Ephb2 (Eph receptor B2) - Rat Genome Database

Name: Ephb2
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Ephb2 (Eph receptor B2) Rattus norvegicus

Analyze

Symbol:

Ephb2

Name:

Eph receptor B2

RGD ID:

1564232

Description:

Predicted to have several functions, including amyloid-beta binding activity; identical protein binding activity; and transmembrane signaling receptor activity. Involved in positive regulation of gene expression and positive regulation of protein localization to plasma membrane. Predicted to localize to several cellular components, including glutamatergic synapse; integral component of synaptic membrane; and neuronal cell body. Human ortholog(s) of this gene implicated in blood platelet disease. Orthologous to human EPHB2 (EPH receptor B2); PARTICIPATES IN ephrin - ephrin receptor bidirectional signaling axis; syndecan signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

ephrin type-B receptor 2; LOC313633; RGD1564232; similar to Ephb2 protein

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):	EPHB2 (EPH receptor B2)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Ephb2 (Eph receptor B2)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Ephb2 (EPH receptor B2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	EPHB2 (EPH receptor B2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	EPHB2 (EPH receptor B2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Ephb2 (EPH receptor B2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	EPHB2 (EPH receptor B2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	EPHB2 (EPH receptor B2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Ephb2 (EPH receptor B2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	EPHB3 (EPH receptor B3)	HGNC	OrthoDB
Homo sapiens (human):	EPHB1 (EPH receptor B1)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	EPHB2 (EPH receptor B2)	Alliance	DIOPT (HGNC\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Ephb2 (Eph receptor B2)	Alliance	DIOPT (PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	ephb2b (eph receptor B2b)	Alliance	DIOPT (PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	ephb2a (eph receptor B2a)	Alliance	DIOPT (PhylomeDB\|TreeFam)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

NCBI Annotation Information:

Annotation category: partial on reference assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	5	155,024,478 - 155,143,539 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	155,022,493 - 155,204,456 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	158,789,192 - 158,907,248 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Rnor_5.0	5	156,786,985 - 156,811,195 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	155,423,035 - 155,605,384 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	5	147,297,353 - 147,415,432 (-)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Colorectal Neoplasms (ISO)

COVID-19 (ISO)

Ependymomas (ISO)

Peters anomaly (ISO)

Platelet-Type Bleeding Disorder 22 (ISO)

Prostate Cancer/Brain Cancer Susceptibility (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

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

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

4-hydroxyphenyl retinamide (ISO)

6-propyl-2-thiouracil (EXP)

aflatoxin B1 (ISO)

aflatoxin B2 (ISO)

aflatoxin M1 (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

atrazine (ISO)

belinostat (ISO)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

bortezomib (ISO)

Brodifacoum (EXP)

butanal (ISO)

C60 fullerene (EXP)

cadmium atom (ISO)

choline (ISO)

cisplatin (ISO)

cobalt dichloride (ISO)

cocaine (EXP)

columbamine (ISO)

CU-O LINKAGE (ISO)

decabromodiphenyl ether (EXP)

diethyl malate (ISO)

dorsomorphin (ISO)

folic acid (ISO)

L-methionine (ISO)

lead(0) (ISO)

lead(2+) (ISO)

lipopolysaccharide (ISO)

mercury dibromide (ISO)

methapyrilene (ISO)

methylmercury chloride (ISO)

nitrogen dioxide (ISO)

p-chloromercuribenzoic acid (ISO)

panobinostat (ISO)

paracetamol (ISO)

phenylmercury acetate (ISO)

pirinixic acid (ISO)

ponatinib (ISO)

potassium chromate (ISO)

potassium dichromate (ISO)

propanal (ISO)

SB 431542 (ISO)

sodium arsenite (ISO)

sodium dichromate (ISO)

Soman (EXP)

sunitinib (ISO)

tert-butyl hydroperoxide (ISO)

titanium dioxide (ISO)

triazines (ISO)

trichostatin A (ISO)

tunicamycin (ISO)

urethane (ISO)

valproic acid (EXP,ISO)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

angiogenesis (ISO)

animal organ morphogenesis (ISO)

axon guidance (IBA,ISO)

axonal fasciculation (ISO)

biological_process (ND)

camera-type eye morphogenesis (ISO)

cell morphogenesis (ISO)

central nervous system projection neuron axonogenesis (IBA,ISO)

commissural neuron axon guidance (ISO)

corpus callosum development (ISO)

dendritic spine development (ISO)

dendritic spine morphogenesis (ISO)

ephrin receptor signaling pathway (ISO)

inactivation of MAPKK activity (ISO)

inner ear morphogenesis (ISO)

learning (ISO)

learning or memory (ISO)

multicellular organism development (IBA)

negative regulation of axonogenesis (ISO)

negative regulation of ERK1 and ERK2 cascade (ISO)

negative regulation of NMDA glutamate receptor activity (ISO)

negative regulation of protein phosphorylation (ISO)

negative regulation of Ras protein signal transduction (ISO)

neuron projection retraction (ISO)

optic nerve morphogenesis (ISO)

peptidyl-tyrosine phosphorylation (ISO)

phosphorylation (ISO)

positive regulation of gene expression (IMP)

positive regulation of kinase activity (IBA)

positive regulation of long-term neuronal synaptic plasticity (ISO)

positive regulation of long-term synaptic potentiation (ISO)

positive regulation of NMDA glutamate receptor activity (ISO)

positive regulation of protein localization to plasma membrane (IMP)

positive regulation of synapse assembly (ISO)

positive regulation of synaptic plasticity (ISO)

postsynaptic membrane assembly (IDA,IMP)

protein phosphorylation (ISO)

regulation of axonogenesis (ISO)

regulation of blood coagulation (ISO)

regulation of body fluid levels (ISO)

regulation of neuronal synaptic plasticity (ISO)

regulation of synapse assembly (ISO)

retinal ganglion cell axon guidance (ISO)

roof of mouth development (ISO)

trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission (ISO)

transmembrane receptor protein tyrosine kinase signaling pathway (IBA,ISO)

urogenital system development (ISO)

Cellular Component

axon (ISO)

cellular_component (ND)

dendrite (ISO)

glutamatergic synapse (IDA,IMP,ISO)

integral component of plasma membrane (IBA,ISO)

integral component of postsynaptic membrane (ISO)

integral component of presynaptic membrane (ISO)

neuron projection (IBA)

neuronal cell body (ISO)

nucleoplasm (IEA,ISO)

plasma membrane (ISO)

receptor complex (IBA)

Molecular Function

amyloid-beta binding (ISO)

ATP binding (IEA)

axon guidance receptor activity (ISO)

ephrin receptor activity (ISO)

identical protein binding (ISO)

molecular_function (ND)

protein binding (ISO)

protein tyrosine kinase activity (ISO)

protein-containing complex binding (IPI,ISO)

signaling receptor activity (ISO)

signaling receptor binding (ISO)

transmembrane receptor protein tyrosine kinase activity (IBA)

transmembrane-ephrin receptor activity (IBA,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

ephrin - ephrin receptor bidirectional signaling axis (ISO)

syndecan signaling pathway (ISO)

References

References - curated


1.	Cissé M, etal., Nature. 2011 Jan 6;469(7328):47-52. doi: 10.1038/nature09635. Epub 2010 Nov 28.
2.	Dalva MB, etal., Cell. 2000 Dec 8;103(6):945-56.
3.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4.	OMIM Disease Annotation Pipeline
5.	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
6.	RGD automated data pipeline
7.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8.	RGD automated import pipeline for gene-chemical interactions
9.	RGD comprehensive gene curation

Additional References at PubMed

PMID:8689685	PMID:8947026	PMID:9883737	PMID:9990854	PMID:10839360	PMID:11532925	PMID:11585923	PMID:11754835	PMID:11754836	PMID:11780069	PMID:12052960	PMID:12971893
PMID:14691139	PMID:14988728	PMID:15223334	PMID:16977320	PMID:17122040	PMID:17310244	PMID:17440041	PMID:17686994	PMID:18410519	PMID:19302865	PMID:21029865	PMID:21364901
PMID:21471370	PMID:21608225	PMID:21746865	PMID:23831214	PMID:23881165	PMID:25834064	PMID:25922200	PMID:28276447	PMID:28358367	PMID:29731254	PMID:30213874

Genomics

Comparative Map Data

Ephb2
(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	5	155,024,478 - 155,143,539 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	155,022,493 - 155,204,456 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	158,789,192 - 158,907,248 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Rnor_5.0	5	156,786,985 - 156,811,195 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	155,423,035 - 155,605,384 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	5	147,297,353 - 147,415,432 (-)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

EPHB2
(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	22,710,839 - 22,921,500 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	22,710,770 - 22,921,500 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	23,037,263 - 23,241,823 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	22,909,918 - 23,114,410 (+)	NCBI	NCBI36		hg18	NCBI36
Celera	1	21,361,651 - 21,563,983 (+)	NCBI
Cytogenetic Map	1	p36.12	NCBI
HuRef	1	21,351,920 - 21,485,793 (+)	NCBI		HuRef
CHM1_1	1	23,149,831 - 23,360,325 (+)	NCBI		CHM1_1

Ephb2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	136,374,850 - 136,563,637 (-)	NCBI	GRCm39		mm39
GRCm38	4	136,647,536 - 136,836,326 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	136,647,539 - 136,835,988 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	136,209,523 - 136,391,850 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	4	135,925,684 - 136,108,011 (-)	NCBI			mm8
Celera	4	134,853,290 - 135,040,552 (-)	NCBI		Celera
Cytogenetic Map	4	D3	NCBI
cM Map	4	69.0	NCBI

Ephb2
(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_004955452	2,844,713 - 2,980,445 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955452	2,844,713 - 2,986,790 (+)	NCBI	ChiLan1.0	ChiLan1.0

EPHB2
(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	22,914,584 - 23,054,752 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	22,912,570 - 23,047,118 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	1	21,895,961 - 22,107,649 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

EPHB2
(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	2	76,428,203 - 76,612,786 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	2	76,427,112 - 76,551,494 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Ephb2
(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_004936474	8,109,800 - 8,203,106 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

EPHB2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	80,649,143 - 80,843,567 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	80,649,098 - 80,849,979 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	74,689,973 - 74,878,715 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

EPHB2
(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	109,746,925 - 109,890,777 (-)	Ensembl
ChlSab1.1	20	109,747,883 - 109,954,936 (-)	NCBI

Ephb2
(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_004624764	7,421,818 - 7,599,800 (+)	NCBI

Position Markers

D5Rat41

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	155,051,873 - 155,052,001	NCBI	Rnor6.0
Rnor_5.0	5	158,816,587 - 158,816,715	UniSTS	Rnor5.0
RGSC_v3.4	5	155,450,540 - 155,450,798	RGD	RGSC3.4
RGSC_v3.4	5	155,450,641 - 155,450,769	UniSTS	RGSC3.4
RGSC_v3.1	5	155,460,680 - 155,460,808	RGD
Celera	5	147,324,795 - 147,324,923	UniSTS
Cytogenetic Map	5	q36	UniSTS
RH 3.4 Map	5	1008.9	RGD
RH 3.4 Map	5	1008.9	UniSTS
FHH x ACI Map	5	84.23	UniSTS
FHH x ACI Map	5	84.23	RGD

D5Uwm43

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	155,136,406 - 155,136,543	NCBI	Rnor6.0
Rnor_5.0	5	158,900,115 - 158,900,252	UniSTS	Rnor5.0
RGSC_v3.4	5	155,536,222 - 155,536,392	RGD	RGSC3.4
RGSC_v3.4	5	155,536,223 - 155,536,392	UniSTS	RGSC3.4
RGSC_v3.1	5	155,546,261 - 155,546,431	RGD
Celera	5	147,408,299 - 147,408,436	UniSTS
Cytogenetic Map	5	q36	UniSTS

RH131438

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	155,022,880 - 155,023,080	NCBI	Rnor6.0
Rnor_5.0	5	158,787,594 - 158,787,794	UniSTS	Rnor5.0
RGSC_v3.4	5	155,421,437 - 155,421,637	UniSTS	RGSC3.4
Celera	5	147,295,755 - 147,295,955	UniSTS
Cytogenetic Map	5	q36	UniSTS
RH 3.4 Map	5	1007.9	UniSTS

UNH1020

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	155,115,890 - 155,116,431	NCBI	Rnor6.0
Rnor_5.0	5	158,879,599 - 158,880,140	UniSTS	Rnor5.0
RGSC_v3.4	5	155,516,031 - 155,516,572	UniSTS	RGSC3.4
Celera	5	147,388,128 - 147,388,669	UniSTS
Cytogenetic Map	5	q36	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
2302369	Scl60	Serum cholesterol level QTL 60	3.13		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	149568588	167739697	Rat
631263	Cm24	Cardiac mass QTL 24	3.5		heart mass (VT:0007028)	heart left ventricle weight to body weight ratio (CMO:0000530)	5	149832180	164807402	Rat
61444	Strs2	Sensitivity to stroke QTL 2	4.7		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	5	142309061	173707219	Rat
70156	Niddm30	Non-insulin dependent diabetes mellitus QTL 30	3.98		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	5	134502140	157212422	Rat
724525	Bp147	Blood pressure QTL 147	4.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	132551937	173707219	Rat
1331721	Bp210	Blood pressure QTL 210	3.413		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	5	149029982	173687766	Rat
1298089	Scl14	Serum cholesterol level QTL 14	5.8	0.0004	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	114140832	159140832	Rat
631562	Apr2	Acute phase response QTL 2	3.7		blood murinoglobulin 1 amount (VT:0010597)	plasma murinoglobulin 1 level (CMO:0001931)	5	142307322	173707219	Rat
738018	Anxrr4	Anxiety related response QTL 4	5.1		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	5	136354114	173707219	Rat
631505	Bp103	Blood pressure QTL 103	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	138154677	172402610	Rat
1302790	Scl20	Serum cholesterol level QTL 20	6.4	0.0001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	84963058	173504662	Rat
1641920	Colcs1	Colorectal carcinoma susceptibility QTL 1	2.99	0.0055	intestine integrity trait (VT:0010554)	benign colorectal tumor surface area measurement (CMO:0001799)	5	128687766	173687766	Rat
1598819	Bp292	Blood pressure QTL 292	4.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	133943857	173707219	Rat
1598847	Cm62	Cardiac mass QTL 62	3.4		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	114140832	159140832	Rat
1598861	Cm64	Cardiac mass QTL 64	2.9		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	133943857	173707219	Rat
2293642	Bss37	Bone structure and strength QTL 37	4.64	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	125455818	157225114	Rat
634349	Bp139	Blood pressure QTL 139		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	134197905	173707219	Rat
1578766	Tcas11	Tongue tumor susceptibility QTL 11	4.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	5	47745646	167946134	Rat
1300119	Bp180	Blood pressure QTL 180	3.82		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	5	150340838	164298744	Rat
1354598	Srn6	Serum renin concentration QTL 6	3.8		blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	5	71552569	157225114	Rat
2317056	Wbc3	White blood cell count QTL 3	2.51	0.01	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	5	111278451	156278451	Rat
1549838	Bss4	Bone structure and strength QTL 4	9.2		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	5	112279412	157279412	Rat
2313096	Bmd78	Bone mineral density QTL 78	3.1	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	5	150360936	167946134	Rat
61393	Bp7	Blood pressure QTL 7	4.5	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	61612600	168109659	Rat
8694441	Bw169	Body weight QTL 169	17.61	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	5	116767924	161767924	Rat
7794791	Mcs33	Mammary carcinoma susceptibility QTL 33	1.93		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	5	136640731	173707219	Rat
8552908	Pigfal4	Plasma insulin-like growth factor 1 level QTL 4	6.6		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	134712342	173707219	Rat
8694198	Abfw3	Abdominal fat weight QTL 3	16.13	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	5	116767924	161767924	Rat
8694389	Bw160	Body weight QTL 160	6.17	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	5	116767924	161767924	Rat
8552960	Pigfal15	Plasma insulin-like growth factor 1 level QTL 15			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	116767924	161767924	Rat
8694169	Bw148	Body weight QTL 148	5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	134712342	173707219	Rat
7207488	Bss110	Bone structure and strength QTL 1	8.4		femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	5	112279412	157279412	Rat
7207491	Bss112	Bone structure and strength QTL 112	7		femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	5	112279412	157279412	Rat
7207481	Bss106	Bone structure and strength QTL 106	7.9		femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	112279412	157279412	Rat
7207486	Bss109	Bone structure and strength QTL 109			femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	5	112279412	157279412	Rat
10053720	Scort26	Serum corticosterone level QTL 26	2.06	0.0147	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	131077716	173707219	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	60
Count of miRNA genes:	60
Interacting mature miRNAs:	60
Transcripts:	ENSRNOT00000016983
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	2	6	10	4	6	4			59	20	28
Low	1	23	20	10	13	10	5	5	15	15	10	11	5
Below cutoff		14	25	25		25	3	6			3		3

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001127319	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AABR07050187	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07050188	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07050189	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07050190	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AABR07073178	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01040332	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01040333	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01040334	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01040335	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC113790	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473968	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	DQ011670	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000016983 ⟹ ENSRNOP00000016983

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	5	155,023,006 - 155,143,539 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000089574 ⟹ ENSRNOP00000070517

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	5	155,022,493 - 155,204,456 (-)	Ensembl

RefSeq Acc Id:

NM_001127319 ⟹ NP_001120791

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	5	155,024,478 - 155,143,539 (-)	NCBI
Rnor_5.0	5	158,789,192 - 158,907,248 (-)	NCBI
RGSC_v3.4	5	155,423,035 - 155,605,384 (-)	RGD
Celera	5	147,297,353 - 147,415,432 (-)	RGD

Sequence:

show sequence

ATGGCCGTGCGCAGGCTGGGGGCCGCGCTGCTGCTGCTGCCGCTGCTAGCCGCCGTGGAAGAAA
CACTGATGGACTCTACTACAGCAACGGCTGAGCTGGGCTGGATGGTACATCCCCCATCAGGGTG
GGAAGAGGTGAGCGGCTACGATGAGAACATGAACACTATCCGTACCTACCAGGTGTGCAATGTC
TTTGAGTCAAGCCAGAACAACTGGCTACGGACCAAATTCATCCGGCGCCGCGGCGCCCACCGCA
TCCACGTGGAGATGAAGTTCTCGGTGCGTGACTGTAGCAGCATTCCCAGCGTGCCCGGCTCCTG
CAAGGAGACCTTCAACCTCTACTACTATGAGGCTGATTTTGACTTAGCCACCAAGACCTTTCCC
AACTGGATGGAGAATCCGTGGGTGAAGGTGGACACCATTGCGGCTGATGAGAGCTTTTCCCAGG
TGGATCTGGGTGGCCGCGTCATGAAAATCAACACTGAGGTGCGAAGCTTCGGTCCCGTGTCCCG
CAATGGTTTCTACCTGGCCTTCCAGGACTACGGCGGCTGTATGTCCCTCATTGCGGTGCGCGTC
TTCTACCGGAAGTGCCCCCGAGTCATCCAGAATGGTGCCATCTTCCAGGAGACACTGTCGGGGG
CTGAGAGCACCTCACTGGTAGCTGCTCGGGGCAGCTGCATCGCCAACGCTGAAGAAGTGGATGT
ACCCATCAAACTCTACTGTAACGGGGACGGCGAATGGCTGGTGCCCATCGGTCGCTGCATGTGC
AAGGCGGGCTTCGAGGCTGTGGAGAACGGTACCGTCTGCCGAGGTTGTCCATCAGGAACCTTCA
AGGCCAACCAAGGGGATGAAGCCTGTACCCACTGTCCCATCAACAGCCGTACCACCTCCGAGGG
TGCCACCAACTGTGTGTGCCGTAACGGCTACTACAGGGCTGACCTGGACCCCTTAGACATGCCT
TGCACAACCATCCCCTCTGCGCCCCAGGCTGTGATCTCCAGTGTCAACGAGACGTCCCTCGTGC
TAGAGTGGACCCCGCCACGAGACTCGGGGGGCCGTGAGGACCTTGTTTATAACATCATCTGCAA
GAGCTGTGGCTCAGGCCGGGGTGCCTGCACGCGCTGTGGAGACAATGTGCAGTACGCACCCCGC
CAGCTAGGCCTGACCGAGCCACGCATCTACATCAGTGACCTGCTGGCACACACACAGTACACCT
TCGAGATCCAGGCCGTGAATGGTGTCACCGACCAGAGTCCCTTCTCACCTCAGTTCGCCTCTGT
GAACATCACCACCAACCAAGCAGCACCGTCGGCCGTGTCCATCATGCACCAGGTGAGCCGCACC
GTGGACAGCATCACCCTGTCGTGGTCCCAGCCAGACCAGCCCAACGGTGTGATCCTGGACTATG
AACTACAGTACTATGAGAAGGAGCTCAGTGAGTACAACGCCACAGCCATAAAAAGCCCCACCAA
CACAGTCACTGTGCAGGGCCTCAAAGCCGGCACCATCTATGTCTTCCAGGTGCGGGCACGCACC
GTCGCAGGCTATGGGCGTTACAGTGGCAAGATGTACTTCCAAACCATGACAGAAGCCGAGTACC
AGACCAGCATCAAGGAAAAGCTGCCCCTCATCGTCGGCTCCTCCGCTGCCGGCGTAGTCTTCGT
CATCGCCGTGGTCGTCATTGCCATCGTATGTAACAGACGGGGGTTTGAGCGTGCCGACTCAGAG
TACACGGACAAGCTGCAGCACTACACCAGCGGCCACATGACCCCAGGCATGAAGATCTATATTG
ACCCTTTCACCTATGAAGATCCTAATGAGGCAGTGCGGGAGTTTGCCAAGGAAATCGACATCTC
CTGTGTCAAGATTGAGCAGGTGATTGGAGCAGGGGAATTTGGTGAGGTCTGCAGTGGCCACTTG
AAGCTGCCAGGGAAGAGAGAGATCTTTGTAGCCATCAAGACCCTCAAGTCAGGATACACAGAGA
AACAGCGCCGGGACTTCCTGAGTGAGGCATCCATCATGGGCCAGTTCGACCACCCCAATGTCAT
CCACCTGGAAGGGGTTGTCACCAAGAGCACACCTGTCATGATCATCACTGAATTCATGGAGAAC
GGTTCCCTGGACTCCTTCCTCCGGCAAAACGATGGGCAGTTCACGGTCATCCAACTGGTGGGCA
TGCTGAGGGGCATCGCAGCTGGCATGAAGTACCTGGCGGACATGAACTATGTGCACCGGGACCT
TGCTGCACGCAACATCCTTGTCAATAGCAACCTGGTGTGCAAGGTGTCTGACTTCGGGCTCTCA
CGCTTCCTGGAGGACGACACATCTGACCCCACCTACACCAGCGCTCTGGGTGGGAAGATCCCCA
TCCGTTGGACAGCACCGGAAGCCATCCAGTACCGGAAATTCACCTCAGCCAGTGATGTGTGGAG
CTATGGCATTGTCATGTGGGAGGTGATGTCCTACGGGGAGCGACCCTACTGGGACATGACCAAC
CAAGACGTAATCAATGCCATCGAGCAGGACTACCGGCTACCTCCGCCCATGGACTGCCCCAGCG
CGCTGCACCAGCTCATGCTGGATTGCTGGCAGAAGGACCGCAACCACCGGCCCAAGTTCGGCCA
GATCGTCAACACGCTGGACAAGATGATCCGAAACCCCAACAGCCTCAAAGCTATGGCGCCCCTG
TCCTCTGGTATCAACCTGCCACTACTGGACCGCACGATACCCGACTACACCAGCTTTAACACAG
TGGATGAGTGGCTGGAGGCCATCAAGATGGGCCAGTACAAGGAGAGCTTTACCAACGCCGGCTT
CACCTCTTTTGACGTCGTATCTCAGATGATGATGGAGGACATTCTCCGGGTTGGGGTCACTCTA
GCTGGCCACCAGAAAAAAATCCTGAACAGTATCCAGGTGATGCGGGCCCAGATGAACCAGATCC
AGTCGGTAGAGGTTTGATGGTCGCCT

hide sequence

Protein Sequences


Protein RefSeqs	NP_001120791	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAY67785	(Get FASTA)	NCBI Sequence Viewer
	EDL80822	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001120791 ⟸ NM_001127319

- Peptide Label:

precursor

- Sequence:

show sequence

MAVRRLGAALLLLPLLAAVEETLMDSTTATAELGWMVHPPSGWEEVSGYDENMNTIRTYQVCNV
FESSQNNWLRTKFIRRRGAHRIHVEMKFSVRDCSSIPSVPGSCKETFNLYYYEADFDLATKTFP
NWMENPWVKVDTIAADESFSQVDLGGRVMKINTEVRSFGPVSRNGFYLAFQDYGGCMSLIAVRV
FYRKCPRVIQNGAIFQETLSGAESTSLVAARGSCIANAEEVDVPIKLYCNGDGEWLVPIGRCMC
KAGFEAVENGTVCRGCPSGTFKANQGDEACTHCPINSRTTSEGATNCVCRNGYYRADLDPLDMP
CTTIPSAPQAVISSVNETSLVLEWTPPRDSGGREDLVYNIICKSCGSGRGACTRCGDNVQYAPR
QLGLTEPRIYISDLLAHTQYTFEIQAVNGVTDQSPFSPQFASVNITTNQAAPSAVSIMHQVSRT
VDSITLSWSQPDQPNGVILDYELQYYEKELSEYNATAIKSPTNTVTVQGLKAGTIYVFQVRART
VAGYGRYSGKMYFQTMTEAEYQTSIKEKLPLIVGSSAAGVVFVIAVVVIAIVCNRRGFERADSE
YTDKLQHYTSGHMTPGMKIYIDPFTYEDPNEAVREFAKEIDISCVKIEQVIGAGEFGEVCSGHL
KLPGKREIFVAIKTLKSGYTEKQRRDFLSEASIMGQFDHPNVIHLEGVVTKSTPVMIITEFMEN
GSLDSFLRQNDGQFTVIQLVGMLRGIAAGMKYLADMNYVHRDLAARNILVNSNLVCKVSDFGLS
RFLEDDTSDPTYTSALGGKIPIRWTAPEAIQYRKFTSASDVWSYGIVMWEVMSYGERPYWDMTN
QDVINAIEQDYRLPPPMDCPSALHQLMLDCWQKDRNHRPKFGQIVNTLDKMIRNPNSLKAMAPL
SSGINLPLLDRTIPDYTSFNTVDEWLEAIKMGQYKESFTNAGFTSFDVVSQMMMEDILRVGVTL
AGHQKKILNSIQVMRAQMNQIQSVEV

hide sequence

RefSeq Acc Id:

ENSRNOP00000070517 ⟸ ENSRNOT00000089574

RefSeq Acc Id:

ENSRNOP00000016983 ⟸ ENSRNOT00000016983

Protein Domains

Eph LBD Fibronectin type-III Protein kinase SAM

Transcriptome

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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

ACI/EurMcwi (RGD)

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

ACI/N (MCW)

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

BBDP/Wor (RGD)

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

BN/SsN (MCW)

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

Buf/N (MCW)

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

COP/CrCrl (MCW & UW)

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

F344/NCrl (RGD)

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

F344/NRrrc (MCW)

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

FHH/EurMcwi (MCW)

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

FHH/EurMcwi (RGD)

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CSV

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

FHL/EurMcwi (MCW)

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

FHL/EurMcwi (RGD)

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CSV

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

GH/OmrMcwi (MCW)

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

GK/Ox (RGD)

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

LE/Stm (RGD)

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CSV

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

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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

LH/MavRrrc (RGD)

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

LL/MavRrrc (RGD)

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

LN/MavRrrc (RGD)

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

M520/N (MCW)

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

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (MCW)

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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CSV

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WKY/Gcrc (RGD)

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

WKY/N (MCW)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (MCW)

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1564232	AgrOrtholog
Ensembl Genes	ENSRNOG00000012531	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000016983	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOP00000070517	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000016983	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOT00000089574	UniProtKB/TrEMBL
Gene3D-CATH	1.10.150.50	UniProtKB/TrEMBL
	2.60.120.260	UniProtKB/TrEMBL
	2.60.40.10	UniProtKB/TrEMBL
InterPro	Eph_TM	UniProtKB/TrEMBL
	EphB2_rcpt_lig-bd	UniProtKB/TrEMBL
	Ephrin_rcpt_lig-bd	UniProtKB/TrEMBL
	FN3_sf	UniProtKB/TrEMBL
	FN_III	UniProtKB/TrEMBL
	Galactose-bd-like	UniProtKB/TrEMBL
	Growth_fac_rcpt	UniProtKB/TrEMBL
	Ig-like_fold	UniProtKB/TrEMBL
	Kinase-like_dom	UniProtKB/TrEMBL
	Prot_kinase_cat_dom	UniProtKB/TrEMBL
	Protein_kinase_ATP_BS	UniProtKB/TrEMBL
	SAM	UniProtKB/TrEMBL
	SAM_type	UniProtKB/TrEMBL
	Ser-Thr/Tyr_kinase	UniProtKB/TrEMBL
	Tyr-kin_ephrin_A/B_rcpt-like	UniProtKB/TrEMBL
	Tyr_kinase_AS	UniProtKB/TrEMBL
	Tyr_kinase_cat_dom	UniProtKB/TrEMBL
	Tyr_kinase_ephrin_rcpt	UniProtKB/TrEMBL
	Tyr_kinase_rcpt_V_CS	UniProtKB/TrEMBL
KEGG Report	rno:313633	UniProtKB/TrEMBL
NCBI Gene	313633	ENTREZGENE
Pfam	EphA2_TM	UniProtKB/TrEMBL
	Ephrin_lbd	UniProtKB/TrEMBL
	fn3	UniProtKB/TrEMBL
	GCC2_GCC3	UniProtKB/TrEMBL
	Pkinase_Tyr	UniProtKB/TrEMBL
	SAM_1	UniProtKB/TrEMBL
PhenoGen	Ephb2	PhenoGen
PIRSF	TyrPK_ephrin_receptor	UniProtKB/TrEMBL
PRINTS	TYRKINASE	UniProtKB/TrEMBL
PROSITE	EPH_LBD	UniProtKB/TrEMBL
	FN3	UniProtKB/TrEMBL
	PROTEIN_KINASE_ATP	UniProtKB/TrEMBL
	PROTEIN_KINASE_DOM	UniProtKB/TrEMBL
	PROTEIN_KINASE_TYR	UniProtKB/TrEMBL
	RECEPTOR_TYR_KIN_V_1	UniProtKB/TrEMBL
	RECEPTOR_TYR_KIN_V_2	UniProtKB/TrEMBL
	SAM_DOMAIN	UniProtKB/TrEMBL
SMART	EPH_lbd	UniProtKB/TrEMBL
	Ephrin_rec_like	UniProtKB/TrEMBL
	FN3	UniProtKB/TrEMBL
	SAM	UniProtKB/TrEMBL
	TyrKc	UniProtKB/TrEMBL
Superfamily-SCOP	FN_III-like	UniProtKB/TrEMBL
	Gal_bind_like	UniProtKB/TrEMBL
	Grow_fac_recept	UniProtKB/TrEMBL
	Kinase_like	UniProtKB/TrEMBL
	SAM_homology	UniProtKB/TrEMBL
UniGene	Rn.229866	ENTREZGENE
UniProt	A0A0G2JY48_RAT	UniProtKB/TrEMBL
	B2B9B0_RAT	UniProtKB/TrEMBL
	F1MAJ0_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Ephb2	Eph receptor B2	Ephb2_predicted	Eph receptor B2 (predicted)	'predicted' is removed	2292626	APPROVED
2006-03-30	Ephb2_predicted	Eph receptor B2 (predicted)	RGD1564232_predicted	similar to Ephb2 protein (predicted)	Symbol and Name updated	1299863	APPROVED
2006-03-07	RGD1564232_predicted	similar to Ephb2 protein (predicted)	LOC313633	similar to Ephb2 protein	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC313633	similar to Ephb2 protein			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

Imported Annotations - PID (archival)