Efna1 (ephrin A1) - Rat Genome Database

Name: Efna1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

	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 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: Efna1 (ephrin A1) Rattus norvegicus

Analyze

Symbol:

Efna1

Name:

ephrin A1

RGD ID:

620388

Description:

Predicted to have ephrin receptor binding activity. Predicted to be involved in several processes, including heart valve morphogenesis; nervous system development; and regulation of protein metabolic process. Predicted to localize to anchored component of plasma membrane. Orthologous to human EFNA1 (ephrin A1); PARTICIPATES IN altered ephrin - ephrin receptor bidirectional signaling pathway; E-cadherin signaling pathway; ephrin - ephrin receptor bidirectional signaling axis; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

B61; EPH-related receptor tyrosine kinase ligand 1; ephrin-A1; immediate early response protein B61; LERK-1

Orthologs:

Homo sapiens (human) : EFNA1 (ephrin A1) HGNC Alliance
Mus musculus (house mouse) : Efna1 (ephrin A1) MGI Alliance
Chinchilla lanigera (long-tailed chinchilla) : Efna1 (ephrin A1)
Pan paniscus (bonobo/pygmy chimpanzee) : EFNA1 (ephrin A1)
Canis lupus familiaris (dog) : EFNA1 (ephrin A1)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Efna1 (ephrin A1)
Sus scrofa (pig) : EFNA1 (ephrin A1)
Chlorocebus sabaeus (African green monkey) : EFNA1 (ephrin A1)
Heterocephalus glaber (naked mole-rat) : Efna1 (ephrin A1)

more info ...

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	EFNA1 (ephrin A1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB
Mus musculus (house mouse):	Efna1 (ephrin A1)	HGNC	EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Efna1 (ephrin A1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	EFNA1 (ephrin A1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	EFNA1 (ephrin A1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Efna1 (ephrin A1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	EFNA1 (ephrin A1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	EFNA1 (ephrin A1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Efna1 (ephrin A1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	EFNA1 (ephrin A1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Mus musculus (house mouse):	Efna1 (ephrin A1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	efna1a (ephrin-A1a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	efna1b (ephrin-A1b)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	efn-4	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|PANTHER)
Drosophila melanogaster (fruit fly):	Ephrin	Alliance	DIOPT (Ensembl Compara\|PANTHER\|PhylomeDB)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	2	188,588,808 - 188,596,156 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	188,588,796 - 188,596,222 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	2	208,002,153 - 208,010,763 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	181,444,599 - 181,451,944 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	2	181,394,706 - 181,402,050 (-)	NCBI
Celera	2	168,623,896 - 168,631,240 (-)	NCBI		Celera
Cytogenetic Map	2	q34	NCBI
RH 3.4 Map	2	1155.2	RGD

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Breast Neoplasms (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-epigallocatechin 3-gallate (ISO)

1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (ISO)

17beta-estradiol (ISO)

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

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

2-hydroxypropanoic acid (ISO)

2-methylcholine (ISO)

3,7-dihydropurine-6-thione (EXP)

3H-1,2-dithiole-3-thione (EXP)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

5-aza-2'-deoxycytidine (ISO)

6-propyl-2-thiouracil (EXP)

acetaldehyde (ISO)

acetamide (EXP)

adefovir pivoxil (ISO)

afimoxifene (ISO)

all-trans-retinoic acid (EXP,ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

belinostat (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

benzo[b]fluoranthene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cadmium dichloride (ISO)

caffeine (ISO)

calcitriol (ISO)

carbon nanotube (ISO)

chloroacetaldehyde (ISO)

cholanic acid (ISO)

choline (ISO)

chromium(6+) (ISO)

chrysene (ISO)

cidofovir anhydrous (ISO)

ciglitazone (ISO)

ciguatoxin CTX1B (ISO)

cisplatin (ISO)

clodronic acid (ISO)

clofibrate (ISO)

clomiphene (ISO)

cocaine (EXP)

copper(II) sulfate (ISO)

coumestrol (ISO)

cyclosporin A (ISO)

cytarabine (ISO)

dextran sulfate (ISO)

diarsenic trioxide (ISO)

diazinon (ISO)

dibenz[a,h]anthracene (ISO)

diethylstilbestrol (ISO)

dioxygen (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

endosulfan (EXP)

Enterolactone (ISO)

entinostat (ISO)

estrone (ISO)

flavonoids (EXP)

flusilazole (ISO)

flutamide (EXP)

folic acid (ISO)

fulvestrant (ISO)

furan (EXP)

genistein (ISO)

glyphosate (ISO)

GW 1929 (EXP)

hemin (ISO)

Heptachlor epoxide (ISO)

hydrogen peroxide (ISO)

hydroquinone (ISO)

ifosfamide (ISO)

indole-3-methanol (EXP)

L-methionine (ISO)

leflunomide (ISO)

lipopolysaccharide (EXP)

lithocholic acid (ISO)

mercaptopurine (EXP)

mercury dibromide (ISO)

mestranol (ISO)

metformin (EXP)

mifepristone (EXP)

monosodium L-glutamate (ISO)

N-acetyl-L-cysteine (EXP)

N-methyl-4-phenylpyridinium (EXP)

N-nitrosodiethylamine (EXP,ISO)

N1'-[2-[[5-[(dimethylamino)methyl]-2-furanyl]methylthio]ethyl]-N1-methyl-2-nitroethene-1,1-diamine (EXP)

nefazodone (EXP)

nickel dichloride (ISO)

nickel sulfate (ISO)

oxaliplatin (EXP)

p-chloromercuribenzoic acid (ISO)

paclitaxel (ISO)

panobinostat (ISO)

paracetamol (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (ISO)

phenobarbital (EXP)

phenylmercury acetate (ISO)

pirinixic acid (EXP,ISO)

potassium chromate (ISO)

progesterone (ISO)

purine-6-thiol (EXP)

quercetin (ISO)

rac-lactic acid (ISO)

raloxifene (ISO)

ranitidine (EXP)

resveratrol (ISO)

rotenone (EXP)

SB 431542 (ISO)

sevoflurane (EXP)

silicon dioxide (ISO)

sulforaphane (ISO)

sunitinib (ISO)

tamoxifen (ISO)

tetrachloromethane (EXP,ISO)

topotecan (EXP)

trichostatin A (ISO)

trimellitic anhydride (ISO)

triphenyl phosphate (EXP)

troglitazone (ISO)

tunicamycin (ISO)

valdecoxib (EXP)

valproic acid (ISO)

vinclozolin (EXP)

vorinostat (ISO)

zinc sulfate (ISO)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

angiogenesis (NAS)

aortic valve morphogenesis (ISO)

axon guidance (IBA)

cell migration (ISO)

endocardial cushion to mesenchymal transition involved in heart valve formation (ISO)

ephrin receptor signaling pathway (IBA,ISO,ISS)

mitral valve morphogenesis (ISO)

negative regulation of dendritic spine morphogenesis (ISO,ISS)

negative regulation of epithelial to mesenchymal transition (ISO)

negative regulation of MAPK cascade (ISO)

negative regulation of proteolysis involved in cellular protein catabolic process (ISO)

negative regulation of thymocyte apoptotic process (ISO)

negative regulation of transcription by RNA polymerase II (ISO)

neuron differentiation (ISO)

notochord formation (ISO)

positive regulation of amyloid-beta formation (ISO)

positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (ISO)

positive regulation of MAPK cascade (ISO)

positive regulation of peptidyl-tyrosine phosphorylation (ISO)

positive regulation of protein phosphorylation (ISO)

positive regulation of protein tyrosine kinase activity (ISO)

protein stabilization (ISO)

regulation of angiogenesis (ISO)

regulation of axonogenesis (ISO)

regulation of blood vessel endothelial cell migration (ISO)

regulation of cell adhesion mediated by integrin (ISO)

regulation of peptidyl-tyrosine phosphorylation (ISO,ISS)

substrate adhesion-dependent cell spreading (ISO)

Cellular Component

anchored component of plasma membrane (IBA,ISO)

extracellular region (IEA)

plasma membrane (IBA)

Molecular Function

ephrin receptor binding (IBA,ISO,TAS)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

altered ephrin - ephrin receptor bidirectional signaling pathway (ISS)

E-cadherin signaling pathway (ISO)

ephrin - ephrin receptor bidirectional signaling axis (ISO,ISS)

hypoxia inducible factor pathway (ISO)

References

References - curated


1.	Deroanne C, etal., J Cell Sci 2003 Apr 1;116(Pt 7):1367-76.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
4.	MGD data from the GO Consortium
5.	Munoz JJ, etal., J Immunol 2002 Jul 1;169(1):177-84.
6.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
7.	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
8.	RGD automated data pipeline
9.	RGD automated import pipeline for gene-chemical interactions
10.	Surawska H, etal., Cytokine Growth Factor Rev 2004 Dec;15(6):419-33.
11.	Takahashi H and Ikeda T, Oncogene 1995 Sep 7;11(5):879-83.

Additional References at PubMed

PMID:10655584	PMID:11287184	PMID:12477932	PMID:14988728	PMID:15145949	PMID:15489334	PMID:15777695	PMID:16547242	PMID:16782872	PMID:17143272	PMID:18794797	PMID:20960543
PMID:21603973	PMID:23376485	PMID:24217950	PMID:25677907	PMID:29350423

Genomics

Comparative Map Data

Efna1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	2	188,588,808 - 188,596,156 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	188,588,796 - 188,596,222 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	2	208,002,153 - 208,010,763 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	181,444,599 - 181,451,944 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	2	181,394,706 - 181,402,050 (-)	NCBI
Celera	2	168,623,896 - 168,631,240 (-)	NCBI		Celera
Cytogenetic Map	2	q34	NCBI
RH 3.4 Map	2	1155.2	RGD

EFNA1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	1	155,127,876 - 155,134,899 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	155,127,876 - 155,134,899 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	155,100,349 - 155,107,386 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	153,366,973 - 153,374,010 (+)	NCBI	NCBI36		hg18	NCBI36
Celera	1	128,171,631 - 128,178,823 (+)	NCBI
Cytogenetic Map	1	q22	NCBI
HuRef	1	126,462,656 - 126,469,862 (+)	NCBI		HuRef
CHM1_1	1	156,496,085 - 156,503,124 (+)	NCBI		CHM1_1

Efna1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	3	89,179,037 - 89,188,258 (-)	NCBI
GRCm38	3	89,271,730 - 89,280,951 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	3	89,271,733 - 89,281,142 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	3	89,075,652 - 89,084,873 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	3	89,357,663 - 89,365,568 (-)	NCBI			mm8
Celera	3	89,306,600 - 89,315,813 (-)	NCBI		Celera
Cytogenetic Map	3	F1	NCBI
cM Map	3	39.04	NCBI

Efna1
(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_004955545	1,610,929 - 1,617,460 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955545	1,610,929 - 1,617,217 (+)	NCBI	ChiLan1.0	ChiLan1.0

EFNA1
(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	1	134,083,855 - 134,091,228 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	134,083,855 - 134,091,228 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	1	130,475,128 - 130,482,531 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

EFNA1
(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	7	42,373,639 - 42,378,946 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	7	42,373,197 - 42,381,161 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Efna1
(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_004936580	4,654,503 - 4,660,950 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

EFNA1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	4	94,666,460 - 94,674,072 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	4	94,666,457 - 94,673,442 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	4	103,449,921 - 103,455,090 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

EFNA1
(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 Ensembl	20	8,696,241 - 8,702,379 (-)	Ensembl
ChlSab1.1	20	8,695,446 - 8,702,556 (-)	NCBI

Efna1
(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_004624885	2,382,712 - 2,388,805 (-)	NCBI

Position Markers

Efna1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	2	188,589,579 - 188,589,883	NCBI	Rnor6.0
Rnor_5.0	2	208,002,924 - 208,003,228	UniSTS	Rnor5.0
RGSC_v3.4	2	181,445,366 - 181,445,670	UniSTS	RGSC3.4
Celera	2	168,624,663 - 168,624,967	UniSTS
Cytogenetic Map	2	q34	UniSTS
RH 3.4 Map	2	1155.2	UniSTS

RH128971

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	2	188,588,874 - 188,589,078	NCBI	Rnor6.0
Rnor_5.0	2	208,002,219 - 208,002,423	UniSTS	Rnor5.0
RGSC_v3.4	2	181,444,661 - 181,444,865	UniSTS	RGSC3.4
Celera	2	168,623,958 - 168,624,162	UniSTS
Cytogenetic Map	2	q34	UniSTS
RH 3.4 Map	2	1156.4	UniSTS

Efna1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	2	188,589,482 - 188,589,632	NCBI	Rnor6.0
Rnor_5.0	2	208,002,827 - 208,002,977	UniSTS	Rnor5.0
RGSC_v3.4	2	181,445,269 - 181,445,419	UniSTS	RGSC3.4
Celera	2	168,624,566 - 168,624,716	UniSTS
Cytogenetic Map	2	q34	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
2293843	Kiddil6	Kidney dilation QTL 6	3.1		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	2	42776916	195645082	Rat
1598805	Memor8	Memory QTL 8	3		exploratory behavior trait (VT:0010471)	average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)	2	157914311	204022555	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	140566078	217498545	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	140566078	217498545	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	140566078	217498545	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	2	140566078	217498545	Rat
70175	BpQTLCluster3	Blood pressure QTL cluster 3	4.128		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	2	140566078	217498545	Rat
71113	Cari2	Carrageenan-induced inflammation QTL 2	2.7	0.009	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	2	147522550	217498710	Rat
631266	Bp132	Blood pressure QTL 132		0.0005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	46537589	217498710	Rat
61457	Niddm8	Non-insulin dependent diabetes mellitus QTL 8	4.1	0.01	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	2	188449158	189857032	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	43133606	217498545	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	43133606	217498545	Rat
61469	Bp16	Blood pressure QTL 16	5.64		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	2	184730446	229730446	Rat
61473	Bp19	Blood pressure QTL 19	6.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	186611811	189857032	Rat
70162	Bp63	Blood pressure QTL 63	5.64		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	2	184730446	229730446	Rat
724568	Uae13	Urinary albumin excretion QTL 13	4.4		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	2	149114878	225501939	Rat
1331734	Bp204	Blood pressure QTL 204	3.61192		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	181990297	240020001	Rat
1331760	Bp206	Blood pressure QTL 206	3.62454		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	56244671	217498710	Rat
1298074	Bp164	Blood pressure QTL 164		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42776916	217498710	Rat
1298076	Bp166	Blood pressure QTL 166		0.0009	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	141583337	217498710	Rat
1298080	Bp163	Blood pressure QTL 163		0.02	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	66828049	217498710	Rat
1298085	Bp165	Blood pressure QTL 165		0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42776916	217498710	Rat
1331794	Bp202	Blood pressure QTL 202	3.66819		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	147122993	240020001	Rat
1331805	Cm29	Cardiac mass QTL 29	3.50746		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	2	147122993	240020001	Rat
2307174	Activ3	Activity QTL 3	4.83	0.000058	locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	2	183984665	228984665	Rat
1581502	Esta3	Estrogen-induced thymic atrophy QTL 3			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	2	142053350	204585731	Rat
631501	Bp101	Blood pressure QTL 101	2.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	157914409	217498545	Rat
631507	Bp105	Blood pressure QTL 105		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	116075644	228737869	Rat
631522	Bp74	Blood pressure QTL 74		0.05	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	186611811	198704485	Rat
1302793	Bw16	Body weight QTL 16	5	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	2	169852800	217498545	Rat
1641891	Alcrsp17	Alcohol response QTL 17			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	2	155965557	254121739	Rat
1641925	Alcrsp2	Alcohol response QTL 2			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	2	155965557	237742948	Rat
1598833	Bp295	Blood pressure QTL 295	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	161745602	206745602	Rat
1598838	Bp290	Blood pressure QTL 290	1.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	181522444	226522444	Rat
2301415	Cm67	Cardiac mass QTL 67		0.003	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	2	172795683	189857032	Rat
634308	Sach6	Saccharin preference QTL 6	4.9		taste sensitivity trait (VT:0001986)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	2	116075644	228737869	Rat
1358356	Srcrt1	Stress Responsive Cort QTL1	3.66		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	2	175403337	239166203	Rat
1578648	Bss11	Bone structure and strength QTL 11	4.7		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	2	118446646	227707979	Rat
1300165	Rf9	Renal function QTL 9	3.28		kidney glomerulus integrity trait (VT:0010546)	index of glomerular damage (CMO:0001135)	2	138901276	217498710	Rat
1354601	Slep1	Serum leptin concentration QTL 1	5.39		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	2	43149788	198704485	Rat
1354605	Rf48	Renal function QTL 48	2.9		blood creatinine amount (VT:0005328)	plasma creatinine level (CMO:0000537)	2	75687495	221880419	Rat
1354609	Niddm62	Non-insulin dependent diabetes mellitus QTL 62	4.72	0.000006	insulin secretion trait (VT:0003564)	plasma insulin level (CMO:0000342)	2	158159186	217498710	Rat
1354622	Kidm16	Kidney mass QTL 16	3		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	2	83819608	239166203	Rat
1354648	Bp239	Blood pressure QTL 239		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	66828236	243550655	Rat
1354649	Kidm17	Kidney mass QTL 17	2.9		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	2	83819608	243901375	Rat
2301966	Bp322	Blood pressure QTL 322	3.58		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	158159186	217498710	Rat
1359022	Ppulsi1	Prepulse inhibition QTL 1	3.63		prepulse inhibition trait (VT:0003088)	acoustic startle response measurement (CMO:0001519)	2	142053350	228984665	Rat
1549833	Bp257	Blood pressure QTL 257		0.003	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	181987080	199696953	Rat
1554319	Bmd2	Bone mineral density QTL 2	13.4	0.0001	lumbar vertebra area (VT:0010570)	lumbar vertebra cross-sectional area (CMO:0001689)	2	118446793	228582621	Rat
2306901	Bp337	Blood pressure QTL 337		0.01	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	177680772	243901375	Rat
1358913	Cm41	Cardiac mass QTL 41	2.73		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	23837491	218957222	Rat
1358917	Cm42	Cardiac mass QTL 42	2.82		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	23837491	218957222	Rat
1359030	Bp277	Blood pressure QTL 277			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	118446646	200453484	Rat
1359030	Bp277	Blood pressure QTL 277			arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	118446646	200453484	Rat
1359032	Hrtrt18	Heart rate QTL 18			heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	2	169852670	207612467	Rat
61374	Edpm2	Estrogen-dependent pituitary mass QTL 2	4.42	0.86	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	2	78321410	217498710	Rat
61401	Niddm2	Non-insulin dependent diabetes mellitus QTL 2	4.54		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	159585731	204585731	Rat
6903312	Bw112	Body weight QTL 112	3.2	0.0013	body mass (VT:0001259)	body weight (CMO:0000012)	2	149614623	198704357	Rat
7488904	Bp363	Blood pressure QTL 363		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	186889035	189857032	Rat
7488925	Bp364	Blood pressure QTL 364		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	174160958	219160958	Rat
7488927	Bp365	Blood pressure QTL 365		0.008	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	177339806	222339806	Rat
8662843	Vetf9	Vascular elastic tissue fragility QTL 9	2.05		thoracic aorta molecular composition trait (VT:0010568)	aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)	2	169852670	243026643	Rat
8662832	Vetf7	Vascular elastic tissue fragility QTL 7	3.5		aorta elastin amount (VT:0003905)	aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)	2	83754907	237610852	Rat
10043136	Iddm54	Insulin dependent diabetes mellitus QTL 54	3.4	0.0001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	2	149614466	205573168	Rat
10043136	Iddm54	Insulin dependent diabetes mellitus QTL 54	3.4	0.0001	blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	2	149614466	205573168	Rat
12879846	Cm90	Cardiac mass QTL 90		0.011	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	2	172795683	189857032	Rat
12879836	Kidm61	Kidney mass QTL 61		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	172795683	199696953	Rat
10755499	Bp389	Blood pressure QTL 389	2.61		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	16679272	245624402	Rat
12879839	Cm85	Cardiac mass QTL 85		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	2	172795683	199696953	Rat
11565181	Bw176	Body weight QTL 176		0.002	body mass (VT:0001259)	body weight (CMO:0000012)	2	172795683	189857032	Rat
12879838	Cm86	Cardiac mass QTL 86		0.002	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	2	172795683	199696953	Rat
12879840	Bw179	Body weight QTL 179		0.005	body mass (VT:0001259)	body weight (CMO:0000012)	2	172795683	199696953	Rat
12879845	Cm89	Cardiac mass QTL 89		0.008	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	2	172795683	189857032	Rat
11565180	Kidm56	Kidney mass QTL 56		0.003	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	172795683	189857032	Rat
12879837	Am2	Aortic mass QTL 2		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	2	172795683	199696953	Rat
12879847	Am4	Aortic mass QTL 4		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	2	172795683	189857032	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	473
Count of miRNA genes:	248
Interacting mature miRNAs:	295
Transcripts:	ENSRNOT00000027920
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	3	36	33	33		33	1	4	1	30	30	11	1
Low		7	24	8	19	8	7	7	73	5	10		7
Below cutoff											1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053599	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008761228	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017591148	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AAHX01018587	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC098750	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC070514	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473976	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	D38056	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000027920 ⟹ ENSRNOP00000027920

