Lypd6 (LY6/PLAUR domain containing 6)

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Gene: Lypd6 (LY6/PLAUR domain containing 6) Rattus norvegicus

Analyze

Symbol:

Lypd6

Name:

LY6/PLAUR domain containing 6

RGD ID:

1587119

Description:

Exhibits acetylcholine receptor inhibitor activity. Predicted to be involved in negative regulation of signaling receptor activity and regulation of neurotransmitter receptor activity. Localizes to membrane and neuron projection. Orthologous to human LYPD6 (LY6/PLAUR domain containing 6); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acrylamide.

Type:

protein-coding

RefSeq Status:

MODEL

Also known as:

hypothetical protein LOC679564; LOC679564; LY6/PLAUR domain containing 6B-like; ly6/PLAUR domain-containing protein 6; uncharacterized protein LOC679564

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):	LYPD6 (LY6/PLAUR domain containing 6)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Lypd6 (LY6/PLAUR domain containing 6)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Lypd6 (LY6/PLAUR domain containing 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LYPD6 (LY6/PLAUR domain containing 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LYPD6 (LY6/PLAUR domain containing 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Lypd6 (LY6/PLAUR domain containing 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LYPD6 (LY6/PLAUR domain containing 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	LYPD6 (LY6/PLAUR domain containing 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Lypd6 (LY6/PLAUR domain containing 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	LYPD6 (LY6/PLAUR domain containing 6)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Lypd6 (LY6/PLAUR domain containing 6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	lypd6 (LY6/PLAUR domain containing 6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

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	3	34,487,222 - 34,632,887 (+)	NCBI
Rnor_6.0 Ensembl	3	35,679,750 - 35,707,410 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	3	35,566,956 - 35,707,416 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	40,681,330 - 40,821,870 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	31,121,163 - 31,145,542 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	3	32,671,498 - 32,812,614 (+)	NCBI		Celera
Cytogenetic Map	3	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-epigallocatechin 3-gallate (ISO)

1,2-dichloroethane (ISO)

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

4,4'-sulfonyldiphenol (ISO)

6-propyl-2-thiouracil (EXP)

acrylamide (EXP)

all-trans-retinoic acid (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

butanal (ISO)

carbon nanotube (ISO)

chromium(6+) (ISO)

cobalt dichloride (ISO)

coumestrol (ISO)

dibutyl phthalate (ISO)

dorsomorphin (ISO)

ethanol (ISO)

methapyrilene (ISO)

nickel atom (ISO)

nickel sulfate (ISO)

phenylmercury acetate (ISO)

potassium chromate (ISO)

resveratrol (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenite (ISO)

sulforaphane (ISO)

sunitinib (ISO)

trichostatin A (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

negative regulation of signaling receptor activity (IEA)

positive regulation of canonical Wnt signaling pathway (IBA)

regulation of neurotransmitter receptor activity (IEA)

Cellular Component

anchored component of membrane (IEA)

cytoplasm (IEA)

extracellular region (IEA)

membrane (IDA)

membrane raft (IEA)

neuron projection (IDA)

plasma membrane (IEA)

synapse (IEA)

Molecular Function

acetylcholine receptor inhibitor activity (IBA,IDA,ISO)

acetylcholine receptor regulator activity (IBA,ISO)

protein binding (ISO)

References

References - curated


1.	Arvaniti M, etal., J Neurochem. 2016 Sep;138(6):806-20. doi: 10.1111/jnc.13718. Epub 2016 Aug 15.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:19403274

Genomics

Comparative Map Data

Lypd6
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	34,487,222 - 34,632,887 (+)	NCBI
Rnor_6.0 Ensembl	3	35,679,750 - 35,707,410 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	3	35,566,956 - 35,707,416 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	40,681,330 - 40,821,870 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	31,121,163 - 31,145,542 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	3	32,671,498 - 32,812,614 (+)	NCBI		Celera
Cytogenetic Map	3	q12	NCBI

LYPD6
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	2	149,329,985 - 149,474,138 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	2	149,329,985 - 149,474,138 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	2	150,186,499 - 150,330,652 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	149,895,359 - 150,038,384 (+)	NCBI	NCBI36		hg18	NCBI36
Celera	2	143,801,045 - 143,944,084 (+)	NCBI
Cytogenetic Map	2	q23.2	NCBI
HuRef	2	142,085,359 - 142,229,514 (+)	NCBI		HuRef
CHM1_1	2	150,192,385 - 150,336,592 (+)	NCBI		CHM1_1

Lypd6
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	49,956,413 - 50,083,581 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	2	49,956,441 - 50,083,581 (+)	Ensembl
GRCm38	2	50,066,400 - 50,193,569 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	50,066,429 - 50,193,569 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	49,921,982 - 50,049,084 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	2	49,950,379 - 50,015,573 (+)	NCBI			mm8
Celera	2	51,740,447 - 51,866,771 (+)	NCBI		Celera
Cytogenetic Map	2	C1.1	NCBI

Lypd6
(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_004955440	15,197,259 - 15,249,407 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955440	15,178,436 - 15,248,791 (+)	NCBI	ChiLan1.0	ChiLan1.0

LYPD6
(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	2B	153,685,720 - 153,828,297 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2B	153,792,413 - 153,828,297 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	2B	10,392,962 - 10,536,125 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

LYPD6
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	19	51,041,219 - 51,067,333 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	19	51,007,147 - 51,069,110 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Lypd6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936469	27,853,111 - 27,992,627 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LYPD6
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	15	2,579,619 - 2,696,153 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	15	2,011,800 - 2,127,992 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LYPD6
(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	10	34,762,531 - 34,912,386 (+)	NCBI
ChlSab1.1 Ensembl	10	34,875,203 - 34,912,737 (+)	Ensembl

Lypd6
(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_004624866	2,103,744 - 2,253,459 (+)	NCBI

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
4889966	Bss95	Bone structure and strength QTL 95	4.4		tibia area (VT:1000281)	tibia-fibula cross-sectional area (CMO:0001718)	3	1	37891710	Rat
2312664	Scl62	Serum cholesterol level QTL 62		0.05	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	1	39773425	Rat
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	95176874	Rat
10401810	Kidm53	Kidney mass QTL 53			kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	2631421	48562146	Rat
70191	BpQTLcluster4	Blood pressure QTL cluster 4	3		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	3	6000748	51687917	Rat
70191	BpQTLcluster4	Blood pressure QTL cluster 4	3		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	3	6000748	51687917	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	10094081	93415837	Rat
2298542	Neuinf11	Neuroinflammation QTL 11	3.9		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	3	10119318	79772001	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	heart rate (CMO:0000002)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	heart rate (CMO:0000002)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	body weight (CMO:0000012)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	body weight (CMO:0000012)	3	13126914	36600143	Rat
631568	Bp92	Blood pressure QTL 92	2.2	0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	13126914	41510346	Rat
731172	Bp151	Blood pressure QTL 151		0.04	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14090411	48562146	Rat
12879849	Bw180	Body weight QTL 180		0.037	body mass (VT:0001259)	body weight (CMO:0000012)	3	14090411	48562146	Rat
12879850	Cm91	Cardiac mass QTL 91		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	3	14090411	48562146	Rat
12879851	Cm92	Cardiac mass QTL 92		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	14090411	48562146	Rat
12879852	Cm93	Cardiac mass QTL 93		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	3	14090411	48562146	Rat
12879853	Am5	Aortic mass QTL 5		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	3	14090411	48562146	Rat
12879854	Kidm63	Kidney mass QTL 63		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	14090411	48562146	Rat
631676	Cm8	Cardiac mass QTL 8	7.03	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	3	18023664	63023664	Rat
10450794	Scl69	Serum cholesterol level QTL 69	6.3	0.001	blood LDL cholesterol amount (VT:0000181)	blood low density lipoprotein cholesterol level (CMO:0000053)	3	21223803	66223803	Rat
10450804	Scl70	Serum cholesterol level QTL 70	4.7	0.001	blood LDL cholesterol amount (VT:0000181)	blood low density lipoprotein cholesterol level (CMO:0000053)	3	21223803	66223803	Rat
631685	Bp118	Blood pressure QTL 118	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	24655225	69655225	Rat
1298073	Cm13	Cardiac mass QTL 13	2.5		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	25633366	39248391	Rat
631832	Sach1	Saccharin preference QTL 1	2.7	0.02	consumption behavior trait (VT:0002069)	calculated saccharin drink intake volume (CMO:0001600)	3	28136728	45772990	Rat
2313049	Bss72	Bone structure and strength QTL 72	2.6	0.0001	tibia area (VT:1000281)	tibia midshaft cross-sectional area (CMO:0001717)	3	28136728	51687917	Rat
2313076	Bss74	Bone structure and strength QTL 74	2	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	3	28136728	51687917	Rat
2313079	Bss73	Bone structure and strength QTL 73	1.5		tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	3	28136728	51687917	Rat
2313093	Bmd77	Bone mineral density QTL 77	2.2	0.0001	tibia mineral mass (VT:1000283)	cortical volumetric bone mineral density (CMO:0001730)	3	28136728	51687917	Rat
2313101	Bmd76	Bone mineral density QTL 76	3.6	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	3	28136728	51687917	Rat
2302055	Pia30	Pristane induced arthritis QTL 30	3.5	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)	3	29321714	74321714	Rat
9590286	Uminl1	Urine mineral level QTL 1	3.5	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	3	29682732	74682732	Rat
9590136	Scort3	Serum corticosterone level QTL 3	23.37	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	29682732	74682732	Rat
8552950	Pigfal12	Plasma insulin-like growth factor 1 level QTL 12	7.3		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	3	29682732	74682732	Rat
8694196	Abfw2	Abdominal fat weight QTL 2	16.58	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	3	29682732	74682732	Rat
8694386	Bw159	Body weight QTL 159	4.52	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	3	29682732	74682732	Rat
1354590	Despr11	Despair related QTL 11		0.000031	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	3	29908255	74908255	Rat
2303593	Gluco46	Glucose level QTL 46	3		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	29908255	74908255	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	30114912	123700444	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	30846101	172879276	Rat
2301400	Cm68	Cardiac mass QTL 68		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	3	31103589	72989078	Rat
11565451	Bw177	Body weight QTL 177		0.002	body mass (VT:0001259)	body weight (CMO:0000012)	3	31103589	72989078	Rat
11565452	Kidm57	Kidney mass QTL 57		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	31103589	72989078	Rat
12879866	Cm94	Cardiac mass QTL 94		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	31103589	72989078	Rat
12879867	Cm95	Cardiac mass QTL 95		0.047	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	3	31103589	72989078	Rat
12879868	Am6	Aortic mass QTL 6		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	3	31103589	72989078	Rat
61356	Bp37	Blood pressure QTL 37	3		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	3	32130997	77130997	Rat
631647	Bp122	Blood pressure QTL 122	6.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	32130997	77130997	Rat
1300169	Bp177	Blood pressure QTL 177	2.96		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	3	33477354	62922975	Rat
1354589	Bw31	Body weight QTL 31	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	3	33477354	81136227	Rat
1354604	Bw36	Body weight QTL 36	2.9		body mass (VT:0001259)	body weight (CMO:0000012)	3	33477354	108914061	Rat
61419	Cia11	Collagen induced arthritis QTL 11	5.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	3	34394121	103141944	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	105
Count of miRNA genes:	88
Interacting mature miRNAs:	93
Transcripts:	ENSRNOT00000059588
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									39	18	10
Low	3	24	21	6	8	6	1	1	35	17	23	1	1
Below cutoff		10	15	14	11	14	6	7			7	10	6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_006234160	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039106250	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473983	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000115	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000059588 ⟹ ENSRNOP00000056346

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	35,679,750 - 35,707,410 (+)	Ensembl

RefSeq Acc Id:

XM_001053512 ⟹ XP_001053512

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	3	35,679,202 - 35,707,416 (+)	NCBI
Rnor_5.0	3	40,681,330 - 40,821,870 (+)	NCBI
RGSC_v3.4	3	31,121,163 - 31,145,542 (+)	RGD

Sequence:

show sequence

GGGTCCAGCATCTGTGTGCGTTTGAAATGCAGAACTGAAAGCTCCACTGTGCCAATCCTCTACC
ACGGTCTCAAGTGCCCCCTCTGAGGCCCTCTGTATGAGTGACACGCCAGTCGGCCATGGAACCC
AGCCCTGCCCTGGCCTGGCTCCTGCTGCTGAGCCTGGTGGCCGACTGTCTGAAAGCTGCCCAGT
CCCGAGACTTCACAGTGAAAGACATCATCTACCTCCATCCTTCAACCACTCCATATCCTGGTGG
ATTTAAATGTTTCACCTGTGAAAAAGCAGCAGACAATTATGAATGCAACCGATGGGCTCCTGAC
ATCTACTGTCCTCGAGACACCAGATACTGCTACACTCAGCACACGATGGAAGTCACAGGGAATA
GCATCTCTGTTACCAAACGCTGTGTCCCACTGGAGGAGTGCTTATCCACAGGCTGCCGAGACTC
GGAGCATGAAGGCTACAAGATCTGCACCTCCTGCTGTGAAGGAAATATCTGTAATCTACCGCTC
CCTCGAAATGACACTGATGCCACATTTGCCACCACGTCCCCTATAAACCAGACAAACGGGCACC
CACACTGTGTGTCAGTGATTGTGTCCTGCTTGTGGGTGTGGCTGGGACTCACCTTATAGTAACC
CTCCCTACCCAATGTAGGTGAGCTCTGTGGTTTCACCGTGGCCATAGTCATGCATGAGTCATCA
GCTTGGCAGCAGCGACACAATGCAACCACAGCACCCCGAGACGTCATCACAGCCAGCCATTACC
ATTCCTATGAAGAGCAAGCATTGCTCCCTCCCGTGCTGTCATTTCCAGCCTAACCACAACCCCG
CCTGAGTCAGCCTGTCCCCGATACGGACCCTGATTCTTACACCACGAACCTGTTATTTCGCTCC
AAGAAAGACCTCTGCTTTTATTGATGTCTGGGGTTCCTGCTTCAGCATCCATGCCTGAGCTGCA
GGAGGTCCTGGGCCCTCTGAAGAATAAGCTATGGATACAGGAGATATTCATTCTCCTCAGGAAA
AGAGTAAAGAACCATTGGTTTCATTGCAACCACACCTGCACCTAGAGCTTTAGAAGTTTAAAAC
TAAATCCAAAATAAATGGAATCGTTTCTTTGAGATTCTGATGGAGTCCCCGAAAGAGCAGAAAG
AGCTTTGCTCGATTTAATTTCCCCAGCCTTCTTATCTTAACATTGGGAAACATGTTCCTTCTGC
TCTTTGTAGAAGATTAAAAAAAAAAGCAATTATAAAAGTTTGCCGTATTTGTAGGAGTGAAAAG
AGAACAATTTCCTTCAACTTGATGAAATTAGCATCCTCAAGATGACGTTATCCCTTCTTGTAAC
TGAACAGATTGGCCTTGACTCGGGAACTAATTATGCTTCCCGAGTTCCCGGATTCCAGGTGGAC
CAGTAGCATCTAAAAAGTTACTAAATGAATGGGATGATTTTCTCCAGGTGTTGCATTCCATTCA
GATATAGCTGATCTCGTCAGAGAGAGGACTTCAGAATAAAAGGAAGCTCTGTGGAGGTTAGTCC
TAGTTCATTTTGAAGGCTCAGAAATGGCTAAGCAAAAGTCTTTCTCTTTCCATAGTATTTACTG
CCAAAGAGCTGTCTCCTTCCACAATCACAGTGACTTGAAAGAGAAAGTTCTGAGCTAAATTCTC
ATTAGATCAATAAGATAAGAGCACACCTGTGCTAGAATAAGAAAAAGATGGATCGTAAGTAGTA
CGGTGGCCTAAGATTTGTTTCTCTCAGTTACCGTTTTTGAAGTAGAAGGAAAGGCTTTTATTGT
CCGTGTATTTTTTTTAACCTATGAAGTTGCATAGTTGTTTTCTTCTCCCATGTAAATTCTTTAA
ATGACATTTATTTTTGTATGGTATAAACTGAAAACTATATTTCAAAAAAAATTCTTTTCTTTTT
CTCCACAAAGTATCAGTTAGAATGCTCGCTTTCAACAGCGGGAGGAATTGTCATCACTCCTGAT
CATGGGAAGTTATCTGTGATCCTAGGACTGATGCTGAAAAAAATTATTGCTATGAACAAGAGTT
GTGCATTTGCCTCAAGGGTTTGCCTCATTGTCTCCTCAGAAAGGTTGCCCGAGAAATATTAGGG
TGAAGGCCATCACTGGTGTGACCGTCTTTGCAGGGCTGTGGGGTGTGTCCACAGGGAACTGGGC
GGAGCTATGTCTCCAAGAGGTCAATGATGTTAAAATATATCTGCCCTGCACAGAGAACTTTAGC
TTAAATGAGACTCCCCCACCCCCTCAGGGACCAAATCTGAACTGAGGGCAGAAACTCTGATGCA
AATCATTGACGTTGCATCACACAGCCTTAATGAAGAGTTTGACAGGCGTATCAATTTCTTGCTT
ATGACTGCAGATGGGAGAGCAGGAGAGAACGACCTGTAGTAAGCACCTCTTATGTGCCCGGCAC
TTTGCTAAGCACTTTACATAGTTAGGCCATATAACCCTACATCAATTCTGTAAGGACAGAACCT
ATTGATGTGTACACATGAAGGTCCCAAGGCTCAAGGAAGTTTGATAAATGAAGCCTTTTCCTTC
AGATTTAGTTTATGTGGGATGCGACATGTTTGGGAGAAAAAAAAACGGGGGAGGGGGGATGGAA
TTTCTCAGCTAGGAAAAACTCTAGGCCTGACTTCATGGGAATTTCCCCCATCCTATCATATAGA
ACGTATCCTGCTTCTCAGGATGACATTTGCATGTGTCCCCAGTTGTCACTTTTCCTTTGGGGAG
TAAAGTTATAGCTTCCTTATTTATCCTCTCGTACAGAGAGGAGGTAGTTGACCTTGCATCTAAA
GATGCTCTAAGACAATGAGAATTTGATGTCGTACATGTCTGCAAGTACTGTTTTTGTGCATGGC
CACATTCCACTGACATTTGCCAAGTCTGCATGCAATCAGAACAAGAGACAAGGGACTGACCATA
CGAGAGCCTCCCTGCCTGGTTTTCAGGGATTGGATCTCAAGGGTACAGACTGTCCTCACCTGGG
GAGTAATGGCAGCCATTGTACACGTGTGCTGCATACGTCCATAATGCCTTTCAAAGTGTCTTTT
TCATTCTCTTGAAAGAGCGTGGATTTGCTCACCACCCCCAGCACCAAGAAACCAAGGTGGGACC
ATTCATGTTGAAGGTCCAGGACTAGTTACCCATGTGACTGTAGTCACTTTAAACTTTCCATTAA
ACCTCACCATTGGTGATGGCTTACAGTGCAAAGAGCCATGATGTGTATATTAACCTATGCTCTA
CATATTTATTTTTAGACTTTCTTCAGCATCCATGTTAGTATGGGATCGATGCCTATATGTAAAT
ATTGTACACTTTGTAAATCAATGAATAAAGATTTTAAGTGTCTTTCATTAGGCTTCTTCCTGCA
AGTGTGTATGTCAATGATTAATATATCAGGTATGGGCTTAGCACCACAGTGGGTTTCTTTCCAT
CACCTACTTTCCAGATATGTCAAGAAATACACACATTAAAGAGACTCATCCCAAATGGTTCATA
CAGGTGATGAGTGCTCCAAAAATAAAAGAAGAGGTTGTCAGACTGTT

hide sequence

RefSeq Acc Id:

XM_003753721 ⟹ XP_003753769

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Celera	3	32,784,395 - 32,812,614 (+)	NCBI

Sequence:

show sequence

GGGTCCAGCATCTGTGTGCGTTTGAAATGCAGAACTGAAAGCTCCACTGTGCCAATCCTCTACC
ACGGTCTCAAGTGCCCCCTCTGAGGCCCTCTGTATGAGTGACACGCCAGTCGGCCATGGAACCC
AGCCCTGCCCTGGCCTGGCTCCTGCTGCTGAGCCTGGTGGCCGACTGTCTGAAAGCTGCCCAGT
CCCGAGACTTCACAGTGAAAGACATCATCTACCTCCATCCTTCAACCACTCCATATCCTGGTGG
ATTTAAATGTTTCACCTGTGAAAAAGCAGCAGACAATTATGAATGCAACCGATGGGCTCCTGAC
ATCTACTGTCCTCGAGACACCAGATACTGCTACACTCAGCACACGATGGAAGTCACAGGGAATA
GCATCTCTGTTACCAAACGCTGTGTCCCACTGGAGGAGTGCTTATCCACAGGCTGCCGAGACTC
GGAGCATGAAGGCTACAAGATCTGCACCTCCTGCTGTGAAGGAAATATCTGTAATCTACCGCTC
CCTCGAAATGACACTGATGCCACATTTGCCACCACGTCCCCTATAAACCAGACAAACGGGCACC
CACACTGTGTGTCAGTGATTGTGTCCTGCTTGTGGGTGTGGCTGGGACTCACCTTATAGTAACC
CTCCCTACCCAATGTAGGTGAGCTCTGTGGTTTCACCGTGGCCATAGTCATGCATGAGTCATCA
GCTTGGCAGCAGCGACACAATGCAACCACAGCACCCCGAGACGTCATCACAGCCAGCCATTACC
ATTCCTATGAAGAGCAAGCATTGCTCCCTCCCGTGCTGTCATTTCCAGCCTAACCACAACCCCG
CCTGAGTCAGCCTGTCCCCGATACGGACCCTGATTCTTACACCACGAACCTGTTATTTCGCTCC
AAGAAAGACCTCTGCTTTTATTGATGTCTGGGGTTCCTGCTTCAGCATCCATGCCTGAGCTGCA
GGAGGTCCTGGGCCCTCTGAAGAATAAGCTATGGATACAGGAGATATTCATTCTCCTCAGGAAA
AGAGTAAAGAACCATGGTTTCATTGCAACCACACCTGCACCTAGAGCTTTAGAAGTTTAAAACT
AAATCCAAAATAAATGGAATCGTTTCTTTGAGATTCTGATGGAGTCCCCGAAAGAGCAGAAAGA
GCTTTGCTCGATTTAATTTCCCCAGCCTTCTTATCTTAACATTGGGAAACATGTTCCTTCTGCT
CTTTGTAGAAGATTAAAAAAAAAAGCAATTATAAAAGTTTGCCGTATTTGTAGGAGTGAAAAGA
GAACAATTTCCTTCAACTTGATGAAATTAGCATCCTCAAGATGACGTTATCCCTTCTTGTAACT
GAACAGATTGGCCTTGACTCGGGAACTAATTATGCTTCCCGAGTTCCCGGATTCCAGGTGGACC
AGTAGCATCTAAAAAGTTACTAAATGAATGGGATGATTTTCTCCAGGTGTTGCATTCCATTCAG
ATATAGCTGATCTCGTCAGAGAGAGGACTTCAGAATAAAAGGAAGCTCTGTGGAGGTTAGTCCT
AGTTCATTTTGAAGGCTCAGAAATGGCTAAGCAAAAGTCTTTCTCTTTCCATAGTATTTACTGC
CAAAGAGCTGTCTCCTTCCACAATCACAGTGACTTGAAAGAGAAAGTTCTGAGCTAAATTCTCA
TTAGATCAATAAGATAAGAGCACACCTGTGCTAGAATAAGAAAAAGATGGATCGTAAGTAGTAC
GGTGGCCTAAGATTTGTTTCTCTCAGTTACCGTTTTTGAAGTAGAAGGAAAGGCTTTTATTGTC
CGTGTATTTTTTTTAACCTATGAAGTTGCATAGTTGTTTTCTTCTCCCATGTAAATTCTTTAAA
TGACATTTATTTTTGTATGGTATAAACTGAAAACTATATTTCAAAAAAAATTCTTTTCTTTTTC
TCCACAAAGTATCAGTTAGAATGCTCGCTTTCAACAGCGGGAGGAATTGTCATCACTCCTGATC
ATGGGAAGTTATCTGTGATCCTAGGACTGATGCTGAAAAAAATTATTGCTATGAACAAGAGTTG
TGCATTTGCCTCAAGGGTTTGCCTCATTGTCTCCTCAGAAAGGTTGCCCGAGAAATATTAGGGT
GAAGGCCATCACTGGTGTGACCGTCTTTGCAGGGCTGTGGGGTGTGTCCACAGGGAACTGGGCG
GAGCTATGTCTCCAAGAGGTCAATGATGTTAAAATATATCTGCCCTGCACAGAGAACTTTAGCT
TAAATGAGACTCCCCCACCCCCTCAGGGACCAAATCTGAACTGAGGGCAGAAACTCTGATGCAA
ATCATTGACGTTGCATCACACAGCCTTAATGAAGAGTTTGACAGGCGTATCAATTTCTTGCTTA
TGACTGCAGATGGGAGAGCAGGAGAGAACGACCTGTAGTAAGCACCTCTTATGTGCCCGGCACT
TTGCTAAGCACTTTACATAGTTAGGCCATATAACCCTACATCAATTCTGTAAGGACAGAACCTA
TTGATGTGTACACATGAAGGTCCCAAGGCTCAAGGAAGTTTGATAAATGAAGCCTTTTCCTTCA
GATTTAGTTTATGTGGGATGCGACATGTTTGGGAGAAAAAAAAACGGGGGAGGGGGGATGGAAT
TTCTCAGCTAGGAAAAACTCTAGGCCTGACTTCATGGGAATTTCCCCCATCCTATCATATAGAA
CGTATCCTGCTTCTCAGGATGACATTTGCATGTGTCCCCAGTTGTCACTTTTCCTTTGGGGAGT
AAAGTTATAGCTTCCTTATTTATCCTCTCGTACAGAGAGGAGGTAGTTGACCTTGCATCTAAAG
ATGCTCTAAGACAATGAGAATTTGATGTCGTACATGTCTGCAAGTACTGTTTTTGTGCATGGCC
ACATTCCACTGACATTTGCCAAGTCTGCATGCAATCAGAACAAGAGACAAGGGACTGACCATAC
GAGAGCCTCCCTGCCTGGTTTTCAGGGATTGGATCTCAAGGGTACAGACTGTCCTCACCTGGGG
AGTAATGGCAGCCATTGTACACGTGTGCTGCATACGTCCATAATGCCTTTCAAAGTGTCTTTTT
CATTCTCTTGAAAGAGCGTGGATTTGCTCACCACCCCCAGCACCAAGAAACCAAGGTGGGACCA
TTCATGTTGAAGGTCCAGGACTAGTTACCCATGTGACTGTAGTCACTTTAAACTTTCCATTAAA
CCTCACCATTGGTGATGGCTTACAGTGCAAAGAGCCATGATGTGTATATTAACCTATGCTCTAC
ATATTTATTTTTAGACTTTCTTCAGCATCCATGTTAGTATGGGATCGATGCCTATATGTAAATA
TTGTACACTTTGTAAATCAATGAATAAAGATTTTAAGTGTCTTTCATTAGGCTTCTTCCTGCAA
GTGTGTATGTCAATGATTAATATATCAGGTATGGGCTTAGCACCACAGTGGGTTTCTTTCCATC
ACCTACTTTCCAGATATGTCAAGAAATACACACATTAAAGAGACTCATCCCAAATGGTTCATAC
AGGTGATGAGTGCTCCAAAAATAAAAGAAGAGGTTGTCAGACTGTT

hide sequence

RefSeq Acc Id:

XM_006224410 ⟹ XP_006224472

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Celera	3	32,671,498 - 32,812,614 (+)	NCBI

Sequence:

show sequence

GCAGGCGGCGCTCCGCATTGCACACGCGGGGGTCGCCGCAGTGTTCGTGGGATGGGGCAGCGGG
CTGCCTCTGGTGGCAGGGACGCGTGCAGCCCGGGTGCCAATCCTCTACCACGGTCTCAAGTGCC
CCCTCTGAGGCCCTCTGTATGAGTGACACGCCAGTCGGCCATGGAACCCAGCCCTGCCCTGGCC
TGGCTCCTGCTGCTGAGCCTGGTGGCCGACTGTCTGAAAGCTGCCCAGTCCCGAGACTTCACAG
TGAAAGACATCATCTACCTCCATCCTTCAACCACTCCATATCCTGGTGGATTTAAATGTTTCAC
CTGTGAAAAAGCAGCAGACAATTATGAATGCAACCGATGGGCTCCTGACATCTACTGTCCTCGA
GACACCAGATACTGCTACACTCAGCACACGATGGAAGTCACAGGGAATAGCATCTCTGTTACCA
AACGCTGTGTCCCACTGGAGGAGTGCTTATCCACAGGCTGCCGAGACTCGGAGCATGAAGGCTA
CAAGATCTGCACCTCCTGCTGTGAAGGAAATATCTGTAATCTACCGCTCCCTCGAAATGACACT
GATGCCACATTTGCCACCACGTCCCCTATAAACCAGACAAACGGGCACCCACACTGTGTGTCAG
TGATTGTGTCCTGCTTGTGGGTGTGGCTGGGACTCACCTTATAGTAACCCTCCCTACCCAATGT
AGGTGAGCTCTGTGGTTTCACCGTGGCCATAGTCATGCATGAGTCATCAGCTTGGCAGCAGCGA
CACAATGCAACCACAGCACCCCGAGACGTCATCACAGCCAGCCATTACCATTCCTATGAAGAGC
AAGCATTGCTCCCTCCCGTGCTGTCATTTCCAGCCTAACCACAACCCCGCCTGAGTCAGCCTGT
CCCCGATACGGACCCTGATTCTTACACCACGAACCTGTTATTTCGCTCCAAGAAAGACCTCTGC
TTTTATTGATGTCTGGGGTTCCTGCTTCAGCATCCATGCCTGAGCTGCAGGAGGTCCTGGGCCC
TCTGAAGAATAAGCTATGGATACAGGAGATATTCATTCTCCTCAGGAAAAGAGTAAAGAACCAT
GGTTTCATTGCAACCACACCTGCACCTAGAGCTTTAGAAGTTTAAAACTAAATCCAAAATAAAT
GGAATCGTTTCTTTGAGATTCTGATGGAGTCCCCGAAAGAGCAGAAAGAGCTTTGCTCGATTTA
ATTTCCCCAGCCTTCTTATCTTAACATTGGGAAACATGTTCCTTCTGCTCTTTGTAGAAGATTA
AAAAAAAAAGCAATTATAAAAGTTTGCCGTATTTGTAGGAGTGAAAAGAGAACAATTTCCTTCA
ACTTGATGAAATTAGCATCCTCAAGATGACGTTATCCCTTCTTGTAACTGAACAGATTGGCCTT
GACTCGGGAACTAATTATGCTTCCCGAGTTCCCGGATTCCAGGTGGACCAGTAGCATCTAAAAA
GTTACTAAATGAATGGGATGATTTTCTCCAGGTGTTGCATTCCATTCAGATATAGCTGATCTCG
TCAGAGAGAGGACTTCAGAATAAAAGGAAGCTCTGTGGAGGTTAGTCCTAGTTCATTTTGAAGG
CTCAGAAATGGCTAAGCAAAAGTCTTTCTCTTTCCATAGTATTTACTGCCAAAGAGCTGTCTCC
TTCCACAATCACAGTGACTTGAAAGAGAAAGTTCTGAGCTAAATTCTCATTAGATCAATAAGAT
AAGAGCACACCTGTGCTAGAATAAGAAAAAGATGGATCGTAAGTAGTACGGTGGCCTAAGATTT
GTTTCTCTCAGTTACCGTTTTTGAAGTAGAAGGAAAGGCTTTTATTGTCCGTGTATTTTTTTTA
ACCTATGAAGTTGCATAGTTGTTTTCTTCTCCCATGTAAATTCTTTAAATGACATTTATTTTTG
TATGGTATAAACTGAAAACTATATTTCAAAAAAAATTCTTTTCTTTTTCTCCACAAAGTATCAG
TTAGAATGCTCGCTTTCAACAGCGGGAGGAATTGTCATCACTCCTGATCATGGGAAGTTATCTG
TGATCCTAGGACTGATGCTGAAAAAAATTATTGCTATGAACAAGAGTTGTGCATTTGCCTCAAG
GGTTTGCCTCATTGTCTCCTCAGAAAGGTTGCCCGAGAAATATTAGGGTGAAGGCCATCACTGG
TGTGACCGTCTTTGCAGGGCTGTGGGGTGTGTCCACAGGGAACTGGGCGGAGCTATGTCTCCAA
GAGGTCAATGATGTTAAAATATATCTGCCCTGCACAGAGAACTTTAGCTTAAATGAGACTCCCC
CACCCCCTCAGGGACCAAATCTGAACTGAGGGCAGAAACTCTGATGCAAATCATTGACGTTGCA
TCACACAGCCTTAATGAAGAGTTTGACAGGCGTATCAATTTCTTGCTTATGACTGCAGATGGGA
GAGCAGGAGAGAACGACCTGTAGTAAGCACCTCTTATGTGCCCGGCACTTTGCTAAGCACTTTA
CATAGTTAGGCCATATAACCCTACATCAATTCTGTAAGGACAGAACCTATTGATGTGTACACAT
GAAGGTCCCAAGGCTCAAGGAAGTTTGATAAATGAAGCCTTTTCCTTCAGATTTAGTTTATGTG
GGATGCGACATGTTTGGGAGAAAAAAAAACGGGGGAGGGGGGATGGAATTTCTCAGCTAGGAAA
AACTCTAGGCCTGACTTCATGGGAATTTCCCCCATCCTATCATATAGAACGTATCCTGCTTCTC
AGGATGACATTTGCATGTGTCCCCAGTTGTCACTTTTCCTTTGGGGAGTAAAGTTATAGCTTCC
TTATTTATCCTCTCGTACAGAGAGGAGGTAGTTGACCTTGCATCTAAAGATGCTCTAAGACAAT
GAGAATTTGATGTCGTACATGTCTGCAAGTACTGTTTTTGTGCATGGCCACATTCCACTGACAT
TTGCCAAGTCTGCATGCAATCAGAACAAGAGACAAGGGACTGACCATACGAGAGCCTCCCTGCC
TGGTTTTCAGGGATTGGATCTCAAGGGTACAGACTGTCCTCACCTGGGGAGTAATGGCAGCCAT
TGTACACGTGTGCTGCATACGTCCATAATGCCTTTCAAAGTGTCTTTTTCATTCTCTTGAAAGA
GCGTGGATTTGCTCACCACCCCCAGCACCAAGAAACCAAGGTGGGACCATTCATGTTGAAGGTC
CAGGACTAGTTACCCATGTGACTGTAGTCACTTTAAACTTTCCATTAAACCTCACCATTGGTGA
TGGCTTACAGTGCAAAGAGCCATGATGTGTATATTAACCTATGCTCTACATATTTATTTTTAGA
CTTTCTTCAGCATCCATGTTAGTATGGGATCGATGCCTATATGTAAATATTGTACACTTTGTAA
ATCAATGAATAAAGATTTTAAGTGTCTTTCATTAGGCTTCTTCCTGCAAGTGTGTATGTCAATG
ATTAATATATCAGGTATGGGCTTAGCACCACAGTGGGTTTCTTTCCATCACCTACTTTCCAGAT
ATGTCAAGAAATACACACATTAAAGAGACTCATCCCAAATGGTTCATACAGGTGATGAGTGCTC
CAAAAATAAAAGAAGAGGTTGTCAGACTGTT

hide sequence

RefSeq Acc Id:

XM_006234160 ⟹ XP_006234222

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	34,487,222 - 34,632,887 (+)	NCBI
Rnor_6.0	3	35,566,956 - 35,707,416 (+)	NCBI
Rnor_5.0	3	40,681,330 - 40,821,870 (+)	NCBI

Sequence:

show sequence

GCAGGCGGCGCTCCGCATTGCACACGCGGGGGTCGCCGCAGTGTTCGTGGGATGGGGCAGCGGG
CTGCCTCTGGTGGCAGGGACGCGTGCAGCCCGGGTGCCAATCCTCTACCACGGTCTCAAGTGCC
CCCTCTGAGGCCCTCTGTATGAGTGACACGCCAGTCGGCCATGGAACCCAGCCCTGCCCTGGCC
TGGCTCCTGCTGCTGAGCCTGGTGGCCGACTGTCTGAAAGCTGCCCAGTCCCGAGACTTCACAG
TGAAAGACATCATCTACCTCCATCCTTCAACCACTCCATATCCTGGTGGATTTAAATGTTTCAC
CTGTGAAAAAGCAGCAGACAATTATGAATGCAACCGATGGGCTCCTGACATCTACTGTCCTCGA
GACACCAGATACTGCTACACTCAGCACACGATGGAAGTCACAGGGAATAGCATCTCTGTTACCA
AACGCTGTGTCCCACTGGAGGAGTGCTTATCCACAGGCTGCCGAGACTCGGAGCATGAAGGCTA
CAAGATCTGCACCTCCTGCTGTGAAGGAAATATCTGTAATCTACCGCTCCCTCGAAATGACACT
GATGCCACATTTGCCACCACGTCCCCTATAAACCAGACAAACGGGCACCCACACTGTGTGTCAG
TGATTGTGTCCTGCTTGTGGGTGTGGCTGGGACTCACCTTATAGTAACCCTCCCTACCCAATGT
AGGTGAGCTCTGTGGTTTCACCGTGGCCATAGTCATGCATGAGTCATCAGCTTGGCAGCAGCGA
CACAATGCAACCACAGCACCCCGAGACGTCATCACAGCCAGCCATTACCATTCCTATGAAGAGC
AAGCATTGCTCCCTCCCGTGCTGTCATTTCCAGCCTAACCACAACCCCGCCTGAGTCAGCCTGT
CCCCGATACGGACCCTGATTCTTACACCACGAACCTGTTATTTCGCTCCAAGAAAGACCTCTGC
TTTTATTGATGTCTGGGGTTCCTGCTTCAGCATCCATGCCTGAGCTGCAGGAGGTCCTGGGCCC
TCTGAAGAATAAGCTATGGATACAGGAGATATTCATTCTCCTCAGGAAAAGAGTAAAGAACCAT
TGGTTTCATTGCAACCACACCTGCACCTAGAGCTTTAGAAGTTTAAAACTAAATCCAAAATAAA
TGGAATCGTTTCTTTGAGATTCTGATGGAGTCCCCGAAAGAGCAGAAAGAGCTTTGCTCGATTT
AATTTCCCCAGCCTTCTTATCTTAACATTGGGAAACATGTTCCTTCTGCTCTTTGTAGAAGATT
AAAAAAAAAAGCAATTATAAAAGTTTGCCGTATTTGTAGGAGTGAAAAGAGAACAATTTCCTTC
AACTTGATGAAATTAGCATCCTCAAGATGACGTTATCCCTTCTTGTAACTGAACAGATTGGCCT
TGACTCGGGAACTAATTATGCTTCCCGAGTTCCCGGATTCCAGGTGGACCAGTAGCATCTAAAA
AGTTACTAAATGAATGGGATGATTTTCTCCAGGTGTTGCATTCCATTCAGATATAGCTGATCTC
GTCAGAGAGAGGACTTCAGAATAAAAGGAAGCTCTGTGGAGGTTAGTCCTAGTTCATTTTGAAG
GCTCAGAAATGGCTAAGCAAAAGTCTTTCTCTTTCCATAGTATTTACTGCCAAAGAGCTGTCTC
CTTCCACAATCACAGTGACTTGAAAGAGAAAGTTCTGAGCTAAATTCTCATTAGATCAATAAGA
TAAGAGCACACCTGTGCTAGAATAAGAAAAAGATGGATCGTAAGTAGTACGGTGGCCTAAGATT
TGTTTCTCTCAGTTACCGTTTTTGAAGTAGAAGGAAAGGCTTTTATTGTCCGTGTATTTTTTTT
AACCTATGAAGTTGCATAGTTGTTTTCTTCTCCCATGTAAATTCTTTAAATGACATTTATTTTT
GTATGGTATAAACTGAAAACTATATTTCAAAAAAAATTCTTTTCTTTTTCTCCACAAAGTATCA
GTTAGAATGCTCGCTTTCAACAGCGGGAGGAATTGTCATCACTCCTGATCATGGGAAGTTATCT
GTGATCCTAGGACTGATGCTGAAAAAAATTATTGCTATGAACAAGAGTTGTGCATTTGCCTCAA
GGGTTTGCCTCATTGTCTCCTCAGAAAGGTTGCCCGAGAAATATTAGGGTGAAGGCCATCACTG
GTGTGACCGTCTTTGCAGGGCTGTGGGGTGTGTCCACAGGGAACTGGGCGGAGCTATGTCTCCA
AGAGGTCAATGATGTTAAAATATATCTGCCCTGCACAGAGAACTTTAGCTTAAATGAGACTCCC
CCACCCCCTCAGGGACCAAATCTGAACTGAGGGCAGAAACTCTGATGCAAATCATTGACGTTGC
ATCACACAGCCTTAATGAAGAGTTTGACAGGCGTATCAATTTCTTGCTTATGACTGCAGATGGG
AGAGCAGGAGAGAACGACCTGTAGTAAGCACCTCTTATGTGCCCGGCACTTTGCTAAGCACTTT
ACATAGTTAGGCCATATAACCCTACATCAATTCTGTAAGGACAGAACCTATTGATGTGTACACA
TGAAGGTCCCAAGGCTCAAGGAAGTTTGATAAATGAAGCCTTTTCCTTCAGATTTAGTTTATGT
GGGATGCGACATGTTTGGGAGAAAAAAAAACGGGGGAGGGGGGATGGAATTTCTCAGCTAGGAA
AAACTCTAGGCCTGACTTCATGGGAATTTCCCCCATCCTATCATATAGAACGTATCCTGCTTCT
CAGGATGACATTTGCATGTGTCCCCAGTTGTCACTTTTCCTTTGGGGAGTAAAGTTATAGCTTC
CTTATTTATCCTCTCGTACAGAGAGGAGGTAGTTGACCTTGCATCTAAAGATGCTCTAAGACAA
TGAGAATTTGATGTCGTACATGTCTGCAAGTACTGTTTTTGTGCATGGCCACATTCCACTGACA
TTTGCCAAGTCTGCATGCAATCAGAACAAGAGACAAGGGACTGACCATACGAGAGCCTCCCTGC
CTGGTTTTCAGGGATTGGATCTCAAGGGTACAGACTGTCCTCACCTGGGGAGTAATGGCAGCCA
TTGTACACGTGTGCTGCATACGTCCATAATGCCTTTCAAAGTGTCTTTTTCATTCTCTTGAAAG
AGCGTGGATTTGCTCACCACCCCCAGCACCAAGAAACCAAGGTGGGACCATTCATGTTGAAGGT
CCAGGACTAGTTACCCATGTGACTGTAGTCACTTTAAACTTTCCATTAAACCTCACCATTGGTG
ATGGCTTACAGTGCAAAGAGCCATGATGTGTATATTAACCTATGCTCTACATATTTATTTTTAG
ACTTTCTTCAGCATCCATGTTAGTATGGGATCGATGCCTATATGTAAATATTGTACACTTTGTA
AATCAATGAATAAAGATTTTAAGTGTCTTTCATTAGGCTTCTTCCTGCAAGTGTGTATGTCAAT
GATTAATATATCAGGTATGGGCTTAGCACCACAGTGGGTTTCTTTCCATCACCTACTTTCCAGA
TATGTCAAGAAATACACACATTAAAGAGACTCATCCCAAATGGTTCATACAGGTGATGAGTGCT
CCAAAAATAAAAGAAGAGGTTGTCAGACTGTT

hide sequence

RefSeq Acc Id:

XM_008775373 ⟹ XP_008773595

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Celera	3	32,785,066 - 32,812,614 (+)	NCBI

Sequence:

show sequence

CTGCGTTTGTATTCCAGGTGCCAATCCTCTACCACGGTCTCAAGTGCCCCCTCTGAGGCCCTCT
GTATGAGTGACACGCCAGTCGGCCATGGAACCCAGCCCTGCCCTGGCCTGGCTCCTGCTGCTGA
GCCTGGTGGCCGACTGTCTGAAAGCTGCCCAGTCCCGAGACTTCACAGTGAAAGACATCATCTA
CCTCCATCCTTCAACCACTCCATATCCTGGTGGATTTAAATGTTTCACCTGTGAAAAAGCAGCA
GACAATTATGAATGCAACCGATGGGCTCCTGACATCTACTGTCCTCGAGACACCAGATACTGCT
ACACTCAGCACACGATGGAAGTCACAGGGAATAGCATCTCTGTTACCAAACGCTGTGTCCCACT
GGAGGAGTGCTTATCCACAGGCTGCCGAGACTCGGAGCATGAAGGCTACAAGATCTGCACCTCC
TGCTGTGAAGGAAATATCTGTAATCTACCGCTCCCTCGAAATGACACTGATGCCACATTTGCCA
CCACGTCCCCTATAAACCAGACAAACGGGCACCCACACTGTGTGTCAGTGATTGTGTCCTGCTT
GTGGGTGTGGCTGGGACTCACCTTATAGTAACCCTCCCTACCCAATGTAGGTGAGCTCTGTGGT
TTCACCGTGGCCATAGTCATGCATGAGTCATCAGCTTGGCAGCAGCGACACAATGCAACCACAG
CACCCCGAGACGTCATCACAGCCAGCCATTACCATTCCTATGAAGAGCAAGCATTGCTCCCTCC
CGTGCTGTCATTTCCAGCCTAACCACAACCCCGCCTGAGTCAGCCTGTCCCCGATACGGACCCT
GATTCTTACACCACGAACCTGTTATTTCGCTCCAAGAAAGACCTCTGCTTTTATTGATGTCTGG
GGTTCCTGCTTCAGCATCCATGCCTGAGCTGCAGGAGGTCCTGGGCCCTCTGAAGAATAAGCTA
TGGATACAGGAGATATTCATTCTCCTCAGGAAAAGAGTAAAGAACCATGGTTTCATTGCAACCA
CACCTGCACCTAGAGCTTTAGAAGTTTAAAACTAAATCCAAAATAAATGGAATCGTTTCTTTGA
GATTCTGATGGAGTCCCCGAAAGAGCAGAAAGAGCTTTGCTCGATTTAATTTCCCCAGCCTTCT
TATCTTAACATTGGGAAACATGTTCCTTCTGCTCTTTGTAGAAGATTAAAAAAAAAAGCAATTA
TAAAAGTTTGCCGTATTTGTAGGAGTGAAAAGAGAACAATTTCCTTCAACTTGATGAAATTAGC
ATCCTCAAGATGACGTTATCCCTTCTTGTAACTGAACAGATTGGCCTTGACTCGGGAACTAATT
ATGCTTCCCGAGTTCCCGGATTCCAGGTGGACCAGTAGCATCTAAAAAGTTACTAAATGAATGG
GATGATTTTCTCCAGGTGTTGCATTCCATTCAGATATAGCTGATCTCGTCAGAGAGAGGACTTC
AGAATAAAAGGAAGCTCTGTGGAGGTTAGTCCTAGTTCATTTTGAAGGCTCAGAAATGGCTAAG
CAAAAGTCTTTCTCTTTCCATAGTATTTACTGCCAAAGAGCTGTCTCCTTCCACAATCACAGTG
ACTTGAAAGAGAAAGTTCTGAGCTAAATTCTCATTAGATCAATAAGATAAGAGCACACCTGTGC
TAGAATAAGAAAAAGATGGATCGTAAGTAGTACGGTGGCCTAAGATTTGTTTCTCTCAGTTACC
GTTTTTGAAGTAGAAGGAAAGGCTTTTATTGTCCGTGTATTTTTTTTAACCTATGAAGTTGCAT
AGTTGTTTTCTTCTCCCATGTAAATTCTTTAAATGACATTTATTTTTGTATGGTATAAACTGAA
AACTATATTTCAAAAAAAATTCTTTTCTTTTTCTCCACAAAGTATCAGTTAGAATGCTCGCTTT
CAACAGCGGGAGGAATTGTCATCACTCCTGATCATGGGAAGTTATCTGTGATCCTAGGACTGAT
GCTGAAAAAAATTATTGCTATGAACAAGAGTTGTGCATTTGCCTCAAGGGTTTGCCTCATTGTC
TCCTCAGAAAGGTTGCCCGAGAAATATTAGGGTGAAGGCCATCACTGGTGTGACCGTCTTTGCA
GGGCTGTGGGGTGTGTCCACAGGGAACTGGGCGGAGCTATGTCTCCAAGAGGTCAATGATGTTA
AAATATATCTGCCCTGCACAGAGAACTTTAGCTTAAATGAGACTCCCCCACCCCCTCAGGGACC
AAATCTGAACTGAGGGCAGAAACTCTGATGCAAATCATTGACGTTGCATCACACAGCCTTAATG
AAGAGTTTGACAGGCGTATCAATTTCTTGCTTATGACTGCAGATGGGAGAGCAGGAGAGAACGA
CCTGTAGTAAGCACCTCTTATGTGCCCGGCACTTTGCTAAGCACTTTACATAGTTAGGCCATAT
AACCCTACATCAATTCTGTAAGGACAGAACCTATTGATGTGTACACATGAAGGTCCCAAGGCTC
AAGGAAGTTTGATAAATGAAGCCTTTTCCTTCAGATTTAGTTTATGTGGGATGCGACATGTTTG
GGAGAAAAAAAAACGGGGGAGGGGGGATGGAATTTCTCAGCTAGGAAAAACTCTAGGCCTGACT
TCATGGGAATTTCCCCCATCCTATCATATAGAACGTATCCTGCTTCTCAGGATGACATTTGCAT
GTGTCCCCAGTTGTCACTTTTCCTTTGGGGAGTAAAGTTATAGCTTCCTTATTTATCCTCTCGT
ACAGAGAGGAGGTAGTTGACCTTGCATCTAAAGATGCTCTAAGACAATGAGAATTTGATGTCGT
ACATGTCTGCAAGTACTGTTTTTGTGCATGGCCACATTCCACTGACATTTGCCAAGTCTGCATG
CAATCAGAACAAGAGACAAGGGACTGACCATACGAGAGCCTCCCTGCCTGGTTTTCAGGGATTG
GATCTCAAGGGTACAGACTGTCCTCACCTGGGGAGTAATGGCAGCCATTGTACACGTGTGCTGC
ATACGTCCATAATGCCTTTCAAAGTGTCTTTTTCATTCTCTTGAAAGAGCGTGGATTTGCTCAC
CACCCCCAGCACCAAGAAACCAAGGTGGGACCATTCATGTTGAAGGTCCAGGACTAGTTACCCA
TGTGACTGTAGTCACTTTAAACTTTCCATTAAACCTCACCATTGGTGATGGCTTACAGTGCAAA
GAGCCATGATGTGTATATTAACCTATGCTCTACATATTTATTTTTAGACTTTCTTCAGCATCCA
TGTTAGTATGGGATCGATGCCTATATGTAAATATTGTACACTTTGTAAATCAATGAATAAAGAT
TTTAAGTGTCTTTCATTAGGCTTCTTCCTGCAAGTGTGTATGTCAATGATTAATATATCAGGTA
TGGGCTTAGCACCACAGTGGGTTTCTTTCCATCACCTACTTTCCAGATATGTCAAGAAATACAC
ACATTAAAGAGACTCATCCCAAATGGTTCATACAGGTGATGAGTGCTCCAAAAATAAAAGAAGA
GGTTGTCAGACTGTT

hide sequence

RefSeq Acc Id:

XM_039106250 ⟹ XP_038962178

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	34,549,038 - 34,632,887 (+)	NCBI

Protein Sequences


Protein RefSeqs	XP_006234222	(Get FASTA)	NCBI Sequence Viewer
	XP_038962178	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	D3ZTT2	(Get FASTA)	NCBI Sequence Viewer
	EDM00460	(Get FASTA)	NCBI Sequence Viewer
	EDM00461	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	XP_001053512 ⟸ XM_001053512
- Sequence:	show sequence MEPSPALAWLLLLSLVADCLKAAQSRDFTVKDIIYLHPSTTPYPGGFKCFTCEKAADNYECNRW APDIYCPRDTRYCYTQHTMEVTGNSISVTKRCVPLEECLSTGCRDSEHEGYKICTSCCEGNICN LPLPRNDTDATFATTSPINQTNGHPHCVSVIVSCLWVWLGLTL hide sequence

RefSeq Acc Id:	XP_003753769 ⟸ XM_003753721
- Sequence:	show sequence MEPSPALAWLLLLSLVADCLKAAQSRDFTVKDIIYLHPSTTPYPGGFKCFTCEKAADNYECNRW APDIYCPRDTRYCYTQHTMEVTGNSISVTKRCVPLEECLSTGCRDSEHEGYKICTSCCEGNICN LPLPRNDTDATFATTSPINQTNGHPHCVSVIVSCLWVWLGLTL hide sequence

RefSeq Acc Id:	XP_006224472 ⟸ XM_006224410
- Sequence:	show sequence MEPSPALAWLLLLSLVADCLKAAQSRDFTVKDIIYLHPSTTPYPGGFKCFTCEKAADNYECNRW APDIYCPRDTRYCYTQHTMEVTGNSISVTKRCVPLEECLSTGCRDSEHEGYKICTSCCEGNICN LPLPRNDTDATFATTSPINQTNGHPHCVSVIVSCLWVWLGLTL hide sequence

RefSeq Acc Id:	XP_006234222 ⟸ XM_006234160
- UniProtKB:	D3ZTT2 (UniProtKB/TrEMBL)
- Sequence:	show sequence MEPSPALAWLLLLSLVADCLKAAQSRDFTVKDIIYLHPSTTPYPGGFKCFTCEKAADNYECNRW APDIYCPRDTRYCYTQHTMEVTGNSISVTKRCVPLEECLSTGCRDSEHEGYKICTSCCEGNICN LPLPRNDTDATFATTSPINQTNGHPHCVSVIVSCLWVWLGLTL hide sequence

RefSeq Acc Id:	XP_008773595 ⟸ XM_008775373
- Sequence:	show sequence MEPSPALAWLLLLSLVADCLKAAQSRDFTVKDIIYLHPSTTPYPGGFKCFTCEKAADNYECNRW APDIYCPRDTRYCYTQHTMEVTGNSISVTKRCVPLEECLSTGCRDSEHEGYKICTSCCEGNICN LPLPRNDTDATFATTSPINQTNGHPHCVSVIVSCLWVWLGLTL hide sequence

RefSeq Acc Id:

ENSRNOP00000056346 ⟸ ENSRNOT00000059588

RefSeq Acc Id:

XP_038962178 ⟸ XM_039106250

Protein Domains

UPAR/Ly6

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1587119	AgrOrtholog
Ensembl Genes	ENSRNOG00000038980	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000056346	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000059588	UniProtKB/Swiss-Prot
InterPro	LYPD6	UniProtKB/Swiss-Prot
	LYPD6-like	UniProtKB/Swiss-Prot
KEGG Report	rno:679564	UniProtKB/Swiss-Prot
NCBI Gene	679564	ENTREZGENE
PANTHER	PTHR31171	UniProtKB/Swiss-Prot
	PTHR31171:SF0	UniProtKB/Swiss-Prot
PhenoGen	Lypd6	PhenoGen
UniProt	D3ZTT2	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2013-05-24	Lypd6	LY6/PLAUR domain containing 6	LOC100365115	LY6/PLAUR domain containing 6B-like	Data Merged	1643240	APPROVED
2010-05-05	LOC100365115	LY6/PLAUR domain containing 6B-like			Symbol and Name status set to provisional	70820	PROVISIONAL
2008-03-05	Lypd6	LY6/PLAUR domain containing 6	LOC679564	hypothetical protein LOC679564	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-01-09	LOC679564	hypothetical protein LOC679564	LOC682476	hypothetical protein LOC682476	Data Merged	1643240	APPROVED
2006-11-19	LOC679564	hypothetical protein LOC679564			Symbol and Name status set to provisional	70820	PROVISIONAL
2006-11-19	LOC682476	hypothetical protein LOC682476			Symbol and Name status set to provisional	70820	PROVISIONAL

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

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

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

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