Wnt1 (Wnt family member 1) - Rat Genome Database

Name: Wnt1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Wnt1 (Wnt family member 1) Rattus norvegicus

Analyze

Symbol:

Wnt1

Name:

Wnt family member 1

RGD ID:

1597195

Description:

Predicted to have cytokine activity; frizzled binding activity; and protein domain specific binding activity. Involved in animal organ regeneration; cellular response to peptide hormone stimulus; and hepatocyte differentiation. Predicted to localize to cell surface; cytoplasm; and extracellular space. Human ortholog(s) of this gene implicated in osteogenesis imperfecta type 15 and osteoporosis. Orthologous to human WNT1 (Wnt family member 1); PARTICIPATES IN Wnt signaling pathway; Wnt signaling, canonical pathway; basal cell carcinoma pathway; INTERACTS WITH atrazine; benzo[a]pyrene; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

Int1; proto-oncogene Wnt-1; wingless-related MMTV integration site 1; Wingless-type MMTV integration site 1 homolog; Wingless-type MMTV integration site 1, homolog; wingless-type MMTV integration site family, member 1; wingless-type MMTV integration site family, member 1 (mapped); Wnt1_mapped

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	WNT1 (Wnt family member 1)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, Panther
Mus musculus (house mouse):	Wnt1 (wingless-type MMTV integration site family, member 1)	HGNC	NCBI, HomoloGene, Inparanoid, Panther, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Wnt1 (Wnt family member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	WNT1 (Wnt family member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	WNT1 (Wnt family member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Wnt1 (Wnt family member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	WNT1 (Wnt family member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	WNT1 (Wnt family member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Wnt1 (Wnt family member 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Wnt1 (wingless-type MMTV integration site family, member 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Homo sapiens (human):	WNT1 (Wnt family member 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	wnt1 (wingless-type MMTV integration site family, member 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	wg	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

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	7	129,938,604 - 129,942,651 (+)	NCBI
Rnor_6.0 Ensembl	7	140,464,999 - 140,469,046 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	7	140,464,999 - 140,469,046 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	X	114,975,118 - 114,979,165 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	137,557,836 - 137,561,883 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	7	126,427,473 - 126,431,520 (+)	NCBI		Celera
Cytogenetic Map	7	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Animal Mammary Neoplasms (ISO)

breast cancer (ISS)

genetic disease (ISO)

keratoconus (ISO)

Mammary Neoplasms, Experimental (ISO)

osteogenesis imperfecta (ISO)

osteogenesis imperfecta type 15 (ISO)

osteogenesis imperfecta type 3 (ISO)

osteoporosis (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

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

3-methyl-3H-imidazo[4,5-f]quinolin-2-amine (ISO)

4,4'-sulfonyldiphenol (ISO)

5-aza-2'-deoxycytidine (ISO)

aldehydo-D-glucose (ISO)

arsenite(3-) (ISO)

atrazine (EXP)

benzene (ISO)

benzo[a]pyrene (EXP,ISO)

bis(2-chloroethyl) sulfide (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cadmium dichloride (ISO)

cannabidiol (ISO)

carbon nanotube (ISO)

chlorpyrifos (EXP)

copper(II) sulfate (ISO)

curcumin (EXP)

D-glucose (ISO)

delta-tocotrienol (ISO)

dexamethasone (ISO)

dibenz[a,h]anthracene (ISO)

dichromium trioxide (ISO)

dimethylarsinic acid (ISO)

ethosuximide (EXP)

folic acid (ISO)

glucose (ISO)

hydralazine (ISO)

hydrogen peroxide (ISO)

lead diacetate (ISO)

linalool (ISO)

lithium chloride (ISO)

losartan (ISO)

maneb (EXP)

methylarsonic acid (ISO)

methylmercury chloride (ISO)

N-acetyl-L-cysteine (ISO)

nickel atom (EXP)

ochratoxin A (ISO)

paracetamol (ISO)

paraquat (EXP,ISO)

phenytoin (ISO)

reactive oxygen species (ISO)

resveratrol (EXP)

simazine (ISO)

sodium arsenite (ISO)

tebuconazole (ISO)

triptonide (ISO)

valproic acid (EXP,ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

animal organ regeneration (IMP)

astrocyte-dopaminergic neuron signaling (ISO)

bone development (ISO)

branching involved in ureteric bud morphogenesis (ISO)

canonical Wnt signaling pathway (IBA,ISO)

canonical Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation (ISO)

cell fate commitment (IBA)

cell proliferation in midbrain (ISO)

cell-cell signaling (ISO)

cellular response to peptide hormone stimulus (IEP)

central nervous system morphogenesis (ISO)

cerebellum development (ISO)

cerebellum formation (ISO)

diencephalon development (ISO)

dopaminergic neuron differentiation (ISO)

embryonic axis specification (ISO)

embryonic brain development (ISO)

forebrain anterior/posterior pattern specification (ISO)

hematopoietic stem cell proliferation (ISO)

hepatocyte differentiation (IMP)

inner ear morphogenesis (ISO)

metencephalon development (ISO)

midbrain development (ISO)

midbrain dopaminergic neuron differentiation (ISO)

midbrain-hindbrain boundary development (ISO)

midbrain-hindbrain boundary maturation during brain development (ISO)

myoblast fusion (ISO)

myotube differentiation (ISO)

negative regulation of apoptotic process (ISO)

negative regulation of BMP signaling pathway (ISO)

negative regulation of cell aging (ISO)

negative regulation of cell differentiation (ISO)

negative regulation of cell-cell adhesion (ISO)

negative regulation of cell-substrate adhesion (ISO)

negative regulation of fat cell differentiation (ISO)

negative regulation of oxidative stress-induced neuron death (ISO)

negative regulation of transforming growth factor beta receptor signaling pathway (ISO)

negative regulation of ubiquitin-dependent protein catabolic process (ISO)

neurogenesis (ISO)

neuron differentiation (IBA)

neuron fate commitment (ISO)

neuron fate determination (ISO)

positive regulation of cell population proliferation (ISO)

positive regulation of dermatome development (ISO)

positive regulation of DNA-binding transcription factor activity (ISO)

positive regulation of fibroblast proliferation (ISO)

positive regulation of insulin-like growth factor receptor signaling pathway (ISO)

positive regulation of lamellipodium assembly (ISO)

positive regulation of Notch signaling pathway (ISO)

positive regulation of protein phosphorylation (ISO)

positive regulation of transcription by RNA polymerase II (ISO)

positive regulation of transcription, DNA-templated (ISO)

response to wounding (ISO)

signal transduction in response to DNA damage (ISO)

Spemann organizer formation (ISO)

spinal cord association neuron differentiation (ISO)

T cell differentiation in thymus (ISO)

ubiquitin-dependent SMAD protein catabolic process (ISO)

Wnt signaling pathway (ISO)

Cellular Component

cell surface (ISO)

cellular_component (ND)

cytoplasm (ISO)

extracellular region (ISO)

extracellular space (IBA)

Molecular Function

cytokine activity (IBA,ISO)

frizzled binding (IBA)

molecular_function (ND)

protein binding (ISO)

protein domain specific binding (ISO)

receptor ligand activity (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

basal cell carcinoma pathway (IEA)

Hedgehog signaling pathway (IEA)

Wnt signaling pathway (IEA,ISO)

Wnt signaling, canonical pathway (ISO)

References

References - curated


1.	Castelo-Branco G, etal., Proc Natl Acad Sci U S A 2003 Oct 28;100(22):12747-52. Epub 2003 Oct 13.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	Heo JS, etal., Mol Cells. 2010 Nov;30(5):449-54. doi: 10.1007/s10059-010-0139-3. Epub 2010 Sep 10.
4.	Ikeya M, etal., Nature. 1997 Oct 30;389(6654):966-70.
5.	Kim WB, etal., J Endocrinol. 2007 Apr;193(1):93-106.
6.	OMIM Disease Annotation Pipeline
7.	Pipeline to import KEGG annotations from KEGG into RGD
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.	Schroeder JA, etal., Oncogene. 2000 Jun 29;19(28):3193-9.
13.	Shimizu H, etal., Cell Growth Differ. 1997 Dec;8(12):1349-58.
14.	van Amerongen R, etal., Sci Signal. 2008 Sep 2;1(35):re9.
15.	Williams JM, etal., Am J Pathol. 2010 Jun;176(6):2732-42. Epub 2010 Apr 22.
16.	Wong GT, etal., Mol Cell Biol. 1994 Sep;14(9):6278-86.

Additional References at PubMed

PMID:1300513	PMID:2202907	PMID:2205396	PMID:2534596	PMID:8555108	PMID:8710372	PMID:8848044	PMID:9160667	PMID:9192640	PMID:9356179	PMID:9473323	PMID:9505170
PMID:9601103	PMID:9652750	PMID:9769173	PMID:10557084	PMID:10644691	PMID:10654605	PMID:10937998	PMID:11265645	PMID:11336703	PMID:11357136	PMID:11793365	PMID:11877374
PMID:12121999	PMID:12154096	PMID:12937339	PMID:14641328	PMID:15035989	PMID:15064719	PMID:15121182	PMID:15143170	PMID:15265686	PMID:15282335	PMID:15454084	PMID:15574752
PMID:15728361	PMID:15961523	PMID:16054034	PMID:16194878	PMID:16207730	PMID:16339193	PMID:16501043	PMID:16543246	PMID:16601693	PMID:17072303	PMID:17239604	PMID:17982423
PMID:17988238	PMID:18004065	PMID:18094027	PMID:18347988	PMID:19348510	PMID:19594026	PMID:19734317	PMID:19756656	PMID:19778454	PMID:19847889	PMID:19931241	PMID:19951692
PMID:20383322	PMID:20499363	PMID:21443457	PMID:21752258	PMID:21935365	PMID:22406377	PMID:23152495	PMID:23324743	PMID:23499309	PMID:23585476	PMID:24961246	PMID:26054493
PMID:28177765	PMID:28733458	PMID:29152652	PMID:31356809	PMID:31886199

Genomics

Comparative Map Data

Wnt1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	7	129,938,604 - 129,942,651 (+)	NCBI
Rnor_6.0 Ensembl	7	140,464,999 - 140,469,046 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	7	140,464,999 - 140,469,046 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	X	114,975,118 - 114,979,165 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	137,557,836 - 137,561,883 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	7	126,427,473 - 126,431,520 (+)	NCBI		Celera
Cytogenetic Map	7	q36	NCBI

WNT1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	12	48,978,322 - 48,982,620 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	12	48,978,322 - 48,982,620 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	12	49,372,105 - 49,376,403 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	47,658,503 - 47,662,746 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	12	47,658,502 - 47,662,746	NCBI
Celera	12	48,167,028 - 48,171,188 (+)	NCBI
Cytogenetic Map	12	q13.12	NCBI
HuRef	12	46,403,758 - 46,407,918 (+)	NCBI		HuRef
CHM1_1	12	49,338,028 - 49,342,188 (+)	NCBI		CHM1_1

Wnt1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	15	98,687,738 - 98,691,711 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	15	98,687,738 - 98,691,718 (+)	Ensembl
GRCm38	15	98,789,857 - 98,793,830 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	15	98,789,857 - 98,793,837 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	15	98,620,288 - 98,624,261 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	15	98,617,891 - 98,621,864 (+)	NCBI			mm8
Celera	15	100,939,306 - 100,943,279 (+)	NCBI		Celera
Cytogenetic Map	15	F1	NCBI
cM Map	15	54.65	NCBI

Wnt1
(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_004955500	7,797,060 - 7,811,167 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955500	7,797,063 - 7,811,142 (+)	NCBI	ChiLan1.0	ChiLan1.0

WNT1
(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	12	40,648,413 - 40,652,583 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	40,648,413 - 40,652,583 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	12	39,767,839 - 39,772,460 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

WNT1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	27	5,588,151 - 5,592,254 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	27	5,574,940 - 5,592,060 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	27	40,665,906 - 40,669,560 (+)	NCBI
ROS_Cfam_1.0	27	5,639,156 - 5,642,810 (-)	NCBI
UMICH_Zoey_3.1	27	5,603,082 - 5,606,734 (-)	NCBI
UNSW_CanFamBas_1.0	27	5,593,278 - 5,596,931 (-)	NCBI
UU_Cfam_GSD_1.0	27	41,058,211 - 41,061,867 (+)	NCBI

Wnt1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404945	66,379,465 - 66,383,960 (-)	NCBI
SpeTri2.0	NW_004936512	6,781,001 - 6,785,358 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

WNT1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	15,010,985 - 15,014,079 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	15,010,607 - 15,015,007 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	15,420,829 - 15,425,219 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

WNT1
(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	11	45,217,402 - 45,222,996 (+)	NCBI
ChlSab1.1 Ensembl	11	45,219,027 - 45,222,017 (+)	Ensembl

Wnt1
(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_004624816	3,209,605 - 3,212,969 (-)	NCBI

Position Markers

D7Kyo2

No map positions available.

Wnt1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	7	129,940,800 - 129,941,417 (+)	MAPPER
Rnor_6.0	7	140,467,196 - 140,467,812	NCBI	Rnor6.0
Rnor_5.0	X	114,977,315 - 114,977,931	UniSTS	Rnor5.0
RGSC_v3.4	7	137,560,033 - 137,560,649	UniSTS	RGSC3.4
Celera	7	126,429,670 - 126,430,286	UniSTS
Cytogenetic Map	7	q35	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
1300179	Kidm5	Kidney mass QTL 5	3.51		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	7	51251919	145729302	Rat
70173	Niddm19	Non-insulin dependent diabetes mellitus QTL 19	4.33	0.00005	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	7	71448715	145729302	Rat
634331	Pia17	Pristane induced arthritis QTL 17	4.7		joint integrity trait (VT:0010548)	arthritic paw count (CMO:0001460)	7	81645773	140745067	Rat
1358914	Bp266	Blood pressure QTL 266			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	7	91832949	145158140	Rat
1358891	Bp265	Blood pressure QTL 265	2.21		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	7	91832949	145158140	Rat
1558655	Swd4	Spike wave discharge measurement QTL 4	3.68	0.0002	brain electrophysiology trait (VT:0010557)	brain spike-and-wave discharge severity grade (CMO:0001988)	7	96630946	141630946	Rat
2299163	Iddm34	Insulin dependent diabetes mellitus QTL 34	2.71		blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	7	100028953	145729302	Rat
1549899	Stresp8	Stress response QTL 8	4.37	0.0008	stress-related behavior trait (VT:0010451)	defensive burying duration (CMO:0001961)	7	100192194	145192194	Rat
731176	Glom5	Glomerulus QTL 5	2.5	0.0035	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	7	106564316	145729302	Rat
1331731	Bp216	Blood pressure QTL 216	2.851		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	7	111519266	143965591	Rat
731174	Uae23	Urinary albumin excretion QTL 23	2.4	0.0042	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	7	114825174	145729302	Rat
2306821	Bp335	Blood pressure QTL 335		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	7	115922628	145729302	Rat
631663	Bw6	Body weight QTL 6	3.4		body mass (VT:0001259)	body weight (CMO:0000012)	7	120746024	145692398	Rat
1300112	Bp183	Blood pressure QTL 183	3.51		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	7	121654760	145729302	Rat
1331748	Bp215	Blood pressure QTL 215	4.043		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	7	121986439	143965591	Rat
1357339	Stl14	Serum triglyceride level QTL 14	3.45	0.0001	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	7	122421276	143965415	Rat
1354582	Stl11	Serum triglyceride level QTL 11	3.42		blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	7	129412003	145729302	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	507
Count of miRNA genes:	237
Interacting mature miRNAs:	297
Transcripts:	ENSRNOT00000019641, ENSRNOT00000067581
Prediction methods:	Microtar, Miranda, Pita, Pita,Targetscan, 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

	circulatory system	nervous system	reproductive system	respiratory system
High
Medium
Low		31	2
Below cutoff	1	11	5	1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001105714	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC114446	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474035	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000187	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000090156 ⟹ ENSRNOP00000071688

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	7	140,464,999 - 140,469,046 (+)	Ensembl

RefSeq Acc Id:

NM_001105714 ⟹ NP_001099184

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	7	129,938,604 - 129,942,651 (+)	NCBI
Rnor_6.0	7	140,464,999 - 140,469,046 (+)	NCBI
Rnor_5.0	X	114,975,118 - 114,979,165 (+)	NCBI
RGSC_v3.4	7	137,557,836 - 137,561,883 (+)	RGD
Celera	7	126,427,473 - 126,431,520 (+)	RGD

Sequence:

show sequence

TTTGCTCAGACCGGCTAGAGCCACAGCTTCGCTCGCTACTCATTGTCTGTGGCCCTGACCAGTG
CGCCCTGGTGCTTTAGTGCGGCCCGGAGGGGCAGCCTCTTCTCACTGCAGTCAGCGCCGCAACT
ATAAGAGGCGGTGCCTCCTGCAGCGGCTGCTTCAGCCCACCAGCCGGGACAGCGAACCATGCTG
CCTGCGGCCCGCCTCCAGACTTTCTAGAGCCAGCCTGAGAATACTCACCACTGCCCTCACCGCT
GTGTCCAGTCCCACCGTCGCGGGGAGCAACCAAAGTCGCCAGAACCGCAGCACAGAACCAGCAA
GGCCAGGCAGGCCATGGGGCTCTGGGCGCTGCTGCCCAGCTGGGTTTCTGCTACGTTGCTACTG
GCACTGACCGCTCTGCCCGCAGCCCTGGGCGCCAACAGTAGTGGCCGATGGTGGGGCATCGTGA
ACATAGCCTCCTCCACGAACCTGCTGACAGATTCCAAGAGTCTACAGCTGGTGCTAGAGCCCAG
CCTGCAGCTACTGAGCCGCAAGCAGCGACGACTGATCCGACAGAACCCGGGGATCCTGCACAGC
GTGAGCGGAGGGCTGCAGAGCGCCGTTCGAGAGTGCAAGTGGCAATTCCGAAACCGCCGCTGGA
ACTGCCCCACTGCTCCCGGGCCCCACCTCTTCGGCAAGATCGTCAACCGAGGCTGCCGAGAAAC
AGCGTTTATCTTCGCAATCACCTCCGCCGGGGTCACACATTCTGTGGCGCGCTCCTGCTCCGAA
GGCTCCATCGAATCCTGCACCTGCGACTACAGGCGGCGCGGTCCTGGGGGCCCCGACTGGCACT
GGGGGGGTTGCAGCGACAACATCGATTTCGGTCGCCTCTTCGGCCGAGAGTTCGTGGACTCTGG
GGAGAAGGGGCGGGACCTACGCTTCCTCATGAACCTTCACAATAACGAGGCAGGGCGCACGACC
GTGTTCTCTGAGATGCGCCAAGAGTGCAAATGCCACGGGATGTCCGGTTCCTGCACCGTGCGCA
CGTGTTGGATGCGGCTGCCCACACTGCGCGCTGTGGGCGACGTGCTGCGCGACCGCTTCGACGG
CGCCTCCCGCGTCCTTTACGGCAACCGAGGCAACAACCGCGCTTCGCGGGCGGAGCTGCTGCGC
CTGGAGCCCGAAGACCCTGCGCACAAGCCGCCCTCCCCTCACGACCTGGTCTACTTCGAGAAAT
CGCCCAACTTCTGCACGTACAGTGGACGCCTGGGCACAGCTGGCACAGCTGGGCGAGCTTGCAA
CAGCTCATCTCCAGCGCTGGACGGCTGCGAGCTGCTGTGCTGTGGCCGAGGCCATCGCACGCGC
ACGCAGCGCGTCACCGAGCGCTGCAACTGCACCTTCCACTGGTGCTGCCACGTCAGCTGCCGCA
ACTGCACGCACACGCGCGTACTGCACGAGTGTCTATGAGGCGCTGCGCCTCCGGGAACGCTCTC
TTCCAGTTCTCCTCAGACAAACTCGCTGGCTCTGATGTTCGCCCACCCTAGCGCGTACAGCCAC
AGTCCCGAGGTTCACAGTGACCCATCTCTCCCACCTCCTACCTGGGGACTCCTAAAACCACTTG
CCTGAGGCAGCTCGAACCCTTTTGCCATCCTGCGGGCCCTGCCCAAGCCTACCTCCCTCCCTCT
TCTCGGGAGACCCCTTTTGCACTGCCCCCCCAATTTGGCCAGAGGGTGAGAGGGAAATTCTTCT
TGGGTGTGGGTGGTGGTGGTGGGTCAGCTTGTGAAGGCGTTGCTGTCCCTGTGGTATTGTGCCC
CCTCTCCCCGTGACCTCTCTGTGTATCACCTTCCGGTTTTCTCTCCGTGTCCCTATAGGTCCCT
AACCACCACACCTGGGCTTCAAGCCCCCCTACACACACCTGTAGCTGAAGTGTTTCCGAGGTGA
AAGGGCAAGGAAAGCTGTGATGACGTGGGAAATAAGGTTGGGGAGCCCAGCAGGAAAAACCTAC
ATTCTCCTAGTCTCTGTCACCGAGCCACTGAACAGTGAACCATGCCTCCCTCAGCCACCTCCCA
CCCCTTCCTGTCCTGCTCCCTCTTCATCAGTGTGTAAATAATTTGCACCGGAACGCGGCCACAC
AGAGCCACGCGTTCGGTTATGTAAATAAAACTATTTATTGTGCCGGGGGTTTCAGCCTGGGTTG
CAGAGCCCACCCTCATCCCAACTCACTCCTCTTGTCTGCCAGCCTTTTTGTTACCCGACCTTTT
CTCCAAGGCACCCTGCCCACCGGATCAGCATCTCCTGCCGCTGTAGCTATTAGTGGCTCTTCGC
CCCCACCGATGTAGTATCTTCCTCTGAGGAATAAAACATCTATTTTTATCAATGAC

hide sequence

Protein Sequences


Protein RefSeqs	NP_001099184	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL87034	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001099184 ⟸ NM_001105714
- Peptide Label:	precursor
- UniProtKB:	D4A9J2 (UniProtKB/TrEMBL)
- Sequence:	show sequence MGLWALLPSWVSATLLLALTALPAALGANSSGRWWGIVNIASSTNLLTDSKSLQLVLEPSLQLL SRKQRRLIRQNPGILHSVSGGLQSAVRECKWQFRNRRWNCPTAPGPHLFGKIVNRGCRETAFIF AITSAGVTHSVARSCSEGSIESCTCDYRRRGPGGPDWHWGGCSDNIDFGRLFGREFVDSGEKGR DLRFLMNLHNNEAGRTTVFSEMRQECKCHGMSGSCTVRTCWMRLPTLRAVGDVLRDRFDGASRV LYGNRGNNRASRAELLRLEPEDPAHKPPSPHDLVYFEKSPNFCTYSGRLGTAGTAGRACNSSSP ALDGCELLCCGRGHRTRTQRVTERCNCTFHWCCHVSCRNCTHTRVLHECL hide sequence

RefSeq Acc Id:

ENSRNOP00000071688 ⟸ ENSRNOT00000090156

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

GH/OmrMcwi (MCW)

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

GK/Ox (RGD)

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

LE/Stm (RGD)

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

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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

LH/MavRrrc (RGD)

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

LL/MavRrrc (RGD)

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

LN/MavRrrc (RGD)

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

M520/N (MCW)

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

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (MCW)

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WKY/Gcrc (RGD)

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

WKY/N (MCW)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (MCW)

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

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
X	114975521	114975522	C	T	snv	WKY/Gcrc (KNAW), WKY/N (KNAW), DOB/Oda (KyushuU), WKY/NHsd (KNAW), WKY/NCrl (KNAW)

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
7	140465402	140465403	C	T	snv	WKY/Gcrc (RGD), WKY/NCrl (RGD)

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
7	137558239	137558240	C	T	snv	WKY/Gcrc (ICL), WKY/NHsd (ICL), LCR/2Mco (UMich), LCR/1Mco (UMich), WKY/NCrl (ICL)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1597195	AgrOrtholog
Ensembl Genes	ENSRNOG00000061818	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000071688	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000090156	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	3.30.2460.20	UniProtKB/TrEMBL
InterPro	Wnt1	UniProtKB/TrEMBL
	Wnt_C	UniProtKB/TrEMBL
	Wnt_grthfactor_CS	UniProtKB/TrEMBL
	Wnt_SF	UniProtKB/TrEMBL
KEGG Report	rno:24881	UniProtKB/TrEMBL
NCBI Gene	24881	ENTREZGENE
PANTHER	Wnt	UniProtKB/TrEMBL
Pfam	wnt	UniProtKB/TrEMBL
PhenoGen	Wnt1	PhenoGen
PRINTS	WNT1PROTEIN	UniProtKB/TrEMBL
	WNTPROTEIN	UniProtKB/TrEMBL
PROSITE	WNT1	UniProtKB/TrEMBL
SMART	WNT1	UniProtKB/TrEMBL
UniProt	D4A9J2	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2017-03-29	Wnt1	Wnt family member 1	Wnt1	wingless-type MMTV integration site family, member 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-11-14	Wnt1	wingless-type MMTV integration site family, member 1	Wnt1	wingless-related MMTV integration site 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-03-04	Wnt1	wingless-related MMTV integration site 1	Wnt1	wingless-type MMTV integration site family, member 1 (mapped)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2007-04-13	Wnt1	wingless-type MMTV integration site family, member 1 (mapped)	Wnt1_mapped	wingless-type MMTV integration site family, member 1 (mapped)	Data Merged	737654	APPROVED
2006-11-20	Wnt1	wingless-type MMTV integration site family, member 1 (mapped)			Symbol and Name status set to provisional	70820	PROVISIONAL
2005-11-17	Wnt1_mapped	wingless-type MMTV integration site family, member 1 (mapped)	Wnt1	wingless-type MMTV integration site family, member 1	Symbol and Name updated	1556543	APPROVED
2003-04-09	Wnt1	wingless-type MMTV integration site family, member 1		Wingless-type MMTV integration site 1, homolog	Name updated	629478	APPROVED
2002-06-10	Wnt1	Wingless-type MMTV integration site 1, homolog			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_product	predicted to be a member of the Wnt family of secreted glycoproteins which regulate cell proliferation, cell differentiation, and determination of cell fate	1300513

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 - MGI

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)