Wnt9a (Wnt family member 9A) - Rat Genome Database

Name: Wnt9a
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Wnt9a (Wnt family member 9A) Rattus norvegicus

Analyze

Symbol:

Wnt9a

Name:

Wnt family member 9A

RGD ID:

1305018

Description:

Predicted to have receptor ligand activity. Predicted to be involved in several processes, including embryonic morphogenesis; negative regulation of chondrocyte differentiation; and positive regulation of smoothened signaling pathway. Human ortholog(s) of this gene implicated in pancreatic cancer. Orthologous to human WNT9A (Wnt family member 9A); PARTICIPATES IN altered Wnt signaling, canonical pathway; pancreatic cancer pathway; Wnt signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; bisphenol A.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

LOC287357; protein Wnt-9a; wingless related MMTV integration site 9A; wingless-type MMTV integration site 9A; wingless-type MMTV integration site family, member 9A

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	10	44,094,140 - 44,121,134 (+)	NCBI
Rnor_6.0 Ensembl	10	45,659,143 - 45,681,393 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	10	45,659,045 - 45,686,103 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	10	45,414,100 - 45,441,651 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	45,613,668 - 45,641,488 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	45,611,817 - 45,652,968 (+)	NCBI
Celera	10	43,356,927 - 43,383,916 (+)	NCBI		Celera
Cytogenetic Map	10	q22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

breast cancer (ISO)

pancreatic cancer (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

17beta-estradiol (ISO)

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

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

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

5-aza-2'-deoxycytidine (ISO)

6-propyl-2-thiouracil (EXP)

aflatoxin B1 (ISO)

avobenzone (ISO)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cadmium dichloride (ISO)

calcitriol (ISO)

carbon nanotube (ISO)

chlorpyrifos (EXP)

cisplatin (ISO)

copper atom (ISO)

copper(0) (ISO)

Deguelin (ISO)

diazinon (EXP)

dieldrin (EXP)

dioxygen (ISO)

ethanol (ISO)

fenamidone (ISO)

fluoranthene (ISO)

lead diacetate (ISO)

methapyrilene (ISO)

mitomycin C (ISO)

nickel atom (EXP)

nickel subsulfide (EXP)

potassium dichromate (ISO)

Soman (EXP)

testosterone (ISO)

tetrachloromethane (ISO)

triclosan (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anatomical structure development (ISO)

biological_process (ND)

canonical Wnt signaling pathway (IBA,ISO)

cell fate commitment (IBA)

embryonic forelimb morphogenesis (ISO)

embryonic skeletal system morphogenesis (ISO)

negative regulation of cartilage development (ISO)

negative regulation of cell death (ISO)

negative regulation of cell population proliferation (ISO)

negative regulation of chondrocyte differentiation (ISO)

negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (ISO)

neuron differentiation (IBA)

positive regulation of cell differentiation (ISO)

positive regulation of smoothened signaling pathway (ISO)

Cellular Component

cellular_component (ND)

extracellular space (IBA)

Molecular Function

cytokine activity (IBA)

frizzled binding (IBA)

molecular_function (ND)

protein binding (ISO)

receptor ligand activity (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

altered Wnt signaling, canonical pathway (ISO)

basal cell carcinoma pathway (IEA)

Hedgehog signaling pathway (IEA)

pancreatic cancer pathway (ISO)

Wnt signaling pathway (IEA,ISO)

Wnt signaling, canonical pathway (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	GOA data from the GO Consortium
3.	Jones S, etal., Science. 2008 Sep 26;321(5897):1801-6. Epub 2008 Sep 4.
4.	Kirikoshi H, etal., Int J Oncol. 2001 Dec;19(6):1221-5.
5.	MGD data from the GO Consortium
6.	Pipeline to import KEGG annotations from KEGG into RGD
7.	RGD automated data pipeline
8.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9.	RGD automated import pipeline for gene-chemical interactions
10.	RGD comprehensive gene curation
11.	Roel Nusse - Howard Hughes Medical Institute and the Department of Developmental Biology at Stanford University, California, USA
12.	Spater D, etal., Development. 2006 Aug;133(15):3039-49. Epub 2006 Jul 3.
13.	van Amerongen R, etal., Sci Signal. 2008 Sep 2;1(35):re9.

Additional References at PubMed

PMID:15371327	PMID:15809769	PMID:17351820	PMID:18056042	PMID:19047045	PMID:19422823	PMID:23376485	PMID:28733458

Genomics

Comparative Map Data

Wnt9a
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	10	44,094,140 - 44,121,134 (+)	NCBI
Rnor_6.0 Ensembl	10	45,659,143 - 45,681,393 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	10	45,659,045 - 45,686,103 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	10	45,414,100 - 45,441,651 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	45,613,668 - 45,641,488 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	45,611,817 - 45,652,968 (+)	NCBI
Celera	10	43,356,927 - 43,383,916 (+)	NCBI		Celera
Cytogenetic Map	10	q22	NCBI

WNT9A
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	1	227,918,656 - 227,947,932 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	227,918,656 - 227,947,932 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	228,106,357 - 228,135,633 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	226,175,320 - 226,202,222 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	1	224,415,431 - 224,442,334	NCBI
Celera	1	201,300,553 - 201,327,066 (-)	NCBI
Cytogenetic Map	1	q42.13	NCBI
HuRef	1	198,625,076 - 198,651,433 (-)	NCBI		HuRef
CHM1_1	1	229,381,547 - 229,408,063 (-)	NCBI		CHM1_1

Wnt9a
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	59,197,675 - 59,224,378 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	11	59,197,754 - 59,224,378 (+)	Ensembl
GRCm38	11	59,306,849 - 59,333,552 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	59,306,928 - 59,333,552 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	59,120,432 - 59,147,054 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	11	59,123,125 - 59,149,747 (+)	NCBI			mm8
Celera	11	64,072,296 - 64,098,904 (+)	NCBI		Celera
Cytogenetic Map	11	B1.3	NCBI

Wnt9a
(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_004955581	421,451 - 438,380 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955581	422,028 - 438,321 (+)	NCBI	ChiLan1.0	ChiLan1.0

WNT9A
(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	1	208,299,208 - 208,306,332 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	208,300,609 - 208,327,191 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	1	203,320,990 - 203,350,599 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

WNT9A
(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	14	953,244 - 959,295 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	14	946,843 - 959,289 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Wnt9a
(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_004936864	216,381 - 245,885 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

WNT9A
(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	51,102,757 - 51,128,347 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	51,102,757 - 51,128,346 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	53,983,861 - 54,009,486 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

WNT9A
(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	25	1,759,047 - 1,787,510 (+)	NCBI
ChlSab1.1 Ensembl	25	1,781,826 - 1,788,663 (+)	Ensembl

Wnt9a
(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_004624937	776,810 - 797,365 (-)	NCBI

