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 ephrin receptor signaling pathway; regulation of neuron projection development; and regulation of synapse organization. Located in several cellular components, including dendrite; distal axon; and perikaryon. 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
Previously 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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8986,263,982 - 86,406,744 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl986,263,982 - 86,406,755 (-)EnsemblGRCr8
mRatBN7.2978,815,460 - 78,958,139 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl978,815,460 - 78,958,139 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx987,245,229 - 87,387,938 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0992,374,666 - 92,517,486 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0990,760,851 - 90,903,498 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0983,111,222 - 83,253,486 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl983,111,222 - 83,253,458 (-)Ensemblrn6Rnor6.0
Rnor_5.0982,880,599 - 83,022,444 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4976,676,778 - 76,820,752 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera976,344,796 - 76,487,530 (-)NCBICelera
Cytogenetic Map9q33NCBI
JBrowse:




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)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (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)
amitrole  (EXP)
amphetamine  (EXP)
aristolochic acid A  (ISO)
Aroclor 1254  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
avobenzone  (ISO)
benzo[a]pyrene  (ISO)
benzoic acid  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol AF  (EXP)
Butylbenzyl phthalate  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calciol  (ISO)
carbamazepine  (ISO)
CGP 52608  (ISO)
chloroprene  (ISO)
chlorpyrifos  (EXP)
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)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (ISO)
diethyl phthalate  (ISO)
diethylstilbestrol  (ISO)
diisobutyl phthalate  (ISO)
diisononyl phthalate  (ISO)
dimethyl sulfoxide  (ISO)
diquat  (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)
gardiquimod  (ISO)
genistein  (ISO)
gentamycin  (EXP)
hexadecanoic acid  (ISO)
hexestrol  (ISO)
indometacin  (ISO)
iron dichloride  (ISO)
kojic acid  (ISO)
malathion  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (EXP,ISO)
mestranol  (ISO)
methimazole  (EXP)
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)
sulfadimethoxine  (EXP)
sunitinib  (ISO)
temozolomide  (ISO)
terbufos  (ISO)
testosterone  (EXP,ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
thiram  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adherens junction organization  (IEA,ISO)
adult walking behavior  (ISO)
axon guidance  (IBA,ISO)
cell adhesion  (IEA)
cell surface receptor protein tyrosine kinase signaling pathway  (IEA)
cellular response to amyloid-beta  (IEA,ISO)
cochlea development  (IEA,ISO)
corticospinal tract morphogenesis  (IEA,ISO,ISS)
ephrin receptor signaling pathway  (IBA,IEA,IGI,ISO,ISS)
fasciculation of motor neuron axon  (IEA,ISO,ISS)
fasciculation of sensory neuron axon  (IEA,ISO)
glial cell migration  (IMP)
innervation  (ISO)
motor neuron axon guidance  (IEA,ISO,ISS)
negative regulation of axon regeneration  (IMP,ISO,ISS)
negative regulation of cell adhesion  (IEA,ISO)
negative regulation of cell migration  (IEA,ISO)
negative regulation of cellular response to hypoxia  (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  (IEA,ISO)
negative regulation of neuron apoptotic process  (ISO)
negative regulation of neuron projection development  (IEA,ISO)
negative regulation of proteolysis involved in protein catabolic process  (IEA,ISO)
nephric duct morphogenesis  (ISO)
nervous system development  (IEA)
neuron projection fasciculation  (IEA,ISO)
neuron projection guidance  (IEA,ISO)
positive regulation of amyloid precursor protein catabolic process  (IEA,ISO)
positive regulation of amyloid-beta formation  (IEA,ISO)
positive regulation of cell adhesion  (IEA,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 intracellular signal transduction  (IEA,ISO)
positive regulation of JNK cascade  (IEA,ISO)
positive regulation of leukocyte adhesion to arterial endothelial cell  (IEA,ISO)
protein stabilization  (IEA,ISO)
regulation of astrocyte differentiation  (IEA,ISO,ISS)
regulation of axonogenesis  (IEA,ISO,ISS)
regulation of dendritic spine morphogenesis  (IEA,ISO,ISS)
regulation of modification of synaptic structure  (IEA,IGI,ISO)
regulation of synapse pruning  (EXP,IDA,IEP,IMP)
synapse pruning  (IEA,ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Astrocyte-produced ephrins inhibit schwann cell migration via VAV2 signaling. Afshari FT, etal., J Neurosci. 2010 Mar 24;30(12):4246-55.
2. Blocking EphA4 upregulation after spinal cord injury results in enhanced chronic pain. Cruz-Orengo L, etal., Exp Neurol. 2006 Dec;202(2):421-33. Epub 2006 Sep 7.
3. Reduction of EphA4 receptor expression after spinal cord injury does not induce axonal regeneration or return of tcMMEP response. Cruz-Orengo L, etal., Neurosci Lett. 2007 May 11;418(1):49-54. Epub 2007 Mar 12.
4. Regeneration-enhancing effects of EphA4 blocking peptide following corticospinal tract injury in adult rat spinal cord. Fabes J, etal., Eur J Neurosci. 2007 Nov;26(9):2496-505. Epub 2007 Oct 26.
5. Expression and Activation of EphA4 in the Human Brain After Traumatic Injury. Frugier T, etal., J Neuropathol Exp Neurol. 2012 Mar;71(3):242-50.
6. Cdk5 regulates EphA4-mediated dendritic spine retraction through an ephexin1-dependent mechanism. Fu WY, etal., Nat Neurosci. 2007 Jan;10(1):67-76. Epub 2006 Dec 3.
7. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Axonal regeneration and lack of astrocytic gliosis in EphA4-deficient mice. Goldshmit Y, etal., J Neurosci. 2004 Nov 10;24(45):10064-73.
9. EphA4 blockers promote axonal regeneration and functional recovery following spinal cord injury in mice. Goldshmit Y, etal., PLoS One. 2011;6(9):e24636. Epub 2011 Sep 13.
10. EphA4 deficient mice maintain astroglial-fibrotic scar formation after spinal cord injury. Herrmann JE, etal., Exp Neurol. 2010 Jun;223(2):582-98. Epub 2010 Feb 17.
11. Synaptic activity prompts gamma-secretase-mediated cleavage of EphA4 and dendritic spine formation. Inoue E, etal., J Cell Biol. 2009 May 4;185(3):551-64.
12. Ephrin-A binding and EphA receptor expression delineate the matrix compartment of the striatum. Janis LS, etal., J Neurosci. 1999 Jun 15;19(12):4962-71.
13. Expression of Eph receptors in skeletal muscle and their localization at the neuromuscular junction. Lai KO, etal., Mol Cell Neurosci. 2001 Jun;17(6):1034-47.
14. Up-regulation of Eph tyrosine kinase receptors after excitotoxic injury in adult hippocampus. Moreno-Flores MT and Wandosell F, Neuroscience. 1999;91(1):193-201.
15. EphA4-mediated Rho activation via Vsm-RhoGEF expressed specifically in vascular smooth muscle cells. Ogita H, etal., Circ Res. 2003 Jul 11;93(1):23-31. Epub 2003 May 29.
16. Attenuation of scratch-induced reactive astrogliosis by novel EphA4 kinase inhibitors. 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. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
18. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
20. Early changes in hippocampal Eph receptors precede the onset of memory decline in mouse models of Alzheimer's disease. Simon AM, etal., J Alzheimers Dis. 2009;17(4):773-86.
21. Ephrin-B3-EphA4 interactions regulate the growth of specific thalamocortical axon populations in vitro. Takemoto M, etal., Eur J Neurosci. 2002 Sep;16(6):1168-72.
22. Developmental course of EphA4 cellular and subcellular localization in the postnatal rat hippocampus. Tremblay ME, etal., J Comp Neurol. 2009 Feb 20;512(6):798-813.
23. EphA4 activation of c-Abl mediates synaptic loss and LTP blockade caused by amyloid-ß oligomers. 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   PMID:36416239   PMID:37064501  


Genomics

Comparative Map Data
Epha4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8986,263,982 - 86,406,744 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl986,263,982 - 86,406,755 (-)EnsemblGRCr8
mRatBN7.2978,815,460 - 78,958,139 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl978,815,460 - 78,958,139 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx987,245,229 - 87,387,938 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0992,374,666 - 92,517,486 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0990,760,851 - 90,903,498 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0983,111,222 - 83,253,486 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl983,111,222 - 83,253,458 (-)Ensemblrn6Rnor6.0
Rnor_5.0982,880,599 - 83,022,444 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4976,676,778 - 76,820,752 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera976,344,796 - 76,487,530 (-)NCBICelera
Cytogenetic Map9q33NCBI
EPHA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382221,418,027 - 221,574,202 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2221,418,027 - 221,574,202 (-)Ensemblhg38GRCh38
GRCh372222,282,747 - 222,438,922 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362221,990,991 - 222,145,254 (-)NCBIBuild 36Build 36hg18NCBI36
Build 342222,108,253 - 222,262,515NCBI
Celera2216,050,899 - 216,205,191 (-)NCBICelera
Cytogenetic Map2q36.1NCBI
HuRef2214,137,116 - 214,291,409 (-)NCBIHuRef
CHM1_12222,288,287 - 222,442,879 (-)NCBICHM1_1
T2T-CHM13v2.02221,903,096 - 222,059,275 (-)NCBIT2T-CHM13v2.0
Epha4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39177,343,819 - 77,491,763 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl177,343,822 - 77,491,725 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38177,367,182 - 77,515,107 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl177,367,185 - 77,515,088 (-)Ensemblmm10GRCm38
MGSCv37177,363,760 - 77,511,663 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36177,250,333 - 77,398,236 (-)NCBIMGSCv36mm8
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 (+)Ensembl
ChiLan1.0NW_00495545312,099,800 - 12,240,199 (+)NCBIChiLan1.0ChiLan1.0
EPHA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213124,035,467 - 124,192,876 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B124,050,435 - 124,207,734 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B108,664,475 - 108,818,802 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B227,246,593 - 227,402,791 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B227,248,958 - 227,402,790 (-)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3728,506,808 - 28,649,559 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03727,690,393 - 27,834,663 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3727,697,197 - 27,834,652 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13727,600,660 - 27,743,768 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03727,535,209 - 27,678,026 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03727,555,060 - 27,698,047 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Epha4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303177,190,052 - 177,327,435 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365693,540,053 - 3,670,348 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365693,539,269 - 3,670,322 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
EPHA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15123,352,816 - 123,503,126 (-)EnsemblsusScr11Sscrofa11.1
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 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10107,352,530 - 107,499,788 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604091,884,095 - 92,041,139 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Epha4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248233,555,288 - 3,698,990 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248233,555,273 - 3,697,794 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Epha4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v14150,608,437 - 150,751,233 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Epha4
997 total Variants
miRNA Target Status (No longer updated)

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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)956047863101047863Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)963376862108376862Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94445825699506504Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)965657365108376720Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)98216882386720295Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)94172029586720295Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)964220169109220169Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)944458256121768150Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)964220169109220169Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)964220169109220169Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)968875497121768150Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)983161999118999486Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)985262459109044727Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)985262459118999486Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)948718864108376862Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)95450650499506504Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)964220169109220169Rat

Markers in Region
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
Celera976,434,592 - 76,434,713UniSTS
RGSC_v3.1976,950,651 - 76,950,773RGD
RH 3.4 Map9763.6RGD
RH 3.4 Map9763.6UniSTS
Cytogenetic Map9q33UniSTS
D9Mco4  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8986,306,965 - 86,307,150 (+)Marker Load Pipeline
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
Celera976,387,780 - 76,387,966UniSTS
RGSC_v3.1976,903,285 - 76,903,470RGD
Cytogenetic Map9q33UniSTS
D9Mco7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2268,443,402 - 68,443,753 (+)MAPPERmRatBN7.2
mRatBN7.2978,858,448 - 78,858,739 (+)MAPPERmRatBN7.2
Rnor_6.0983,153,934 - 83,154,224NCBIRnor6.0
Rnor_6.0269,224,232 - 69,224,582NCBIRnor6.0
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


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 162 91 90 59 51 59 6 314 151 11 141 80 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000041689   ⟹   ENSRNOP00000051316
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl986,263,982 - 86,406,697 (-)Ensembl
mRatBN7.2 Ensembl978,815,460 - 78,958,139 (-)Ensembl
Rnor_6.0 Ensembl983,111,222 - 83,253,458 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000134527   ⟹   ENSRNOP00000103263
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl986,263,982 - 86,406,755 (-)Ensembl
RefSeq Acc Id: NM_001162411   ⟹   NP_001155883
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8986,263,982 - 86,406,697 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8986,263,982 - 86,406,734 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8986,263,982 - 86,406,744 (-)NCBI
mRatBN7.2978,817,889 - 78,958,128 (-)NCBI
RefSeq Acc Id: XM_039083684   ⟹   XP_038939612
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8986,263,982 - 86,334,316 (-)NCBI
mRatBN7.2978,817,889 - 78,885,774 (-)NCBI
RefSeq Acc Id: NP_001155883   ⟸   NM_001162411
- Peptide Label: precursor
- UniProtKB: A6JW54 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008765471   ⟸   XM_008767249
- Peptide Label: isoform X1
- UniProtKB: D3ZZK3 (UniProtKB/TrEMBL),   A6JW54 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000051316   ⟸   ENSRNOT00000041689
RefSeq Acc Id: XP_038939611   ⟸   XM_039083683
- Peptide Label: isoform X2
- UniProtKB: A6JW54 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038939612   ⟸   XM_039083684
- Peptide Label: isoform X3
Ensembl Acc Id: ENSRNOP00000103263   ⟸   ENSRNOT00000134527
Protein Domains
Eph LBD   Fibronectin type-III   Protein kinase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZZK3-F1-model_v2 AlphaFold D3ZZK3 1-986 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560587 AgrOrtholog
BioCyc Gene G2FUF-27041 BioCyc
Ensembl Genes ENSRNOG00000013213 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041689 ENTREZGENE
  ENSRNOT00000041689.6 UniProtKB/TrEMBL
  ENSRNOT00000134527 ENTREZGENE
  ENSRNOT00000134527.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/TrEMBL
  ephrin a2 ectodomain UniProtKB/TrEMBL
  Galactose-binding domain-like UniProtKB/TrEMBL
  Phosphorylase Kinase, domain 1 UniProtKB/TrEMBL
  Transferase(Phosphotransferase) domain 1 UniProtKB/TrEMBL
  Tumor Necrosis Factor Receptor, subunit A, domain 2 UniProtKB/TrEMBL
InterPro Eph_TM UniProtKB/TrEMBL
  EphA4_rcpt_lig-bd UniProtKB/TrEMBL
  Ephrin_rcpt_lig-bd UniProtKB/TrEMBL
  Ephrin_rcpt_TKs 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-kin_ephrin_A/B_rcpt-like 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
NCBI Gene 316539 ENTREZGENE
PANTHER EPH RECEPTOR A5 UniProtKB/TrEMBL
  EPHRIN TYPE-A RECEPTOR 4 UniProtKB/TrEMBL
Pfam EphA2_TM UniProtKB/TrEMBL
  Ephrin_CRD UniProtKB/TrEMBL
  Ephrin_lbd UniProtKB/TrEMBL
  Ephrin_rec_like UniProtKB/TrEMBL
  fn3 UniProtKB/TrEMBL
  Pkinase_Tyr UniProtKB/TrEMBL
  SAM_2 UniProtKB/TrEMBL
PhenoGen Epha4 PhenoGen
PIRSF TyrPK_ephrin_receptor UniProtKB/TrEMBL
PRINTS FNTYPEIII UniProtKB/TrEMBL
  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
RatGTEx ENSRNOG00000013213 RatGTEx
SMART EPH_lbd UniProtKB/TrEMBL
  Ephrin_rec_like UniProtKB/TrEMBL
  FN3 UniProtKB/TrEMBL
  S_TKc 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 A0ABK0LMR9_RAT UniProtKB/TrEMBL
  A6JW54 ENTREZGENE, UniProtKB/TrEMBL
  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