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	12	45,076,183 - 45,080,354 (-)	NCBI			mm8
Celera	12	45,576,005 - 45,580,176 (-)	NCBI		Celera
Cytogenetic Map	12	B2	NCBI

Dnajb9
(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_004955410	12,814,479 - 12,822,777 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955410	12,814,993 - 12,820,852 (+)	NCBI	ChiLan1.0	ChiLan1.0

DNAJB9
(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	7	113,273,844 - 113,279,105 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	7	113,274,015 - 113,279,105 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	7	100,555,527 - 100,560,052 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

DNAJB9
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	14	48,879,963 - 48,885,616 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	14	48,879,914 - 48,884,361 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	14	48,323,737 - 48,329,124 (+)	NCBI
ROS_Cfam_1.0	14	48,829,357 - 48,834,752 (+)	NCBI
UMICH_Zoey_3.1	14	48,926,451 - 48,931,836 (+)	NCBI
UNSW_CanFamBas_1.0	14	48,610,313 - 48,615,689 (+)	NCBI
UU_Cfam_GSD_1.0	14	48,983,891 - 48,989,289 (+)	NCBI

Dnajb9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405118	68,402,977 - 68,407,460 (+)	NCBI
SpeTri2.0	NW_004936653	1,554,534 - 1,558,832 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

DNAJB9
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	18	36,549,544 - 36,584,130 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	18	36,578,928 - 36,584,211 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	18	40,219,853 - 40,224,716 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

DNAJB9
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	21	77,477,177 - 77,482,190 (+)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	21	77,479,112 - 77,482,571 (+)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666042	26,381,126 - 26,386,050 (-)	NCBI	Vero_WHO_p1.0

Dnajb9
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624739	21,187,581 - 21,193,345 (-)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

RH140278

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	61,271,115 - 61,271,332 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	64,166,175 - 64,166,391	NCBI	Rnor6.0
Rnor_5.0	6	73,754,822 - 73,755,038	UniSTS	Rnor5.0
RGSC_v3.4	6	63,583,295 - 63,583,511	UniSTS	RGSC3.4
Celera	6	60,267,511 - 60,267,727	UniSTS
RH 3.4 Map	6	433.3	UniSTS
Cytogenetic Map	6	q16-q23	UniSTS

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2301972	Bp325	Blood pressure QTL 325	4.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	1	72227641	Rat
4145119	Mcs25	Mammary carcinoma susceptibility QTL 25		0.0001	mammary gland integrity trait (VT:0010552)	ratio of deaths to total study population during a period of time (CMO:0001023)	6	10894415	110548006	Rat
1578665	Bss16	Bone structure and strength QTL 16	4.4		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	6	11735669	72593685	Rat
1578668	Bmd14	Bone mineral density QTL 14	3.8		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	6	11735669	72593685	Rat
1576309	Emca7	Estrogen-induced mammary cancer QTL 7	4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	15107216	107351382	Rat
2292589	Emca10	Estrogen-induced mammary cancer QTL 10		0.048	mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	6	16536140	61536140	Rat
1354664	Slep2	Serum leptin concentration QTL 2	4.49		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	6	16536140	71636405	Rat
1641898	Colcr4	Colorectal carcinoma resistance QTL4	3.71	0.0007	intestine integrity trait (VT:0010554)	well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)	6	20338777	62613667	Rat
2293839	Kiddil2	Kidney dilation QTL 2	4.8		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	20866422	81133036	Rat
2293841	Kiddil4	Kidney dilation QTL 4	4.4		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	20866422	81133036	Rat
1331779	Rf38	Renal function QTL 38	2.876		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	6	32074428	72227641	Rat
6893340	Cm77	Cardiac mass QTL 77	0.26	0.57	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	6	33309549	81132889	Rat
1300143	Rf14	Renal function QTL 14	2.92		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	34434137	77102317	Rat
1354632	Scl29	Serum cholesterol level QTL 29	3.74		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	6	35098709	71636405	Rat
634307	Bp141	Blood pressure QTL 141	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	35230417	80230417	Rat
9590290	Uminl2	Urine mineral level QTL 2	3.96	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	6	38783989	83783989	Rat
9590306	Scort18	Serum corticosterone level QTL 18	2.88	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	38783989	83783989	Rat
9590140	Scort4	Serum corticosterone level QTL 4	14.49	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	38783989	83783989	Rat
634330	Pia16	Pristane induced arthritis QTL 16	3.9		joint integrity trait (VT:0010548)	arthritic paw count (CMO:0001460)	6	45790088	104200226	Rat
4889848	Pur25	Proteinuria QTL 25	14	0.003	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	6	56728562	90198260	Rat
6893332	Cm74	Cardiac mass QTL 74	0.4	0.64	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	6	57730540	104085867	Rat
1558641	Cm47	Cardiac mass QTL 47	2.9	0.001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	6	57730540	104085867	Rat
70176	Mcsm1	Mammary carcinoma susceptibility modifier QTL 1			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	58632962	103632962	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	109
Count of miRNA genes:	87
Interacting mature miRNAs:	90
Transcripts:	ENSRNOT00000005363
Prediction methods:	Miranda, Rnahybrid
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	3	43	57	41	19	41	8	10	74	35	41	11	8
Low								1
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_012699	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006240065	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039111791	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC133400	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC070915	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473947	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ225630	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ230361	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ234282	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000164	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X98993	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000005363 ⟹ ENSRNOP00000005363

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	6	61,269,913 - 61,275,063 (-)	Ensembl
Rnor_6.0 Ensembl	6	64,165,913 - 64,170,151 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000093248 ⟹ ENSRNOP00000076154

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	6	64,167,798 - 64,170,122 (-)	Ensembl

RefSeq Acc Id:

NM_012699 ⟹ NP_036831

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	6	61,270,854 - 61,275,063 (-)	NCBI
Rnor_6.0	6	64,165,913 - 64,170,122 (-)	NCBI
Rnor_5.0	6	73,754,560 - 73,770,497 (-)	NCBI
RGSC_v3.4	6	63,583,033 - 63,587,247 (-)	RGD
Celera	6	60,267,249 - 60,271,433 (-)	RGD

Sequence:

show sequence

GCCAGTAGTGAGCGGGCCGAACAGGACGAAGGTTGCTCGGCTGTTAGAGGCGAGGTCGGAGCGT
GTGCGGCGAGGGTGAGGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGGCCGCCGCGG
TTTGGAGAAGCTGCGTCGGGGCGCACGGGTTATTAGAAATGGCAACTCCACAGTCAGTTTTCGT
CTTTGCCATCTGCATTCTAATGATAACAGAATTAATCCTGGCCTCAAAAAACTACTATGATATC
TTAGGTGTGCCAAAGTCAGCCTCAGAGAGACAAATCAAAAAGGCCTTTCACAAATTAGCCATGA
AGTACCACCCTGATAAAAATAAAAGCCCTGATGCTGAAGCAAAATTCAGAGAGATTGCAGAAGC
ATATGAAACACTCTCGGATGCCAATAGACGGAAAGAGTATGATATAATTGGACACAGTGCTTTT
ACTAATGGCAAAGGACAAAGAAGCAATGGAAGTCCTTTTGAGCAGTCATTTAACTTCAATTTTG
ATGACTTATTTAAAGACTTTAATTTGTTTGGTCAGAACCAGAACACTCGGTCTAAGAAGCATTT
TGAAAATCACTTCCAGACACGCCAGGATGGTTCCAGTAGACAAAGGCATCACTTCCAGGAGTTT
TCTTTTGGAGGTGGATTGTTTGATGATATGTTTGAAGACATGGAGAAGATGTTTTCTTTTAGTG
GCTTTGATAGCACCAATCGACGCACAGTACAGACTGAAAATAGATTTCATGGATCCAGCAAGCA
CTGCAGGACCGTCACTCAGCGGAGAGGGAATATGGTTACTACGTACACCGACTGTTCAGGACAG
TAGTTGGATCTTTTCCTGTGTCCACTAAGCCCACCTAGTTTACTCTTCCTCACTATGTCTGATG
AAAAAAGTTTTCTGTGAACTAGTTTGGCATGATTTCACTTATGTTAAGCAGTTTGTTATTAGGT
ATTTCATATATTGAAATTTTTTTTTTTTTTTTTAACAAAACACATTCAGCTAGTAAACAATTCT
AATTTTCCTGATTAGGAAAAGTTCTTTTGAAAGATCATTTGAAAGATAGATTTTCCTCTTTACC
TGTCCTTTGGCTCATTAATTTGCCCCTCCCTCCCCCAACAAAAAAAGAAAATCCCAAACAACTC
AGTTAGCCCCAACATACTTAATGATTAAATAATGATTAAATTTTAAGTTATCATAGATTTGCAT
TGTATGAACTTGAATAATATTTGCAGTGAAACCTCTGGGAACTTAAAACTACACAGCCTATGGT
CCCTGTAACTCGGGCTACTAAATGTATATGAAGCTGTAATTGAGTCATTTAGTGAAGACCACCA
TTGTTTTTGGCTCTTTGCCACTGAAAGCTTTAGAAAGTGATGGTTTGATGTCTATCACAGAAAG
ATTCCTCTTCTACAGGAGAATTGGTGTGATGGGGATGATTGTATTGCACGTAGTTAAGCTGAAG
AAAGTTTAAAATTTATAAACTATTGCCAAGAAATTGTGTTTTAGTAATGGGCTAATGATTTTGT
ATGATCAAAATCATAGCTTTGTAAACTTCTTTTTGAATATTTTTGTTTGTTGACTTTCTAGGTC
TTCGTATGAATTTGTTTTTTGTTTTTGGTGTGTGTGTGTGTAGTTACTCTGTTGCACTTATCTT
TATCTAGAGATTGACTAATACCTCATTCTTTTTGTAAAAGCAGCCAGTAATTTCTGTGCAACCT
TACTATGTGCAATATTTTTAAATTTTAAGAAACGTGTGCTTCTTTTGTTGTTAGAGTTATTTCT
TTAGTTCTGCACTTTTCCATGTTATACTCCATATGAGTATTAATCCTATGGATGCATATGAAAA
CTAGTAATGTCTCATACAATATTGTGTGTGAGTGAGAGAAACTATAAATATTTACAACCTGAAA
AAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006240065 ⟹ XP_006240127

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	6	61,270,385 - 61,274,760 (-)	NCBI
Rnor_6.0	6	64,165,913 - 64,169,806 (-)	NCBI
Rnor_5.0	6	73,754,560 - 73,770,497 (-)	NCBI

Sequence:

show sequence

GGGTCAGCTTCCCCGGGGCCGGGCCGGCGGAGCTCGCCGGTGGGGTCGGAGCAGGCAGTTGCCG
CACTGAGTGGAGTGGGCCGGGATGCCGGACCGACCCAATGGCAGGGTCGGGGAGGACGTTCCCA
TTGTTTAAACCGAGTTATTAGAAATGGCAACTCCACAGTCAGTTTTCGTCTTTGCCATCTGCAT
TCTAATGATAACAGAATTAATCCTGGCCTCAAAAAACTACTATGATATCTTAGGTGTGCCAAAG
TCAGCCTCAGAGAGACAAATCAAAAAGGCCTTTCACAAATTAGCCATGAAGTACCACCCTGATA
AAAATAAAAGCCCTGATGCTGAAGCAAAATTCAGAGAGATTGCAGAAGCATATGAAACACTCTC
GGATGCCAATAGACGGAAAGAGTATGATATAATTGGACACAGTGCTTTTACTAATGGCAAAGGA
CAAAGAAGCAATGGAAGTCCTTTTGAGCAGTCATTTAACTTCAATTTTGATGACTTATTTAAAG
ACTTTAATTTGTTTGGTCAGAACCAGAACACTCGGTCTAAGAAGCATTTTGAAAATCACTTCCA
GACACGCCAGGATGGTTCCAGTAGACAAAGGCATCACTTCCAGGAGTTTTCTTTTGGAGGTGGA
TTGTTTGATGATATGTTTGAAGACATGGAGAAGATGTTTTCTTTTAGTGGCTTTGATAGCACCA
ATCGACGCACAGTACAGACTGAAAATAGATTTCATGGATCCAGCAAGCACTGCAGGACCGTCAC
TCAGCGGAGAGGGAATATGGTTACTACGTACACCGACTGTTCAGGACAGTAGTTGGATCTTTTC
CTGTGTCCACTAAGCCCACCTAGTTTACTCTTCCTCACTATGTCTGATGAAAAAAGTTTTCTGT
GAACTAGTTTGGCATGATTTCACTTATGTTAAGCAGTTTGTTATTAGGTATTTCATATATTGAA
ATTTTTTTTTTTTTTTAACAAAACACATTCAGCTAGTAAACAATTCTAATTTTCCTGATTAGGA
AAAGTTCTTTTGAAAGATCATTTGAAAGATAGATTTTCCTCTTTACCTGTCCTTTGGCTCATTA
ATTTGCCCCTCCCTCCCCCAACAAAAAAAGAAAATCCCAAACAACTCAGTTAGCCCAACATACT
TAATGATTAAATAATGATTAAATTTTAAGTTATCATAGATTTGCATTGTATGAACTTGAATAAT
ATTTGCAGTGAAACCTCTGGGAACTTAAAACTACACAGCCTATGGTCCCTGTAACTCGGGCTAC
TAAATGTATATGAAGCTGTAATTGAGTCATTTAGTGAAGACCACCATTGTTTTTGGCTCTTTGC
CACTGAAAGCTTTAGAAAGTGATGGTTTGATGTCTATCACAGAAAGATTCCTCTTCTACAGGAG
AATTGGTGTGATGGGGATGATTGTATTGCACGTAGTTAAGCTGAAGAAAGTTTAAAATTTATAA
ACTATTGCCAAGAAATTGTGTTTTAGTAATGGGCTAATGATTTTGTATGATCAAAATCATAGCT
TTGTAAACTTCTTTTTGAATATTTTTGTTTGTTGACTTTCTAGGTCTTCGTATGAATTTGTTTT
TTGTTTTTGGTGTGTGTGTGTGTAGTTACTCTGTTGCACTTATCTTTATCTAGAGATTGACTAA
TACCTCATTCTTTTTGTAAAAGCAGCCAGTAATTTCTGTGCAACCTTACTATGTGCAATATTTT
TAAATTTTAAGAAACGTGTGCTTCTTTTGTTGTTAGAGTTATTTCTTTAGTTCTGCACTTTTCC
ATGTTATACTCCATATGAGTATTAATCCTATGGATGCATATGAAAACTAGTAATGTCTCATACA
ATATTGTGTGTGAGTGAGAGAAACTATAAATATTTACAACCTGA

hide sequence

RefSeq Acc Id:

XM_039111791 ⟹ XP_038967719

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	6	61,270,385 - 61,276,795 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_036831	(Get FASTA)	NCBI Sequence Viewer
	XP_006240127	(Get FASTA)	NCBI Sequence Viewer
	XP_038967719	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH70915	(Get FASTA)	NCBI Sequence Viewer
	CAA67434	(Get FASTA)	NCBI Sequence Viewer
	EDM03348	(Get FASTA)	NCBI Sequence Viewer
	P97554	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_036831 ⟸ NM_012699
- Peptide Label:	precursor
- UniProtKB:	P97554 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MATPQSVFVFAICILMITELILASKNYYDILGVPKSASERQIKKAFHKLAMKYHPDKNKSPDAE AKFREIAEAYETLSDANRRKEYDIIGHSAFTNGKGQRSNGSPFEQSFNFNFDDLFKDFNLFGQN QNTRSKKHFENHFQTRQDGSSRQRHHFQEFSFGGGLFDDMFEDMEKMFSFSGFDSTNRRTVQTE NRFHGSSKHCRTVTQRRGNMVTTYTDCSGQ hide sequence

RefSeq Acc Id:	XP_006240127 ⟸ XM_006240065
- Peptide Label:	isoform X2
- UniProtKB:	P97554 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MATPQSVFVFAICILMITELILASKNYYDILGVPKSASERQIKKAFHKLAMKYHPDKNKSPDAE AKFREIAEAYETLSDANRRKEYDIIGHSAFTNGKGQRSNGSPFEQSFNFNFDDLFKDFNLFGQN QNTRSKKHFENHFQTRQDGSSRQRHHFQEFSFGGGLFDDMFEDMEKMFSFSGFDSTNRRTVQTE NRFHGSSKHCRTVTQRRGNMVTTYTDCSGQ hide sequence

RefSeq Acc Id:

ENSRNOP00000005363 ⟸ ENSRNOT00000005363

RefSeq Acc Id:

ENSRNOP00000076154 ⟸ ENSRNOT00000093248

RefSeq Acc Id:	XP_038967719 ⟸ XM_039111791
- Peptide Label:	isoform X1

Protein Domains

Transcriptome

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

Promoters

RGD ID:

13694575

Promoter ID:

EPDNEW_R5100

Type:

initiation region

Name:

Dnajb9_1

Description:

DnaJ heat shock protein family member B9

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	6	64,170,122 - 64,170,182	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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 (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/N (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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-Lx/CubMcwi (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (MCW)

Visual

CSV

TAB

Printer

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 (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

Buf/N (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

DA/OlaHsd (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (RGD)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

F344/Stm (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

FXLE16/Stm (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GH/OmrMcwi (MCW)

Visual

CSV

TAB

Printer

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/FarMcwi (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GK/Ox (RGD)

Visual

CSV

TAB

Printer

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

HXB10/IpcvMcwi (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (RGD)

Visual

CSV

TAB

Printer

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 (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEW/Crl (RGD)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

LEXF10A/StmMcwi (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LH/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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/MavRrrcAek (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LL/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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/MavRrrcAek (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LN/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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/MavRrrcAek (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (MCW)

Visual

CSV

TAB

Printer

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

M520/NRrrcMcwi (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MHS/Gib (RGD)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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 (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MR/N (MCW)

Visual

CSV

TAB

Printer

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

MWF/Hsd (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SBH/Ygl (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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/OlalpcvMcwi (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/Gcrc (RGD)

Visual

CSV

TAB

Printer

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 (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SR/JrHsd (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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 (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SS/JrHsdMcwi (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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/RijCrl (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/Gcrc (RGD)

Visual

CSV

TAB

Printer

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 (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/N (MCW)

Visual

CSV

TAB

Printer

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 (2019)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/NCrl (RGD)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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 (2020)

Visual

CSV

TAB

Printer

Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WN/N (MCW)

Visual

CSV

TAB

Printer

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:3070	AgrOrtholog
Ensembl Genes	ENSRNOG00000004006	Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000005363	UniProtKB/Swiss-Prot
	ENSRNOP00000076154	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000005363	UniProtKB/Swiss-Prot
	ENSRNOT00000093248	UniProtKB/TrEMBL
Gene3D-CATH	1.10.287.110	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7104653	IMAGE-MGC_LOAD
InterPro	DnaJ_domain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	DnaJ_domain_CS	UniProtKB/Swiss-Prot
	J_dom_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:24908	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:91708	IMAGE-MGC_LOAD
NCBI Gene	24908	ENTREZGENE
Pfam	DnaJ	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Dnajb9	PhenoGen
PRINTS	JDOMAIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	DNAJ_1	UniProtKB/Swiss-Prot
	DNAJ_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	DnaJ	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF46565	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR	TC229679
UniProt	A0A1W2Q662_RAT	UniProtKB/TrEMBL
	DNJB9_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-11-25	Dnajb9	DnaJ heat shock protein family (Hsp40) member B9	Dnajb9	DnaJ (Hsp40) homolog, subfamily B, member 9	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-09-10	Dnajb9	DnaJ (Hsp40) homolog, subfamily B, member 9		dnaJ homolog, subfamily b, member 9	Name updated	1299863	APPROVED
2002-06-10	Dnajb9	dnaJ homolog, subfamily b, member 9			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_cellular_localization	localizes to the cytoplasm, nucleus and nucleoli	1300442
gene_cellular_localization	translocates to the nucleus after stress	1300442
gene_domains	contains a J-domain	1300442
gene_function	mammalian chaperone	1300443
gene_process	protects endoplasmic reticulum stressed cells from apoptosis	1300443
gene_product	member of the HSP40 protein family	1300443
gene_regulation	upregulated in primary endothelial and mesangial cells by stress	1300442

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

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

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

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

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Send us a Message

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD