Emx2 (empty spiracles homeobox 2)

	Submit Data \| Help \| Video Tutorials \| News \| Publications \| FTP Download \| REST API \| Citing RGD \| Contact
	Search RGD Grant Resources Citing RGD About Us Contact Us Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References FTP Download Submit Data OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper Genome Scanner Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease Find Models new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive Pathways Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
	Advanced Search (OLGA)

Gene: Emx2 (empty spiracles homeobox 2) Rattus norvegicus

Analyze

Symbol:

Emx2

Name:

empty spiracles homeobox 2

RGD ID:

1564797

Description:

Predicted to have sequence-specific double-stranded DNA binding activity. Predicted to be involved in several processes, including forebrain development; response to drug; and ureter morphogenesis. Orthologous to human EMX2 (empty spiracles homeobox 2); INTERACTS WITH bis(2-ethylhexyl) phthalate; bisphenol A; Butylbenzyl phthalate.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

empty spiracles homolog 2; homeobox protein EMX2; LOC499380; RGD1564797; similar to empty spiracles-like protein 2

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):	EMX2 (empty spiracles homeobox 2)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, PhylomeDB
Mus musculus (house mouse):	Emx2 (empty spiracles homeobox 2)	HGNC	NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Emx2 (empty spiracles homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	EMX2 (empty spiracles homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	EMX2 (empty spiracles homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Emx2 (empty spiracles homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	EMX2 (empty spiracles homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	EMX2 (empty spiracles homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Emx2 (empty spiracles homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	EMX1 (empty spiracles homeobox 1)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	EMX2 (empty spiracles homeobox 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Emx2 (empty spiracles homeobox 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	emx2 (empty spiracles homeobox 2)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	ceh-2	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Drosophila melanogaster (fruit fly):	E5	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Drosophila melanogaster (fruit fly):	ems	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|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	258,626,584 - 258,633,594 (+)	NCBI
Rnor_6.0 Ensembl	1	280,633,938 - 280,640,946 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	280,633,938 - 280,640,946 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	287,993,648 - 288,000,656 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	266,004,257 - 266,011,265 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	1	254,275,943 - 254,282,950 (+)	NCBI		Celera
Cytogenetic Map	1	q55	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

epilepsy (ISO)

Female Urogenital Diseases (ISO)

Lung Neoplasms (ISO)

Schizencephaly (ISO)

visual epilepsy (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

15-acetyldeoxynivalenol (ISO)

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

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

4,4'-sulfonyldiphenol (ISO)

aflatoxin B1 (ISO)

antirheumatic drug (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (EXP,ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

Butylbenzyl phthalate (EXP)

cisplatin (ISO)

dexamethasone (ISO)

dibutyl phthalate (EXP)

diethyl phthalate (EXP)

diethylstilbestrol (EXP)

diisobutyl phthalate (EXP)

diisononyl phthalate (EXP)

dorsomorphin (ISO)

endosulfan (EXP)

entinostat (ISO)

ethanol (ISO)

fluoranthene (ISO)

folic acid (ISO)

furan (EXP)

hydroquinone O-beta-D-glucopyranoside (ISO)

indometacin (ISO)

melphalan (ISO)

mercury atom (ISO)

mercury(0) (ISO)

methylmercury chloride (ISO)

N-ethyl-N-nitrosourea (ISO)

nickel atom (ISO)

ochratoxin A (ISO)

phenylmercury acetate (ISO)

phenytoin (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

silver atom (ISO)

silver(0) (ISO)

Soman (EXP)

trichostatin A (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anterior/posterior pattern specification (ISO)

brain development (IBA,ISO)

cell proliferation in forebrain (ISO)

central nervous system development (IBA)

cerebral cortex development (ISO)

cerebral cortex regionalization (ISO)

dentate gyrus development (ISO)

forebrain cell migration (ISO)

forebrain development (ISO)

neuron differentiation (IBA,ISO)

regulation of gene expression (ISO)

regulation of transcription by RNA polymerase II (IBA)

response to drug (ISO)

ureter morphogenesis (ISO)

Cellular Component

nucleus (IBA)

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA)

protein binding (ISO)

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

sequence-specific double-stranded DNA binding (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	OMIM Disease Annotation Pipeline
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:9098922	PMID:10729342	PMID:12091317	PMID:12196586	PMID:12209834	PMID:12561075	PMID:12764040	PMID:15147765	PMID:15294144	PMID:15917450	PMID:16919471	PMID:21731775

Genomics

Comparative Map Data

Emx2
(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	258,626,584 - 258,633,594 (+)	NCBI
Rnor_6.0 Ensembl	1	280,633,938 - 280,640,946 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	280,633,938 - 280,640,946 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	287,993,648 - 288,000,656 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	266,004,257 - 266,011,265 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	1	254,275,943 - 254,282,950 (+)	NCBI		Celera
Cytogenetic Map	1	q55	NCBI

EMX2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	10	117,542,445 - 117,549,546 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	10	117,542,746 - 117,549,546 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	10	119,302,257 - 119,309,057 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	10	119,291,946 - 119,299,043 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	10	119,291,945 - 119,299,043	NCBI
Celera	10	113,031,949 - 113,039,046 (+)	NCBI
Cytogenetic Map	10	q26.11	NCBI
HuRef	10	112,930,193 - 112,937,289 (+)	NCBI		HuRef
CHM1_1	10	119,586,078 - 119,593,194 (+)	NCBI		CHM1_1

Emx2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	19	59,447,122 - 59,453,789 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	19	59,446,804 - 59,453,789 (+)	Ensembl
GRCm38	19	59,458,690 - 59,465,357 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	19	59,458,372 - 59,465,357 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	19	59,533,180 - 59,539,847 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	19	59,511,622 - 59,518,607 (+)	NCBI			mm8
Celera	19	61,658,178 - 61,664,837 (+)	NCBI		Celera
Cytogenetic Map	19	D3	NCBI
cM Map	19	56.28	NCBI

Emx2
(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_004955431	22,192,446 - 22,199,279 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955431	22,192,446 - 22,199,141 (+)	NCBI	ChiLan1.0	ChiLan1.0

EMX2
(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	10	117,551,451 - 117,557,972 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	10	117,551,451 - 117,557,972 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	10	114,124,759 - 114,132,109 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

EMX2
(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	28	28,003,710 - 28,009,035 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	28	28,002,966 - 28,009,955 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Emx2
(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_004936486	7,313,689 - 7,319,971 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

EMX2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	14	127,650,688 - 127,655,706 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	14	127,649,675 - 127,656,972 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	139,052,130 - 139,055,522 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

EMX2
(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	9	110,347,043 - 110,353,647 (+)	NCBI
ChlSab1.1 Ensembl	9	110,347,379 - 110,353,643 (+)	Ensembl

Emx2
(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_004624737	29,103,378 - 29,110,356 (-)	NCBI

Position Markers

D1Mit14

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	280,632,517 - 280,632,620	NCBI	Rnor6.0
Rnor_5.0	1	287,992,227 - 287,992,330	UniSTS	Rnor5.0
RGSC_v3.4	1	266,002,835 - 266,002,939	RGD	RGSC3.4
RGSC_v3.4	1	266,002,836 - 266,002,939	UniSTS	RGSC3.4
RGSC_v3.1	1	266,213,881 - 266,213,984	RGD
Celera	1	254,274,522 - 254,274,625	UniSTS
RH 3.4 Map	1	1706.6	UniSTS
RH 3.4 Map	1	1706.6	RGD
RH 2.0 Map	1	1324.4999	RGD
FHH x ACI Map	1	132.1799	RGD
Cytogenetic Map	1	q55	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
70211	Niddm24	Non-insulin dependent diabetes mellitus QTL 24	3.79		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	236795785	281795785	Rat
631215	Stl8	Serum triglyceride level QTL 8	9.27	0.0001	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	1	245529606	282763074	Rat
2302040	Pia35	Pristane induced arthritis QTL 35	3.8	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	1	236265430	281265430	Rat
724552	Glom2	Glomerulus QTL 2	3.3	0.0001	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)	1	243272341	282763074	Rat
734767	Niddm57	Non-insulin dependent diabetes mellitus QTL 57			body mass (VT:0001259)	body weight (CMO:0000012)	1	244401175	282365384	Rat
734768	Niddm59	Non-insulin dependent diabetes mellitus QTL 59			body mass (VT:0001259)	body weight (CMO:0000012)	1	235850810	280850810	Rat
734769	Niddm58	Non-insulin dependent diabetes mellitus QTL 58			body mass (VT:0001259)	body weight (CMO:0000012)	1	244992467	282365384	Rat
631690	Scl5	Serum cholesterol level QTL 5	2.1		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	1	258132568	282763074	Rat
1581544	Rf52	Renal function QTL 52		0.05	total urine protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	1	252948438	281795785	Rat
731175	Uae20	Urinary albumin excretion QTL 20	3.5	0.0018	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	241482188	281795785	Rat
631536	Lnnr2	Liver neoplastic nodule remodeling QTL 2	2.9	0.0005	liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)	1	255728828	282763074	Rat
631836	Stl31	Serum triglyceride level QTL 31	4.64	0.00000487	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	1	259295704	282763074	Rat
631837	Niddm35	Non-insulin dependent diabetes mellitus QTL 35		0.01	blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	258709726	281795785	Rat
631843	Bw116	Body weight QTL 116	4.1	0.016	abdominal adipose amount (VT:1000220)	abdominal fat pad weight (CMO:0000088)	1	244401175	282365384	Rat
634313	Niddm43	Non-insulin dependent diabetes mellitus QTL 43			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	217054291	281795785	Rat
1600392	Bw123	Body weight QTL 123		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	1	244087148	282763074	Rat
1578763	Kidm29	Kidney mass QTL 29	3.3	0.0001	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	1	196395041	282763074	Rat
1300108	Rf8	Renal function QTL 8	3.75		renal blood flow trait (VT:2000006)	absolute change in renal vascular resistance (CMO:0001900)	1	249206242	281795785	Rat
1549910	Bw54	Body weight QTL 54		0.05	body mass (VT:0001259)	body weight (CMO:0000012)	1	236795785	281795785	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	163796316	282763074	Rat
1358890	Bp259	Blood pressure QTL 259	3.06		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	230420627	282645769	Rat
61327	Eae7	Experimental allergic encephalomyelitis QTL 7	5.6		body mass (VT:0001259)	change in body weight (CMO:0002045)	1	236265430	281265430	Rat
7387289	Uae45	Urinary albumin excretion QTL 45	2.86	0.0021	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	244148899	282763074	Rat
10053715	Scort24	Serum corticosterone level QTL 24	2.13	0.0088	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	1	242302911	282763074	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	449
Count of miRNA genes:	242
Interacting mature miRNAs:	287
Transcripts:	ENSRNOT00000012564
Prediction methods:	Microtar, Miranda
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium									37	34	28
Low			4	4		4	2	4	31	1	7	2	2
Below cutoff	2	33	29	13	18	13	6	7	2		6	9	6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001109169	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473986	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000055	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000012564 ⟹ ENSRNOP00000012564

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	280,633,938 - 280,640,946 (+)	Ensembl

RefSeq Acc Id:

NM_001109169 ⟹ NP_001102639

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	258,626,584 - 258,633,594 (+)	NCBI
Rnor_6.0	1	280,633,938 - 280,640,946 (+)	NCBI
Rnor_5.0	1	287,993,648 - 288,000,656 (+)	NCBI
RGSC_v3.4	1	266,004,257 - 266,011,265 (+)	RGD
Celera	1	254,275,943 - 254,282,950 (+)	RGD

Sequence:

show sequence

GAGCAGGAGGAGGAGAGGAACGAGGAAGAGGAGGAGAAGAGGGAAGCGGAGGAGCCCAAGGAGG
AGGAGAGAAACTGCAGCGGGTGCCGCGAGAGCGAGGGAGCTAGCCCGGAGCGCAGGGCGAAGAC
ACCAAGAGGTCTGCGGCCGGGCGGGCGGCTGGAGGCACGGCCGGGGCAGTGGCGCCGACTCCGT
TCCATTCTGGGACCGGATCCAGGCCTCCGGGTTCCCAGGCGTTCGCCTCCCTCTGACGCACTTT
AAAGAGTCTCCCCCCCTTCCACCTCAGGGCGAGTAATAGCGACCAATCATCAAGCCATTTACCA
GGCTTCGGAGGAAGCTGTTTATGTGATCCCCGCACTAATTAGGCTCATGAACTAACAAATCGTT
TGCACTACTAGTGAAGAAGCGAACACTTCCATGGATTGTCCTTGGACTTAGGGCGCCCTGCCCG
CCTTTTGCAAAGGAAAGAAAACTTTTTTTTGCCTCCCCGAGAACCCCCCTCCCTGCCTCTAACT
CCAACCCCCCCCCAACGCCACCTCGCTCAAAAAAATATTACCCCAATCCACGCCTGCAAATTCT
TCTGGAAGGATTTTCCCCCCTCTCTCCAGGTTGGGCGCGTTTGGTGCAAGATTCTCGGGATCTT
CGGCTTTGCCTCTCCTCCCCCTCCCCCTCCTTTCCTTTTTCCTTTCCTTTCTTTCTTCCTTCCT
TTCTTTTCCTTACCCCCACCCCCACCCCAAACAAACGAGTCCCCCATTCTCCTCGGTCTTCGCC
GCGGGCAGCGGGCGGCGGAGGCAGCGCGCCGCGGTCGCCGGGAGCAGGGAGCCCAGGGCGCCCG
CTCCTCGGCGCAGCATGTTTCAGCCGGCGCCTAAGCGCTGCTTCACCATCGAGTCGCTGGTGGC
CAAGGACAGTCCCCTGCCTGCCTCACGCTCCGAGGATCCCATCCGTCCCGCGGCGCTCAGCTAC
GCCAATTCCAGCCCCATAAATCCGTTCCTCAACGGCTTCCACTCGGCCGCCGCCGCCGCCGCCG
CGGGCAGGGGCGTCTACTCCAACCCGGACTTGGTGTTCGCCGAGGCGGTCTCGCACCCGCCCAA
CCCCGCCGTGCCGGTGCACCCGGTGCCGCCGCCGCACGCCCTGGCCGCCCACCCCCTGCCCTCC
TCGCATTCGCCACACCCCCTCTTCGCCTCGCAGCAGCGGGACCCGTCCACCTTCTACCCCTGGC
TCATCCACCGCTACCGATATCTGGGTCATCGCTTCCAAGGGAACGACACAAGTCCCGAGAGTTT
CCTTTTGCACAACGCTCTGGCTCGAAAGCCGAAGCGGATTCGAACCGCCTTCTCTCCGTCCCAG
CTTTTAAGGCTAGAACACGCGTTCGAGAAGAATCATTACGTGGTGGGAGCGGAAAGGAAGCAGC
TGGCGCACAGTCTCAGCCTTACGGAAACTCAGGTAAAAGTATGGTTTCAGAACCGGAGAACGAA
ATTCAAAAGGCAAAAGCTAGAGGAAGAAGGCTCAGATTCCCAACAAAAGAAAAAAGGGACACAC
CACATTAACCGGTGGAGAATTGCTACCAAGCAGGCGAGTCCGGAGGAAATAGACGTGACCTCAG
ACGATTAAAAGTACAAACCTATTCCCACAGAAATGGACAGCACGGAGCAAGAGAGACAGGGAGA
GGAGGGGAAGAAAAACCCTACAGAACAAAAAACAAACTGCACACACATTCACCGAGAAAGGGGG
AGAGGGAATCACAGCAGACTTTGGACATCGAGGGCACTGGACCGGGACCCGGCGCTGGGGCACC
ACTCACGGGACAGGAACGGCAGAGGACCGAGGCCCCTTCATCAACATGCAACCCTCGTCTAAAG
AGGCAGCTGAGTGAGTGAGAGAGACAGAGACTGGGAGGGAGAGAGAAAGGAGAGAGAGAGAGAG
AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAATGAGAATGAATGATCTGGTCCTTCTGAG
GCAAAGGCACATTCTGACAAGGGGAGCTGTCAGTCAAATGCCAAACCAGGGAAACAAGATGATT
GGCGGCGTATTCCGCTTATCGAAGTCCATTTAGAAATGATAATGATTTTTTTTTTGGAAAAAAA
AGGCACAGGACTTTTAATTTTGCACTTCGCAGTGTTTCTCCCTCATCTTTAATTAGAAATAACA
TGCAAAATTCCATGTCTAGCCCCACCCTACACCTGTTTCAAAAACTTGAATTGCATGTAACAGT
TGTTGGGCGAATGGTGTCTAAAAACTGAATTGTAATTTTACTCTTCCTTTAAAGGCAGGTTCTG
TGTATTTTTATTTTTTATTTTTTCTGAGAAATGTGCAGTCTGTAAAAACACTTTTTTTTTGATA
CCTTCTATTGTCAAAGTGATTGTGAAAGCTAAATGAAGTAGGCTCGGAAATAGTGGTCCTCTGA
CAGAGAAATGAGGGAGCAGGATGGGGATGGAGGGCGGGGGAGGGTGCCCCTGAGAAGAGTCAGG
ACTTACACTAGGGGTTAAAAACAACACATGATAAAGACCCAAATTAATTCTATTTCTTGGATAT
TTCCTTTTCTAACATTCTGATTCTTTAAATCACCAAATCAACCTTTCCTTTTAGTGGTTGGAGA
CATTGACCGCATTCAACCACTCAACACAATGGCCATTCAGAACTTTTAAGTCTGTTTATTGCAA
AAGTGGAAGGAAGGACTGTAGTTAATGGGGTGATAGTGGCGTGGCCAAGGACATGGGAGTTTTC
AAGCACTGAGTTTCTCTTCCAAGACCATAGACTTACTAAAGAGGGTTACAAATGCTTCCTTAGT
GTCTTCTATACCAGAATGTAAATATTTTTGTGTTTTGTGTTAATTTGTTAGAATTCTAACACAC
TATATACTTCCAAGAAGTATGTCAATGTCAATATTTTGTCAATAAAGATTTATCAATATGCCCT
CA

hide sequence

RefSeq Acc Id:

XM_017589593 ⟹ XP_017445082

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	280,634,757 - 280,639,542 (+)	NCBI

Sequence:

show sequence

CCCAGGGCGCCCGCTCCTCGGCGCAGCATGTTTCAGCCGGCGCCTAAGCGCTGCTTCACCATCG
AGTCGCTGGTGGCCAAGGACAGTCCCCTGCCTGCCTCACGCTCCGAGGATCCCATCCGTCCCGC
GGCGCTCAGCTACGCCAATTCCAGCCCCATAAATCCGTTCCTCAACGGCTTCCACTCGGCCGCC
GCCGCCGCCGCCGCGGGCAGGGGCGTCTACTCCAACCCGGACTTGGTGTTCGCCGAGGCGGTCT
CGCACCCGCCCAACCCCGCCGTGCCGGTGCACCCGGTGCCGCCGCCGCACGCCCTGGCCGCCCA
CCCCCTGCCCTCCTCGCATTCGCCACACCCCCTCTTCGCCTCGCAGCAGCGGGACCCGTCCACC
TTCTACCCCTGGCTCATCCACCGCTACCGATATCTGGGTCATCGCTTCCAAGGTAAAAGTATGG
TTTCAGAACCGGAGAACGAAATTCAAAAGGCAAAAGCTAGAGGAAGAAGGCTCAGATTCCCAAC
AAAAGAAAAAAGGGACACACCACATTAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001102639	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL94560	(Get FASTA)	NCBI Sequence Viewer
	EDL94561	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001102639 ⟸ NM_001109169

- UniProtKB:

D3ZCK7 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MFQPAPKRCFTIESLVAKDSPLPASRSEDPIRPAALSYANSSPINPFLNGFHSAAAAAAAGRGV
YSNPDLVFAEAVSHPPNPAVPVHPVPPPHALAAHPLPSSHSPHPLFASQQRDPSTFYPWLIHRY
RYLGHRFQGNDTSPESFLLHNALARKPKRIRTAFSPSQLLRLEHAFEKNHYVVGAERKQLAHSL
SLTETQVKVWFQNRRTKFKRQKLEEEGSDSQQKKKGTHHINRWRIATKQASPEEIDVTSDD

hide sequence

RefSeq Acc Id:	XP_017445082 ⟸ XM_017589593
- Peptide Label:	isoform X1
- Sequence:	show sequence MFQPAPKRCFTIESLVAKDSPLPASRSEDPIRPAALSYANSSPINPFLNGFHSAAAAAAAGRGV YSNPDLVFAEAVSHPPNPAVPVHPVPPPHALAAHPLPSSHSPHPLFASQQRDPSTFYPWLIHRY RYLGHRFQGKSMVSEPENEIQKAKARGRRLRFPTKEKRDTPH hide sequence

RefSeq Acc Id:

ENSRNOP00000012564 ⟸ ENSRNOT00000012564

Protein Domains

Homeobox

Transcriptome

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

Promoters

RGD ID:

13691015

Promoter ID:

EPDNEW_R1540

Type:

single initiation site

Name:

Emx2_1

Description:

empty spiracles homeobox 2

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	280,633,971 - 280,634,031	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
1	287994786	287994787	A	C	snv	F344/Jcl (KyushuU)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1564797	AgrOrtholog
Ensembl Genes	ENSRNOG00000009482	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000012564	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000012564	ENTREZGENE, UniProtKB/TrEMBL
InterPro	Homeobox	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_region	UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/TrEMBL
	HTH_lambrepressr	UniProtKB/TrEMBL
KEGG Report	rno:499380	UniProtKB/TrEMBL
NCBI Gene	499380	ENTREZGENE
Pfam	Homeobox	UniProtKB/TrEMBL
PhenoGen	Emx2	PhenoGen
PRINTS	HOMEOBOX	UniProtKB/TrEMBL
	HTHREPRESSR	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	Homeodomain_like	UniProtKB/TrEMBL
UniProt	D3ZCK7	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-03-07	Emx2	empty spiracles homeobox 2	RGD1564797_predicted	similar to empty spiracles-like protein 2 (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-07	RGD1564797_predicted	similar to empty spiracles-like protein 2 (predicted)	LOC499380	similar to empty spiracles-like protein 2	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC499380	similar to empty spiracles-like protein 2			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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM