Ntn1 (netrin 1) - Rat Genome Database

Name: Ntn1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Ntn1 (netrin 1) Rattus norvegicus

Analyze

Symbol:

Ntn1

Name:

netrin 1

RGD ID:

619809

Description:

Predicted to enable cytokine activity. Involved in several processes, including Cdc42 protein signal transduction; positive regulation of axon extension; and substrate-dependent cell migration, cell extension. Located in extracellular matrix. Human ortholog(s) of this gene implicated in congenital mirror movement disorder. Orthologous to human NTN1 (netrin 1); INTERACTS WITH 17beta-estradiol; 2,3,7,8-Tetrachlorodibenzofuran; acetamide.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

netrin-1

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):	NTN1 (netrin 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Ntn1 (netrin 1)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Ntn1 (netrin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	NTN1 (netrin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	NTN1 (netrin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Ntn1 (netrin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	NTN1 (netrin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	NTN1 (netrin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Ntn1 (netrin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	NTN3 (netrin 3)	HGNC	OrthoDB
Homo sapiens (human):	LAMC1 (laminin subunit gamma 1)	HGNC	OrthoDB
Homo sapiens (human):	LAMC3 (laminin subunit gamma 3)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	NTN1 (netrin 1)	Alliance	DIOPT (HGNC\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Ntn1 (netrin 1)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	ntn1a (netrin 1a)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	ntn1b (netrin 1b)	Alliance	DIOPT (OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	NetA	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	unc-6	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	10	52,899,933 - 53,098,591 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	10	52,899,934 - 53,085,326 (-)	Ensembl
Rnor_6.0	10	54,761,925 - 54,982,072 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	54,761,871 - 54,967,585 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	54,507,464 - 54,725,989 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	54,950,521 - 55,133,536 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	54,964,143 - 55,147,159 (-)	NCBI
Celera	10	52,078,465 - 52,253,812 (-)	NCBI		Celera
Cytogenetic Map	10	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

Alzheimer's disease (ISO)

brain edema (ISO)

cleft lip (ISO)

Mirror Movements 4 (ISO)

Neurobehavioral Manifestations (ISO)

Subarachnoid Hemorrhage (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17beta-estradiol (EXP)

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

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

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

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

acetamide (EXP)

aflatoxin B1 (ISO)

ammonium chloride (EXP)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

benzo[e]pyrene (ISO)

Benzo[k]fluoranthene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

Bisphenol A diglycidyl ether (ISO)

bisphenol F (ISO)

butanal (ISO)

cadmium atom (ISO)

cadmium dichloride (EXP)

chrysene (ISO)

cisplatin (ISO)

clobetasol (ISO)

cocaine (EXP)

curcumin (EXP)

DDT (EXP)

dexamethasone (ISO)

diazinon (EXP)

dieldrin (EXP)

doxorubicin (ISO)

ethanol (ISO)

folic acid (ISO)

indometacin (ISO)

kainic acid (EXP)

lithium chloride (ISO)

maneb (ISO)

methapyrilene (ISO)

N-methyl-4-phenylpyridinium (ISO)

N-nitrosodiethylamine (ISO)

nickel dichloride (EXP)

paracetamol (ISO)

paraquat (ISO)

pentanal (ISO)

phenobarbital (ISO)

pirinixic acid (ISO)

propanal (ISO)

rimonabant (ISO)

rotenone (ISO)

silicon dioxide (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenite (ISO)

streptozocin (ISO)

sunitinib (ISO)

tetrachloromethane (ISO)

tetraphene (ISO)

titanium dioxide (ISO)

trichostatin A (ISO)

triclosan (ISO)

troglitazone (ISO)

valproic acid (ISO)

WIN 55212-2 (ISO)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

animal organ morphogenesis (IBA)

anterior/posterior axon guidance (IEA,ISO)

apoptotic process (IEA)

axon guidance (ISO,NAS)

axonogenesis (ISO)

B cell mediated immunity (ISS)

B cell proliferation (ISS)

Cdc42 protein signal transduction (IDA)

cell-cell adhesion (IEA,ISO)

chemorepulsion of axon (IEA,ISO,ISS)

dendrite development (IBA)

inner ear morphogenesis (IEA,ISO)

mammary gland development (ISO)

mammary gland duct morphogenesis (IEA,ISO)

motor neuron axon guidance (IBA)

negative regulation of axon extension (IEA,ISO)

neuron migration (IEA,ISO)

nuclear migration (IEA,ISO)

positive regulation of axon extension (IDA,IEA,ISO)

positive regulation of cell motility (IDA)

positive regulation of cell population proliferation (IEA,ISO)

Ras protein signal transduction (IDA)

regulation of cell migration (IEA,ISO)

regulation of synapse assembly (IEA,ISO)

substrate-dependent cell migration, cell extension (IDA)

T cell mediated immunity (ISS)

tissue development (IBA)

Cellular Component

basement membrane (IBA,IEA,ISO)

cytoplasm (IEA,ISO)

extracellular matrix (IDA)

extracellular region (IEA,ISO,TAS)

Molecular Function

cytokine activity (ISS)

protein binding (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.	Manitt C, etal., J Neurosci 2001 Jun 1;21(11):3911-22.
4.	MGD data from the GO Consortium
5.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	RGD automated data pipeline
7.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8.	RGD automated import pipeline for gene-chemical interactions
9.	Toriyama M, etal., Curr Biol. 2013 Mar 18;23(6):529-34. doi: 10.1016/j.cub.2013.02.017. Epub 2013 Feb 28.
10.	Zamani E, etal., Clin Exp Pharmacol Physiol. 2018 Aug 1. doi: 10.1111/1440-1681.13020.

Additional References at PubMed

PMID:9143559	PMID:10399920	PMID:10704383	PMID:10908620	PMID:12051827	PMID:12679031	PMID:12819897	PMID:14750959	PMID:15737744	PMID:16267219	PMID:16439476	PMID:16481423
PMID:17086203	PMID:17574219	PMID:17616930	PMID:17825258	PMID:17898206	PMID:17995930	PMID:18234888	PMID:18425773	PMID:18479186	PMID:18757743	PMID:18932228	PMID:19858080
PMID:20052412	PMID:21726647	PMID:21820492	PMID:22323486	PMID:22997549	PMID:23230270	PMID:24174661	PMID:25240286	PMID:25834042	PMID:26116534	PMID:26482371	PMID:26787017
PMID:26818229	PMID:27060954	PMID:27176224	PMID:28084632	PMID:28483977	PMID:28526701	PMID:28931811	PMID:28945198	PMID:30626732	PMID:30789913	PMID:31846437	PMID:32251100
PMID:32688140

Genomics

Comparative Map Data

Ntn1
(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	52,899,933 - 53,098,591 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	10	52,899,934 - 53,085,326 (-)	Ensembl
Rnor_6.0	10	54,761,925 - 54,982,072 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	54,761,871 - 54,967,585 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	54,507,464 - 54,725,989 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	54,950,521 - 55,133,536 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	54,964,143 - 55,147,159 (-)	NCBI
Celera	10	52,078,465 - 52,253,812 (-)	NCBI		Celera
Cytogenetic Map	10	q24	NCBI

NTN1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	17	9,021,510 - 9,244,000 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	17	9,021,510 - 9,244,000 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	17	8,924,827 - 9,147,317 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	8,865,584 - 9,088,042 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	17	8,865,583 - 9,084,078	NCBI
Celera	17	8,956,718 - 9,179,095 (+)	NCBI
Cytogenetic Map	17	p13.1	NCBI
HuRef	17	8,823,748 - 9,046,260 (+)	NCBI		HuRef
CHM1_1	17	8,934,056 - 9,156,348 (+)	NCBI		CHM1_1

Ntn1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	68,100,190 - 68,277,652 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	11	68,100,190 - 68,291,649 (-)	Ensembl
GRCm38	11	68,209,364 - 68,386,826 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	68,209,364 - 68,400,823 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	68,022,866 - 68,200,328 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	11	68,029,201 - 68,202,315 (-)	NCBI			mm8
Celera	11	75,146,897 - 75,324,142 (-)	NCBI		Celera
Cytogenetic Map	11	B3	NCBI

Ntn1
(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_004955467	7,794,735 - 7,991,695 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955467	7,795,175 - 7,991,597 (-)	NCBI	ChiLan1.0	ChiLan1.0

NTN1
(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	17	47,148,384 - 47,368,127 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	17	47,152,225 - 47,368,134 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	17	42,409,797 - 42,631,930 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

NTN1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	5	33,654,723 - 33,825,832 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	5	33,637,142 - 33,825,899 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	5	33,791,096 - 33,962,030 (+)	NCBI
ROS_Cfam_1.0	5	33,758,267 - 33,929,266 (+)	NCBI
UMICH_Zoey_3.1	5	33,725,541 - 33,896,204 (+)	NCBI
UNSW_CanFamBas_1.0	5	33,683,225 - 33,853,961 (+)	NCBI
UU_Cfam_GSD_1.0	5	33,859,633 - 34,030,422 (+)	NCBI

Ntn1
(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_024405602	48,672,178 - 48,849,151 (+)	NCBI
SpeTri2.0	NW_004936595	2,146,371 - 2,323,346 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NTN1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	12	54,089,472 - 54,308,355 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	12	54,089,444 - 54,292,191 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	12	56,822,597 - 57,056,391 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NTN1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	16	8,359,682 - 8,603,231 (+)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	16	8,379,129 - 8,603,223 (+)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666059	12,748,497 - 13,022,123 (-)	NCBI	Vero_WHO_p1.0

Ntn1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624786	11,508,643 - 11,707,060 (+)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

D10Rat59

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	52,957,296 - 52,957,442 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	54,816,216 - 54,816,361	NCBI	Rnor6.0
Rnor_5.0	10	54,561,755 - 54,561,900	UniSTS	Rnor5.0
RGSC_v3.4	10	55,004,338 - 55,004,484	RGD	RGSC3.4
RGSC_v3.4	10	55,004,339 - 55,004,484	UniSTS	RGSC3.4
RGSC_v3.1	10	55,017,915 - 55,018,228	RGD
Celera	10	52,132,256 - 52,132,401	UniSTS
FHH x ACI Map	10	42.61	RGD
FHH x ACI Map	10	42.61	UniSTS
Cytogenetic Map	10	q24	UniSTS

AU046514

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	53,067,284 - 53,067,487 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	54,950,669 - 54,950,871	NCBI	Rnor6.0
Rnor_5.0	10	54,694,720 - 54,694,922	UniSTS	Rnor5.0
RGSC_v3.4	10	55,116,482 - 55,116,684	UniSTS	RGSC3.4
Celera	10	52,239,613 - 52,239,820	UniSTS
Cytogenetic Map	10	q24	UniSTS

ha2998

Rat Assembly	Chr	Position (strand)	Source	JBrowse
RGSC_v3.4	10	55,083,506 - 55,084,899	UniSTS	RGSC3.4
Cytogenetic Map	10	q24	UniSTS

NZPR1680

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	53,079,913 - 53,081,309 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	54,963,269 - 54,964,663	NCBI	Rnor6.0
Rnor_5.0	10	54,707,260 - 54,708,654	UniSTS	Rnor5.0
RGSC_v3.4	10	55,129,134 - 55,130,528	UniSTS	RGSC3.4
Cytogenetic Map	10	q24	UniSTS

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
70223	Bp57	Blood pressure QTL 57	5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	1	80676123	Rat
631554	Bp133	Blood pressure QTL 133		0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	743364	63851208	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	5801990	62146030	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	6154182	73453136	Rat
61427	Cia16	Collagen induced arthritis QTL 16	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	6357896	96121100	Rat
2303118	Mamtr7	Mammary tumor resistance QTL 7		0.003	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	9658275	104670812	Rat
9590310	Scort19	Serum corticosterone level QTL 19	6.3	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	11474010	56474010	Rat
9590268	Scort13	Serum corticosterone level QTL 13	3.26	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	11474010	56474010	Rat
9589136	Insul27	Insulin level QTL 27	10.46	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	10	11474010	56474010	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	14487011	89062041	Rat
631268	Cia21	Collagen induced arthritis QTL 21	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	14487011	104060283	Rat
2316949	Gluco60	Glucose level QTL 60	3.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	14487011	107057807	Rat
1354587	Kidm21	Kidney mass QTL 21	3.3		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	10	15028513	60430477	Rat
631564	Apr3	Acute phase response QTL 3	3.9		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	10	15275955	60275955	Rat
6893350	Bw99	Body weight QTL 99	0.87	0.16	body mass (VT:0001259)	body weight (CMO:0000012)	1	15906665	60906665	Rat
6893352	Bw100	Body weight QTL 100	0.33	0.6	body mass (VT:0001259)	body weight (CMO:0000012)	1	15906665	60906665	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	18167841	63167841	Rat
2313055	Bw96	Body weight QTL 96	3.6	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	10	19606483	64606483	Rat
2313087	Bmd80	Bone mineral density QTL 80	3.2	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	10	19606483	64606483	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	19816042	99406971	Rat
1581497	Esta1	Estrogen-induced thymic atrophy QTL 1			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	10	21329805	61345413	Rat
724556	Pur2	Proteinuria QTL 2	5.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	22427500	90627625	Rat
61354	Pia10	Pristane induced arthritis QTL 10		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	23444813	104060283	Rat
631267	Cia20	Collagen induced arthritis QTL 20	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	23444813	104060283	Rat
61325	Aia5	Adjuvant induced arthritis QTL 5		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	23444813	104060283	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	26521957	61345413	Rat
1298069	Bp168	Blood pressure QTL 168	5.5		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	10	26521957	98003205	Rat
631542	Bp82	Blood pressure QTL 82	6.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	26521957	98952741	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	26944628	71944628	Rat
10402859	Bp381	Blood pressure QTL 381		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	27606468	72606468	Rat
2292441	Bp308	Blood pressure QTL 308			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	27606468	72606468	Rat
724527	Bp148	Blood pressure QTL 148		0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	28453136	73453136	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	29299504	64155584	Rat
1331791	Cm31	Cardiac mass QTL 31	3.84606		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	29299504	107211142	Rat
631557	Bp136	Blood pressure QTL 136		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	30632053	75632053	Rat
1576311	Pia26	Pristane induced arthritis QTL 26			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	31224026	75632053	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	31297439	76297439	Rat
1576319	Cia29	Collagen induced arthritis QTL 29			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	33973921	78973921	Rat
1358897	Stresp6	Stress response QTL 6	4.17	0.022	blood norepinephrine amount (VT:0005663)	plasma norepinephrine level (CMO:0001010)	10	35392267	64155584	Rat
61441	Btemp1	Thermal response to stress QTL 1	4		body temperature trait (VT:0005535)	core body temperature (CMO:0001036)	10	35392457	63642539	Rat
2317042	Aia20	Adjuvant induced arthritis QTL 20	3.38		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	10	37565079	82565079	Rat
2317043	Aia7	Adjuvant induced arthritis QTL 7	3.82		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	10	37565079	82565079	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	40035094	102359817	Rat
631269	Cia22	Collagen induced arthritis QTL 22	8.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	40035094	104060283	Rat
631270	Cia23	Collagen induced arthritis QTL 23	3.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	40035094	104060283	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	41142633	86142633	Rat
61463	Bp12	Blood pressure QTL 12	6.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	41333258	86333258	Rat
8552805	Bw145	Body weight QTL 145	2.2		body mass (VT:0001259)	change in body weight to body weight ratio (CMO:0002216)	10	41944526	78307017	Rat
1298078	Stresp5	Stress response QTL 5	2.99	0.00025	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	42045676	104670812	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	42323132	87323132	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	42323132	87323132	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	42323132	87323132	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	42323132	87323132	Rat
70198	BpQTLcluster9	Blood pressure QTL cluster 9	2.94		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	42323132	87323132	Rat
6893342	Cm78	Cardiac mass QTL 78	0.1	0.88	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	10	42876766	79813922	Rat
9589030	Epfw9	Epididymal fat weight QTL 9	19.24	0.001	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	10	44441699	89441699	Rat
7411614	Foco18	Food consumption QTL 18		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	10	44441699	89441699	Rat
8694173	Bw149	Body weight QTL 149	4.38	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	10	44441699	89441699	Rat
2300218	Hpcl2	Hepatic cholesterol level QTL 2			liver cholesterol amount (VT:0010498)	liver cholesterol level (CMO:0001597)	10	45029650	95600334	Rat
631547	Bp87	Blood pressure QTL 87	4.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	47369470	92369470	Rat
2293705	Bmd25	Bone mineral density QTL 25	7.1	0.0001	femur mineral mass (VT:0010011)	cortical volumetric bone mineral density (CMO:0001730)	10	49444551	81709989	Rat
7207811	Bmd90	Bone mineral density QTL 90	5.2		femur size trait (VT:1000369)	femoral neck cross-sectional area (CMO:0001697)	10	49444551	81709989	Rat
2293652	Bmd22	Bone mineral density QTL 22	4.9	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	10	49444551	81709989	Rat
2293669	Bmd33	Bone mineral density QTL 33	4.5	0.0001	femur strength trait (VT:0010010)	femoral neck polar moment of inertia (CMO:0001670)	10	49444551	81709989	Rat
2293679	Bmd30	Bone mineral density QTL 30	3.5	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	10	49444551	81709989	Rat
1549846	Scl47	Serum cholesterol level QTL 47	3.6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	10	50574707	95574707	Rat
70364	Bp72	Blood pressure QTL 72			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	51121100	96121100	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	51770177	107211142	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	51770177	107211142	Rat
1359017	Hrtrt21	Heart rate QTL 21	2.4		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	10	51772940	96772940	Rat
631530	Tls3	T-lymphoma susceptibility QTL 3	0	0.0001	thymus integrity trait (VT:0010555)	percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)	10	51774612	95600334	Rat
631535	Cm51	Cardiac mass QTL 51	3		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	10	51786282	91669536	Rat
1578762	Toxo1	Toxoplasma gondii resistance QTL 1			brain integrity trait (VT:0010579)	percentage of study population displaying Toxoplasma gondii brain cysts at a point in time (CMO:0002028)	10	52200030	59378278	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	131
Count of miRNA genes:	102
Interacting mature miRNAs:	108
Transcripts:	ENSRNOT00000005255
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium		37	1						55	35	25	6
Low	3	6	52	37	19	37	8	11	19		16	5	8
Below cutoff			4	4		4

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053731	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006246567	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006246568	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AY028417	(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
	Y11353	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000005255 ⟹ ENSRNOP00000005255

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	52,899,934 - 53,085,326 (-)	Ensembl
Rnor_6.0 Ensembl	10	54,761,871 - 54,967,585 (-)	Ensembl

RefSeq Acc Id:

NM_053731 ⟹ NP_446183

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	52,903,477 - 53,084,319 (-)	NCBI
Rnor_6.0	10	54,761,997 - 54,967,671 (-)	NCBI
Rnor_5.0	10	54,507,464 - 54,725,989 (-)	NCBI
RGSC_v3.4	10	54,950,521 - 55,133,536 (-)	RGD
Celera	10	52,078,465 - 52,253,812 (-)	RGD

Sequence:

show sequence

ATGATGCGCGCTGTGTGGGAGGCGCTGGCGGCGCTGGCGGCGGTGGCGTGCCTGGTGGGCGCGG
TGCGCGGCGGGCCCGGGCTTAGCATGTTCGCCGGCCAGGCGGCGCAGCCTGATCCTTGCTCGGA
TGAGAACGGGCACCCACGCCGCTGCATCCCGGACTTTGTCAACGCGGCTTTCGGCAAGGACGTG
CGCGTGTCCAGCACCTGCGGCCGGCCCCCGGCGCGCTACTGCGTGGTGAGCGAGCGTGGCGAGG
AGCGGCTGCGCTCCTGTCACCTCTGCAACTCTTCCGATCCCAAGAAAGCGCATCCGCCCGCCTT
CCTCACCGACCTCAACAATCCGCACAACCTGACGTGCTGGCAGTCTGAGAACTACCTGCAGTTC
CCGCACAACGTTACGCTCACTCTGTCGCTCGGCAAGAAGTTTGAGGTGACCTATGTGAGCCTGC
AATTCTGCTCGCCCCGGCCAGAGTCCATGGCCATCTACAAGTCCATGGACTACGGGCGCACGTG
GGTGCCCTTCCAATTCTATTCCACTCAGTGCCGCAAAATGTACAACCGGCCGCACCGCGCGCCC
ATCACTAAGCAGAACGAGCAGGAGGCGGTGTGCACCGACTCGCACACCGACATGCGCCCGCTCT
CCGGCGGGCTGATCGCTTTCAGCACGCTGGACGGGCGGCCCTCGGCGCACGACTTCGACAACTC
GCCGGTGCTGCAGGACTGGGTCACCGCCACAGACATCCGCGTGGCTTTCAGCCGCCTGCACACG
TTTGGCGACGAGAACGAAGATGACTCGGAGCTGGCTCGCGACTCCTATTACTATGCAGTATCTG
ACCTGCAGGTTGGCGGCCGCTGCAAGTGCAATGGCCACGCGGCGCGTTGCGTGCGCGACCGAGA
CGACAGTCTGGTGTGTGACTGTAGGCACAACACGGCCGGCCCTGAATGCGACCGTTGCAAGCCC
TTCCACTACGATCGGCCCTGGCAGCGCGCCACGGCTCGCGAGGCCAACGAGTGCGTGGCCTGCA
ACTGCAACCTTCATGCTCGGCGCTGCAGATTCAACATGGAGCTTTACAAGCTATCAGGGCGCAA
GAGCGGGGGTGTCTGTCTCAACTGCCGCCACAACACTGCCGGCCGCCACTGCCACTACTGCAAG
GAGGGCTTCTACCGAGACATGGGCAAGCCTATCACCCACCGGAAGGCTTGCAAAGCCTGTGATT
GCCACCCTGTGGGTGCTGCTGGTAAGACCTGCAATCAAACCACCGGCCAGTGTCCCTGCAAGGA
CGGCGTGACAGGCATCACCTGCAACCGCTGTGCCAAAGGCTACCAGCAGAGCCGCTCCCCCATC
GCCCCTTGCATTAAGATTCCTGTAGCGCCACCCACCACTGCAGCCAGCAGCATGGAAGAACCTG
AAGACTGTGACTCCTACTGCAAGGCTTCCAAAGGAAAACTGAAGATGAACATGAAGAAATACTG
CAGGAAGGACTATGCTGTCCAGATCCACATTCTGAAGGCGGACAAAGCAGGGGACTGGTGGAAG
TTCACAGTGAACATCATCTCCGTGTACAAGCAGGGCACAAGTCGTATACGCCGTGGTGACCAGA
GTTTGTGGATCCGTTCGCGAGACATCGCTTGCAAGTGTCCCAAAATCAAGCCCCTCAAGAAGTA
CCTGCTGCTGGGCAATGCTGAGGACTCGCCTGACCAGAGTGGCATCGTGGCAGACAAGAGCAGC
CTGGTGATCCAGTGGCGGGACACATGGGCACGACGGCTGCGCAAGTTCCAGCAGCGGGAGAAGA
AGGGCAAGTGCAAGAAGGCCTAG

hide sequence

RefSeq Acc Id:

XM_006246567 ⟹ XP_006246629

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	52,899,933 - 53,085,124 (-)	NCBI
Rnor_6.0	10	54,761,925 - 54,968,438 (-)	NCBI
Rnor_5.0	10	54,507,464 - 54,725,989 (-)	NCBI

Sequence:

show sequence

GTGTGTGAGTGCGCGCCAGCGAGCGTGAGTGTGTGTGTGCGCCCCGGGCGCGGGCAGGGCAACA
CTCGGACCGCGGCGGGAGCCGGGCGGCTGCGTCGTCACTCAGTAGGAAGAGGCGGCGGCGGTGG
CGGCCGGGGCCGGGGCTAGGGCAGCGGCGGCCGTGCGGGGCATGGAGCTGGCAAGCCCGCGTTG
AGACAGGACGCTCCTGCTAGCGGCCAGCGAGAGGCTCTCTGCGGTCCGGCGCGCGGGCTCCCCG
GCTGGGGCCAGGCAAACTTTTCTTTCTCTTTTGCCATCACTTAGAGGCGTCTGGTGCGGCGGGC
GAACCGACTCCTCGGCGCGGCGCGGCCGGGGCAAGCTGGCCACGGCATGATGCGCGCTGTGTGG
GAGGCGCTGGCGGCGCTGGCGGCGGTGGCGTGCCTGGTGGGCGCGGTGCGCGGCGGGCCCGGGC
TTAGCATGTTCGCCGGCCAGGCGGCGCAGCCTGATCCTTGCTCGGATGAGAACGGGCACCCACG
CCGCTGCATCCCGGACTTTGTCAACGCGGCTTTCGGCAAGGACGTGCGCGTGTCCAGCACCTGC
GGCCGGCCCCCGGCGCGCTACTGCGTGGTGAGCGAGCGTGGCGAGGAGCGGCTGCGCTCCTGTC
ACCTCTGCAACTCTTCCGATCCCAAGAAAGCGCATCCGCCCGCCTTCCTCACCGACCTCAACAA
TCCGCACAACCTGACGTGCTGGCAGTCTGAGAACTACCTGCAGTTCCCGCACAACGTTACGCTC
ACTCTGTCGCTCGGCAAGAAGTTTGAGGTGACCTATGTGAGCCTGCAATTCTGCTCGCCCCGGC
CAGAGTCCATGGCCATCTACAAGTCCATGGACTACGGGCGCACGTGGGTGCCCTTCCAATTCTA
TTCCACTCAGTGCCGCAAAATGTACAACCGGCCGCACCGCGCGCCCATCACTAAGCAGAACGAG
CAGGAGGCGGTGTGCACCGACTCGCACACCGACATGCGCCCGCTCTCCGGCGGGCTGATCGCTT
TCAGCACGCTGGACGGGCGGCCCTCGGCGCACGACTTCGACAACTCGCCGGTGCTGCAGGACTG
GGTCACCGCCACAGACATCCGCGTGGCTTTCAGCCGCCTGCACACGTTTGGCGACGAGAACGAA
GATGACTCGGAGCTGGCTCGCGACTCCTATTACTATGCAGTATCTGACCTGCAGGTTGGCGGCC
GCTGCAAGTGCAATGGCCACGCGGCGCGTTGCGTGCGCGACCGAGACGACAGTCTGGTGTGTGA
CTGTAGGCACAACACGGCCGGCCCTGAATGCGACCGTTGCAAGCCCTTCCACTACGATCGGCCC
TGGCAGCGCGCCACGGCTCGCGAGGCCAACGAGTGCGTGGCCTGCAACTGCAACCTTCATGCTC
GGCGCTGCAGATTCAACATGGAGCTTTACAAGCTATCAGGGCGCAAGAGCGGGGGTGTCTGTCT
CAACTGCCGCCACAACACTGCCGGCCGCCACTGCCACTACTGCAAGGAGGGCTTCTACCGAGAC
ATGGGCAAGCCTATCACCCACCGGAAGGCTTGCAAAGCCTGTGATTGCCACCCTGTGGGTGCTG
CTGGTAAGACCTGCAATCAAACCACCGGCCAGTGTCCCTGCAAGGACGGCGTGACAGGCATCAC
CTGCAACCGCTGTGCCAAAGGCTACCAGCAGAGCCGCTCCCCCATCGCCCCTTGCATTAAGATT
CCTGTAGCGCCACCCACCACTGCAGCCAGCAGCATGGAAGAACCTGAAGACTGTGACTCCTACT
GCAAGGCTTCCAAAGGAAAACTGAAGATGAACATGAAGAAATACTGCAGGAAGGACTATGCTGT
CCAGATCCACATTCTGAAGGCGGACAAAGCAGGGGACTGGTGGAAGTTCACAGTGAACATCATC
TCCGTGTACAAGCAGGGCACAAGTCGTATACGCCGTGGTGACCAGAGTTTGTGGATCCGTTCGC
GAGACATCGCTTGCAAGTGTCCCAAAATCAAGCCCCTCAAGAAGTACCTGCTGCTGGGCAATGC
TGAGGACTCGCCTGACCAGAGTGGCATCGTGGCAGACAAGAGCAGCCTGGTGATCCAGTGGCGG
GACACATGGGCACGACGGCTGCGCAAGTTCCAGCAGCGGGAGAAGAAGGGCAAGTGCAAGAAGG
CCTAGCGTGGAGGTGGCGCAGGCTCCAGGAGGGCGGGCAGGGCGCTGGCAGGGGCTGGCAGCCT
TGGACTTGGCCCG

hide sequence

RefSeq Acc Id:

XM_006246568 ⟹ XP_006246630

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	52,899,933 - 53,098,591 (-)	NCBI
Rnor_6.0	10	54,761,925 - 54,982,072 (-)	NCBI
Rnor_5.0	10	54,507,464 - 54,725,989 (-)	NCBI

Sequence:

show sequence

GGGCAGGCGTAACACCACCTGGCGGAACCTGGGGGAAGAGTCTTAAAAGAGGGCGCTCCTCCGC
TCCCAGTGCAATCCAGCAGGATCTACCTAGTGCTCGCTTCCCTCCGATGCCCAGCAGTCGCGTC
CTCCCAATCCCAACCCTCCCACCTCAGGCGTCTGGTGCGGCGGGCGAACCGACTCCTCGGCGCG
GCGCGGCCGGGGCAAGCTGGCCACGGCATGATGCGCGCTGTGTGGGAGGCGCTGGCGGCGCTGG
CGGCGGTGGCGTGCCTGGTGGGCGCGGTGCGCGGCGGGCCCGGGCTTAGCATGTTCGCCGGCCA
GGCGGCGCAGCCTGATCCTTGCTCGGATGAGAACGGGCACCCACGCCGCTGCATCCCGGACTTT
GTCAACGCGGCTTTCGGCAAGGACGTGCGCGTGTCCAGCACCTGCGGCCGGCCCCCGGCGCGCT
ACTGCGTGGTGAGCGAGCGTGGCGAGGAGCGGCTGCGCTCCTGTCACCTCTGCAACTCTTCCGA
TCCCAAGAAAGCGCATCCGCCCGCCTTCCTCACCGACCTCAACAATCCGCACAACCTGACGTGC
TGGCAGTCTGAGAACTACCTGCAGTTCCCGCACAACGTTACGCTCACTCTGTCGCTCGGCAAGA
AGTTTGAGGTGACCTATGTGAGCCTGCAATTCTGCTCGCCCCGGCCAGAGTCCATGGCCATCTA
CAAGTCCATGGACTACGGGCGCACGTGGGTGCCCTTCCAATTCTATTCCACTCAGTGCCGCAAA
ATGTACAACCGGCCGCACCGCGCGCCCATCACTAAGCAGAACGAGCAGGAGGCGGTGTGCACCG
ACTCGCACACCGACATGCGCCCGCTCTCCGGCGGGCTGATCGCTTTCAGCACGCTGGACGGGCG
GCCCTCGGCGCACGACTTCGACAACTCGCCGGTGCTGCAGGACTGGGTCACCGCCACAGACATC
CGCGTGGCTTTCAGCCGCCTGCACACGTTTGGCGACGAGAACGAAGATGACTCGGAGCTGGCTC
GCGACTCCTATTACTATGCAGTATCTGACCTGCAGGTTGGCGGCCGCTGCAAGTGCAATGGCCA
CGCGGCGCGTTGCGTGCGCGACCGAGACGACAGTCTGGTGTGTGACTGTAGGCACAACACGGCC
GGCCCTGAATGCGACCGTTGCAAGCCCTTCCACTACGATCGGCCCTGGCAGCGCGCCACGGCTC
GCGAGGCCAACGAGTGCGTGGCCTGCAACTGCAACCTTCATGCTCGGCGCTGCAGATTCAACAT
GGAGCTTTACAAGCTATCAGGGCGCAAGAGCGGGGGTGTCTGTCTCAACTGCCGCCACAACACT
GCCGGCCGCCACTGCCACTACTGCAAGGAGGGCTTCTACCGAGACATGGGCAAGCCTATCACCC
ACCGGAAGGCTTGCAAAGCCTGTGATTGCCACCCTGTGGGTGCTGCTGGTAAGACCTGCAATCA
AACCACCGGCCAGTGTCCCTGCAAGGACGGCGTGACAGGCATCACCTGCAACCGCTGTGCCAAA
GGCTACCAGCAGAGCCGCTCCCCCATCGCCCCTTGCATTAAGATTCCTGTAGCGCCACCCACCA
CTGCAGCCAGCAGCATGGAAGAACCTGAAGACTGTGACTCCTACTGCAAGGCTTCCAAAGGAAA
ACTGAAGATGAACATGAAGAAATACTGCAGGAAGGACTATGCTGTCCAGATCCACATTCTGAAG
GCGGACAAAGCAGGGGACTGGTGGAAGTTCACAGTGAACATCATCTCCGTGTACAAGCAGGGCA
CAAGTCGTATACGCCGTGGTGACCAGAGTTTGTGGATCCGTTCGCGAGACATCGCTTGCAAGTG
TCCCAAAATCAAGCCCCTCAAGAAGTACCTGCTGCTGGGCAATGCTGAGGACTCGCCTGACCAG
AGTGGCATCGTGGCAGACAAGAGCAGCCTGGTGATCCAGTGGCGGGACACATGGGCACGACGGC
TGCGCAAGTTCCAGCAGCGGGAGAAGAAGGGCAAGTGCAAGAAGGCCTAGCGTGGAGGTGGCGC
AGGCTCCAGGAGGGCGGGCAGGGCGCTGGCAGGGGCTGGCAGCCTTGGACTTGGCCCG

hide sequence

Protein Sequences


Protein RefSeqs	NP_446183	(Get FASTA)	NCBI Sequence Viewer
	XP_006246629	(Get FASTA)	NCBI Sequence Viewer
	XP_006246630	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAK17014	(Get FASTA)	NCBI Sequence Viewer
	CAA72188	(Get FASTA)	NCBI Sequence Viewer
	EDM04807	(Get FASTA)	NCBI Sequence Viewer
	EDM04808	(Get FASTA)	NCBI Sequence Viewer
	Q924Z9	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_446183 ⟸ NM_053731

- Peptide Label:

precursor

- Sequence:

show sequence

MMRAVWEALAALAAVACLVGAVRGGPGLSMFAGQAAQPDPCSDENGHPRRCIPDFVNAAFGKDV
RVSSTCGRPPARYCVVSERGEERLRSCHLCNSSDPKKAHPPAFLTDLNNPHNLTCWQSENYLQF
PHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGRTWVPFQFYSTQCRKMYNRPHRAP
ITKQNEQEAVCTDSHTDMRPLSGGLIAFSTLDGRPSAHDFDNSPVLQDWVTATDIRVAFSRLHT
FGDENEDDSELARDSYYYAVSDLQVGGRCKCNGHAARCVRDRDDSLVCDCRHNTAGPECDRCKP
FHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCK
EGFYRDMGKPITHRKACKACDCHPVGAAGKTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPI
APCIKIPVAPPTTAASSMEEPEDCDSYCKASKGKLKMNMKKYCRKDYAVQIHILKADKAGDWWK
FTVNIISVYKQGTSRIRRGDQSLWIRSRDIACKCPKIKPLKKYLLLGNAEDSPDQSGIVADKSS
LVIQWRDTWARRLRKFQQREKKGKCKKA

hide sequence

RefSeq Acc Id:

XP_006246630 ⟸ XM_006246568

- Peptide Label:

isoform X1

- Sequence:

show sequence

MMRAVWEALAALAAVACLVGAVRGGPGLSMFAGQAAQPDPCSDENGHPRRCIPDFVNAAFGKDV
RVSSTCGRPPARYCVVSERGEERLRSCHLCNSSDPKKAHPPAFLTDLNNPHNLTCWQSENYLQF
PHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGRTWVPFQFYSTQCRKMYNRPHRAP
ITKQNEQEAVCTDSHTDMRPLSGGLIAFSTLDGRPSAHDFDNSPVLQDWVTATDIRVAFSRLHT
FGDENEDDSELARDSYYYAVSDLQVGGRCKCNGHAARCVRDRDDSLVCDCRHNTAGPECDRCKP
FHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCK
EGFYRDMGKPITHRKACKACDCHPVGAAGKTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPI
APCIKIPVAPPTTAASSMEEPEDCDSYCKASKGKLKMNMKKYCRKDYAVQIHILKADKAGDWWK
FTVNIISVYKQGTSRIRRGDQSLWIRSRDIACKCPKIKPLKKYLLLGNAEDSPDQSGIVADKSS
LVIQWRDTWARRLRKFQQREKKGKCKKA

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RefSeq Acc Id:

XP_006246629 ⟸ XM_006246567

- Peptide Label:

isoform X1

- Sequence:

show sequence

MMRAVWEALAALAAVACLVGAVRGGPGLSMFAGQAAQPDPCSDENGHPRRCIPDFVNAAFGKDV
RVSSTCGRPPARYCVVSERGEERLRSCHLCNSSDPKKAHPPAFLTDLNNPHNLTCWQSENYLQF
PHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGRTWVPFQFYSTQCRKMYNRPHRAP
ITKQNEQEAVCTDSHTDMRPLSGGLIAFSTLDGRPSAHDFDNSPVLQDWVTATDIRVAFSRLHT
FGDENEDDSELARDSYYYAVSDLQVGGRCKCNGHAARCVRDRDDSLVCDCRHNTAGPECDRCKP
FHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCK
EGFYRDMGKPITHRKACKACDCHPVGAAGKTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPI
APCIKIPVAPPTTAASSMEEPEDCDSYCKASKGKLKMNMKKYCRKDYAVQIHILKADKAGDWWK
FTVNIISVYKQGTSRIRRGDQSLWIRSRDIACKCPKIKPLKKYLLLGNAEDSPDQSGIVADKSS
LVIQWRDTWARRLRKFQQREKKGKCKKA

hide sequence

RefSeq Acc Id:

ENSRNOP00000005255 ⟸ ENSRNOT00000005255

Protein Domains

Laminin EGF-like Laminin N-terminal NTR

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 (2019)

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

ACI/EurMcwi (MCW)

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

ACI/EurMcwi (RGD)

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

ACI/N (2020)

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

ACI/N (MCW)

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

BBDP/Wor (RGD)

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

BN-Lx/CubMcwi (2019)

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

BN/NHsdMcwi (2019)

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

BN/NHsdMcwi (2020)

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

BN/SsN (2020)

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

BN/SsN (MCW)

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

BUF/N (2020)

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

BXH2/CubMcwi (2020)

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

BXH3/CubMcwi (2020)

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

Buf/N (MCW)

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

COP/CrCrl (MCW & UW)

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

DA/OlaHsd (2019)

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

F344/DuCrl (2019)

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

F344/N (2020)

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

F344/NCrl (2019)

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

F344/NCrl (RGD)

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

F344/NRrrc (MCW)

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

F344/Stm (2019)

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

FHH/EurMcwi (2019)

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

FHH/EurMcwi (MCW)

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

FHH/EurMcwi (RGD)

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

FHL/EurMcwi (MCW)

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

FHL/EurMcwi (RGD)

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

FXLE16/Stm (2020)

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

FXLE18/Stm (2020)

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

GH/OmrMcwi (MCW)

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

GK/FarMcwi (2019)

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

GK/Ox (RGD)

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

HXB10/IpcvMcwi (2019)

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

HXB2/IpcvMcwi (2019)

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

HXB20/IpcvMcwi (2020)

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

HXB31/IpcvMcwi (2019)

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

HXB4/IpcvMcwi (2020)

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

LE/Stm (2019)

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

LE/Stm (RGD)

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

LEW/Crl (2019)

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

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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

LEXF10A/StmMcwi (2020)

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

LEXF11/Stm (2020)

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

LEXF1A/Stm (2019)

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

LEXF1C/Stm (2019)

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

LEXF2B/Stm (2019)

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

LEXF3/Stm (2020)

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

LEXF4/Stm (2020)

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

LH/MavRrrc (RGD)

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

LH/MavRrrcAek (2020)

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

LL/MavRrrc (RGD)

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

LL/MavRrrcAek (2020)

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

LN/MavRrrc (RGD)

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

LN/MavRrrcAek (2020)

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

M520/N (2020)

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

M520/N (MCW)

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

M520/NRrrcMcwi (2019)

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

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (2020)

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

MR/N (MCW)

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

MWF/Hsd (2019)

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

PVG/Seac (2019)

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHR/OlalpcvMcwi (2019)

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

SHRSP/A3NCrl (2019)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (2020)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (2019)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WAG/RijCrl (2020)

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

WKY/Gcrc (RGD)

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

WKY/N (2020)

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

WKY/N (MCW)

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

WKY/NCrl (2019)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (2020)

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

WN/N (MCW)

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:619809	AgrOrtholog
Ensembl Genes	ENSRNOG00000003947	Ensembl, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000005255	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000005255	UniProtKB/TrEMBL
Gene3D-CATH	2.40.50.120	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	Galactose-bd-like_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Laminin_EGF	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Laminin_N	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Netrin_domain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Netrin_module_non-TIMP	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	TIMP-like_OB-fold	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene	114523	ENTREZGENE
Pfam	Laminin_EGF	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Laminin_N	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	NTR	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Ntn1	PhenoGen
PROSITE	EGF_1	UniProtKB/Swiss-Prot
	EGF_LAM_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	EGF_LAM_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	LAMININ_NTER	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	NTR	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	C345C	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	EGF_Lam	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	LamNT	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF49785	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF50242	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	F1LPC8_RAT	UniProtKB/TrEMBL
	NET1_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2004-02-26	Ntn1	netrin 1			Symbol and Name status set to approved	625702	APPROVED
2002-08-07	Ntn1	netrin 1			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expressed in spinal inteneurons, motoneurons, and oligodendrocytes in the adult spinal cord	633501

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)

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Imported Disease Annotations - OMIM

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