Eed (embryonic ectoderm development)

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Gene: Eed (embryonic ectoderm development) Rattus norvegicus

Analyze

Symbol:

Eed

Name:

embryonic ectoderm development

RGD ID:

1309782

Description:

Exhibits chromatin binding activity. Is predicted to contribute to histone methyltransferase activity (H3-K27 specific). Involved in negative regulation of transcription by RNA polymerase II and spinal cord development. Localizes to nucleus. Used to study transient cerebral ischemia. Orthologous to human EED (embryonic ectoderm development); PARTICIPATES IN histone modification pathway; INTERACTS WITH 2,4-dinitrotoluene; amphetamine; benzo[a]pyrene.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

LOC293104; polycomb protein EED

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):	EED (embryonic ectoderm development)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Eed (embryonic ectoderm development)	HGNC	Treefam, EggNOG, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Eed (embryonic ectoderm development)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	EED (embryonic ectoderm development)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	EED (embryonic ectoderm development)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Eed (embryonic ectoderm development)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	EED (embryonic ectoderm development)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	EED (embryonic ectoderm development)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Eed (embryonic ectoderm development)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	EED (embryonic ectoderm development)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Eed (embryonic ectoderm development)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	eed (embryonic ectoderm development)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	esc	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	escl	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	mes-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	1	143,867,875 - 143,895,008 (-)	NCBI
Rnor_6.0 Ensembl	1	154,189,260 - 154,216,340 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	154,189,252 - 154,216,340 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	160,493,753 - 160,520,834 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	146,563,961 - 146,591,042 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	146,642,345 - 146,669,450 (-)	NCBI
Celera	1	142,108,258 - 142,135,298 (-)	NCBI		Celera
Cytogenetic Map	1	q32	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Cohen-Gibson Syndrome (ISO)

exudative vitreoretinopathy 1 (ISO)

Nerve Sheath Neoplasms (ISO)

neurilemmoma (ISO)

transient cerebral ischemia (IDA)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

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

2,4-dinitrotoluene (EXP)

aflatoxin B1 (ISO)

amiodarone (ISO)

amphetamine (EXP)

arsane (ISO)

arsenic atom (ISO)

benzene (ISO)

benzo[a]pyrene (EXP,ISO)

benzo[a]pyrene diol epoxide I (ISO)

bisphenol A (EXP,ISO)

copper atom (ISO)

copper(0) (ISO)

copper(II) sulfate (ISO)

coumestrol (ISO)

cyclosporin A (ISO)

disulfiram (ISO)

dorsomorphin (ISO)

Enterolactone (ISO)

folic acid (ISO)

formaldehyde (ISO)

leflunomide (ISO)

methapyrilene (EXP)

methotrexate (ISO)

methyl methanesulfonate (ISO)

methylmercury chloride (ISO)

N-methyl-N-nitrosourea (ISO)

paracetamol (ISO)

quinolin-8-ol (ISO)

resveratrol (ISO)

SB 431542 (ISO)

tetrachloromethane (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cellular response to leukemia inhibitory factor (ISO)

chromatin silencing (IBA)

histone H3-K27 methylation (IEA)

histone methylation (ISO)

negative regulation of transcription by RNA polymerase II (IBA,IDA,ISO)

oligodendrocyte differentiation (ISO)

positive regulation of histone H3-K27 methylation (ISO)

regulation of adaxial/abaxial pattern formation (ISO)

regulation of gene expression by genetic imprinting (ISO)

spinal cord development (IEP)

Cellular Component

chromatin silencing complex (ISO)

cytosol (ISO)

ESC/E(Z) complex (IBA,ISO)

nucleoplasm (ISO)

nucleus (IDA,ISO)

pronucleus (ISO)

sex chromatin (ISO)

Molecular Function

chromatin binding (IDA,ISO)

histone methyltransferase activity (ISO)

histone methyltransferase activity (H3-K27 specific) (IBA,ISO)

identical protein binding (ISO)

nucleosome binding (IBA)

protein binding (IPI,ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (ISO)

