Dnajb1 (DnaJ heat shock protein family (Hsp40) member B1)

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Gene: Dnajb1 (DnaJ heat shock protein family (Hsp40) member B1) Rattus norvegicus

Analyze

Symbol:

Dnajb1

Name:

DnaJ heat shock protein family (Hsp40) member B1

RGD ID:

1304725

Description:

Predicted to enable several functions, including ATPase binding activity; Hsp70 protein binding activity; and chaperone binding activity. Involved in forebrain development. Located in several cellular components, including dendritic spine; postsynaptic cytosol; and sperm head. Is active in glutamatergic synapse and postsynaptic density. Orthologous to human DNAJB1 (DnaJ heat shock protein family (Hsp40) member B1); PARTICIPATES IN chaperone mediated autophagy pathway; Endoplasmic Reticulum-associated degradation pathway; influenza A pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

DnaJ (Hsp40) homolog, subfamily B, member 1; dnaJ homolog subfamily B member 1; LOC361384

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	19	24,522,717 - 24,526,458 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	19	24,522,717 - 24,526,458 (-)	Ensembl
Rnor_6.0	19	24,747,178 - 24,750,919 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	19	24,747,178 - 24,750,919 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	19	35,726,334 - 35,730,075 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	19	26,213,739 - 26,217,480 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	19	26,218,578 - 26,222,306 (-)	NCBI
Celera	19	24,065,512 - 24,069,253 (-)	NCBI		Celera
Cytogenetic Map	19	q11	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

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP,ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

1H-pyrazole (ISO)

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

2,4-dinitrotoluene (EXP)

2-hydroxypropanoic acid (ISO)

2-methylcholine (ISO)

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

4,4'-sulfonyldiphenol (ISO)

4-amino-2,6-dinitrotoluene (EXP)

acetamide (EXP)

acrolein (ISO)

acrylamide (ISO)

aflatoxin B1 (ISO)

albendazole (ISO)

all-trans-retinoic acid (ISO)

alpha-pinene (ISO)

antimonite (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

azoxystrobin (EXP)

bathocuproine disulfonic acid (ISO)

belinostat (ISO)

benzene (ISO)

benzene-1,2,4-triol (ISO)

benzo[a]pyrene (ISO)

Benzo[k]fluoranthene (ISO)

bilirubin IXalpha (ISO)

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

bisphenol A (EXP)

bortezomib (ISO)

buspirone (EXP)

cadmium atom (EXP,ISO)

cadmium dichloride (EXP,ISO)

cadmium sulfate (ISO)

cannabidiol (ISO)

carbamazepine (ISO)

carbon nanotube (ISO)

chenodeoxycholic acid (ISO)

chloropicrin (ISO)

chloroprene (ISO)

chlorpyrifos (EXP)

chromium(6+) (ISO)

ciguatoxin CTX1B (ISO)

cisplatin (ISO)

clofibrate (ISO)

cobalt dichloride (EXP,ISO)

copper atom (ISO)

copper(0) (ISO)

copper(II) chloride (ISO)

copper(II) sulfate (ISO)

crocidolite asbestos (ISO)

crotonaldehyde (ISO)

CU-O LINKAGE (ISO)

cyclophosphamide (EXP,ISO)

cyclosporin A (ISO)

deguelin (ISO)

deoxycholic acid (ISO)

dexamethasone (ISO)

diarsenic trioxide (ISO)

diazinon (ISO)

dibenz[a,h]anthracene (ISO)

dibutyl phthalate (EXP)

diclofenac (ISO)

dieldrin (ISO)

diethyl maleate (ISO)

dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate (ISO)

disulfiram (ISO)

diuron (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

elesclomol (ISO)

emodin (ISO)

endosulfan (EXP)

epoxiconazole (EXP)

ethanol (ISO)

fenofibrate (EXP)

flutamide (EXP)

gefitinib (ISO)

gliotoxin (EXP)

glycochenodeoxycholic acid (ISO)

glycocholic acid (ISO)

glycodeoxycholic acid (ISO)

glyphosate (EXP)

hydrogen peroxide (ISO)

hydroquinone (ISO)

imidacloprid (EXP)

indometacin (EXP,ISO)

iron(2+) sulfate (anhydrous) (ISO)

ivermectin (ISO)

lead diacetate (ISO)

leflunomide (EXP,ISO)

Licochalcone B (ISO)

linalool (EXP)

lipopolysaccharide (ISO)

menadione (ISO)

mercury dibromide (ISO)

metacetamol (ISO)

methamphetamine (EXP)

methotrexate (ISO)

methyl methanesulfonate (ISO)

methylisothiazolinone (ISO)

methylmercury chloride (ISO)

mono(2-ethylhexyl) phthalate (ISO)

motexafin gadolinium (ISO)

N-acetyl-L-cysteine (ISO)

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

N-methyl-4-phenylpyridinium (ISO)

N-nitrosodiethylamine (EXP,ISO)

nefazodone (EXP,ISO)

nickel atom (ISO)

nimesulide (EXP)

organoselenium compound (ISO)

ozone (ISO)

p-chloromercuribenzoic acid (ISO)

paracetamol (EXP,ISO)

paraquat (ISO)

perfluorooctanoic acid (EXP,ISO)

phenobarbital (EXP,ISO)

phlorizin (ISO)

pirinixic acid (EXP,ISO)

piroxicam (ISO)

progesterone (ISO)

propanil (ISO)

propiconazole (ISO)

Propiverine (EXP)

pyrrolidine dithiocarbamate (ISO)

rac-lactic acid (ISO)

raloxifene (ISO)

resorcinol (ISO)

resveratrol (ISO)

SB 431542 (ISO)

SCH 23390 (EXP)

silicon dioxide (ISO)

silver atom (ISO)

silver(0) (ISO)

silver(1+) nitrate (ISO)

sodium arsenite (EXP,ISO)

sodium dichromate (ISO)

Soman (EXP)

sulforaphane (ISO)

sunitinib (ISO)

tamoxifen (ISO)

tebufenpyrad (ISO)

temozolomide (ISO)

tert-butyl hydroperoxide (ISO)

tetrachloromethane (EXP,ISO)

tetraphene (ISO)

thalidomide (ISO)

thiabendazole (EXP)

thimerosal (ISO)

thioacetamide (EXP)

titanium dioxide (EXP,ISO)

toluene (EXP)

trichostatin A (ISO)

triptonide (ISO)

troglitazone (ISO)

tunicamycin (ISO)

urethane (ISO)

valproic acid (ISO)

vinclozolin (EXP)

vincristine (ISO)

zinc acetate (ISO)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

chaperone cofactor-dependent protein refolding (IBA,ISO)

forebrain development (IEP)

negative regulation of inclusion body assembly (ISO)

negative regulation of transcription by RNA polymerase II (IBA)

negative regulation of transcription from RNA polymerase II promoter in response to stress (ISO)

positive regulation of ATP-dependent activity (ISO)

protein folding (ISO)

regulation of catalytic activity (IEA)

Cellular Component

cytoplasm (ISO)

cytosol (IBA,ISO)

dendritic spine (IDA)

glutamatergic synapse (IDA)

neuronal cell body (IDA)

nucleoplasm (IEA,ISO)

postsynapse (IDA)

postsynaptic cytosol (IDA)

postsynaptic density (IDA)

sperm head (IDA)

Molecular Function

ATPase activator activity (ISO)

ATPase binding (ISO)

chaperone binding (IBA,ISO)

Hsp70 protein binding (IBA,ISO)

molecular_function (ND)

protein binding (ISO)

protein folding chaperone (ISO)

transcription corepressor activity (IBA,ISO)

unfolded protein binding (IBA,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

chaperone mediated autophagy pathway (ISO)

Endoplasmic Reticulum-associated degradation pathway (IEA)

influenza A pathway (IEA)

References

References - curated


1.	Doiguchi M, etal., Mol Reprod Dev. 2007 Feb;74(2):223-32. doi: 10.1002/mrd.20609.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	GOA data from the GO Consortium
4.	Lee KJ, etal., Cell Stress Chaperones. 2004 Mar;9(1):58-68.
5.	MGD data from the GO Consortium
6.	Pipeline to import KEGG annotations from KEGG into RGD
7.	RGD automated import pipeline for gene-chemical interactions
8.	RGD comprehensive gene curation
9.	Suzuki T, etal., Brain Res. 1999 Jan 16;816(1):99-110.
10.	Xilouri M and Stefanis L, Mol Cell Neurosci. 2015 May;66(Pt A):29-36. doi: 10.1016/j.mcn.2015.01.003. Epub 2015 Feb 25.

Additional References at PubMed

PMID:9499401	PMID:12477932	PMID:14644449	PMID:18620420	PMID:19056867	PMID:20060297	PMID:21231916	PMID:21630459	PMID:22022600	PMID:23376485	PMID:23921388	PMID:24318877
PMID:25468996	PMID:27496612

Genomics

Comparative Map Data

Dnajb1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	19	24,522,717 - 24,526,458 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	19	24,522,717 - 24,526,458 (-)	Ensembl
Rnor_6.0	19	24,747,178 - 24,750,919 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	19	24,747,178 - 24,750,919 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	19	35,726,334 - 35,730,075 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	19	26,213,739 - 26,217,480 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	19	26,218,578 - 26,222,306 (-)	NCBI
Celera	19	24,065,512 - 24,069,253 (-)	NCBI		Celera
Cytogenetic Map	19	q11	NCBI

DNAJB1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	19	14,514,769 - 14,560,391 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	19	14,514,769 - 14,530,597 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	19	14,625,581 - 14,640,083 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	19	14,486,582 - 14,490,201 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	19	14,486,581 - 14,490,201	NCBI
Celera	19	14,519,709 - 14,523,328 (-)	NCBI
Cytogenetic Map	19	p13.12	NCBI
HuRef	19	14,195,571 - 14,199,191 (-)	NCBI		HuRef
CHM1_1	19	14,625,542 - 14,629,161 (-)	NCBI		CHM1_1

Dnajb1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	8	84,334,804 - 84,339,282 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	8	84,334,822 - 84,339,282 (+)	Ensembl
GRCm38	8	83,608,175 - 83,612,653 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	8	83,608,193 - 83,612,653 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	8	86,132,074 - 86,135,802 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	8	86,498,298 - 86,502,008 (+)	NCBI			mm8
Celera	8	87,895,947 - 87,899,699 (+)	NCBI		Celera
Cytogenetic Map	8	C2	NCBI

Dnajb1
(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_004955415	33,098,210 - 33,103,143 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955415	33,098,503 - 33,102,125 (-)	NCBI	ChiLan1.0	ChiLan1.0

DNAJB1
(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	19	14,921,219 - 14,926,473 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	19	14,922,389 - 14,926,268 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	19	14,078,201 - 14,081,884 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

DNAJB1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	20	48,120,604 - 48,131,091 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	20	48,121,379 - 48,130,060 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	20	47,997,072 - 48,007,556 (+)	NCBI
ROS_Cfam_1.0	20	48,637,524 - 48,648,012 (+)	NCBI
UMICH_Zoey_3.1	20	47,851,456 - 47,861,943 (+)	NCBI
UNSW_CanFamBas_1.0	20	48,277,833 - 48,288,317 (+)	NCBI
UU_Cfam_GSD_1.0	20	48,520,662 - 48,531,368 (+)	NCBI

Dnajb1
(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	207,303,265 - 207,315,402 (+)	NCBI
SpeTri2.0	NW_004936659	3,039,304 - 3,051,373 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

DNAJB1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	64,750,820 - 64,765,485 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	64,761,672 - 64,764,482 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	65,176,572 - 65,180,388 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

DNAJB1
(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	6	13,173,197 - 13,176,826 (-)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	6	13,173,157 - 13,176,877 (-)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666074	6,478,080 - 6,481,855 (+)	NCBI	Vero_WHO_p1.0

Dnajb1
(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_004624901	1,631,789 - 1,643,026 (-)	NCBI	HetGla_female_1.0		hetGla2

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
7411590	Foco7	Food consumption QTL 7	6.8	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	19	1	24688055	Rat
10054132	Srcrt9	Stress Responsive Cort QTL 9	2.87	0.0017	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	19	1	27355345	Rat
631678	Cm9	Cardiac mass QTL 9	4.27	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	19	1	28982497	Rat
631681	Cm12	Cardiac mass QTL 12	3.33	0.00053	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	19	1	28982497	Rat
1549847	Bss8	Bone structure and strength QTL 8	4		lumbar vertebra strength trait (VT:0010574)	vertebra ultimate force (CMO:0001678)	19	1	31963836	Rat
9590298	Uminl5	Urine mineral level QTL 5	3.59	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	19	1	36824771	Rat
8552935	Pigfal10	Plasma insulin-like growth factor 1 level QTL 10	5.7		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	19	1	36824771	Rat
9590250	Scort11	Serum corticosterone level QTL 11	23.45	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	19	1	36824771	Rat
9590090	Insglur8	Insulin/glucose ratio QTL 8	10.81	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	19	1	36824771	Rat
9589102	Slep13	Serum leptin concentration QTL 13	4.63	0.001	blood leptin amount (VT:0005667)	plasma leptin level (CMO:0000781)	19	569374	45569374	Rat
8694186	Bw152	Body weight QTL 152	3.34	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	19	569374	45569374	Rat
7247442	Uae39	Urinary albumin excretion QTL 39			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	19	2187927	46708701	Rat
724566	Uae12	Urinary albumin excretion QTL 12	5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	19	2187927	56457239	Rat
61447	Tcas1	Tongue tumor susceptibility QTL 1	6.08		tongue integrity trait (VT:0010553)	squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)	19	2316121	47316121	Rat
2317848	Alcrsp21	Alcohol response QTL 21	1.899999976158142	0.05	response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	19	3204777	48204777	Rat
1331737	Uae29	Urinary albumin excretion QTL 29	5.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	19	4096155	55283277	Rat
724518	Uae19	Urinary albumin excretion QTL 19	5.5		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	19	7457249	42983518	Rat
724565	Tcas5	Tongue tumor susceptibility QTL 5	10.04		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	19	9977753	39654489	Rat
61423	Cia14	Collagen induced arthritis QTL 14	3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	19	10827970	43544039	Rat
61407	Scl12	Serum cholesterol level QTL 12		0.001	blood HDL cholesterol amount (VT:0000184)	serum high density lipoprotein cholesterol level (CMO:0000361)	19	13926401	30303727	Rat
1558656	Prcs1	Prostate cancer susceptibility QTL 1	5		prostate integrity trait (VT:0010571)	percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)	19	15114598	34521833	Rat
7411549	Bw130	Body weight QTL 130	5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	19	15455860	57337602	Rat
1331788	Rf45	Renal function QTL 45	2.818		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	19	15605023	46559041	Rat
1578764	Stresp19	Stress response QTL 19	3.6	0.001	blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	19	15630201	57337602	Rat
2298478	Eau8	Experimental allergic uveoretinitis QTL 8		0.0163	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	19	17154433	57337602	Rat
61350	Bp32	Blood pressure QTL 32		0.012	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	19	20483575	57337602	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	393
Count of miRNA genes:	215
Interacting mature miRNAs:	259
Transcripts:	ENSRNOT00000038879
Prediction methods:	Microtar, 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	36	57	41	19	41	1	2	74	35	41	11	1
Low		7					7	9					7
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001108441	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NM_001395149	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006255282	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017601314	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017601315	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC102976	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC159430	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473972	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ227374	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ227962	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000313	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000038879 ⟹ ENSRNOP00000032313

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	19	24,522,717 - 24,526,458 (-)	Ensembl
Rnor_6.0 Ensembl	19	24,747,178 - 24,750,919 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000079106 ⟹ ENSRNOP00000072055

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	19	24,747,216 - 24,750,904 (+)	Ensembl

RefSeq Acc Id:

NM_001108441 ⟹ NP_001101911

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	19	24,522,717 - 24,526,458 (-)	NCBI
Rnor_6.0	19	24,747,178 - 24,750,919 (+)	NCBI
Rnor_5.0	19	35,726,334 - 35,730,075 (+)	NCBI
RGSC_v3.4	19	26,213,739 - 26,217,480 (-)	RGD
Celera	19	24,065,512 - 24,069,253 (-)	RGD

Sequence:

show sequence

GGTGTGGGGCGACGCATCGGGAGGGGCGGAAGGTTCTGGAGGGCTGGCGGGATCTGGAAGCTTC
CGCCGGACGGGTATATAGAGTCCGGGACGGGGCAGCAGCGGAGCCGGAGGCGGCGACAGCTGGG
CGGCGGTGGCCATGGGCAAGGACTACTACCAGACGCTGGGCCTGGCCCGCGGCGCGTCCGACGA
CGAGATCAAGCGGGCCTACCGCCGCCAGGCGCTGCGCTACCACCCGGACAAGAACAAGGAGCCC
GGCGCCGAGGAGAAGTTCAAGGAGATCGCCGAGGCCTACGACGTGCTCAGCGACCCGCGCAAGC
GCGAGATTTTCGACCGCTATGGAGAGGAAGGCCTGAAGGGTGGTGGCCCCAGTGGCGGGAGCAG
TGGTGGTGCTAATGGTACCTCTTTCAGCTACACATTCCATGGAGACCCTCATGCTATGTTTGCT
GAGTTCTTCGGTGGCAGGAATCCCTTTGATACCTTTTTTGGGCAGCGCAACGGGGAAGAAGGCA
TGGACATCGATGACCCGTTCTCTAGCTTTCCGATGGGTATGGGCGGCTTCACCAATATGAACTT
TGGACGTTCCCGCCCTACTCAAGAGCCCACCCGGAAGAAGCAAGATCCCCCAGTCACCCACGAC
CTTCGGGTCTCCCTTGAAGAGATCTACAGCGGCTGTACCAAGAAGATGAAAATCTCCCACAAGC
GGCTGAACCCTGATGGAAAGAGCATTCGAAATGAAGATAAGATCCTGACCATCGAAGTGAAGAG
GGGCTGGAAAGAAGGGACCAAAATCACCTTTCCCAAGGAAGGGGACCAGACCTCGAACAACATT
CCAGCTGACATCGTCTTTGTTTTAAAGGACAAGCCACACAATATCTTCAAGAGAGATGGTTCTG
ATGTCATTTATCCAGCCAGGATTAGCCTTCGGGAGGCTCTCTGTGGTTGCACTGTGAATGTTCC
TACTCTGGACAAGGCCTCCCCCTCCCCAAAACACCTGAGAAACGTGGAGACCTTGTTATCGAAT
TTGAAGTCATCTTCCCTGATAGGATCCCCATCTCATCCAGAACCATCCTGGAGCAGGTTCTTCC
CATATAGCTGCCTGCATTCCTCAAGGACTGAGCCAGGGACCTTTCCAGAGCTGCAGATTTCCAG
ACCGTTCCACTGGTTGCATACTGCGGGAGGGCCCAGGGAGGGCTTTTGCTCTGCCGAATGTTTT
CCACAGAATATATTACAATCTTTCAAAGTCGCGCACTAGACTACAGTGGTTTTTCGAGCGATAG
GCAGGCGGTGGGAACAGCAGCCCTCCTGGAATGGACCCACCCTTTGCACCCCAGCTCCTGCCCG
AGGGTGTGAGGCAGGCCTGCAACTGGACTCTTCCCCTCTGCTGTCCTTAGGTTCTGGCTGTCAC
GTGACAGTGGCCCACCATCTCGGTTGCCAGACCCTGTGCACTAATCAGTCTCCACTGTGTGAGA
GGTTCTTGTTTTATTCTGTATTTGTCCCCTGCCTTGTCCTCCTCCCCAGAAGAATCCTGTCTTG
TCTTGGCCATCTCAAATTGAGACCAATTCTTTAGAACTGCCAGGCCAGCATCACAAGCAATACC
TGGTTGCAGGACCACAGGGCCAGCCTCCTTCCAGGTTCTGGGGCCTGGACAGCCAGGAGATCCC
CTGGACCTCTGGCTCTCTTGAAATCAGATGGCTGCCTTACAGTCACAGTACTTGCTGGTCCAGA
GGTAGCCCTTGGCCACACCTGGCACTTCTCAGAGGTGCAGGTGACTTTTTTGTGTGTGTGTATG
TGTGTGTGTAATGGACTCAACTTTCTCAAAAGGATACAGTCCTTTTGAATTTTGCACAGCCCTA
GATATAATCCCTTTTGATAAAAGGGCCTTTGCTTCTGATGAAAGGAGCACCGTGGAACGTATGT
AAATATGTTTTTATAATTCCATGCAAAGCTGGTGTGCACTTGGATGAAAGCAGTCCCTGTCAAC
TACTGCCTGTCCAGGGCTGTGATGAGTCAGACCTGGGGAGGGAATGGATCTGTTCTTTGGAGCT
AGCCTGGTGCTCTGACCATTCGACTCATTGTAAGTTGCCACTACCAACACAAGACCAAAGTGTG
TGACTTGTCATTATGCAGTGTGACAGCATTAAAGACTGATGCTAAACCTCAGGGGAGCAGTCCT
T

hide sequence

RefSeq Acc Id:

XM_006255282 ⟹ XP_006255344

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	19	24,522,731 - 24,526,417 (-)	NCBI
Rnor_6.0	19	24,747,207 - 24,750,905 (+)	NCBI
Rnor_5.0	19	35,726,334 - 35,730,075 (+)	NCBI

Sequence:

show sequence

AAGGTTCTGGAGGGCTGGCGGGATCTGGAAGCTTCCGCCGGACGGGTATATAGAGTCCGGGACG
GGGCAGCAGCGGAGCCGGAGGCGGCGACAGCTGGGCGGCGGTGGCCATGGGCAAGGACTACTAC
CAGACGCTGGGCCTGGCCCGCGGCGCGTCCGACGACGAGATCAAGCGGGCCTACCGCCGCCAGG
CGCTGCGCTACCACCCGGACAAGAACAAGGAGCCCGGCGCCGAGGAGAAGTTCAAGGAGATCGC
CGAGGCCTACGACGTGCTCAGCGACCCGCGCAAGCGCGAGATTTTCGACCGCTATGGAGAGGAA
GGCCTGAAGGGTGGTGGCCCCAGTGGCGGGAGCAGTGGTGGTGCTAATGGTACCTCTTTCAGCT
ACACATTCCATGGAGACCCTCATGCTATGTTTGCTGAGTTCTTCGGTGGCAGGAATCCCTTTGA
TACCTTTTTTGGGCAGCGCAACGGGGAAGAAGGCATGGACATCGATGACCCGTTCTCTAGCTTT
CCGATGGGTATGGGCGGCTTCACCAATATGAACTTTGGACGTTCCCGCCCTACTCAAGAGCCCA
CCCGGAAGAAGCAAGATCCCCCAGTCACCCACGACCTTCGGGTCTCCCTTGAAGAGATCTACAG
CGGCTGTACCAAGAAGATGAAAATCTCCCACAAGCGGCTGAACCCTGATGGAAAGAGCATTCGA
AATGAAGATAAGATCCTGACCATCGAAGTGAAGAGGGGCTGGAAAGAAGGGACCAAAATCACCT
TTCCCAAGGAAGGGGACCAGACCTCGAACAACATTCCAGCTGACATCGTCTTTGTTTTAAAGGA
CAAGCCACACAATATCTTCAAGAGAGATGGTTCTGATGTCATTTATCCAGCCAGGATTAGCCTT
CGGGAGGCTCTCTGTGGTTGCACTGTGAATGTTCCTACTCTGGACGGCAGGACCATTCCTGTTG
TATTCAAAGATGTCATCAGGCCTGGCATGCGGAGGAAAGTTCCTGGAGAAGGCCTCCCCCTCCC
CAAAACACCTGAGAAACGTGGAGACCTTGTTATCGAATTTGAAGTCATCTTCCCTGATAGGATC
CCCATCTCATCCAGAACCATCCTGGAGCAGGTTCTTCCCATATAGCTGCCTGCATTCCTCAAGG
ACTGAGCCAGGGACCTTTCCAGAGCTGCAGATTTCCAGACCGTTCCACTGGTTGCATACTGCGG
GAGGGCCCAGGGAGGGCTTTTGCTCTGCCGAATGTTTTCCACAGAATATATTACAATCTTTCAA
AGTCGCGCACTAGACTACAGTGGTTTTTCGAGCGATAGGCAGGCGGTGGGAACAGCAGCCCTCC
TGGAATGGACCCACCCTTTGCACCCCAGCTCCTGCCCGAGGGTGTGAGGCAGGCCTGCAACTGG
ACTCTTCCCCTCTGCTGTCCTTAGGTTCTGGCTGTCACGTGACAGTGGCCCACCATCTCGGTTG
CCAGACCCTGTGCACTAATCAGTCTCCACTGTGTGAGAGGTTCTTGTTTTATTCTGTATTTGTC
CCCTGCCTTGTCCTCCTCCCCAGAAGAATCCTGTCTTGTCTTGGCCATCTCAAATTGAGACCAA
TTCTTTAGAACTGCCAGGCCAGCATCACAAGCAATACCTGGTTGCAGGACCACAGGGCCAGCCT
CCTTCCAGGTTCTGGGGCCTGGACAGCCAGGAGATCCCCTGGACCTCTGGCTCTCTTGAAATCA
GATGGCTGCCTTACAGTCACAGTACTTGCTGGTCCAGAGGTAGCCCTTGGCCACACCTGGCACT
TCTCAGAGGTGCAGGTGACTTTTTTGTGTGTGTGTATGTGTGTGTGTAATGGACTCAACTTTCT
CAAAAGGATACAGTCCTTTTGAATTTTGCACAGCCCTAGATATAATCCCTTTTGATAAAAGGGC
CTTTGCTTCTGATGAAAGGAGCACCGTGGAACGTATGTAAATATGTTTTTATAATTCCATGCAA
AGCTGGTGTGCACTTGGATGAAAGCAGTCCCTGTCAACTACTGCCTGTCCAGGGCTGTGATGAG
TCAGACCTGGGGAGGGAATGGATCTGTTCTTTGGAGCTAGCCTGGTGCTCTGACCATTCGACTC
ATTGTAAGTTGCCACTACCAACACAAGACCAAAGTGTGTGACTTGTCATTATGCAGTGTGACAG
CATTAAAGACTGATGCTAAACCTCA

hide sequence

RefSeq Acc Id:

XM_017601314 ⟹ XP_017456803

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	19	24,522,731 - 24,526,101 (-)	NCBI
Rnor_6.0	19	24,747,541 - 24,750,905 (+)	NCBI

Sequence:

show sequence

CGGCCCGGGTGACCCGCCGTTTGACAGGCGAGGAAACCGAGGCACTCGGGGCCTCTCTGAGGCT
TCGGCGGGGGACAGATGGTCCGGGGATCCCGCGGCGGCGCTGCCTCCTCCACCTTCTCTCTAAT
CGGCGGCCTCAGACGGGAGGAGGAGCTCTGGGCCTGAAGGGTGGTGGCCCCAGTGGCGGGAGCA
GTGGTGGTGCTAATGGTACCTCTTTCAGCTACACATTCCATGGAGACCCTCATGCTATGTTTGC
TGAGTTCTTCGGTGGCAGGAATCCCTTTGATACCTTTTTTGGGCAGCGCAACGGGGAAGAAGGC
ATGGACATCGATGACCCGTTCTCTAGCTTTCCGATGGGTATGGGCGGCTTCACCAATATGAACT
TTGGACGTTCCCGCCCTACTCAAGAGCCCACCCGGAAGAAGCAAGATCCCCCAGTCACCCACGA
CCTTCGGGTCTCCCTTGAAGAGATCTACAGCGGCTGTACCAAGAAGATGAAAATCTCCCACAAG
CGGCTGAACCCTGATGGAAAGAGCATTCGAAATGAAGATAAGATCCTGACCATCGAAGTGAAGA
GGGGCTGGAAAGAAGGGACCAAAATCACCTTTCCCAAGGAAGGGGACCAGACCTCGAACAACAT
TCCAGCTGACATCGTCTTTGTTTTAAAGGACAAGCCACACAATATCTTCAAGAGAGATGGTTCT
GATGTCATTTATCCAGCCAGGATTAGCCTTCGGGAGGCTCTCTGTGGTTGCACTGTGAATGTTC
CTACTCTGGACGGCAGGACCATTCCTGTTGTATTCAAAGATGTCATCAGGCCTGGCATGCGGAG
GAAAGTTCCTGGAGAAGGCCTCCCCCTCCCCAAAACACCTGAGAAACGTGGAGACCTTGTTATC
GAATTTGAAGTCATCTTCCCTGATAGGATCCCCATCTCATCCAGAACCATCCTGGAGCAGGTTC
TTCCCATATAGCTGCCTGCATTCCTCAAGGACTGAGCCAGGGACCTTTCCAGAGCTGCAGATTT
CCAGACCGTTCCACTGGTTGCATACTGCGGGAGGGCCCAGGGAGGGCTTTTGCTCTGCCGAATG
TTTTCCACAGAATATATTACAATCTTTCAAAGTCGCGCACTAGACTACAGTGGTTTTTCGAGCG
ATAGGCAGGCGGTGGGAACAGCAGCCCTCCTGGAATGGACCCACCCTTTGCACCCCAGCTCCTG
CCCGAGGGTGTGAGGCAGGCCTGCAACTGGACTCTTCCCCTCTGCTGTCCTTAGGTTCTGGCTG
TCACGTGACAGTGGCCCACCATCTCGGTTGCCAGACCCTGTGCACTAATCAGTCTCCACTGTGT
GAGAGGTTCTTGTTTTATTCTGTATTTGTCCCCTGCCTTGTCCTCCTCCCCAGAAGAATCCTGT
CTTGTCTTGGCCATCTCAAATTGAGACCAATTCTTTAGAACTGCCAGGCCAGCATCACAAGCAA
TACCTGGTTGCAGGACCACAGGGCCAGCCTCCTTCCAGGTTCTGGGGCCTGGACAGCCAGGAGA
TCCCCTGGACCTCTGGCTCTCTTGAAATCAGATGGCTGCCTTACAGTCACAGTACTTGCTGGTC
CAGAGGTAGCCCTTGGCCACACCTGGCACTTCTCAGAGGTGCAGGTGACTTTTTTGTGTGTGTG
TATGTGTGTGTGTAATGGACTCAACTTTCTCAAAAGGATACAGTCCTTTTGAATTTTGCACAGC
CCTAGATATAATCCCTTTTGATAAAAGGGCCTTTGCTTCTGATGAAAGGAGCACCGTGGAACGT
ATGTAAATATGTTTTTATAATTCCATGCAAAGCTGGTGTGCACTTGGATGAAAGCAGTCCCTGT
CAACTACTGCCTGTCCAGGGCTGTGATGAGTCAGACCTGGGGAGGGAATGGATCTGTTCTTTGG
AGCTAGCCTGGTGCTCTGACCATTCGACTCATTGTAAGTTGCCACTACCAACACAAGACCAAAG
TGTGTGACTTGTCATTATGCAGTGTGACAGCATTAAAGACTGATGCTAAACCTCA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001101911	(Get FASTA)	NCBI Sequence Viewer
	NP_001382078	(Get FASTA)	NCBI Sequence Viewer
	XP_006255344	(Get FASTA)	NCBI Sequence Viewer
	XP_017456803	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI59431	(Get FASTA)	NCBI Sequence Viewer
	EDL92266	(Get FASTA)	NCBI Sequence Viewer
	EDL92267	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001101911 ⟸ NM_001108441

- Sequence:

show sequence

MGKDYYQTLGLARGASDDEIKRAYRRQALRYHPDKNKEPGAEEKFKEIAEAYDVLSDPRKREIF
DRYGEEGLKGGGPSGGSSGGANGTSFSYTFHGDPHAMFAEFFGGRNPFDTFFGQRNGEEGMDID
DPFSSFPMGMGGFTNMNFGRSRPTQEPTRKKQDPPVTHDLRVSLEEIYSGCTKKMKISHKRLNP
DGKSIRNEDKILTIEVKRGWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIY
PARISLREALCGCTVNVPTLDKASPSPKHLRNVETLLSNLKSSSLIGSPSHPEPSWSRFFPYSC
LHSSRTEPGTFPELQISRPFHWLHTAGGPREGFCSAECFPQNILQSFKVAH

hide sequence

RefSeq Acc Id:	XP_006255344 ⟸ XM_006255282
- Peptide Label:	isoform X1
- UniProtKB:	B0K030 (UniProtKB/TrEMBL)
- Sequence:	show sequence MGKDYYQTLGLARGASDDEIKRAYRRQALRYHPDKNKEPGAEEKFKEIAEAYDVLSDPRKREIF DRYGEEGLKGGGPSGGSSGGANGTSFSYTFHGDPHAMFAEFFGGRNPFDTFFGQRNGEEGMDID DPFSSFPMGMGGFTNMNFGRSRPTQEPTRKKQDPPVTHDLRVSLEEIYSGCTKKMKISHKRLNP DGKSIRNEDKILTIEVKRGWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIY PARISLREALCGCTVNVPTLDGRTIPVVFKDVIRPGMRRKVPGEGLPLPKTPEKRGDLVIEFEV IFPDRIPISSRTILEQVLPI hide sequence

RefSeq Acc Id:

XP_017456803 ⟸ XM_017601314

- Peptide Label:

isoform X2

- Sequence:

show sequence

MFAEFFGGRNPFDTFFGQRNGEEGMDIDDPFSSFPMGMGGFTNMNFGRSRPTQEPTRKKQDPPV
THDLRVSLEEIYSGCTKKMKISHKRLNPDGKSIRNEDKILTIEVKRGWKEGTKITFPKEGDQTS
NNIPADIVFVLKDKPHNIFKRDGSDVIYPARISLREALCGCTVNVPTLDGRTIPVVFKDVIRPG
MRRKVPGEGLPLPKTPEKRGDLVIEFEVIFPDRIPISSRTILEQVLPI

hide sequence

RefSeq Acc Id:

ENSRNOP00000072055 ⟸ ENSRNOT00000079106

RefSeq Acc Id:

ENSRNOP00000032313 ⟸ ENSRNOT00000038879

Protein Domains

Transcriptome

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

Promoters

RGD ID:

13701008

Promoter ID:

EPDNEW_R11525

Type:

initiation region

Name:

Dnajb1_1

Description:

DnaJ heat shock protein family member B1

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	19	24,747,258 - 24,747,318	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (2019)

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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)

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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 (2020)

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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)

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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-Lx/CubMcwi (2019)

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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)

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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)

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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)

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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)

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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 (2020)

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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)

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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)

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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)

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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)

DA/OlaHsd (2019)

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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)

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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)

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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)

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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)

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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

F344/Stm (2019)

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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)

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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)

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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

FXLE16/Stm (2020)

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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)

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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)

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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/FarMcwi (2019)

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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)

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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

HXB10/IpcvMcwi (2019)

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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)

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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)

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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)

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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)

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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)

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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)

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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 (2019)

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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)

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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

LEXF10A/StmMcwi (2020)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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/MavRrrcAek (2020)

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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)

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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/MavRrrcAek (2020)

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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)

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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/MavRrrcAek (2020)

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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)

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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)

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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

M520/NRrrcMcwi (2019)

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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)

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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 (2020)

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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)

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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

MWF/Hsd (2019)

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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)

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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)

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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

SHR/OlalpcvMcwi (2019)

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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)

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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)

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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 (2020)

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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)

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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 (2019)

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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)

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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

WAG/RijCrl (2020)

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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)

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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 (2020)

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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)

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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 (2019)

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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)

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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 (2020)

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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)

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1304725	AgrOrtholog
Ensembl Genes	ENSRNOG00000021824	Ensembl, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000032313	UniProtKB/TrEMBL
	ENSRNOP00000072055	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000038879	UniProtKB/TrEMBL
	ENSRNOT00000079106	UniProtKB/TrEMBL
Gene3D-CATH	1.10.287.110	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:9089687	IMAGE-MGC_LOAD
InterPro	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
KEGG Report	rno:361384	UniProtKB/TrEMBL
MGC_CLONE	MGC:188751	IMAGE-MGC_LOAD
NCBI Gene	361384	ENTREZGENE
Pfam	CTDII	UniProtKB/TrEMBL
	DnaJ	UniProtKB/TrEMBL
PhenoGen	Dnajb1	PhenoGen
PRINTS	DNAJPROTEIN	UniProtKB/TrEMBL
PROSITE	DNAJ_1	UniProtKB/TrEMBL
	DNAJ_2	UniProtKB/TrEMBL
SMART	DnaJ	UniProtKB/TrEMBL
Superfamily-SCOP	DnaJ_N	UniProtKB/TrEMBL
	HSP40_DnaJ_pep	UniProtKB/TrEMBL
UniProt	B0K030	ENTREZGENE, UniProtKB/TrEMBL
	D3ZUU5_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-11-25	Dnajb1	DnaJ heat shock protein family (Hsp40) member B1	Dnajb1	DnaJ (Hsp40) homolog, subfamily B, member 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Dnajb1	DnaJ (Hsp40) homolog, subfamily B, member 1	Dnajb1_predicted	DnaJ (Hsp40) homolog, subfamily B, member 1 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Dnajb1_predicted	DnaJ (Hsp40) homolog, subfamily B, member 1 (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)

RGD Manual Annotations

Imported Annotations - KEGG (archival)

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RGD Manual Annotations

Imported Annotations - KEGG (archival)