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
631554	Bp133	Blood pressure QTL 133		0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	764421	66221621	Rat
2298544	Neuinf9	Neuroinflammation QTL 9	4.6		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	10	5877536	64401490	Rat
8662860	Vetf10	Vascular elastic tissue fragility QTL 10			artery integrity trait (VT:0010639)	number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)	10	6229095	75983805	Rat
61427	Cia16	Collagen induced arthritis QTL 16	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	6429075	99492409	Rat
1578761	Stresp21	Stress response QTL 21	3.3		thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	10	7521450	52521450	Rat
2303118	Mamtr7	Mammary tumor resistance QTL 7		0.003	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	9841807	108540162	Rat
9590310	Scort19	Serum corticosterone level QTL 19	6.3	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	12639513	57639513	Rat
9590268	Scort13	Serum corticosterone level QTL 13	3.26	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	12639513	57639513	Rat
9589136	Insul27	Insulin level QTL 27	10.46	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	10	12639513	57639513	Rat
2301967	Cm73	Cardiac mass QTL 73	4.55		heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	10	14827894	92423564	Rat
631268	Cia21	Collagen induced arthritis QTL 21	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	14827894	107857673	Rat
2316949	Gluco60	Glucose level QTL 60	3.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	14827894	110992275	Rat
1354587	Kidm21	Kidney mass QTL 21	3.3		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	10	15375474	62469074	Rat
631564	Apr3	Acute phase response QTL 3	3.9		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	10	16468736	61468736	Rat
6893350	Bw99	Body weight QTL 99	0.87	0.16	body mass (VT:0001259)	body weight (CMO:0000012)	1	17121542	62121542	Rat
6893352	Bw100	Body weight QTL 100	0.33	0.6	body mass (VT:0001259)	body weight (CMO:0000012)	1	17121542	62121542	Rat
631532	Cm50	Cardiac mass QTL 50	6.6		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	10	18246394	53637634	Rat
1598852	Anxrr19	Anxiety related response QTL 19	5.07		body movement coordination trait (VT:0005424)	number of rearing movements in an experimental apparatus (CMO:0001752)	10	19402814	64402814	Rat
1554317	Bmd4	Bone mineral density QTL 4	9.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	20170031	102897474	Rat
70223	Bp57	Blood pressure QTL 57	5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	21523906	83549467	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	21523906	90312401	Rat
70198	BpQTLcluster9	Blood pressure QTL cluster 9	2.94		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	21523906	90312401	Rat
1581497	Esta1	Estrogen-induced thymic atrophy QTL 1			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	10	21707766	64648311	Rat
724556	Pur2	Proteinuria QTL 2	5.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	22901497	93886300	Rat
1331762	Rf40	Renal function QTL 40	3.873		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	10	23861015	66539843	Rat
1331791	Cm31	Cardiac mass QTL 31	3.84606		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	23861015	112626471	Rat
631267	Cia20	Collagen induced arthritis QTL 20	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61325	Aia5	Adjuvant induced arthritis QTL 5		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61354	Pia10	Pristane induced arthritis QTL 10		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
634329	Pia15	Pristane induced arthritis QTL 15	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24884084	47487910	Rat
70224	Eae3	Experimental allergic encephalomyelitis QTL 3	4.1		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	10	27237530	64648311	Rat
1298069	Bp168	Blood pressure QTL 168	5.5		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	10	27237530	101482600	Rat
631542	Bp82	Blood pressure QTL 82	6.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	27237530	102427718	Rat
2300171	Bmd58	Bone mineral density QTL 58	4.9	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	28789280	73789280	Rat
1600371	Mcs21	Mammary carcinoma susceptibility QTL 21	3		mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	30021354	54057745	Rat
2292441	Bp308	Blood pressure QTL 308			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30099909	75099909	Rat
10402859	Bp381	Blood pressure QTL 381		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30099909	75099909	Rat
724527	Bp148	Blood pressure QTL 148		0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30983805	75983805	Rat
1576311	Pia26	Pristane induced arthritis QTL 26			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	31919397	78343192	Rat
1578779	Tcas10	Tongue tumor susceptibility QTL 10	3.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	10	33179030	78179030	Rat
631557	Bp136	Blood pressure QTL 136		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	33343192	78343192	Rat
1576319	Cia29	Collagen induced arthritis QTL 29			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	35139424	80139424	Rat
61332	Eau3	Experimental allergic uveoretinitis QTL 3		0.004	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	10	35669465	46851407	Rat
6893342	Cm78	Cardiac mass QTL 78	0.1	0.88	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	10	36185929	82675365	Rat
631552	Vetf2	Vascular elastic tissue fragility QTL 2	4.5	0.0002	aorta elastic tissue integrity trait (VT:0010556)	artery internal elastic lamina non-tumorous lesion count (CMO:0001913)	10	36185929	95845311	Rat
1354614	Hpcl1	Hepatic cholesterol level QTL 1	3.3		liver cholesterol amount (VT:0010498)	liver cholesterol level (CMO:0001597)	10	36584373	53645194	Rat
1358897	Stresp6	Stress response QTL 6	4.17	0.022	blood norepinephrine amount (VT:0005663)	plasma norepinephrine level (CMO:0001010)	10	36584373	66539843	Rat
61441	Btemp1	Thermal response to stress QTL 1	4		body temperature trait (VT:0005535)	core body temperature (CMO:0001036)	10	36584560	66015527	Rat
2317042	Aia20	Adjuvant induced arthritis QTL 20	3.38		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	10	40514044	85514044	Rat
2317043	Aia7	Adjuvant induced arthritis QTL 7	3.82		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	10	40514044	85514044	Rat
1576308	Schws1	Schwannoma susceptibility QTL 1		0.0041	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	10	41260363	106105607	Rat
631269	Cia22	Collagen induced arthritis QTL 22	8.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	41260363	107857673	Rat
631270	Cia23	Collagen induced arthritis QTL 23	3.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	41260363	107857673	Rat
8552805	Bw145	Body weight QTL 145	2.2		body mass (VT:0001259)	change in body weight to body weight ratio (CMO:0002216)	10	43188659	81042642	Rat
1298078	Stresp5	Stress response QTL 5	2.99	0.00025	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	43289657	108540162	Rat
61463	Bp12	Blood pressure QTL 12	6.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	43704955	88704955	Rat
11528628	Bss116	Bone structure and strength QTL 116	6.46	0.00000038	femur morphology trait (VT:0000559)	femur length (CMO:0000442)	10	45114283	45744081	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	439
Count of miRNA genes:	223
Interacting mature miRNAs:	296
Transcripts:	ENSRNOT00000058327
Prediction methods:	Miranda, Targetscan
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium								1			1
Low	1	38	4	3	1	3	8	10	74	19	29	11	8
Below cutoff	2	5	39	25	14	25				14	6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001105783	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC121055	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473948	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000220	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000058327 ⟹ ENSRNOP00000055129

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	10	45,659,143 - 45,681,393 (+)	Ensembl

RefSeq Acc Id:

NM_001105783 ⟹ NP_001099253

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	44,094,140 - 44,121,134 (+)	NCBI
Rnor_6.0	10	45,659,056 - 45,686,089 (+)	NCBI
Rnor_5.0	10	45,414,100 - 45,441,651 (+)	NCBI
RGSC_v3.4	10	45,613,668 - 45,641,488 (+)	RGD
Celera	10	43,356,927 - 43,383,916 (+)	RGD

Sequence:

show sequence

GGCTGCGGACGCTATAAGAGGGCGGCGGTCGCGGCGCGCCCTGCGCGGAGCCCGGAGCGCGATG
GTCAGCCGCCGCGGCGCGGCAAGATGCTGGATGGGTCCCTTCTGGCGCGCTGGCTGGCCGCGGC
CTTCGGGCTGACGCTGCTGCTCGCCGCGCTGCGCCCTTCGGCCGCCTACTTCGGGCTAACAGGC
AGTGAACCCCTGACTATACTCCCTCTAACCCTGGAGACCGAGGCTGCAGCCCAAGCTCACTACA
AGGCCTGCGACAGGCTGAAGCTGGAGCGCAAGCAGCGTCGCATGTGCCGCAGGGACCCGGGCGT
GGCGGAGACACTGGTGGAGGCTGTGAGCATGAGTGCCCTGGAGTGCCAGTACCAGTTCCGCTTC
GAGCGCTGGAACTGCACCCTGGAGGGCCGCTACCGAGCCAGCCTGCTCAAGCGAGGCTTCAAGG
AGACTGCTTTCCTCTACGCCATCTCTTCTGCGGGTCTGACGCATGCACTAGCCAAGGCCTGCAG
TGCAGGTCGCATGGAGCGCTGCACTTGTGACGAGGCACCTGACCTGGAAAACCGCGAGGCCTGG
CAGTGGGGCGGCTGTGGGGACAACCTCAAGTACAGCAGCAAGTTTGTCAAGGAGTTCCTGGGCC
GGCGGTCTACAAGGATCTGCGAGCCCGAGTGGACTTCCACAACAACCTCGTGGGTGTGAAGGCA
AGCTGGGTAATAAAGGCTGGAGTGGAGACCACTTGCAAATGCCATGGCGTGTCTGGCTCCTGCA
CGGTGCGGACCTGCTGGCGGCAGCTAGCACCCTTCCACGAGGTGGGCAAGCACCTAAAACACAA
ATATGAGACCTCTCTCAAGGTGGGCAGCACTACCAATGAAGCCACCGGCGAGGCGGGTGCCATC
TCCCCACCGCGGGGCCGGGCGTCCGGGTCCGGAGGCGGTGACCCCTTACCCCGAACACCAGAGC
TGGTACACCTGGACGACTCTCCCAGCTTCTGCCTGGCTGGCCGATTTTCCCCTGGCACGGCAGG
CCGCAGGTGTCACCGAGAGAAGAACTGTGAGAGTATTTGTTGTGGCCGCGGCCACAACACACAG
AGCCGTGTGGTGACAAGGCCCTGCCAATGCCAGGTCCGCTGGTGCTGCTATGTGGAGTGCAGGC
AGTGTACACAGAGAGAGGAGGTCTATACCTGCAAGGGCTGACCCGAGGCCCTGCGGCCCCGCCA
CAAGCGGTGTGGGCTTTGCATACAGCGCCGGAAGAATTCTACGCCTGCAGGAGCTGACTCCCCG
GCCCTGCCAGCCTTTCAGCGGGGAGTGTAGGCTTTGCACACAGTGCAAAGGGTCTTAACCTGCG
TGGAGTGAGCCCTGCAGGTCCAGCCTGTCCTGCTGTGTGGGGCACGGGTGTTATAAACAACACA
AAAGGTCTGCAAGGAAGGAGAGATGCCCCCAGCACTTGGGCCCTGGTATACAGACAGCTGGTTG
GCTGTCTCCCGGCCCAGAGGGCGGGGCTGGCCCCTGTCTGGCCTCCTCGACCCTTTGCTTATGC
CTTGGGCCTGAGCTTCCCGCCCCTCCTGACCCGAGAGCGTTGCAGTAATGCTTTCTCAGTTGCC
TGTGTCCCTGACATATCAGTATAGCCCTTGTCAGGGACCAGTGTGTCGACTAGCCCTCCGTGCC
TCTTGGCTTCCTCTGAGGCTTGGAGGGCAGGTGCACCTTCATAATCACATGGCCTCATCTGGCC
CAGCAGCCTGACGCCAGCACTGTCTTCAGAGAGCCAAACCACTAGGAGAGGGCAGCCACTCCAT
CTACAGGGCGTAGCCTCTGGCCCTCTGACCCTGAGCACTTCCTTGGAGTATCAGTGACTTTTAA
ATTATTATTATTTAACTAATATAGTAATTATTATTTTCCCTGTCCCCTTACCTCCTAATCTGTG
GCTTTTTCCGTCTGACCTGCCCCAGGCCCAGTCAAGCCAATCTGGGAGGCCTTGCCTTCCCTCC
CTTCATACTCCCTCCTCGTCTGCTTGCTCTAGTTTGAAACCACTAAATCAAGGTCACGTTTGGA
AAGAATGGAGCAATAGAGTCTAGCCGTGGCCCACAAGGCTTCTGGAAGCCCACTCCCCGATTCT
ACCTTACCTGGGGTCAGAGACCCTTGGTGGTCCCTGCTCTGTGCCCTGCCGGTGCAGAGATCAG
GTTGCTGGATATAGATTGGGGGTCTGGGGCACTAGAGCCATGGGCTCGGCGACAGGGGCAGGGT
CAGCTTTTTGATTGTCCATCTCAGGAAGCCATTCTTGCTCTGTGTCCCCAAGGGAGGTATGGAG
ACAGACACACTTGCTCTCATCAGGTCTCGCTGATGTCTCTGCAGGGGAAAGGTGGCTACACTGA
GCTGGCGATGAGTGTGTGTGCATGTGTTGTGTGAGTGTGCGAGTGTATGTATTCCGAGCTGGCA
TGGTCAGCATCCAGCGGCCCGTGTCCCTCTGCAGTATGGTGACTCTTTGGCTCCCAGAAAGCCC
AGCCTTAGGTCCGTGGGAACCCCATGGCTGTACAGGCTAGAGTGTAGGCAGGTGGCAGGCAAGG
AGTCAGGCACTACTGAGGAAAGAAGCACCAGGGGTCCAGAAGACCCAAGCATGGGGTGGCGGTG
GGACTGTGTCTTAAAGGAAACCTATTTATGTGGATGAGAGCCTCTGGTCTCTATTGGATGTGTA
AATAGCAAAGTTTATTCTCCTGTGGTTCCTAGAGCCCACCGATGAATGCCACGTTCCCAGGATG
CGTGTGGGTGGCGGTATGCAGTGGCTGGTGGGTGGGAGTGTACCCCGTACTCTTCAGATGCCTG
TACCCAGTCACACTACCACCGCCGACTGGAGCTCCATCTCTGTCAGATCTGGGGGAAAGAGCCT
ACCAGTCCAGAGGAAAGAATATTTTTATCGAATGCCACATTTAGCTCTATGTCCTCAATATTCA
GAAAAGCTATTTTTTAAAACAAGGCAGAATGAAACTATCTGCCGGCTGGTTTGTTTCTGTATAA
ATATATACTAGAATGTCTTTCTGGATGAAGCGACTCCCACAGGCCAAAGCCTCTTTGATCTTCT
TCTCTTCTATGGGCAGTAGAGTGAGCAGCTGCCCTGCTCCCGCCGGCCACCCAGGTTATGCCGG
CACTGAGGCGCACTGCTGGCCCGCCTGGCAGTGGACACACAAGGGAGCTGTCTTTGTGTGGAGT
CCTGTGCAGCCTGTGATTTCTCTACCTCAACTGTGTGGCGAGTAGGTGTGAACCTGAGTGACTG
CAGAGAATGTATTTATTTAACAGCTTTGTGTAACAAAACCAGAAACAAATGGAAACACTAAATA
AATGTATTT

hide sequence

RefSeq Acc Id:

XM_006246448 ⟹ XP_006246510

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	45,659,045 - 45,686,103 (+)	NCBI
Rnor_5.0	10	45,414,100 - 45,441,651 (+)	NCBI

Sequence:

show sequence

CCGCGGACCGCGGCTGCGGACGCTATAAGAGGGCGGCGGTCGCGGCGCGCCCTGCGCGGAGCCC
GGAGCGCGATGGTCAGCCGCCGCGGCGCGGCAAGATGCTGGATGGGTCCCTTCTGGCGCGCTGG
CTGGCCGCGGCCTTCGGGCTGACGCTGCTGCTCGCCGCGCTGCGCCCTTCGGCCGCCTACTTCG
GGCTAACAGGCAGTGAACCCCTGACTATACTCCCTCTAACCCTGGAGACCGAGGCTGCAGCCCA
AGCTCACTACAAGGCCTGCGACAGGCTGAAGCTGGAGCGCAAGCAGCGTCGCATGTGCCGCAGG
GACCCGGGCGTGGCGGAGACACTGGTGGAGGCTGTGAGCATGAGTGCCCTGGAGTGCCAGTACC
AGTTCCGCTTCGAGCGCTGGAACTGCACCCTGGAGGGCCGCTACCGAGCCAGCCTGCTCAAGCG
AGGCTTCAAGGAGACTGCTTTCCTCTACGCCATCTCTTCTGCGGGTCTGACGCATGCACTAGCC
AAGGCCTGCAGTGCAGGTCGCATGGAGCGCTGCACTTGTGACGAGGCACCTGACCTGGAAAACC
GCGAGGCCTGGCAGTGGGGCGGCTGTGGGGACAACCTCAAGTACAGCAGCAAGTTTGTCAAGGA
GTTCCTGGGCCGGCGGTCTAGCAAGGATCTGCGAGCCCGAGTGGACTTCCACAACAACCTCGTG
GGTGTGAAGGTAATAAAGGCTGGAGTGGAGACCACTTGCAAATGCCATGGCGTGTCTGGCTCCT
GCACGGTGCGGACCTGCTGGCGGCAGCTAGCACCCTTCCACGAGGTGGGCAAGCACCTAAAACA
CAAATATGAGACCTCTCTCAAGGTGGGCAGCACTACCAATGAAGCCACCGGCGAGGCGGGTGCC
ATCTCCCCACCGCGGGGCCGGGCGTCCGGGTCCGGAGGCGGTGACCCCTTACCCCGAACACCAG
AGCTGGTACACCTGGACGACTCTCCCAGCTTCTGCCTGGCTGGCCGATTTTCCCCTGGCACGGC
AGGCCGCAGGTGTCACCGAGAGAAGAACTGTGAGAGTATTTGTTGTGGCCGCGGCCACAACACA
CAGAGCCGTGTGGTGACAAGGCCCTGCCAATGCCAGGTCCGCTGGTGCTGCTATGTGGAGTGCA
GGCAGTGTACACAGAGAGAGGAGGTCTATACCTGCAAGGGCTGACCCGAGGCCCTGCGGCCCCG
CCACAAGCGGTGTGGGCTTTGCATACAGCGCCGGAAGAATTCTACGCCTGCAGGAGCTGACTCC
CCGGCCCTGCCAGCCTTTCAGCGGGGAGTGTAGGCTTTGCACACAGTGCAAAGGGTCTTAACCT
GCGTGGAGTGAGCCCTGCAGGTCCAGCCTGTCCTGCTGTGTGGGGCACGGGTGTTATAAACAAC
ACAAAAGGTCTGCAAGGAAGGAGAGATGCCCCCAGCACTTGGGCCCTGGTATACAGACAGCTGG
TTGGCTGTCTCCCGGCCCAGAGGGCGGGGCTGGCCCCTGTCTGGCCTCCTCGACCCTTTGCTTA
TGCCTTGGGCCTGAGCTTCCCGCCCCTCCTGACCCGAGAGCGTTGCAGTAATGCTTTCTCAGTT
GCCTGTGTCCCTGACATATCAGTATAGCCCTTGTCAGGGACCAGTGTGTCGACTAGCCCTCCGT
GCCTCTTGGCTTCCTCTGAGGCTTGGAGGGCAGGTGCACCTTCATAATCACATGGCCTCATCTG
GCCCAGCAGCCTGACGCCAGCACTGTCTTCAGAGAGCCAAACCACTAGGAGAGGGCAGCCACTC
CATCTACAGGGCGTAGCCTCTGGCCCTCTGACCCTGAGCACTTCCTTGGAGTATCAGTGACTTT
TAAATTATTATTATTTAACTAATATAGTAATTATTATTTTCCCTGTCCCCTTACCTCCTAATCT
GTGGCTTTTTCCGTCTGACCTGCCCCAGGCCCAGTCAAGCCAATCTGGGAGGCCTTGCCTTCCC
TCCCTTCATACTCCCTCCTCGTCTGCTTGCTCTAGTTTGAAACCACTAAATCAAGGTCACGTTT
GGAAAGAATGGAGCAATAGAGTCTAGCCGTGGCCCACAAGGCTTCTGGAAGCCCACTCCCCGAT
TCTACCTTACCTGGGGTCAGAGACCCTTGGTGGTCCCTGCTCTGTGCCCTGCCGGTGCAGAGAT
CAGGTTGCTGGATATAGATTGGGGGTCTGGGGCACTAGAGCCATGGGCTCGGCGACAGGGGCAG
GGTCAGCTTTTTGATTGTCCATCTCAGGAAGCCATTCTTGCTCTGTGTCCCCAAGGGAGGTATG
GAGACAGACACACTTGCTCTCATCAGGTCTCGCTGATGTCTCTGCAGGGGAAAGGTGGCTACAC
TGAGCTGGCGATGAGTGTGTGTGCATGTGTTGTGTGAGTGTGCGAGTGTATGTATTCCGAGCTG
GCATGGTCAGCATCCAGCGGCCCGTGTCCCTCTGCAGTATGGTGACTCTTTGGCTCCCAGAAAG
CCCAGCCTTAGGTCCGTGGGAACCCCATGGCTGTACAGGCTAGAGTGTAGGCAGGTGGCAGGCA
AGGAGTCAGGCACTACTGAGGAAAGAAGCACCAGGGGTCCAGAAGACCCAAGCATGGGGTGGCG
GTGGGACTGTGTCTTAAAGGAAACCTATTTATGTGGATGAGAGCCTCTGGTCTCTATTGGATGT
GTAAATAGCAAAGTTTATTCTCCTGTGGTTCCTAGAGCCCACCGATGAATGCCACGTTCCCAGG
ATGCGTGTGGGTGGCGGTATGCAGTGGCTGGTGGGTGGGAGTGTACCCCGTACTCTTCAGATGC
CTGTACCCAGTCACACTACCACCGCCGACTGGAGCTCCATCTCTGTCAGATCTGGGGGAAAGAG
CCTACCAGTCCAGAGGAAAGAATATTTTTATCGAATGCCACATTTAGCTCTATGTCCTCAATAT
TCAGAAAAGCTATTTTTTAAAACAAGGCAGAATGAAACTATCTGCCGGCTGGTTTGTTTCTGTA
TAAATATATACTAGAATGTCTTTCTGGATGAAGCGACTCCCACAGGCCAAAGCCTCTTTGATCT
TCTTCTCTTCTATGGGCAGTAGAGTGAGCAGCTGCCCTGCTCCCGCCGGCCACCCAGGTTATGC
CGGCACTGAGGCGCACTGCTGGCCCGCCTGGCAGTGGACACACAAGGGAGCTGTCTTTGTGTGG
AGTCCTGTGCAGCCTGTGATTTCTCTACCTCAACTGTGTGGCGAGTAGGTGTGAACCTGAGTGA
CTGCAGAGAATGTATTTATTTAACAGCTTTGTGTAACAAAACCAGAAACAAATGGAAACACTAA
ATAAATGTATTTTAAATTATAGACAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001099253	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM04607	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001099253 ⟸ NM_001105783

- Peptide Label:

precursor

- Sequence:

show sequence

MLDGSLLARWLAAAFGLTLLLAALRPSAAYFGLTGSEPLTILPLTLETEAAAQAHYKACDRLKL
ERKQRRMCRRDPGVAETLVEAVSMSALECQYQFRFERWNCTLEGRYRASLLKRGFKETAFLYAI
SSAGLTHALAKACSAGRMERCTCDEAPDLENREAWQWGGCGDNLKYSSKFVKEFLGRRSTRICE
PEWTSTTTSWV

hide sequence

RefSeq Acc Id:

XP_006246510 ⟸ XM_006246448

- Peptide Label:

isoform X1

- Sequence:

show sequence

MLDGSLLARWLAAAFGLTLLLAALRPSAAYFGLTGSEPLTILPLTLETEAAAQAHYKACDRLKL
ERKQRRMCRRDPGVAETLVEAVSMSALECQYQFRFERWNCTLEGRYRASLLKRGFKETAFLYAI
SSAGLTHALAKACSAGRMERCTCDEAPDLENREAWQWGGCGDNLKYSSKFVKEFLGRRSSKDLR
ARVDFHNNLVGVKVIKAGVETTCKCHGVSGSCTVRTCWRQLAPFHEVGKHLKHKYETSLKVGST
TNEATGEAGAISPPRGRASGSGGGDPLPRTPELVHLDDSPSFCLAGRFSPGTAGRRCHREKNCE
SICCGRGHNTQSRVVTRPCQCQVRWCCYVECRQCTQREEVYTCKG

hide sequence

RefSeq Acc Id:

ENSRNOP00000055129 ⟸ ENSRNOT00000058327

Transcriptome

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

Promoters

RGD ID:

13697234

Promoter ID:

EPDNEW_R7758

Type:

single initiation site

Name:

Wnt9a_1

Description:

Wnt family member 9A

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	45,659,098 - 45,659,158	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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

ACI/EurMcwi (RGD)

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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

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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CSV

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

F344/NRrrc (MCW)

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

FHH/EurMcwi (MCW)

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CSV

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

FHH/EurMcwi (RGD)

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CSV

TAB

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

FHL/EurMcwi (MCW)

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CSV

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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)

Visual

CSV

TAB

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

GH/OmrMcwi (MCW)

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CSV

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

GK/Ox (RGD)

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CSV

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

LE/Stm (RGD)

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CSV

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

LEW/Crl (RGD)

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CSV

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

LEW/NCrlBR (RGD)

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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

LH/MavRrrc (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

LL/MavRrrc (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

LN/MavRrrc (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

M520/N (MCW)

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CSV

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

MHS/Gib (RGD)

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CSV

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

MNS/Gib (RGD)

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CSV

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

MR/N (MCW)

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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CSV

TAB

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

SBN/Ygl (MCW)

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CSV

TAB

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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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CSV

TAB

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

SHR/NHsd (RGD)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WKY/Gcrc (RGD)

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

WKY/N (MCW)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (MCW)

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1305018	AgrOrtholog
Ensembl Genes	ENSRNOG00000003066	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000055129	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000058327	ENTREZGENE, UniProtKB/TrEMBL
InterPro	Wnt14	UniProtKB/TrEMBL
	Wnt_SF	UniProtKB/TrEMBL
NCBI Gene	287357	ENTREZGENE
PANTHER	PTHR12027:SF75	UniProtKB/TrEMBL
	Wnt	UniProtKB/TrEMBL
Pfam	wnt	UniProtKB/TrEMBL
PhenoGen	Wnt9a	PhenoGen
PRINTS	WNT14PROTEIN	UniProtKB/TrEMBL
	WNTPROTEIN	UniProtKB/TrEMBL
SMART	WNT1	UniProtKB/TrEMBL
UniProt	D3ZF63_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2017-03-29	Wnt9a	Wnt family member 9A	Wnt9a	wingless-type MMTV integration site family, member 9A	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-11-14	Wnt9a	wingless-type MMTV integration site family, member 9A	Wnt9a	wingless-type MMTV integration site 9A	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-03-07	Wnt9a	wingless-type MMTV integration site 9A	Wnt9a_predicted	wingless related MMTV integration site 9A (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Wnt9a_predicted	wingless related MMTV integration site 9A (predicted)		wingless-type MMTV integration site 9A (predicted)	Name updated	1299863	APPROVED
2005-01-12	Wnt9a_predicted	wingless-type MMTV integration site 9A (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)