RNA polymerase II transcription corepressor binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

histone modification pathway (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	GOA data from the GO Consortium
3.	Gu L, etal., J Neuroinflammation. 2013 Sep 3;10:109. doi: 10.1186/1742-2094-10-109.
4.	Herz HM, etal., Trends Biochem Sci. 2013 Dec;38(12):621-39. doi: 10.1016/j.tibs.2013.09.004. Epub 2013 Oct 20.
5.	Lomniczi A, etal., Nat Neurosci. 2013 Mar;16(3):281-9. doi: 10.1038/nn.3319. Epub 2013 Jan 27.
6.	MGD data from the GO Consortium
7.	RGD automated import pipeline for gene-chemical interactions
8.	Simon JA and Kingston RE, Mol Cell. 2013 Mar 7;49(5):808-24. doi: 10.1016/j.molcel.2013.02.013.
9.	Wang C, etal., Front Biosci (Landmark Ed). 2010 Jun 1;15:1018-22.

Additional References at PubMed

PMID:9584197	PMID:11124122	PMID:11555636	PMID:12477932	PMID:12627233	PMID:12900441	PMID:15385962	PMID:15525528	PMID:15916951	PMID:16687444	PMID:17107999	PMID:17997413
PMID:18483221	PMID:19796622	PMID:20064375	PMID:20064376	PMID:20075857	PMID:20144788	PMID:20439489	PMID:22438827	PMID:22573614	PMID:23104054	PMID:23273982	PMID:24105743
PMID:26658965	PMID:28041882	PMID:28229514	PMID:31451685

Genomics

Comparative Map Data

Eed
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	143,867,875 - 143,895,008 (-)	NCBI
Rnor_6.0 Ensembl	1	154,189,260 - 154,216,340 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	154,189,252 - 154,216,340 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	160,493,753 - 160,520,834 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	146,563,961 - 146,591,042 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	146,642,345 - 146,669,450 (-)	NCBI
Celera	1	142,108,258 - 142,135,298 (-)	NCBI		Celera
Cytogenetic Map	1	q32	NCBI

EED
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	11	86,244,753 - 86,278,813 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	11	86,244,753 - 86,285,420 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	11	85,955,795 - 85,989,852 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	11	85,633,463 - 85,667,429 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	11	85,633,462 - 85,667,426	NCBI
Celera	11	83,265,529 - 83,300,439 (+)	NCBI
Cytogenetic Map	11	q14.2	NCBI
HuRef	11	82,243,000 - 82,278,147 (+)	NCBI		HuRef
CHM1_1	11	85,841,200 - 85,875,657 (+)	NCBI		CHM1_1

Eed
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	89,603,862 - 89,630,184 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	7	89,603,862 - 89,630,191 (-)	Ensembl
GRCm38	7	89,954,654 - 89,980,976 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	89,954,654 - 89,980,983 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	97,103,164 - 97,129,486 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	7	89,829,868 - 89,857,005 (-)	NCBI			mm8
Celera	7	87,275,683 - 87,302,613 (-)	NCBI		Celera
Cytogenetic Map	7	D3	NCBI

Eed
(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_004955414	6,659,055 - 6,685,530 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955414	6,659,144 - 6,685,530 (-)	NCBI	ChiLan1.0	ChiLan1.0

EED
(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	11	84,902,330 - 84,937,906 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	11	84,902,330 - 84,937,906 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	11	81,295,068 - 81,330,321 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

EED
(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	21	13,260,002 - 13,289,337 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	21	13,260,062 - 13,289,511 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Eed
(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_004936498	14,050,731 - 14,082,410 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

EED
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	9	20,123,857 - 20,158,816 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	9	20,123,077 - 20,158,747 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	9	22,382,548 - 22,417,549 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

EED
(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	1	77,496,266 - 77,531,439 (+)	NCBI
ChlSab1.1 Ensembl	1	77,496,086 - 77,531,499 (+)	Ensembl

Eed
(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_004624845	3,679,163 - 3,712,153 (-)	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
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34993530	173445086	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	35377692	217372257	Rat
2313402	Anxrr24	Anxiety related response QTL 24			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	1	49147799	156446783	Rat
1578654	Bss10	Bone structure and strength QTL 10	4		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	1	49578577	169852184	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49578693	217054291	Rat
2298545	Neuinf8	Neuroinflammation QTL 8	4.6		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	1	58354072	161711996	Rat
1578780	Cm52	Cardiac mass QTL 52	3.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	1	82788437	239853971	Rat
724529	Cm16	Cardiac mass QTL 16	2.7		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	1	90804143	161321256	Rat
724521	Uae1	Urinary albumin excretion QTL 1	3.8	0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	94201400	184846632	Rat
1358902	Bw47	Body weight QTL 47	1.67		body mass (VT:0001259)	body weight (CMO:0000012)	1	94201400	197187904	Rat
724567	Tcas6	Tongue tumor susceptibility QTL 6	6.85		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	1	95304961	156446783	Rat
1331793	Bp200	Blood pressure QTL 200	3.71601		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	99983293	188289386	Rat
1331751	Bp199	Blood pressure QTL 199	3.60022		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	99983293	198656062	Rat
1331749	Hrtrt11	Heart rate QTL 11	2.973		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	99983293	216213510	Rat
70209	Niddm23	Non-insulin dependent diabetes mellitus QTL 23	2.82		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	99983293	216325819	Rat
731168	Bp154	Blood pressure QTL 154	3.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	100131562	236763528	Rat
8655649	Arrd1	Age-related retinal degeneration QTL 1	4.89		retinal layer morphology trait (VT:0003727)	percentage of study population developing retinopathy during a period of time (CMO:0002453)	1	106002252	202571904	Rat
61370	Mcs3	Mammary carcinoma susceptibility QTL 3	2.15		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	1	108057233	167517487	Rat
1354623	Rf46	Renal function QTL 46	3.8		blood creatinine amount (VT:0005328)	plasma creatinine level (CMO:0000537)	1	108986301	161784422	Rat
1354591	Cm36	Cardiac mass QTL 36	4.1		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	108986301	219232156	Rat
1354615	Cm32	Cardiac mass QTL 32	5.2		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	1	108986301	219232156	Rat
1354606	Bp246	Blood pressure QTL 246	3.6		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	108986301	238830534	Rat
2303591	Gluco41	Glucose level QTL 41	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	109634374	154634374	Rat
9590300	Scort16	Serum corticosterone level QTL 16	4.39	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	1	110620749	155620749	Rat
8694370	Bw154	Body weight QTL 154	8.91	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	1	110620749	155620749	Rat
61399	Tcat1	Tongue tumor resistance QTL 1	3.3		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 5 mm (CMO:0001879)	1	111446783	156446783	Rat
61346	Rf2	Renal disease susceptibility QTL 2	3.7		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	1	111446783	156446783	Rat
631496	Bp97	Blood pressure QTL 97	3.08		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	113593576	158593576	Rat
1300158	Bp173	Blood pressure QTL 173	3.48		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	1	122614824	201146953	Rat
7794788	Mcs32	Mammary carcinoma susceptibility QTL 32	2.61		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	1	122614824	262664716	Rat
2313060	Bss71	Bone structure and strength QTL 71	2.6	0.0001	long bone metaphysis morphology trait (VT:0000133)	tibia midshaft total cross-sectional area (CMO:0001715)	1	124090312	169090312	Rat
631199	Cm23	Cardiac mass QTL 23	4.6	0.0004	heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	1	124603592	188289386	Rat
7421630	Bp362	Blood pressure QTL 362		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	125875758	262433692	Rat