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	2	188,588,796 - 188,596,222 (-)	Ensembl

RefSeq Acc Id:

NM_053599 ⟹ NP_446051

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	2	188,588,812 - 188,596,156 (-)	NCBI
Rnor_5.0	2	208,002,153 - 208,010,763 (-)	NCBI
RGSC_v3.4	2	181,444,599 - 181,451,944 (-)	RGD
Celera	2	168,623,896 - 168,631,240 (-)	RGD

Sequence:

show sequence

GCCAGTGGGAACCTTACACTGCGGAGCTTTCGTCCTGGCCTGGCCCGGCCCGGCCCCGCGCTAT
GGAGTTCCTTTGGGCCCCTCTCTTGGGTCTGTGCTGCAGTCTGGCCGCTGCTGACCGCCACATC
GTCTTCTGGAACAGTTCAAATCCCAAGTTCCGAGAGGAGGACTACACCGTGCACGTGCAGCTGA
ATGACTATCTGGACATCATCTGCCCACATTACGAGGACGACTCTGTGGCAGATGCTGCCATGGA
GAGATACACGCTGTACATGGTGGAACACCAGGAGTATGTGACATGCGAGCCCCAGTCCAAGGAC
CAGGTTCGCTGGAAGTGCAACCAGCCCAGTGCCAAGCACGGCCCGGAGAAGCTGTCTGAGAAAT
TCCAGCGCTTCACGCCTTTCACCTTGGGCAAGGAGTTCAAGGAAGGACACAGCTACTACTACAT
CTCCAAACCTATCTACCATCAGGAAACCCAGTGCCTGAAGTTGAAGGTGACTGTCAATGGCAAA
ATCACTCACAGCCCCCACGCCCATGCCAACCCACAGGAGAAGAGACTCCAAGCAGATGACCCGG
AAGTGCAGGTTTTGCACAGCATTGGTCACAGCGCCGCCCCCCGCCTCTTCCCATTGGTCTGGGC
AGTATTGCTCCTACCACTGCTGCTGCTGCAAACTCAGTGAAGGTATTTGCTTGCCCTGGCTTAC
GGATTGGAACGGGACTAAGGGGCAGGGTTAAGCACCCCCAAAGCCCCAGCCCTGGGAACCTCTC
CCACTACACGCACAAGACGCCACCACGAAGCCTCAGAAAGGTTCAGTATTAAGGGTTTTAACCG
AAAGGAGTTCAACCAGCCCAACTGGGCCATCCCTGCCTCCACTTCAGAGGGATGGAGAAAGAAG
TGGAGAAGGTCCTTTCCCTGTGGTTTCTACCTTTAAGCCAAAGAAACAAGCTGTGCGGACCTGG
CCCATTAAGAGCACCCACTGGGAGATGCGCTGAAAGAGCCTGAGGCCATGCAGTTGGACACTGA
ACTTGGTAAAAATGTCCTTCCCCAAGGAAGCCATAATGTGCAGATGAACTGACCAAAGGAAAAG
CTTGAGACAGCTTCCTGCGGGGAAGCCAGGTACAAGAGAGACAGCTTGGGCTGACCCAGCATCT
CTGCAAGATTTCCACCTGCTGGGCTGCCAGAGAGTTTTGTAGCCCGGCACTGACTGCATCCTCC
CCTTCCCTGGGGCAGCATTCCCTGAAGCTGTGCCAGCAGGAGGACTATAGCAGCCTGGTTTTGG
AGTATAGCTGTAAGGGCAGTGCCCATGTGTATAGTCTGTGGAGTTTAGCTTAAAGGGCAGGGCC
CACATGTACAGTGTCTGTATATAAACGTGCTGTCTGTTCATTTCTACGACTGGAGGTTTTTTAT
ACAGTGTTCTTGGATTCATAATAAAGTGATGTTTTTGGTTTTTTAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_008761228 ⟹ XP_008759450

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	2	188,588,808 - 188,595,996 (-)	NCBI

Sequence:

show sequence

CATGGGACTCCCTGGCAGCCTGGGTGCCGGGTTGGCAATGCCCTTTCCCAGGGTAACTGTCCCT
GCCAACCCCTGGTCAGGGGTGGGAAGGATTCTATAGCTCCTCACCTCAGTCTGTATCTCCCCTT
AGTACCTGGCAACAGCGGACCAGGGCAGAAACCTGCTCATGCCTACTTGCACAGGCGCTGTTTC
AGTCCTTTGGCATCCTATCACTCTAAAGTAAGGCTCTCATGCTGAGCGCTCCTGCCTTGATAGT
GGAACGTTGGCCTGGCCTCTGGGGGTTCTTTAAGTACCCCCTCGAAACTTCTGTGGACTCCCTT
TTTGGTGTGCCACTTGGGCATTTGTATCCTGACAGGCACCTACTGACGACTCTTGCCATCAAGA
GTAAGCACAATGCTCAGAGTAGCCCTGGGAAGACCCTTAGGAGAGACCCACGTTTGGGGTATTA
GGTATGCAGTCTGTATTTAAGATGAGTCTGGAGAGTACCTCCGAGGATTTTGGAGAGGGAGGCA
TAAATTAGGCACATGCTGAGCATGGGTAGACCAAGGGAGTGGCTGAGGTGGTCACACTAAGGAA
CCGGTAAGAGGAGTAGTGTCACTGGAAAGCTTGGGGAGGAGCCGAGTGGGGCTTCACAGGGCTA
CAAAGGCTGTAACAGGAAGGAGGTAATTTCTCCCGGGCAGGTTTTAGGGCAATGAAGCAAATGG
TATTGAGAGGAAGACACTGCCGGGCCCTTTGTTCTTGCCCTTGAGTTTCCTCAAGTTAGGAGAA
CAGTAATGGGCAAAACCTAAGAGGGAGGTATGGTGGACCAAGGAGAAAGCGGCCTAGCAGTTGA
GGTGAGGGGTCGAGGCCACAAAATACCACTAAACCACTCCTAGCTCCAGTGAGCCAGTTTCCTC
TGGCATTGCCTATTGAGGGTCTGTTGTCTAGGGCATGTCAGAGGGCAAGATGAAGCCAGCTGCC
ACCCCTAAAGGGGGTGCCTTCCCAGCCCCGGGTACTAACTACCACCTCCCAGCCAGCCCTTGGG
CCTTGCCCCTTGCCTCCCTGACCTAGTCCCGTCCTGGTAGTGGGAAAGAGCAAAGTCCCTGTTT
ATGCCCATGCCAGGTGTTGGCTGAAGGAGGAGGAGGGGACAGGAAGCCATGAGTAGGGAGGGGG
GAACCCTGGCCTTTTCCGTTCCCAAGCTCCCAGGTTTCCTCTCTTTCAGGAAGGAGCCTCTTCC
TTACCCCCCTCCCTGTCTTCTCCACCACTAATGTAACCCCCTTTTCCAGATGGAGACTAAGTGT
CAGGGGCGGGCTAAGTGTAGGAGATAGGACGCTAAGTATAGCTTCAGCCCTGGCCCTCTGGACA
CACACATACCCTGTCTTATTTACAGCTACAGGAAAGTCCGTCTAGAGTGGAGGTCATGGGCGGT
CTAGCCAGGCCCAGCTTGGGGGAAGAGATGAGGTGGCAATGAACAGGGCGGGTGTAGGGTTGCA
TAGGTGACTCAGGGTAGTGGGCATTAGTCCTGGGATCACCAGGCTCCAGGCAGAGGCAGTGTCA
GAGAAAGGTGCCACTGTGAGCTGGACCCTGGTCCTGGAGAGAGGTACCCTAGCTCTTCAGACTT
CTCTGCTCCTTTTGCCCAGAAGCTGGCACTGGGCAAACCGGTACTGGGCTGTCCTGGGGTCCAG
GGGGCAGCTCACATTTGACAAGGTTCCGAGAGGAGGACTACACCGTGCACGTGCAGCTGAATGA
CTATCTGGACATCATCTGCCCACATTACGAGGACGACTCTGTGGCAGATGCTGCCATGGAGAGA
TACACGCTGTACATGGTGGAACACCAGGAGTATGTGACATGCGAGCCCCAGTCCAAGGACCAGG
TTCGCTGGAAGTGCAACCAGCCCAGTGCCAAGCACGGCCCGGAGAAGCTGTCTGAGAAATTCCA
GCGCTTCACGCCTTTCACCTTGGGCAAGGAGTTCAAGGAAGGACACAGCTACTACTACATCTCC
AAACCTATCTACCATCAGGAAACCCAGTGCCTGAAGTTGAAGGTGACTGTCAATGGCAAAATCA
CTCACAGCCCCCACGCCCATGCCAACCCACAGGAGAAGAGACTCCAAGCAGATGACCCGGAAGT
GCAGGTTTTGCACAGCATTGGTCACAGCGCCGCCCCCCGCCTCTTCCCATTGGTCTGGGCAGTA
TTGCTCCTACCACTGCTGCTGCTGCAAACTCAGTGAAGGTATTTGCTTGCCCTGGCTTACGGAT
TGGAACGGGACTAAGGGGCAGGGTTAAGCACCCCCAAAGCCCCAGCCCTGGGAACCTCTCCCAC
TACACGCACAAGACGCCACCACGAAGCCTCAGAAAGGTTCAGTATTAAGGGTTTTAACCGAAAG
GAGTTCAACCAGCCCAACTGGGCCATCCCTGCCTCCACTTCAGAGGGATGGAGAAAGAAGTGGA
GAAGGTCCTTTCCCTGTGGTTTCTACCTTTAAGCCAAAGAAACAAGCTGTGCGGACCTGGCCCA
TTAAGAGCACCCACTGGGAGATGCGCTGAAAGAGCCTGAGGCCATGCAGTTGGACACTGAACTT
GGTAAAAATGTCCTTCCCCAAGGAAGCCATAATGTGCAGATGAACTGACCAAAGGAAAAGCTTG
AGACAGCTTCCTGCGGGGAAGCCAGGTACAAGAGAGACAGCTTGGGCTGACCCAGCATCTCTGC
AAGATTTCCACCTGCTGGGCTGCCAGAGAGTTTTGTAGCCCGGCACTGACTGCATCCTCCCCTT
CCCTGGGGCAGCATTCCCTGAAGCTGTGCCAGCAGGAGGACTATAGCAGCCTGGTTTTGGAGTA
TAGCTGTAAGGGCAGTGCCCATGTGTATAGTCTGTGGAGTTTAGCTTAAAGGGCAGGGCCCACA
TGTACAGTGTCTGTATATAAACGTGCTGTCTGTTCATTTCTACGACTGGAGGTTTTTTATACAG
TGTTCTTGGATTCATAATAAAGTGATGTTTTTGGTTTTTTAATGGA

hide sequence

RefSeq Acc Id:

XM_017591148 ⟹ XP_017446637

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	2	188,588,808 - 188,594,304 (-)	NCBI

Sequence:

show sequence

TCTCACATGCTCCCAGGAGCGCCTGGGCGGGTAGCAGAGGTGGATGAGGCATGAGTGAGTCAGT
GCCCATCACGGGAATAGGGGAAAGACGCCAGGCCCAGAGCTGAAATACCTGTTCTGAAATGGCT
TCTATGTTTATCTCTCCAGAGAGGAATTTTAAAAGCCTCCCTCTGCTTCTCTCTCTTTTCCCCC
GGGGTGGGGGAGGGGCCTGCTAAGCCTAGTTCTAGAGGCTGCAAGCTGTTGCAAGGCCAGGGCT
CTAAAGGATCATGATGACCGGGTGGTGGGTGGCCACCATGGAACCCCACCATCACCATGGGCAC
CACCCATGCCAAGGACTTTGGTTTAAAGCAAGTTGGCAGCCAGCTCTGCAGAGCATCTCCTGGC
GGTGCTTGGGGGAATTCAGAGAAGCTGACTGGCTTTCAGCGGGAGGAGGGAAGCACTTTCCTAC
AGCTAAGACCCTACCCAGCCTGGAGCCAGGTTCCGAGAGGAGGACTACACCGTGCACGTGCAGC
TGAATGACTATCTGGACATCATCTGCCCACATTACGAGGACGACTCTGTGGCAGATGCTGCCAT
GGAGAGATACACGCTGTACATGGTGGAACACCAGGAGTATGTGACATGCGAGCCCCAGTCCAAG
GACCAGGTTCGCTGGAAGTGCAACCAGCCCAGTGCCAAGCACGGCCCGGAGAAGCTGTCTGAGA
AATTCCAGCGCTTCACGCCTTTCACCTTGGGCAAGGAGTTCAAGGAAGGACACAGCTACTACTA
CATCTCCAAACCTATCTACCATCAGGAAACCCAGTGCCTGAAGTTGAAGGTGACTGTCAATGGC
AAAATCACTCACAGCCCCCACGCCCATGCCAACCCACAGGAGAAGAGACTCCAAGCAGATGACC
CGGAAGTGCAGGTTTTGCACAGCATTGGTCACAGCGCCGCCCCCCGCCTCTTCCCATTGGTCTG
GGCAGTATTGCTCCTACCACTGCTGCTGCTGCAAACTCAGTGAAGGTATTTGCTTGCCCTGGCT
TACGGATTGGAACGGGACTAAGGGGCAGGGTTAAGCACCCCCAAAGCCCCAGCCCTGGGAACCT
CTCCCACTACACGCACAAGACGCCACCACGAAGCCTCAGAAAGGTTCAGTATTAAGGGTTTTAA
CCGAAAGGAGTTCAACCAGCCCAACTGGGCCATCCCTGCCTCCACTTCAGAGGGATGGAGAAAG
AAGTGGAGAAGGTCCTTTCCCTGTGGTTTCTACCTTTAAGCCAAAGAAACAAGCTGTGCGGACC
TGGCCCATTAAGAGCACCCACTGGGAGATGCGCTGAAAGAGCCTGAGGCCATGCAGTTGGACAC
TGAACTTGGTAAAAATGTCCTTCCCCAAGGAAGCCATAATGTGCAGATGAACTGACCAAAGGAA
AAGCTTGAGACAGCTTCCTGCGGGGAAGCCAGGTACAAGAGAGACAGCTTGGGCTGACCCAGCA
TCTCTGCAAGATTTCCACCTGCTGGGCTGCCAGAGAGTTTTGTAGCCCGGCACTGACTGCATCC
TCCCCTTCCCTGGGGCAGCATTCCCTGAAGCTGTGCCAGCAGGAGGACTATAGCAGCCTGGTTT
TGGAGTATAGCTGTAAGGGCAGTGCCCATGTGTATAGTCTGTGGAGTTTAGCTTAAAGGGCAGG
GCCCACATGTACAGTGTCTGTATATAAACGTGCTGTCTGTTCATTTCTACGACTGGAGGTTTTT
TATACAGTGTTCTTGGATTCATAATAAAGTGATGTTTTTGGTTTTTTAATGGA

hide sequence

Protein Sequences


Protein RefSeqs	NP_446051	(Get FASTA)	NCBI Sequence Viewer
	XP_008759450	(Get FASTA)	NCBI Sequence Viewer
	XP_017446637	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH70514	(Get FASTA)	NCBI Sequence Viewer
	BAA07242	(Get FASTA)	NCBI Sequence Viewer
	EDM00644	(Get FASTA)	NCBI Sequence Viewer
	P97553	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_446051 ⟸ NM_053599
- Peptide Label:	precursor
- UniProtKB:	P97553 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MEFLWAPLLGLCCSLAAADRHIVFWNSSNPKFREEDYTVHVQLNDYLDIICPHYEDDSVADAAM ERYTLYMVEHQEYVTCEPQSKDQVRWKCNQPSAKHGPEKLSEKFQRFTPFTLGKEFKEGHSYYY ISKPIYHQETQCLKLKVTVNGKITHSPHAHANPQEKRLQADDPEVQVLHSIGHSAAPRLFPLVW AVLLLPLLLLQTQ hide sequence

RefSeq Acc Id:	XP_008759450 ⟸ XM_008761228
- Peptide Label:	isoform X1
- Sequence:	show sequence MERYTLYMVEHQEYVTCEPQSKDQVRWKCNQPSAKHGPEKLSEKFQRFTPFTLGKEFKEGHSYY YISKPIYHQETQCLKLKVTVNGKITHSPHAHANPQEKRLQADDPEVQVLHSIGHSAAPRLFPLV WAVLLLPLLLLQTQ hide sequence

RefSeq Acc Id:	XP_017446637 ⟸ XM_017591148
- Peptide Label:	isoform X1
- Sequence:	show sequence MERYTLYMVEHQEYVTCEPQSKDQVRWKCNQPSAKHGPEKLSEKFQRFTPFTLGKEFKEGHSYY YISKPIYHQETQCLKLKVTVNGKITHSPHAHANPQEKRLQADDPEVQVLHSIGHSAAPRLFPLV WAVLLLPLLLLQTQ hide sequence

RefSeq Acc Id:

ENSRNOP00000027920 ⟸ ENSRNOT00000027920

Protein Domains

Ephrin RBD

Transcriptome

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

Promoters

RGD ID:

13691468

Promoter ID:

EPDNEW_R1993

Type:

initiation region

Name:

Efna1_1

Description:

ephrin A1

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	2	188,596,193 - 188,596,253	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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620388	AgrOrtholog
Ensembl Genes	ENSRNOG00000020573	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000027920	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000027920	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	2.60.40.420	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7100462	IMAGE-MGC_LOAD
InterPro	Cupredoxin	UniProtKB/Swiss-Prot
	Ephrin	UniProtKB/Swiss-Prot
	Ephrin-A_Ecto	UniProtKB/Swiss-Prot
	Ephrin_CS	UniProtKB/Swiss-Prot
	Ephrin_RBD	UniProtKB/Swiss-Prot
KEGG Report	rno:94268	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:91567	IMAGE-MGC_LOAD
NCBI Gene	94268	ENTREZGENE
PANTHER	PTHR11304	UniProtKB/Swiss-Prot
Pfam	Ephrin	UniProtKB/Swiss-Prot
PhenoGen	Efna1	PhenoGen
PRINTS	EPHRIN	UniProtKB/Swiss-Prot
PROSITE	EPHRIN_RBD_1	UniProtKB/Swiss-Prot
	EPHRIN_RBD_2	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF49503	UniProtKB/Swiss-Prot
UniGene	Rn.8427	ENTREZGENE
UniProt	EFNA1_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary	Q6NS29	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-01-20	Efna1	ephrin A1			Symbol and Name status set to approved	1299863	APPROVED
2002-08-07	Efna1	ephrin A1			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expressed in thymic epithelial cells and thymocytes	625721
gene_expression	expressed in the early stage of thymic development	625721
gene_expression	broadly expressed in both the thymic epithelial cells and thymocytes	625721
gene_expression	expressed in epithelial cells of various organs, developing skeletal system and dorsal root ganglia	632612
gene_process	involved in blood vessel destabilization via the Rac/PAK pathway	1299268

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 - CTD

RGD Manual Annotations

Imported Annotations - PID (archival)