Epha4 (Eph receptor A4) - Rat Genome Database

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Gene: Epha4 (Eph receptor A4) Rattus norvegicus
Analyze
Symbol: Epha4
Name: Eph receptor A4
RGD ID: 1560587
Description: Enables ephrin receptor binding activity. Involved in several processes, including regulation of modification of synaptic structure; regulation of neuron projection development; and synapse pruning. Located in several cellular components, including dendrite; distal axon; and perikaryon. Is integral component of plasma membrane. Is active in glutamatergic synapse. Biomarker of toxic encephalopathy. Orthologous to human EPHA4 (EPH receptor A4); PARTICIPATES IN ephrin - ephrin receptor bidirectional signaling axis; INTERACTS WITH 1,3-dinitrobenzene; 17alpha-ethynylestradiol; 3,4-methylenedioxymethamphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: ephrin type-A receptor 4; LOC316539; RGD1560587; similar to Eph receptor A4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2978,815,460 - 78,958,139 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl978,815,460 - 78,958,139 (-)Ensembl
Rnor_6.0983,111,222 - 83,253,486 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl983,111,222 - 83,253,458 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0982,880,599 - 83,022,444 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4976,676,778 - 76,820,752 (-)NCBIRGSC3.4rn4RGSC3.4
Celera976,344,796 - 76,487,530 (-)NCBICelera
Cytogenetic Map9q33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(R)-adrenaline  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
acetaldehyde  (ISO)
acrylamide  (ISO)
ADP  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
avobenzone  (ISO)
benzo[a]pyrene  (ISO)
benzoic acid  (ISO)
bisphenol A  (EXP,ISO)
C60 fullerene  (EXP)
calciol  (ISO)
carbamazepine  (ISO)
chloroprene  (ISO)
chromium atom  (ISO)
chromium(6+)  (ISO)
cisplatin  (EXP)
cocaine  (EXP)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
DDT  (EXP)
dexamethasone  (ISO)
dibenz[a,h]anthracene  (ISO)
diethylstilbestrol  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
entinostat  (ISO)
estrone  (ISO)
ethanol  (ISO)
fenvalerate  (EXP)
flusilazole  (ISO)
folic acid  (ISO)
fonofos  (ISO)
fulvestrant  (ISO)
furan  (EXP)
genistein  (ISO)
gentamycin  (EXP)
hexestrol  (ISO)
indometacin  (ISO)
kojic acid  (ISO)
malathion  (ISO)
manganese(II) chloride  (EXP)
mestranol  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
nickel sulfate  (ISO)
nitrofen  (EXP)
panobinostat  (ISO)
paracetamol  (EXP)
parathion  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
ponatinib  (ISO)
potassium chromate  (ISO)
protein kinase inhibitor  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP,ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
temozolomide  (ISO)
terbufos  (ISO)
testosterone  (EXP,ISO)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adherens junction organization  (ISO)
adult walking behavior  (ISO)
axon guidance  (IBA,ISO)
cell adhesion  (IEA)
cellular response to amyloid-beta  (ISO)
cochlea development  (ISO)
corticospinal tract morphogenesis  (ISO,ISS)
ephrin receptor signaling pathway  (ISO)
fasciculation of motor neuron axon  (ISO,ISS)
fasciculation of sensory neuron axon  (ISO)
glial cell migration  (IMP)
motor neuron axon guidance  (ISO,ISS)
negative regulation of axon regeneration  (IMP,ISO,ISS)
negative regulation of cell adhesion  (IEA,ISO)
negative regulation of cell migration  (ISO)
negative regulation of cellular response to hypoxia  (IEA,ISO)
negative regulation of epithelial to mesenchymal transition  (IEA,ISO)
negative regulation of ERK1 and ERK2 cascade  (IEA,ISO)
negative regulation of long-term synaptic potentiation  (ISO)
negative regulation of neuron projection development  (ISO)
negative regulation of proteolysis involved in cellular protein catabolic process  (ISO)
nephric duct morphogenesis  (ISO)
neuron projection fasciculation  (ISO)
neuron projection guidance  (ISO)
peptidyl-tyrosine phosphorylation  (ISO,ISS)
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 cell adhesion  (ISO)
positive regulation of cell migration  (IEA,ISO)
positive regulation of cell population proliferation  (IEA,ISO)
positive regulation of dendrite morphogenesis  (IMP)
positive regulation of JUN kinase activity  (ISO)
positive regulation of kinase activity  (IBA)
positive regulation of protein tyrosine kinase activity  (ISO)
positive regulation of Rho guanyl-nucleotide exchange factor activity  (ISO,ISS)
protein autophosphorylation  (ISO,ISS)
protein stabilization  (ISO)
regulation of astrocyte differentiation  (ISO,ISS)
regulation of axonogenesis  (ISO,ISS)
regulation of dendritic spine morphogenesis  (ISO,ISS)
regulation of GTPase activity  (IDA,ISO,ISS)
regulation of modification of synaptic structure  (IGI,ISO)
synapse pruning  (EXP,IDA,IMP,ISO)
transmembrane receptor protein tyrosine kinase signaling pathway  (IBA)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Afshari FT, etal., J Neurosci. 2010 Mar 24;30(12):4246-55.
2. Cruz-Orengo L, etal., Exp Neurol. 2006 Dec;202(2):421-33. Epub 2006 Sep 7.
3. Cruz-Orengo L, etal., Neurosci Lett. 2007 May 11;418(1):49-54. Epub 2007 Mar 12.
4. Fabes J, etal., Eur J Neurosci. 2007 Nov;26(9):2496-505. Epub 2007 Oct 26.
5. Frugier T, etal., J Neuropathol Exp Neurol. 2012 Mar;71(3):242-50.
6. Fu WY, etal., Nat Neurosci. 2007 Jan;10(1):67-76. Epub 2006 Dec 3.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Goldshmit Y, etal., J Neurosci. 2004 Nov 10;24(45):10064-73.
9. Goldshmit Y, etal., PLoS One. 2011;6(9):e24636. Epub 2011 Sep 13.
10. Herrmann JE, etal., Exp Neurol. 2010 Jun;223(2):582-98. Epub 2010 Feb 17.
11. Inoue E, etal., J Cell Biol. 2009 May 4;185(3):551-64.
12. Janis LS, etal., J Neurosci. 1999 Jun 15;19(12):4962-71.
13. Lai KO, etal., Mol Cell Neurosci. 2001 Jun;17(6):1034-47.
14. Moreno-Flores MT and Wandosell F, Neuroscience. 1999;91(1):193-201.
15. Ogita H, etal., Circ Res. 2003 Jul 11;93(1):23-31. Epub 2003 May 29.
16. Parmentier-Batteur S, etal., J Neurochem. 2011 Sep;118(6):1016-31. doi: 10.1111/j.1471-4159.2011.07375.x. Epub 2011 Aug 16.
17. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. Simon AM, etal., J Alzheimers Dis. 2009;17(4):773-86.
21. Takemoto M, etal., Eur J Neurosci. 2002 Sep;16(6):1168-72.
22. Tremblay ME, etal., J Comp Neurol. 2009 Feb 20;512(6):798-813.
23. Vargas LM, etal., PLoS One. 2014 Mar 21;9(3):e92309. doi: 10.1371/journal.pone.0092309. eCollection 2014.
Additional References at PubMed
PMID:9789074   PMID:10523642   PMID:12496762   PMID:12649481   PMID:12761826   PMID:16977320   PMID:17299751   PMID:17719550   PMID:17785183   PMID:17911252   PMID:18094260   PMID:18403711  
PMID:18410519   PMID:20886601   PMID:22580205   PMID:23123677   PMID:23144223   PMID:23689248   PMID:24217950   PMID:25139858   PMID:25268254   PMID:29350423   PMID:29451151   PMID:30639848  
PMID:31469726   PMID:33555537   PMID:33974931  


Genomics

Comparative Map Data
Epha4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2978,815,460 - 78,958,139 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl978,815,460 - 78,958,139 (-)Ensembl
Rnor_6.0983,111,222 - 83,253,486 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl983,111,222 - 83,253,458 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0982,880,599 - 83,022,444 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4976,676,778 - 76,820,752 (-)NCBIRGSC3.4rn4RGSC3.4
Celera976,344,796 - 76,487,530 (-)NCBICelera
Cytogenetic Map9q33NCBI
EPHA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2221,418,027 - 221,574,202 (-)EnsemblGRCh38hg38GRCh38
GRCh382221,418,027 - 221,574,202 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372222,282,747 - 222,438,922 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362221,990,991 - 222,145,254 (-)NCBINCBI36hg18NCBI36
Build 342222,108,253 - 222,262,515NCBI
Celera2216,050,899 - 216,205,191 (-)NCBI
Cytogenetic Map2q36.1NCBI
HuRef2214,137,116 - 214,291,409 (-)NCBIHuRef
CHM1_12222,288,287 - 222,442,879 (-)NCBICHM1_1
Epha4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39177,343,819 - 77,491,763 (-)NCBIGRCm39mm39
GRCm39 Ensembl177,343,822 - 77,491,725 (-)Ensembl
GRCm38177,367,182 - 77,515,107 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl177,367,185 - 77,515,088 (-)EnsemblGRCm38mm10GRCm38
MGSCv37177,363,760 - 77,511,663 (-)NCBIGRCm37mm9NCBIm37
MGSCv36177,250,333 - 77,398,236 (-)NCBImm8
Celera177,858,813 - 78,000,449 (-)NCBICelera
Cytogenetic Map1C4NCBI
cM Map139.55NCBI
Epha4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545312,099,757 - 12,240,199 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545312,099,800 - 12,240,199 (+)NCBIChiLan1.0ChiLan1.0
EPHA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B227,246,593 - 227,402,791 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B227,248,958 - 227,402,790 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B108,664,475 - 108,818,802 (-)NCBIMhudiblu_PPA_v0panPan3
EPHA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13727,670,143 - 27,809,642 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3727,677,566 - 27,809,646 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3728,506,808 - 28,649,559 (-)NCBI
ROS_Cfam_1.03727,690,393 - 27,834,663 (-)NCBI
ROS_Cfam_1.0 Ensembl3727,697,197 - 27,834,652 (-)Ensembl
UMICH_Zoey_3.13727,600,660 - 27,743,768 (-)NCBI
UNSW_CanFamBas_1.03727,535,209 - 27,678,026 (-)NCBI
UU_Cfam_GSD_1.03727,555,060 - 27,698,047 (-)NCBI
Epha4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303177,190,052 - 177,327,435 (-)NCBI
SpeTri2.0NW_0049365693,539,269 - 3,670,322 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
EPHA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15123,352,813 - 123,503,126 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115123,350,867 - 123,501,872 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215136,746,506 - 136,804,962 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Sscrofa10.215136,931,366 - 136,936,233 (+)NCBISscrofa10.2Sscrofa10.2susScr3
EPHA4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110107,344,442 - 107,501,375 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl10107,352,530 - 107,499,788 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604091,884,095 - 92,041,139 (+)NCBIVero_WHO_p1.0
Epha4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248233,555,273 - 3,697,794 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D9Got102  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2978,905,457 - 78,905,579 (+)MAPPERmRatBN7.2
Rnor_6.0983,200,966 - 83,201,087NCBIRnor6.0
Rnor_5.0982,970,038 - 82,970,159UniSTSRnor5.0
RGSC_v3.4976,767,366 - 76,767,488RGDRGSC3.4
RGSC_v3.4976,767,367 - 76,767,488UniSTSRGSC3.4
RGSC_v3.1976,950,651 - 76,950,773RGD
Celera976,434,592 - 76,434,713UniSTS
RH 3.4 Map9763.6UniSTS
RH 3.4 Map9763.6RGD
Cytogenetic Map9q33UniSTS
D9Mco4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2978,858,446 - 78,858,631 (+)MAPPERmRatBN7.2
Rnor_6.0983,153,932 - 83,154,116NCBIRnor6.0
Rnor_5.0982,923,125 - 82,923,309UniSTSRnor5.0
RGSC_v3.4976,720,001 - 76,720,185UniSTSRGSC3.4
RGSC_v3.4976,720,000 - 76,720,185RGDRGSC3.4
RGSC_v3.1976,903,285 - 76,903,470RGD
Celera976,387,780 - 76,387,966UniSTS
Cytogenetic Map9q33UniSTS
D9Mco7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2978,858,448 - 78,858,739 (+)MAPPERmRatBN7.2
mRatBN7.2268,443,402 - 68,443,753 (+)MAPPERmRatBN7.2
Rnor_6.0269,224,232 - 69,224,582NCBIRnor6.0
Rnor_6.0983,153,934 - 83,154,224NCBIRnor6.0
Rnor_5.0982,923,127 - 82,923,417UniSTSRnor5.0
Rnor_5.0288,949,281 - 88,949,631UniSTSRnor5.0
RGSC_v3.1976,903,287 - 76,903,578RGD
Cytogenetic Map9q33UniSTS
D9Mco36  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2978,871,171 - 78,871,387 (+)MAPPERmRatBN7.2
Rnor_6.0983,166,662 - 83,166,877NCBIRnor6.0
Rnor_5.0982,935,724 - 82,935,939UniSTSRnor5.0
RGSC_v3.4976,732,506 - 76,732,721UniSTSRGSC3.4
Celera976,400,538 - 76,400,753UniSTS
Cytogenetic Map9q33UniSTS
D9Mco37  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2978,854,185 - 78,854,389 (+)MAPPERmRatBN7.2
Rnor_6.0983,149,671 - 83,149,874NCBIRnor6.0
Rnor_5.0982,918,864 - 82,919,067UniSTSRnor5.0
RGSC_v3.4976,715,740 - 76,715,943UniSTSRGSC3.4
Celera976,383,513 - 76,383,722UniSTS
Cytogenetic Map9q33UniSTS
D9Mco87  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2978,920,859 - 78,921,073 (+)MAPPERmRatBN7.2
Rnor_6.0983,216,368 - 83,216,581NCBIRnor6.0
Rnor_5.0982,985,440 - 82,985,653UniSTSRnor5.0
RGSC_v3.4976,782,769 - 76,782,982UniSTSRGSC3.4
Celera976,449,994 - 76,450,207UniSTS
Cytogenetic Map9q33UniSTS
RH143200  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2978,816,558 - 78,816,778 (+)MAPPERmRatBN7.2
Rnor_6.0983,112,321 - 83,112,540NCBIRnor6.0
Rnor_5.0982,881,698 - 82,881,917UniSTSRnor5.0
RGSC_v3.4976,677,877 - 76,678,096UniSTSRGSC3.4
Celera976,345,895 - 76,346,114UniSTS
RH 3.4 Map9757.0UniSTS
Cytogenetic Map9q33UniSTS
BE116570  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2978,816,557 - 78,816,709 (+)MAPPERmRatBN7.2
Rnor_6.0983,112,320 - 83,112,471NCBIRnor6.0
Rnor_5.0982,881,697 - 82,881,848UniSTSRnor5.0
RGSC_v3.4976,677,876 - 76,678,027UniSTSRGSC3.4
Celera976,345,894 - 76,346,045UniSTS
RH 3.4 Map9758.2UniSTS
Cytogenetic Map9q33UniSTS
BM389593  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2978,953,915 - 78,954,083 (+)MAPPERmRatBN7.2
Rnor_6.0983,249,208 - 83,249,375NCBIRnor6.0
Rnor_5.0983,018,194 - 83,018,361UniSTSRnor5.0
RGSC_v3.4976,816,501 - 76,816,668UniSTSRGSC3.4
Celera976,483,280 - 76,483,447UniSTS
RH 3.4 Map9761.4UniSTS
Cytogenetic Map9q33UniSTS
PMC23772P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2978,949,661 - 78,950,304 (+)MAPPERmRatBN7.2
Rnor_6.0983,244,957 - 83,245,599NCBIRnor6.0
Rnor_5.0983,013,943 - 83,014,585UniSTSRnor5.0
RGSC_v3.4976,812,250 - 76,812,892UniSTSRGSC3.4
Celera976,479,023 - 76,479,665UniSTS
Cytogenetic Map9q33UniSTS
MARC_49122-49123:1117732036:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2978,830,869 - 78,831,513 (+)MAPPERmRatBN7.2
Rnor_6.0983,126,632 - 83,127,275NCBIRnor6.0
Rnor_5.0982,896,009 - 82,896,652UniSTSRnor5.0
RGSC_v3.4976,692,188 - 76,692,831UniSTSRGSC3.4
Celera976,360,208 - 76,360,851UniSTS
Cytogenetic Map9q33UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92207116986369743Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92375414483851531Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92526804479271759Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94019418885194188Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94019418885194188Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94249534379271511Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94279151387976209Rat
11353951Bp394Blood pressure QTL 394arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94464992189649921Rat
12879506Pur33Proteinuria QTL 33total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)94464992189649921Rat
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94859825193598251Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96207227596470995Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96207227596470995Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
4889852Pur26Proteinuria QTL 26150.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)977813894101597663Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:982
Count of miRNA genes:327
Interacting mature miRNAs:451
Transcripts:ENSRNOT00000041689
Prediction methods:Microtar, Miranda, 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 25 4 4 4 74 22 21 10
Low 3 18 42 26 11 26 8 10 13 20 1 8
Below cutoff 11 11 8 11 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041689   ⟹   ENSRNOP00000051316
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl978,815,460 - 78,958,139 (-)Ensembl
Rnor_6.0 Ensembl983,111,222 - 83,253,458 (-)Ensembl
RefSeq Acc Id: NM_001162411   ⟹   NP_001155883
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2978,815,460 - 78,958,139 (-)NCBI
Rnor_6.0983,111,222 - 83,253,458 (-)NCBI
Rnor_5.0982,880,599 - 83,022,444 (-)NCBI
RGSC_v3.4976,676,778 - 76,820,752 (-)RGD
Celera976,344,796 - 76,487,530 (-)RGD
Sequence:
RefSeq Acc Id: XM_008767249   ⟹   XP_008765471
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2978,815,460 - 78,958,083 (-)NCBI
Rnor_6.0983,117,738 - 83,253,486 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039083683   ⟹   XP_038939611
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2978,817,889 - 78,958,128 (-)NCBI
RefSeq Acc Id: XM_039083684   ⟹   XP_038939612
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2978,817,889 - 78,885,774 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001155883 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765471 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939611 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939612 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL75462 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001155883   ⟸   NM_001162411
- Peptide Label: precursor
- UniProtKB: D3ZZK3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008765471   ⟸   XM_008767249
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000051316   ⟸   ENSRNOT00000041689
RefSeq Acc Id: XP_038939611   ⟸   XM_039083683
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038939612   ⟸   XM_039083684
- Peptide Label: isoform X3
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

Promoters
RGD ID:13696786
Promoter ID:EPDNEW_R7310
Type:initiation region
Name:Epha4_1
Description:Eph receptor A4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0983,253,458 - 83,253,518EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 83121376 83121377 G T snv LEW/Crl (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560587 AgrOrtholog
Ensembl Genes ENSRNOG00000013213 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000051316 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041689 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/TrEMBL
InterPro Eph_TM UniProtKB/TrEMBL
  EphA4_rcpt_lig-bd UniProtKB/TrEMBL
  EphA4_SAM UniProtKB/TrEMBL
  Ephrin_rcpt_lig-bd UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  FN_III UniProtKB/TrEMBL
  Galactose-bd-like 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-Pkinase UniProtKB/TrEMBL
  Tyr_kinase_cat_dom UniProtKB/TrEMBL
  Tyr_prot_kinase_AS UniProtKB/TrEMBL
  Tyr_prot_kinase_ephrin_rcpt UniProtKB/TrEMBL
  Tyr_prot_kinase_rcpt_V_CS UniProtKB/TrEMBL
KEGG Report rno:316539 UniProtKB/TrEMBL
NCBI Gene 316539 ENTREZGENE
Pfam EphA2_TM UniProtKB/TrEMBL
  Ephrin_lbd UniProtKB/TrEMBL
  fn3 UniProtKB/TrEMBL
  Pkinase_Tyr UniProtKB/TrEMBL
  SAM_2 UniProtKB/TrEMBL
PhenoGen Epha4 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
  FN3 UniProtKB/TrEMBL
  S_TKc UniProtKB/TrEMBL
  SAM UniProtKB/TrEMBL
  TyrKc UniProtKB/TrEMBL
Superfamily-SCOP FN_III-like UniProtKB/TrEMBL
  Gal_bind_like UniProtKB/TrEMBL
  Kinase_like UniProtKB/TrEMBL
  SAM_homology UniProtKB/TrEMBL
UniProt D3ZZK3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-28 Epha4  Eph receptor A4  RGD1560587_predicted  similar to Eph receptor A4 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1560587_predicted  similar to Eph receptor A4 (predicted)  LOC316539  similar to Eph receptor A4  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC316539  similar to Eph receptor A4      Symbol and Name status set to provisional 70820 PROVISIONAL