631205	Bp196	Blood pressure QTL 196	4	0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	126240667	217054291	Rat
2293140	Bp313	Blood pressure QTL 313			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	129208943	174208943	Rat
631544	Bp84	Blood pressure QTL 84	5.6		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	130779148	198585664	Rat
1358189	Cstrr1	Cold stress response QTL 1		0.0001	catecholamine amount (VT:0010543)	urine norepinephrine level (CMO:0001629)	1	130779148	199254774	Rat
1578770	Stresp23	Stress response QTL 23			kidney sympathetic nerve activity (VT:0004050)	stimulated renal sympathetic nerve activity to basal renal sympathetic nerve activity ratio (CMO:0001786)	1	130779148	199254774	Rat
1641895	Bp298	Blood pressure QTL 298			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	130779148	199254774	Rat
631549	Bp89	Blood pressure QTL 89	5.7		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	130779320	219238476	Rat
1598850	Bp297	Blood pressure QTL 297	2.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	131334152	176334152	Rat
1598866	Bp287	Blood pressure QTL 287	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	131334152	176334152	Rat
631654	Bp107	Blood pressure QTL 107			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	133076978	178076978	Rat
9685799	Bp375	Blood pressure QTL 375			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	133076978	178076978	Rat
634348	Bp138	Blood pressure QTL 138			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	133076978	184188922	Rat
61442	Strs1	Sensitivity to stroke QTL 1	7.4		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	1	133946489	178946489	Rat
9685802	Bp376	Blood pressure QTL 376			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	134089429	179089429	Rat
724562	Rends1	Renal damage susceptibility QTL 1		0.05	kidney glomerulus integrity trait (VT:0010546)	index of glomerular damage (CMO:0001135)	1	137787261	236763528	Rat
61341	Bp26	Blood pressure QTL 26			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	137787261	236763528	Rat
631202	Gluco13	Glucose level QTL 13		0.0001	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	139523928	170246858	Rat
738006	Anxrr14	Anxiety related response QTL 14	4	0.00035	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	1	141296374	186296374	Rat
738028	Anxrr12	Anxiety related response QTL 12	4.9	0.00001	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	1	141296374	186296374	Rat
1558645	Bw55	Body weight QTL 55	3.2	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	1	144395993	189395993	Rat
6893347	Bw98	Body weight QTL 98	0.2	0.53	body mass (VT:0001259)	body weight (CMO:0000012)	1	144395993	189395993	Rat
6893361	Bw104	Body weight QTL 104	0.59	0.27	body mass (VT:0001259)	body weight (CMO:0000012)	1	144395993	189395993	Rat
7771612	Cm80	Cardiac mass QTL 80	8.4		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	1	144634295	241482368	Rat
631206	Niddm40	Non-insulin dependent diabetes mellitus QTL 40			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	144723107	174343537	Rat
71118	Thym1	Thymus enlargement QTL 1	10.17	0.001	thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	153655976	198655976	Rat
724550	Thym3	Thymus enlargement QTL 3	7.82	0.001	thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	153655976	198655976	Rat
631519	Pia11	Pristane induced arthritis QTL 11	5.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	153656062	198656062	Rat
1598853	Memor3	Memory QTL 3	4.5		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	1	153834077	232297227	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	53
Count of miRNA genes:	42
Interacting mature miRNAs:	51
Transcripts:	ENSRNOT00000024082
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	3	35	47	31	19	31	8	9	74	35	40	11	8
Low		8	10	10		10		2			1
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106278	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006229664	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039105860	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039105864	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC168872	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473956	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000041	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000024082 ⟹ ENSRNOP00000024082

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	154,189,260 - 154,216,340 (-)	Ensembl

RefSeq Acc Id:

NM_001106278 ⟹ NP_001099748

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	143,867,875 - 143,894,958 (-)	NCBI
Rnor_6.0	1	154,189,259 - 154,216,340 (-)	NCBI
Rnor_5.0	1	160,493,753 - 160,520,834 (-)	NCBI
RGSC_v3.4	1	146,563,961 - 146,591,042 (-)	RGD
Celera	1	142,108,258 - 142,135,298 (-)	RGD

Sequence:

show sequence

CAATTGCGGACGAAACGTCTGGGCAAGGAAGGGGGTGAGGGAGCAGCCCTTTGAGTTCCGCCTC
CTCTCTAGGCGCTGGTGGGGAAGGGGGACTAGGAAACCCTGCCCTCTGAGCCAGCAGGTCCGAC
GCCTCGGTGCAAAGTGCCGAGAGGGCGGCGGGAAAACCGCCCGCCGGGACCAGGGGACGGGAAG
CAGCCAGGAAGCCGTACGGGAGGGCGCGCGCGCGCGCGCCCCTTTTTCAGCAGTGTGGCGGGGT
CGCACGCACGCCCGCCTCGGCGGCTGGGCGCGATTTGCGACAGTGGGGGGAGCGGCGGCGGTGG
CGGTGCCGGCAGCTTTGCGGCAGGCTCCGGCCGGGCGTGCTTGACGGCGGTGTGGCGGAGGCCC
CGCCCGAGGCGGCAAGAACCTGGAGGGAGGCGGAGGAATATGTCTGAGAGGGAAGTGTCGACTG
CGCCGGCGGGAACAGACATGCCGGCGGCCAAGAAGCAGAAGTTGAGCAGCGACGAGAACAGCAA
CCCGGACCTCTCGGGAGACGAGAATGACGATGCTGTCAGTATCGAGAGTGGCACAAACACAGAA
CGCCCGGACACACCCACAAATACACCAAATGCACCAGGAAGGAAAAGCTGGGGAAAGGGAAAAT
GGAAGTCGAAGAAATGCAAATATTCTTTCAAATGTGTGAACAGCCTCAAGGAAGATCACAACCA
GCCATTGTTTGGAGTTCAGTTTAACTGGCACAGTAAAGAAGGAGATCCTCTGGTGTTTGCAACT
GTGGGAAGCAACAGAGTAACCTTATATGAATGCCATTCTCAAGGGGAAATACGGTTATTGCAGT
CCTATGTAGATGCTGATGCAGATGAAAACTTTTACACTTGTGCATGGACCTATGATAGCAACAC
CAGCCACCCTCTGCTAGCAGTTGCTGGATCTAGAGGCATAATAAGAATAATTAATCCTATAACA
ATGCAGTGTATAAAGCACTATGTTGGCCATGGGAATGCTATCAATGAGCTGAAATTCCACCCAC
GAGACCCAAACCTTCTCCTGTCAGTAAGTAAAGATCATGCTTTACGATTATGGAATATCCAAAC
AGACACTCTTGTGGCAATATTCGGAGGTGTGGAAGGGCACAGAGATGAAGTGCTGAGTGCTGAT
TATGATCTTTTGGGTGAAAAAATAATGTCCTGTGGTATGGATCACTCTCTTAAACTGTGGAGAA
TCAACTCAAAGAGAATGATGAATGCGATTAAGGAATCTTACGATTATAACCCAAACAAAACTAA
CAGGCCATTTATTTCCCAGAAAATCCACTTTCCTGATTTTTCTACCAGAGACATACATAGGAAT
TATGTTGATTGTGTACGATGGTTAGGCGATTTGATACTTTCCAAGTCTTGTGAAAATGCCATTG
TATGCTGGAAACCTGGCAAAATGGAGGATGATATAGATAAAATTAAACCTAGTGAGTCTAATGT
GACTATTCTTGGGCGATTTGATTACAGCCAGTGTGACATTTGGTACATGAGGTTTTCTATGGAT
TTCTGGCAAAAGATGCTTGCATTGGGCAATCAGGTTGGCAAACTGTATGTTTGGGATTTAGAAG
TAGAAGATCCTCATAAAGCCAAATGCACAACACTGACCCATCATAAATGTGGCGCTGCTATTCG
ACAAACCAGTTTTAGCAGGGATAGCAGCATCCTCATAGCTGTCTGCGATGATGCCAGCATTTGG
CGTTGGGATCGACTTCGATAAACTATTTTTCCCTAGTAAAAATTAGAATATGTTGTCTGTGTAA
AATAGAATTAATGTATCTTGCTAGCAAAGGGACTAGAGCATTTAGACTTGTCTTTCAGCATCCG
ATCAGGCTGAGCTGAATGTAGTGGTGTTTACATTGTTTACATTCTTTGTACTGTCTTCCTGCTC
AGACTTTACTGCTTTTAATAAAAATTTATTTTTGTAAAGCTGTGTTATTTTTATTGTGATGGAA
ACAAACTGGAAGAAATAAAGTTATACCATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006229664 ⟹ XP_006229726

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	143,867,875 - 143,895,006 (-)	NCBI
Rnor_6.0	1	154,189,252 - 154,216,119 (-)	NCBI
Rnor_5.0	1	160,493,753 - 160,520,834 (-)	NCBI

Sequence:

show sequence

GCGCGCGCGCCCCTTTTTCAGCAGTGTGGCGGGGTCGCACGCACGCCCGCCTCGGCGGCTGGGC
GCGATTTGCGACAGTGGGGGGAGCGGCGGCGGTGGCGGTGCCGGCAGCTTTGCGGCAGGCTCCG
GCCGGGCGTGCTTGACGGCGGTGTGGCGGAGGCCCCGCCCGAGGCGGCAAGAACCTGGAGGGAG
GCGGAGGAATATGTCTGAGAGGGAAGTGTCGACTGCGCCGGCGGGAACAGACATGCCGGCGGCC
AAGAAGCAGAAGTTGAGCAGCGACGAGAACAGCAACCCGGACCTCTCGGGAGACGAGAATGACG
ATGCTGTCAGTATCGAGAGTGGCACAAACACAGAACGCCCGGACACACCCACAAATACACCAAA
TGCACCAGGAAGGAAAAGCTGGGGAAAGGGAAAATGGAAGTCGAAGAAATGCAAATATTCTTTC
AAATGTGTGAACAGCCTCAAGGAAGATCACAACCAGCCATTGTTTGGAGTTCAGTTTAACTGGC
ACAGTAAAGAAGGAGATCCTCTGGTGTTTGCAACTGTGGGAAGCAACAGAGTAACCTTATATGA
ATGCCATTCTCAAGGGGAAATACGGTTATTGCAGTCCTATGTAGATGCTGATGCAGATGAAAAC
TTTTACACTTGTGCATGGACCTATGATAGCAACACCAGCCACCCTCTGCTAGCAGTTGCTGGAT
CTAGAGGCATAATAAGAATAATTAATCCTATAACAATGCAGTGTATAAAGCACTATGTTGGCCA
TGGGAATGCTATCAATGAGCTGAAATTCCACCCACGAGACCCAAACCTTCTCCTGTCAGTAAGT
AAAGATCATGCTTTACGATTATGGAATATCCAAACAGACACTCTTGTGGCAATATTCGGAGGTG
TGGAAGGGCACAGAGATGAAGTGCTGAGTGCTGATTATGATCTTTTGGGTGAAAAAATAATGTC
CTGTGGTATGGATCACTCTCTTAAACTGTGGAGAATCAACTCAAAGAGAATGATGAATGCGATT
AAGGAATCTTACGATTATAACCCAAACAAAACTAACAGGCCATTTATTTCCCAGAAAATCCACT
TTCCTGATTTTTCTACCAGAGACATACATAGGAATTATGTTGATTGTGTACGATGGTTAGGCGA
TTTGATACTTTCCAAGTCTTGTGAAAATGCCATTGTATGCTGGAAACCTGGCAAAATGGAGGAT
GATATAGATAAAATTAAACCTAATGCTTGCATTGGGCAATCAGGTTGGCAAACTGTATGTTTGG
GATTTAGAAGTAGAAGATCCTCATAAAGCCAAATGCACAACACTGACCCATCATAAATGTGGCG
CTGCTATTCGACAAACCAGTTTTAGCAGGGATAGCAGCATCCTCATAGCTGTCTGCGATGATGC
CAGCATTTGGCGTTGGGATCGACTTCGATAAACTATTTTTCCCTAGTAAAAATTAGAATATGTT
GTCTGTGTAAAATAGAATTAATGTATCTTGCTAGCAAAGGGACTAGAGCATTTAGACTTGTCTT
TCAGCATCCGATCAGGCTGAGCTGAATGTAGTGGTGTTTACATTGTTTACATTCTTTGTACTGT
CTTCCTGCTCAGACTTTACTGCTTTTAATAAAAATTTATTTTTGTAAAGCTGTGTTATTTTTAT
TGTGATGGAAACAAACTGGAAGAAATAAAGTTATACCATATCTTCTT

hide sequence

RefSeq Acc Id:

XM_039105860 ⟹ XP_038961788

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	143,867,875 - 143,894,339 (-)	NCBI

RefSeq Acc Id:

XM_039105864 ⟹ XP_038961792

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	143,867,875 - 143,895,008 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001099748	(Get FASTA)	NCBI Sequence Viewer
	XP_006229726	(Get FASTA)	NCBI Sequence Viewer
	XP_038961788	(Get FASTA)	NCBI Sequence Viewer
	XP_038961792	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI68872	(Get FASTA)	NCBI Sequence Viewer
	EDM18565	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001099748 ⟸ NM_001106278

- UniProtKB:

B5DF02 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTPNAPG
RKSWGKGKWKSKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHS
QGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNA
INELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGM
DHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLIL
SKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVG
KLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRLR

hide sequence

RefSeq Acc Id:

XP_006229726 ⟸ XM_006229664

- Peptide Label:

isoform X3

- Sequence:

show sequence

MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTPNAPG
RKSWGKGKWKSKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHS
QGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNA
INELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGM
DHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLIL
SKSCENAIVCWKPGKMEDDIDKIKPNACIGQSGWQTVCLGFRSRRSS

hide sequence

RefSeq Acc Id:

ENSRNOP00000024082 ⟸ ENSRNOT00000024082

RefSeq Acc Id:	XP_038961792 ⟸ XM_039105864
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038961788 ⟸ XM_039105860
- Peptide Label:	isoform X1

Protein Domains

WD_REPEATS_REGION

Transcriptome

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

Promoters

RGD ID:

13690185

Promoter ID:

EPDNEW_R710

Type:

multiple initiation site

Name:

Eed_1

Description:

embryonic ectoderm development

SO ACC ID:

SO:0000170

Source:

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

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	154,216,356 - 154,216,416	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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CSV

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

ACI/EurMcwi (RGD)

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CSV

TAB

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

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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CSV

TAB

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

BN/SsN (MCW)

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CSV

TAB

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

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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CSV

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

F344/NCrl (RGD)

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CSV

TAB

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

F344/NRrrc (MCW)

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CSV

TAB

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

FHH/EurMcwi (MCW)

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CSV

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

FHH/EurMcwi (RGD)

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CSV

TAB

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

FHL/EurMcwi (MCW)

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CSV

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

FHL/EurMcwi (RGD)

Visual

CSV

TAB

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

GH/OmrMcwi (MCW)

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CSV

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

GK/Ox (RGD)

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CSV

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

LE/Stm (RGD)

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CSV

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

LEW/Crl (RGD)

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CSV

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

LEW/NCrlBR (RGD)

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CSV

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

LH/MavRrrc (RGD)

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CSV

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

LL/MavRrrc (RGD)

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CSV

TAB

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

LN/MavRrrc (RGD)

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CSV

TAB

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

M520/N (MCW)

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CSV

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

MHS/Gib (RGD)

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CSV

TAB

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

MNS/Gib (RGD)

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CSV

TAB

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

MR/N (MCW)

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CSV

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

SBH/Ygl (MCW)

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CSV

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

SBH/Ygl (RGD)

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CSV

TAB

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

SBN/Ygl (MCW)

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CSV

TAB

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

SBN/Ygl (RGD)

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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:1309782	AgrOrtholog
Ensembl Genes	ENSRNOG00000017509	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000024082	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000024082	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	2.130.10.10	UniProtKB/TrEMBL
InterPro	Polycomb_EED	UniProtKB/TrEMBL
	WD40/YVTN_repeat-like_dom	UniProtKB/TrEMBL
	WD40_repeat	UniProtKB/TrEMBL
	WD40_repeat_CS	UniProtKB/TrEMBL
	WD40_repeat_dom	UniProtKB/TrEMBL
	WD40_repeat_dom_sf	UniProtKB/TrEMBL
KEGG Report	rno:293104	UniProtKB/TrEMBL
NCBI Gene	293104	ENTREZGENE
PANTHER	PTHR10253:SF5	UniProtKB/TrEMBL
Pfam	WD40	UniProtKB/TrEMBL
PhenoGen	Eed	PhenoGen
PROSITE	WD_REPEATS_1	UniProtKB/TrEMBL
	WD_REPEATS_2	UniProtKB/TrEMBL
	WD_REPEATS_REGION	UniProtKB/TrEMBL
SMART	WD40	UniProtKB/TrEMBL
Superfamily-SCOP	WD40_like	UniProtKB/TrEMBL
UniProt	B5DF02	ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary	F1LMC5	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Eed	embryonic ectoderm development	Eed_predicted	embryonic ectoderm development (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Eed_predicted	embryonic ectoderm development (predicted)			Symbol and Name status set to approved	70820	APPROVED

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

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

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

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

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations