Stra6 (signaling receptor and transporter of retinol STRA6)

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Gene: Stra6 (signaling receptor and transporter of retinol STRA6) Rattus norvegicus

Analyze

Symbol:

Stra6

Name:

signaling receptor and transporter of retinol STRA6

RGD ID:

1307551

Description:

Predicted to have retinol transmembrane transporter activity. Involved in response to retinoic acid. Predicted to localize to integral component of plasma membrane and protein-containing complex. Human ortholog(s) of this gene implicated in syndromic microphthalmia 9. Orthologous to human STRA6 (signaling receptor and transporter of retinol STRA6); PARTICIPATES IN retinoic acid metabolic pathway; INTERACTS WITH 17beta-estradiol; 3,3',5,5'-tetrabromobisphenol A; 6-propyl-2-thiouracil.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

LOC363071; MGC114408; receptor for retinol uptake STRA6; retinol-binding protein receptor STRA6; RGD1307551; similar to retinoic acid-responsive protein; stimulated by retinoic acid 6; stimulated by retinoic acid gene 6; stimulated by retinoic acid gene 6 homolog; stimulated by retinoic acid gene 6 homolog (mouse); stimulated by retinoic acid gene 6 protein homolog

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

NCBI Annotation Information:

Annotation category: partial on reference assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	8	58,549,743 - 58,568,861 (+)	NCBI
Rnor_6.0 Ensembl	8	62,925,357 - 62,944,437 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	8	62,925,364 - 62,944,438 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	8	62,701,454 - 62,720,528 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	8	61,920,772 - 61,939,791 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	8	61,939,822 - 61,958,845 (+)	NCBI
Celera	8	58,013,586 - 58,032,719 (+)	NCBI		Celera
Cytogenetic Map	8	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Anophthalmia (ISO)

Cardiovascular Abnormalities (ISO)

congenital heart disease (ISO)

Craniofacial Abnormalities (ISO)

Diaphragmatic Hernia (ISO)

intellectual disability (ISO)

lung disease (ISO)

microphthalmia (ISO)

persistent fetal circulation syndrome (ISO)

schizophrenia (ISO)

syndromic microphthalmia 5 (ISO)

syndromic microphthalmia 9 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (EXP)

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

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

4,4'-diaminodiphenylmethane (ISO)

4,4'-sulfonyldiphenol (ISO)

6-propyl-2-thiouracil (EXP)

8-Br-cAMP (ISO)

acrylamide (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (EXP,ISO)

all-trans-retinol (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cefaloridine (EXP)

choline (ISO)

ciguatoxin CTX1B (ISO)

cisplatin (ISO)

copper atom (EXP)

copper(0) (EXP)

diarsenic trioxide (ISO)

dibutyl phthalate (EXP)

diuron (EXP)

dorsomorphin (ISO)

entinostat (ISO)

ethyl methanesulfonate (ISO)

folic acid (ISO)

formaldehyde (ISO)

hydrogen sulfide (ISO)

L-methionine (ISO)

lead diacetate (EXP)

mercury dichloride (EXP)

methamphetamine (EXP)

methyl methanesulfonate (ISO)

methylmercury chloride (ISO)

ochratoxin A (EXP)

paclitaxel (EXP)

panobinostat (ISO)

pentane-2,3-dione (EXP)

pirinixic acid (ISO)

SB 431542 (ISO)

SCH 23390 (EXP)

silicon dioxide (ISO)

sodium arsenite (ISO)

tamoxifen (ISO)

thapsigargin (ISO)

titanium dioxide (ISO)

toluene (EXP)

trichostatin A (ISO)

valproic acid (ISO)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adrenal gland development (IEA,ISO)

alveolar primary septum development (IEA,ISO)

artery morphogenesis (ISO)

blood vessel development (ISO)

camera-type eye development (ISO,ISS)

cognition (ISO)

developmental growth (IEA,ISO)

diaphragm development (IEA,ISO)

digestive tract morphogenesis (IEA,ISO)

ductus arteriosus closure (IEA,ISO)

ear development (IEA,ISO)

embryonic camera-type eye formation (IEA,ISO)

embryonic digestive tract development (IEA,ISO)

eyelid development in camera-type eye (IEA,ISO)

face morphogenesis (IEA,ISO)

feeding behavior (IEA,ISO)

female genitalia development (IEA,ISO)

head development (ISO)

head morphogenesis (ISO)

heart development (ISO)

kidney development (IEA,ISO)

learning (ISO)

lung alveolus development (ISO)

lung development (ISO)

lung vasculature development (IEA,ISO)

neuromuscular process (IEA,ISO)

nose morphogenesis (IEA,ISO)

paramesonephric duct development (IEA,ISO)

positive regulation of behavior (IEA,ISO)

positive regulation of receptor signaling pathway via JAK-STAT (ISO)

pulmonary artery morphogenesis (IEA,ISO)

pulmonary valve morphogenesis (IEA,ISO)

response to retinoic acid (IEP)

retinol transport (IEA,ISO,ISS)

smooth muscle tissue development (IEA,ISO)

uterus morphogenesis (IEA,ISO)

ventricular septum development (IEA,ISO)

vitamin A import (IBA)

vocal learning (IEA,ISO)

Cellular Component

integral component of plasma membrane (IEA,ISO,ISS)

plasma membrane (IBA,ISO)

protein-containing complex (IEA,ISO)

Molecular Function

protein binding (ISO)

retinal binding (IEA)

retinol binding (IEA)

retinol transmembrane transporter activity (IEA,ISO,ISS)

signaling receptor activity (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

retinoic acid metabolic pathway (ISO)

References

References - curated


1.	Berry DC and Noy N, Biochim Biophys Acta. 2012 Jan;1821(1):168-76. Epub 2011 Jul 12.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	MGD data from the GO Consortium
4.	Napoli JL Biochim Biophys Acta. 2012 Jan;1821(1):152-67. Epub 2011 May 19.
5.	OMIM Disease Annotation 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.	Wu L and Ross AC, J Lipid Res. 2010 Feb;51(2):378-87. Epub 2009 Aug 20.

Additional References at PubMed

PMID:12477932	PMID:17273977	PMID:19500772	PMID:21901792	PMID:23105095	PMID:23839944

Genomics

Comparative Map Data

Stra6
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	8	58,549,743 - 58,568,861 (+)	NCBI
Rnor_6.0 Ensembl	8	62,925,357 - 62,944,437 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	8	62,925,364 - 62,944,438 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	8	62,701,454 - 62,720,528 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	8	61,920,772 - 61,939,791 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	8	61,939,822 - 61,958,845 (+)	NCBI
Celera	8	58,013,586 - 58,032,719 (+)	NCBI		Celera
Cytogenetic Map	8	q24	NCBI

STRA6
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	15	74,179,466 - 74,212,267 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	15	74,179,466 - 74,212,267 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	15	74,471,807 - 74,502,046 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	15	72,258,860 - 72,282,245 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	15	72,258,862 - 72,282,245	NCBI
Celera	15	51,418,988 - 51,448,552 (-)	NCBI
Cytogenetic Map	15	q24.1	NCBI
HuRef	15	51,265,478 - 51,295,736 (-)	NCBI		HuRef
CHM1_1	15	74,590,002 - 74,620,238 (-)	NCBI		CHM1_1

Stra6
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	9	57,971,076 - 58,061,287 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	9	57,971,071 - 58,061,279 (+)	Ensembl
GRCm38	9	58,063,793 - 58,154,004 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	9	58,063,788 - 58,153,996 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	9	57,976,895 - 58,001,804 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	9	57,927,486 - 57,952,090 (+)	NCBI			mm8
Celera	9	55,363,368 - 55,388,212 (+)	NCBI		Celera
Cytogenetic Map	9	B	NCBI

Stra6
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955450	3,580,662 - 3,602,600 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955450	3,579,081 - 3,602,538 (+)	NCBI	ChiLan1.0	ChiLan1.0

STRA6
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	15	72,740,868 - 72,773,802 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	15	72,741,482 - 72,770,876 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	15	53,117,891 - 53,150,790 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

STRA6
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	30	37,331,832 - 37,353,529 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	30	37,331,834 - 37,359,449 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Stra6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936471	33,224,174 - 33,245,076 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

STRA6
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	59,318,010 - 59,347,267 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	7	59,317,930 - 59,347,274 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	63,936,184 - 63,965,508 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

STRA6
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	26	9,275,317 - 9,311,302 (+)	NCBI
ChlSab1.1 Ensembl	26	9,278,303 - 9,311,475 (+)	Ensembl

Stra6
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624781	304,890 - 413,655 (+)	NCBI

Position Markers

AI059311

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	8	62,932,078 - 62,932,286	NCBI	Rnor6.0
Rnor_5.0	8	62,708,168 - 62,708,376	UniSTS	Rnor5.0
RGSC_v3.4	8	61,927,486 - 61,927,694	UniSTS	RGSC3.4
Celera	8	58,020,303 - 58,020,511	UniSTS
RH 3.4 Map	8	673.8	UniSTS
Cytogenetic Map	8	q24	UniSTS

BI284420

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	8	62,943,850 - 62,944,026	NCBI	Rnor6.0
Rnor_5.0	8	62,719,940 - 62,720,116	UniSTS	Rnor5.0
RGSC_v3.4	8	61,939,203 - 61,939,379	UniSTS	RGSC3.4
Celera	8	58,032,131 - 58,032,307	UniSTS
RH 3.4 Map	8	675.3	UniSTS
Cytogenetic Map	8	q24	UniSTS

Stra6

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	8	62,944,265 - 62,944,375	NCBI	Rnor6.0
Rnor_5.0	8	62,720,355 - 62,720,465	UniSTS	Rnor5.0
RGSC_v3.4	8	61,939,618 - 61,939,728	UniSTS	RGSC3.4
Celera	8	58,032,546 - 58,032,656	UniSTS
Cytogenetic Map	8	q24	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2316950	Scl66	Serum cholesterol level QTL 66	4.1		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	8	33558764	113580387	Rat
737824	Hcar10	Hepatocarcinoma resistance QTL 10	2.9		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	8	44219197	89542960	Rat
1298065	Scl16	Serum cholesterol level QTL 16	3.8		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	8	35041414	80041414	Rat
1298079	Activ2	Activity QTL 2	9.5	0.000001	voluntary movement trait (VT:0003491)	rearing measurement (CMO:0001515)	8	45712344	90712344	Rat
631650	Stl6	Serum triglyceride level QTL 6	4	0.0019	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	8	10938911	120496129	Rat
631664	Hcar3	Hepatocarcinoma resistance QTL 3	2.9	0.0005	liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	8	58425510	106526740	Rat
4889938	Bss89	Bone structure and strength QTL 89	3.8		tibia size trait (VT:0100001)	tibia cortical bone volume (CMO:0001725)	8	54065044	89058369	Rat
5684973	Bss100	Bone structure and strength QTL 100	4.7		tibia area (VT:1000281)	tibia area measurement (CMO:0001382)	8	54065044	89058369	Rat
731182	Uae24	Urinary albumin excretion QTL 24	6.4		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	21813070	100873963	Rat
631271	Lecl1	Lens clarity QTL 1		0.001	lens clarity trait (VT:0001304)	age of onset/diagnosis of cataract (CMO:0001584)	8	21464919	91140553	Rat
8662823	Vetf5	Vascular elastic tissue fragility QTL 5	1.9		artery integrity trait (VT:0010639)	patent ductus arteriosus score (CMO:0002566)	8	30918112	107206309	Rat
1300146	Rf17	Renal function QTL 17	2.9		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	8	30918112	75918112	Rat
10402857	Bp380	Blood pressure QTL 380		0.95	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	61394378	106394378	Rat
1331769	Rf39	Renal function QTL 39	3.871		urine output (VT:0003620)	timed urine volume (CMO:0000260)	8	45712344	80003418	Rat
1331838	Niddm61	Non-insulin dependent diabetes mellitus QTL 61	3.53	0.0004	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	8	39230130	106506973	Rat
1300177	Cm2	Cardiac mass QTL 2	3.65		heart mass (VT:0007028)	heart weight (CMO:0000017)	8	59234112	108068306	Rat
1549908	Neudeg1	Neurodegradation QTL 1	5.5	0	nervous system integrity trait (VT:0010566)	logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)	8	32888352	101374135	Rat
1554321	Bmd3	Bone mineral density QTL 3	7.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	8	44458129	118087517	Rat
1358896	Bp262	Blood pressure QTL 262	2.89		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	29867983	106526740	Rat
1358906	Bp253	Blood pressure QTL 253	4	0.0004	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	44219197	100873963	Rat
1359033	Bp273	Blood pressure QTL 273			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	33558660	65717592	Rat
1582254	Kidm31	Kidney mass QTL 31	3		kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	8	58425510	91990535	Rat
1581557	Eae16	Experimental allergic encephalomyelitis QTL 16	3.8		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	8	9531047	119211942	Rat
1578755	Pur5	Proteinuria QTL 5	3.3	0.0001	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	8	33558660	109028082	Rat
1578765	Klgr1	Kidney lesion grade QTL 1	3.3	0.0001	kidney morphology trait (VT:0002135)	organ lesion measurement (CMO:0000677)	8	33558660	109028082	Rat
1578769	Uae31	Urinary albumin excretion QTL 31	3.3	0.001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	33558660	109028082	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	50529480	128036471	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	8	50529480	128036471	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	8	50529480	128036471	Rat
70197	BpQTLcluster8	Blood pressure QTL cluster 8	3.482		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	50529480	128036471	Rat
631216	Stl9	Serum triglyceride level QTL 9	4.71	0.0001	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	8	45712475	75971259	Rat
70161	Bp62	Blood pressure QTL 62	2.9	0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	46588437	96998640	Rat
724514	Uae15	Urinary albumin excretion QTL 15	2.9		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	32201981	75971421	Rat
2303564	Gluco43	Glucose level QTL 43	3		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	8	30144800	75144800	Rat
2303570	Gluco48	Glucose level QTL 48	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	8	55659105	100659105	Rat
2301402	Bp316	Blood pressure QTL 316		0.005	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	61394378	106394378	Rat
61373	Mcs4	Mammary carcinoma susceptibility QTL 4	1.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	8	20717592	65717592	Rat
11556286	Cm81	Cardiac mass QTL 81		0.01	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	33558660	65717592	Rat
631842	Inf1	Infertility severity QTL 1	4.1	0.001	seminal gland mass (VT:0010524)	seminal vesicle wet weight (CMO:0001603)	8	27841496	72841496	Rat
12879882	Am8	Aortic mass QTL 8		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	8	47200750	106394378	Rat
12879879	Cm99	Cardiac mass QTL 99		0.001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	47200750	106394378	Rat
1358912	Bw51	Body weight QTL 51	2.95		body mass (VT:0001259)	body weight (CMO:0000012)	8	55435004	115812386	Rat
1582222	Epfw2	Epididymal fat weight QTL 2	3.2	0.0005	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	8	35925594	80925594	Rat
61464	Niddm11	Non-insulin dependent diabetes mellitus QTL 11	3.1	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	8	39958022	84958022	Rat
12879881	Cm101	Cardiac mass QTL 101		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	8	47200750	106394378	Rat
1582243	Bw66	Body weight QTL 66	3.4	0.0048	body mass (VT:0001259)	body weight (CMO:0000012)	8	58425510	91990535	Rat
2303572	Insul13	Insulin level QTL 13	2		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	8	30144800	75144800	Rat
2293697	Bmd39	Bone mineral density QTL 39			femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	8	58230766	106394378	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	33558660	65717592	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	8	33558660	65717592	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	33558660	65717592	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	8	33558660	65717592	Rat
61358	Bp39	Blood pressure QTL 39	2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	39927901	84927901	Rat
1358907	Cm40	Cardiac mass QTL 40	1.89		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	29867983	106526740	Rat
2313067	Bss77	Bone structure and strength QTL 77	3.1	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	8	33558660	89058369	Rat
12879883	Kidm65	Kidney mass QTL 65		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	8	47200750	106394378	Rat
2313086	Bss60	Bone structure and strength QTL 60	4.1	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	8	54065044	89058369	Rat
2313088	Bss75	Bone structure and strength QTL 75	3.1	0.0001	body length (VT:0001256)	body length, nose to rump (CMO:0000079)	8	33558660	89058369	Rat
2313057	Bss76	Bone structure and strength QTL 76	3	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	8	33558660	89058369	Rat
1358892	Kidm26	Kidney mass QTL 26	3.69		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	8	29867983	106526740	Rat
12879880	Cm100	Cardiac mass QTL 100		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	8	47200750	106394378	Rat
12879878	Bw183	Body weight QTL 183		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	8	47200750	106394378	Rat
1331837	Bw23	Body weight QTL 23	4.19	0.00007	body mass (VT:0001259)	body weight (CMO:0000012)	8	50529563	106506973	Rat
2313046	Bss78	Bone structure and strength QTL 78	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	8	33558660	89058369	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	99
Count of miRNA genes:	66
Interacting mature miRNAs:	78
Transcripts:	ENSRNOT00000011074
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium									26	28	30
Low	2	12	12	6	12	6	1	1	48	7	11	11	1
Below cutoff	1	27	20	10	7	10	6	9					6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001029924	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC097373	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473975	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000198	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000011074 ⟹ ENSRNOP00000011074

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	8	62,925,357 - 62,944,437 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000090588 ⟹ ENSRNOP00000070968

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	8	62,925,376 - 62,943,788 (+)	Ensembl

RefSeq Acc Id:

NM_001029924 ⟹ NP_001025095

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	8	58,549,743 - 58,568,861 (+)	NCBI
Rnor_6.0	8	62,925,364 - 62,944,438 (+)	NCBI
Rnor_5.0	8	62,701,454 - 62,720,528 (+)	NCBI
RGSC_v3.4	8	61,920,772 - 61,939,791 (+)	RGD
Celera	8	58,013,586 - 58,032,719 (+)	RGD

Sequence:

show sequence

GGAAATTGAGAAAGAAAGAAGAGCTGGAGCATGGAATCCCAGGCCTCTGAGAATGGAAGCCAGA
CCTCCTCCGGGGTGACAGATGACTACAGCAGCTGGTACATCGAGGAACCTCTAGGAGCTGAGGA
GGTGCAGCCAGAGGGGGTGAATCCCCTTTGCCAGCCCACTGTACCGCCTGCCCTGCACCATGCC
TGCTTGGCCTCACTGTCGCTCCTGGCTCTGCTGCTGCTGGCCTTACTGGTGAGACGTCGCAGGC
TTTGGCCACACTGTGCTCATTGCAGACCTGGACTGCCCAGCCCTGTGGATTTCTTGGCTGGGAA
CCGATCCTGGACAGTTCCTACTGCTGTCTTTGTGGCCCTCTTCAGCAATCTGTGCCTGTTGCTC
CCTGATGAGAACCCACTGCCTTTCCTGAACCGCACTGCAGCATCCAGTCCAGATGGAGAGCCGG
AGACATCAAGAGGGCCCTGGAAGCTCCTGGCTCTGCTCTACTACCCAGCCCTCTACTACCCTCT
GGCTGCCTGTGCTACGGCAGGGCACCGAGCTGCATACTTACTGGGTACTGTGCTATCTTGGGTT
CACGTCAGTGTTCAGGTCTGGCAGAGAGCAGAGTGTCCTCAGGACCCCAAGATCTACAAGCACT
ACTCCTTGCTGGCCTCCCTGCCTCTGCTTCTGAGTCTTGGATTCCTGAGCCTTTGGTATCCAGT
ACAAGTGGTGCAGAGTATCCGTCATCGGACAGGAGCAGGCTCCCAGGGGCTACAGACCAGCTAC
TCCGAGAAGTATCTGAGAGCCCTCCTCTGTCCAAAGAAGCTGGACAGCTGCTCCCATCCCGCCT
CCAAGCGTAGCCTTCTGTCTCGGGCTTGGGCCTTTTCCCAGCATTCCATCTACACTCCAGAGCC
AGGATTCTGCCTGCCCTTGAAGCTGGTGATCTCGGCCACCCTGACAGGAACAGCCACTTACCAG
GTGGCCCTGCTGTTGCTGGTGAGCGTGGTGCCTACTGTGCAGAAGGTGAGGGCAGGGATCACCA
CAGATGTCTCCTACCTGCTGGCGGGCTTTGGGATTGTGCTCTCTGAAGACAGGCAGGAGGTGGT
AGAGCTGGTGAAGCATCACCTATGGGCCGTGGAAGCATGTTATATCTCAGCTCTGGTCTTGTCC
TGCTCATTAACCTTCCTGCTTCTGATCCGCTCCCTGAGGACTCACAGGGCCAATCTTAAAGCAC
TGCACCGAGGGGCTGCCCTGGATCTGGGTCCCCCTCTTCAGAGTACTCACCCCTCTCGCCAAGC
CATAGTCTGCTGGATGAGCTTCAGTGCCTACCAGACGGCCTTCAGCTGCCTTGGGCTCCTGGTG
CAGCAGGTCATCTTCTTCCTGGGGACCACAATCCTGGCCTTCCTAGTGTTTGTGCCTTTACTCC
ATGGTAGGAACCTCTTGCTCCTCCGGTCCCTGGAATCCACATGGCCCTTCTGGCTGACTCTGGT
CTTGGCTGTAATCCTGCAGAACATAGCAGCCAATTGGGTCTTCCTAGAGTCTCACCACGGATAC
CCGGAGCTGACCAACCGGCGCATGCTCTGCGTAGCCACTTTTCTTCTCTTCCCCATCAACATGC
TGGTGGGAGCCATAATGGCTATTTGGCGGGTGCTCCTCTCTTCTCTCTACAACACTGTTCACCT
CGGCCAGATGGACCTCAGCCTGCTGCCGCAGAGAGCTGCCTCCCTGGATCCAGGCTATCACACA
TACCGAAACTTCCTGAGGATTGAGGCCAGCCAGTCACACCCAGGAGTCATAGCCTTCTGTGCCC
TGCTCCTTCATGTGCCAAGTCCACAGCCCCAGCCCCCACTGGCCCCCCAGGACAGCCTCAGACC
AGCAGCAGAAGAAGAAGGTATGCAATTGCTACAGACCAAGGACCTGATGGCCAAGGGAGCAGGA
CCCAAAGGCAGCCGGAGCAGGGCCCGGTGGGGTCTGGCCTACACATTGCTCCACAACCCAAGTC
TGCAGGCCTTTCGGAAGGCAGCCCTTACTAGTGCCAAGGCCAATGGCACCCAGCCCTGAGGGTG
AAGAAAACCACACCACCCTGCTTTTATGTGCTAAGGCACATTCTTGTCTACATCCTCCCTCTCA
TTCATGTCAGCAAGCCCCTCCCCCAGCAGCAACTCTGCCAACCAGGGGATCAGGGGACTGGAGT
CACTGTGTCTACACCACCAGCTTCCAGAGGACTTTGGTCTGTGCTTGTCCACAAGACTACCAGC
TAGGGCTCTAGAGGAAACAGCTAGTGGGTTCTTTGTCCTGGAACAGTCAGGGAAAGGGTGGGCA
CATTTAGGCCTCTCCTCCGCACACTGGCTCTGCCATCAGCTTGCTGGGCCTCAGTGAGGCCCCT
CTTACTCCCTGTTGGTAATGAAAATCCAGAATATCTCCTATCCCAGCTCGCCCCACCTCAGCCT
CCCACCATAAAGGTGGAGCCTGTGTGGGTTTCCTCTCTGCCCCAGCTCTCTGCTTCCTCTCTCT
TCCACTCCCGCCCCTTCTTGTGCAGCCAAGTCAGACTCCAAGAGGCCCCACGGAACTGCCCTCT
CCAAAAACCAGATTTTTTTTTGTAGTTTTAATGCTGTTAGTTGTCATGAAAGAAGTTAGTGTGC
TCTCTGTAATAAATGTGCCTCTGAGGAACACTCCTCCTCACTGGAGGAGGGCTCTCAGGGGAAC
CACTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001025095	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH97373	(Get FASTA)	NCBI Sequence Viewer
	EDL95664	(Get FASTA)	NCBI Sequence Viewer
	Q4QR83	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001025095 ⟸ NM_001029924

- UniProtKB:

Q4QR83 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MESQASENGSQTSSGVTDDYSSWYIEEPLGAEEVQPEGVNPLCQPTVPPALHHACLASLSLLAL
LLLALLVRRRRLWPHCAHCRPGLPSPVDFLAGNRSWTVPTAVFVALFSNLCLLLPDENPLPFLN
RTAASSPDGEPETSRGPWKLLALLYYPALYYPLAACATAGHRAAYLLGTVLSWVHVSVQVWQRA
ECPQDPKIYKHYSLLASLPLLLSLGFLSLWYPVQVVQSIRHRTGAGSQGLQTSYSEKYLRALLC
PKKLDSCSHPASKRSLLSRAWAFSQHSIYTPEPGFCLPLKLVISATLTGTATYQVALLLLVSVV
PTVQKVRAGITTDVSYLLAGFGIVLSEDRQEVVELVKHHLWAVEACYISALVLSCSLTFLLLIR
SLRTHRANLKALHRGAALDLGPPLQSTHPSRQAIVCWMSFSAYQTAFSCLGLLVQQVIFFLGTT
ILAFLVFVPLLHGRNLLLLRSLESTWPFWLTLVLAVILQNIAANWVFLESHHGYPELTNRRMLC
VATFLLFPINMLVGAIMAIWRVLLSSLYNTVHLGQMDLSLLPQRAASLDPGYHTYRNFLRIEAS
QSHPGVIAFCALLLHVPSPQPQPPLAPQDSLRPAAEEEGMQLLQTKDLMAKGAGPKGSRSRARW
GLAYTLLHNPSLQAFRKAALTSAKANGTQP

hide sequence

RefSeq Acc Id:

ENSRNOP00000070968 ⟸ ENSRNOT00000090588

RefSeq Acc Id:

ENSRNOP00000011074 ⟸ ENSRNOT00000011074

Transcriptome

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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

ACI/EurMcwi (RGD)

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

ACI/N (MCW)

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

BBDP/Wor (RGD)

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

BN/SsN (MCW)

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

Buf/N (MCW)

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

COP/CrCrl (MCW & UW)

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

F344/NCrl (RGD)

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

F344/NRrrc (MCW)

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

FHH/EurMcwi (MCW)

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

FHH/EurMcwi (RGD)

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

FHL/EurMcwi (MCW)

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

FHL/EurMcwi (RGD)

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CSV

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

GH/OmrMcwi (MCW)

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

GK/Ox (RGD)

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

LE/Stm (RGD)

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

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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

LH/MavRrrc (RGD)

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

LL/MavRrrc (RGD)

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

LN/MavRrrc (RGD)

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

M520/N (MCW)

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

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (MCW)

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WKY/Gcrc (RGD)

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

WKY/N (MCW)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (MCW)

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CSV

TAB

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

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
8	62709307	62709308	A	C	snv	IS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1307551	AgrOrtholog
Ensembl Genes	ENSRNOG00000008312	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000011074	UniProtKB/TrEMBL
	ENSRNOP00000070968	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000011074	UniProtKB/TrEMBL
	ENSRNOT00000090588	ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7444462	IMAGE-MGC_LOAD
InterPro	STRA6	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:363071	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:114408	IMAGE-MGC_LOAD
NCBI Gene	363071	ENTREZGENE
PANTHER	PTHR21444:SF16	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Stra6	PhenoGen
UniProt	A0A0H2UHG6_RAT	UniProtKB/TrEMBL
	Q4QR83	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2019-11-11	Stra6	signaling receptor and transporter of retinol STRA6	Stra6	stimulated by retinoic acid 6	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2013-03-01	Stra6	stimulated by retinoic acid 6	Stra6	stimulated by retinoic acid gene 6	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-03-07	Stra6	stimulated by retinoic acid gene 6	Stra6	stimulated by retinoic acid gene 6 homolog (mouse)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Stra6	stimulated by retinoic acid gene 6 homolog (mouse)	RGD1307551	similar to retinoic acid-responsive protein; STRA6	Symbol and Name updated	1299863	APPROVED
2005-12-06	RGD1307551	similar to retinoic acid-responsive protein; STRA6	RGD1307551_predicted	similar to retinoic acid-responsive protein; STRA6 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-20	RGD1307551_predicted	similar to retinoic acid-responsive protein; STRA6 (predicted)	LOC363071_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC363071_predicted	similar to retinoic acid-responsive protein; STRA6 (predicted)			Symbol and Name status set to provisional	70820	PROVISIONAL

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

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

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

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

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations