Rara (retinoic acid receptor, alpha) - Rat Genome Database

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Gene: Rara (retinoic acid receptor, alpha) Rattus norvegicus
Analyze
Symbol: Rara
Name: retinoic acid receptor, alpha
RGD ID: 3534
Description: Enables several functions, including histone deacetylase binding activity; mRNA 5'-UTR binding activity; and mRNA regulatory element binding translation repressor activity. Involved in several processes, including reproductive structure development; response to estradiol; and response to vitamin A. Located in dendrite and perinuclear region of cytoplasm. Biomarker of amyotrophic lateral sclerosis. Human ortholog(s) of this gene implicated in acute promyelocytic leukemia. Orthologous to human RARA (retinoic acid receptor alpha); PARTICIPATES IN retinoic acid signaling pathway; acute myeloid leukemia pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,2',5,5'-tetrachlorobiphenyl; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: retinoic acid receptor alpha
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
GRCr81084,379,780 - 84,424,371 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1084,389,622 - 84,425,160 (+)EnsemblGRCr8
mRatBN7.21083,883,490 - 83,928,932 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1083,893,384 - 83,928,142 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1088,859,187 - 88,872,075 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01088,357,291 - 88,370,179 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01083,749,813 - 83,762,723 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01086,838,819 - 86,884,224 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1086,860,685 - 86,884,210 (+)Ensemblrn6Rnor6.0
Rnor_5.01086,663,856 - 86,681,847 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41087,740,479 - 87,753,265 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1082,656,708 - 82,669,574 (+)NCBICelera
RGSC_v3.11087,754,841 - 87,767,635 (+)NCBI
Cytogenetic Map10q31NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1-(5-isoquinolinesulfonyl)-2-methylpiperazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-(tert-butylimino)-5-phenyl-3-(propan-2-yl)-1,3,5-thiadiazinan-4-one  (ISO)
2-bromohexadecanoic acid  (ISO)
2-palmitoylglycerol  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methyladenine  (ISO)
4'-epidoxorubicin  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-diisothiocyano-trans-stilbene-2,2'-disulfonic acid  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
4-aminopyridine  (EXP)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-(2-methylpiperazine-1-sulfonyl)isoquinoline  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
8'-apo-beta,psi-caroten-8'-al  (ISO)
9-cis-retinoic acid  (EXP,ISO)
adefovir pivoxil  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
alendronic acid  (EXP)
Alisol B  (ISO)
all-trans-4-hydroxyretinoic acid  (ISO)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-4-oxoretinol  (ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (EXP,ISO)
all-trans-retinyl palmitate  (EXP)
allethrin  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
androgen antagonist  (EXP)
Antimony trioxide  (ISO)
antirheumatic drug  (ISO)
arotinoid acid  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
Bardoxolone methyl  (ISO)
benzo[a]pyrene  (ISO)
beta-carotene  (ISO)
bicuculline  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
Bisphenol Z  (ISO)
buprofezin  (ISO)
Butylbenzyl phthalate  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calciol  (EXP,ISO)
camptothecin  (ISO)
cannabidiol  (ISO)
carnosic acid  (ISO)
CGP 52608  (ISO)
chenodeoxycholic acid  (ISO)
CHIR 99021  (ISO)
chloroacetaldehyde  (ISO)
chlorogenic acid  (ISO)
chlorpromazine  (EXP)
chlorpyrifos  (ISO)
choline  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (EXP,ISO)
clodronic acid  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
cortisol  (ISO)
coumaphos  (ISO)
curcumin  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (EXP,ISO)
D-gluconic acid  (EXP)
DAPT  (ISO)
deguelin  (ISO)
deoxycholic acid  (EXP,ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
dieldrin  (EXP)
dioxygen  (ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
dizocilpine maleate  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP)
enilconazole  (ISO)
ethanol  (ISO)
fenofibrate  (EXP,ISO)
folic acid  (ISO)
fonofos  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
furan  (EXP)
gamma-hexachlorocyclohexane  (ISO)
gentamycin  (EXP)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
griseofulvin  (ISO)
hydroxyurea  (ISO)
ibuprofen  (ISO)
Indeno[1,2,3-cd]pyrene  (ISO)
indometacin  (ISO)
isotretinoin  (EXP,ISO)
kojic acid  (EXP)
L-ascorbic acid 2-phosphate  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
limonene  (EXP)
lipopolysaccharide  (ISO)
melatonin  (ISO)
mercury atom  (EXP)
mercury(0)  (EXP)
methoxychlor  (EXP,ISO)
mitoxantrone  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-(6-acetamidohexyl)acetamide  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N-nitrosourea  (EXP,ISO)
N-nitrosodiethylamine  (EXP,ISO)
nickel dichloride  (EXP)
nitrofen  (EXP)
Nor-9-carboxy-delta9-THC  (ISO)
ochratoxin A  (EXP)
okadaic acid  (EXP)
Osajin  (ISO)
oxybenzone  (ISO)
ozone  (ISO)
paracetamol  (EXP)
parathion  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (EXP)
phenethyl caffeate  (ISO)
phenytoin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosalone  (ISO)
picene  (ISO)
Pomiferin  (ISO)
prochloraz  (ISO)
propiconazole  (ISO)
puerarin  (ISO)
quinolines  (ISO)
quinoxyfen  (ISO)
raloxifene  (EXP)
resveratrol  (ISO)
Ro 41-5253  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium cholate  (ISO)
sodium dodecyl sulfate  (EXP)
sunitinib  (ISO)
Sunset Yellow FCF  (ISO)
tamibarotene  (EXP,ISO)
tamoxifen  (ISO)
tartrazine  (ISO)
terbufos  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
tetraphene  (ISO)
thiophenes  (ISO)
titanium dioxide  (ISO)
toluene  (ISO)
trichostatin A  (EXP)
triphenyl phosphate  (ISO)
troglitazone  (ISO)
valproic acid  (EXP,ISO)
vanadyl sulfate  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
XAV939  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
apoptotic cell clearance  (IEA,ISO)
bone development  (ISO)
camera-type eye development  (IEA)
cell differentiation  (IBA)
cellular response to estrogen stimulus  (IEA,ISO)
cellular response to lipopolysaccharide  (IEA,ISO)
cellular response to retinoic acid  (IEA,ISO)
chondroblast differentiation  (ISO)
embryonic camera-type eye development  (ISO)
embryonic morphogenesis  (IEA)
embryonic organ development  (IEA)
face development  (ISO)
female pregnancy  (IEP)
germ cell development  (IEA,ISO)
glandular epithelial cell development  (IEA,ISO)
growth plate cartilage development  (IEA,ISO)
hippocampus development  (IEP)
limb development  (IEA,ISO)
liver development  (IEP)
male gonad development  (IDA)
mRNA transcription by RNA polymerase II  (IEA,ISO)
multicellular organism growth  (IEA,ISO)
negative regulation of apoptotic process  (IEA,ISO)
negative regulation of cartilage development  (IEA,ISO)
negative regulation of cell differentiation  (IEA,ISO)
negative regulation of cell population proliferation  (IDA)
negative regulation of DNA-templated transcription  (IEA,ISO)
negative regulation of gene expression  (ISO)
negative regulation of granulocyte differentiation  (IEA,ISO)
negative regulation of miRNA transcription  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IBA,IEA,ISO)
negative regulation of translation  (IDA)
negative regulation of translational initiation  (ISO)
negative regulation of tumor necrosis factor production  (IEA,ISO)
negative regulation of type II interferon production  (IEA,ISO)
neural tube closure  (ISO)
outflow tract septum morphogenesis  (IEA,ISO)
positive regulation of cell cycle  (IEA,ISO)
positive regulation of cell population proliferation  (IEA,ISO)
positive regulation of DNA-templated transcription  (IEA,ISO)
positive regulation of ERK1 and ERK2 cascade  (IMP)
positive regulation of gene expression  (IEA,ISO)
positive regulation of interleukin-13 production  (IEA,ISO)
positive regulation of interleukin-4 production  (IEA,ISO)
positive regulation of interleukin-5 production  (IEA,ISO)
positive regulation of neuron differentiation  (IDA)
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction  (IMP)
positive regulation of T-helper 2 cell differentiation  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IBA,IEA,ISO)
prostate gland development  (IEP)
protein phosphorylation  (ISO)
regulation of apoptotic process  (IDA)
regulation of DNA-templated transcription  (IEA,ISO)
regulation of granulocyte differentiation  (ISO)
regulation of myelination  (IDA)
regulation of synaptic plasticity  (IDA)
response to cytokine  (IEP)
response to estradiol  (IEP)
response to ethanol  (IDA)
response to retinoic acid  (IEA,ISO)
response to vitamin A  (IEP)
retinoic acid receptor signaling pathway  (IBA,IEA,ISO)
Sertoli cell fate commitment  (IEA,ISO)
spermatogenesis  (ISO)
trachea cartilage development  (ISO)
ureteric bud development  (IEA,ISO)
ventricular cardiac muscle cell differentiation  (IEA,ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Region-specific localization of retinoic acid receptor-alpha expression in the rat epididymis. Akmal KM, etal., Biol Reprod 1996 May;54(5):1111-9.
2. Retinoic acid receptor alpha gene expression in the rat testis: potential role during the prophase of meiosis and in the transition from round to elongating spermatids. Akmal KM, etal., Biol Reprod 1997 Feb;56(2):549-56.
3. Ligand-dependent regulation of retinoic acid receptor alpha in rat testis: in vivo response to depletion and repletion of vitamin A. Akmal KM, etal., Endocrinology 1998 Mar;139(3):1239-48.
4. Synaptic signaling by all-trans retinoic acid in homeostatic synaptic plasticity. Aoto J, etal., Neuron. 2008 Oct 23;60(2):308-20.
5. Multiple mechanisms of ontogenic regulation of nuclear receptors during rat liver development. Balasubramaniyan N, etal., Am J Physiol Gastrointest Liver Physiol. 2005 Feb;288(2):G251-60. Epub 2004 Sep 23.
6. Regulation of the proliferation of cocultured gonocytes and Sertoli cells by retinoids, triiodothyronine, and intracellular signaling factors: differences between fetal and neonatal cells. Boulogne B, etal., Mol Reprod Dev. 2003 Jun;65(2):194-203.
7. Positive regulation of retinoic acid receptor alpha by protein kinase C and mitogen-activated protein kinase in sertoli cells. Braun KW, etal., Biol Reprod 2002 Jul;67(1):29-37.
8. The involvement of retinoic acid receptor-alpha in corticotropin-releasing hormone gene expression and affective disorders. Chen XN, etal., Biol Psychiatry. 2009 Nov 1;66(9):832-9. Epub 2009 Jul 12.
9. Changes in maternal liver Cyp2c and Cyp2d expression and activity during rat pregnancy. Dickmann LJ, etal., Biochem Pharmacol. 2008 Apr 15;75(8):1677-87. Epub 2008 Feb 7.
10. 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.
11. International Union of Pharmacology. LX. Retinoic acid receptors. Germain P, etal., Pharmacol Rev. 2006 Dec;58(4):712-25.
12. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
13. Sequential RARbeta and alpha signalling in vivo can induce adult forebrain neural progenitor cells to differentiate into neurons through Shh and FGF signalling pathways. Goncalves MB, etal., Dev Biol. 2009 Feb 15;326(2):305-13. Epub 2008 Dec 7.
14. NPM mutations in acute myelogenous leukemia. Grisendi S and Pandolfi PP, N Engl J Med. 2005 Jan 20;352(3):291-2.
15. Changes in the expression and subcellular localization of RARalpha in the rat hippocampus during postnatal development. Huang H, et al., Brain Res. 2008 Aug 28;1227:26-33. doi: 10.1016/j.brainres.2008.06.073. Epub 2008 Jun 27.
16. Retinoid receptors in chronic degeneration of the spinal cord: observations in a rat model of amyotrophic lateral sclerosis. Jokic N, etal., J Neurochem. 2007 Dec;103(5):1821-33. Epub 2007 Sep 13.
17. Retinoic acid regulates myelin formation in the peripheral nervous system. Latasa MJ, etal., Glia. 2010 Sep;58(12):1451-64.
18. Retinoic acid inhibits rat XY gonad development by blocking mesonephric cell migration and decreasing the number of gonocytes. Li H and Kim KH, Biol Reprod. 2004 Mar;70(3):687-93. Epub 2003 Nov 12.
19. Effects of ethanol on embryonic and neonatal rat testes in organ cultures. Li H and Kim KH, J Androl. 2003 Sep-Oct;24(5):653-60.
20. Vitamin A regulation of gene expression: molecular mechanism of a prototype gene. McGrane MM J Nutr Biochem. 2007 Aug;18(8):497-508. Epub 2007 Feb 22.
21. Effects of inflammatory cytokines IL-1beta, IL-6, and TNFalpha on the intracellular localization of retinoid receptors in Schwann cells. Mey J, etal., Glia. 2007 Jan 15;55(2):152-64.
22. Insoluble, speckled cytosolic distribution of retinoic acid receptor alpha protein as a marker of hepatic stellate cell activation in vitro. Mezaki Y, etal., J Histochem Cytochem. 2009 Jul;57(7):687-99. Epub 2009 Mar 30.
23. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
24. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
26. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
27. Retinoic acid-gated sequence-specific translational control by RARalpha. Poon MM and Chen L, Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20303-8. Epub 2008 Dec 10.
28. Retinoic acid receptors and retinoids are up-regulated in the developing and adult rat prostate by neonatal estrogen exposure. Prins GS, etal., Endocrinology 2002 Sep;143(9):3628-40.
29. Study of retinoic acid effect upon retinoic acid receptors beta (RAR-beta) in C6 cultured glioma cells. Reboul P, etal., Biochem Mol Biol Int. 1995 Aug;36(5):1097-105.
30. Synergic effect of vitamin A and high-fat diet in adipose tissue development and nuclear receptor expression in young rats. Redonnet A, etal., Br J Nutr. 2008 Oct;100(4):722-30. Epub 2008 Apr 3.
31. GOA pipeline RGD automated data pipeline
32. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
33. Dynamic and combinatorial control of gene expression by nuclear retinoic acid receptors (RARs). Rochette-Egly C and Germain P, Nucl Recept Signal. 2009 May 8;7:e005.
34. Macrophages and neurons are targets of retinoic acid signaling after spinal cord contusion injury. Schrage K, etal., Eur J Neurosci. 2006 Jan;23(2):285-95.
35. Transcriptional induction of mitogen-activated protein kinase phosphatase 1 by retinoids. Selective roles of nuclear receptors and contribution to the antiapoptotic effect. Xu Q, etal., J Biol Chem 2002 Nov 1;277(44):41693-700.
36. Synthetic retinoid Am80 inhibits interaction of KLF5 with RAR alpha through inducing KLF5 dephosphorylation mediated by the PI3K/Akt signaling in vascular smooth muscle cells. Zhang XH, etal., FEBS Lett. 2009 Apr 17;583(8):1231-6. Epub 2009 Mar 16.
37. HDAC2 phosphorylation-dependent Klf5 deacetylation and RARalpha acetylation induced by RAR agonist switch the transcription regulatory programs of p21 in VSMCs. Zheng B, etal., Cell Res. 2011 Oct;21(10):1487-508. doi: 10.1038/cr.2011.34. Epub 2011 Mar 8.
38. Kruppel-like factor 4 inhibits proliferation by platelet-derived growth factor receptor beta-mediated, not by retinoic acid receptor alpha-mediated, phosphatidylinositol 3-kinase and ERK signaling in vascular smooth muscle cells. Zheng B, etal., J Biol Chem. 2009 Aug 21;284(34):22773-85. doi: 10.1074/jbc.M109.026989. Epub 2009 Jun 16.
39. Small ubiquitin-like modifier-2 modification of retinoic acid receptor-alpha regulates its subcellular localization and transcriptional activity. Zhu L, etal., Endocrinology. 2009 Dec;150(12):5586-95. doi: 10.1210/en.2009-0868. Epub 2009 Oct 22.
Additional References at PubMed
PMID:1655807   PMID:2825025   PMID:7566114   PMID:7607067   PMID:7823919   PMID:8152920   PMID:8394014   PMID:9376317   PMID:9428411   PMID:9628876   PMID:9659935   PMID:10684250  
PMID:11222375   PMID:11641275   PMID:12039952   PMID:12101409   PMID:12195422   PMID:12477932   PMID:14980219   PMID:15322135   PMID:15528198   PMID:15766748   PMID:15901285   PMID:16417524  
PMID:16456540   PMID:17195188   PMID:17363140   PMID:17538076   PMID:17641689   PMID:17905941   PMID:17928865   PMID:18026104   PMID:18254374   PMID:18416830   PMID:18495661   PMID:18845237  
PMID:18922886   PMID:19389355   PMID:19628791   PMID:19752193   PMID:19917671   PMID:20080953   PMID:20130111   PMID:20201933   PMID:20215566   PMID:20413580   PMID:20649843   PMID:20945395  
PMID:21131358   PMID:21882190   PMID:22337869   PMID:22351778   PMID:23327965   PMID:23613978   PMID:24859384   PMID:25127741   PMID:25209250   PMID:25359573   PMID:27073891   PMID:28570942  
PMID:28645189   PMID:32205185   PMID:33411644   PMID:36768908  


Genomics

Comparative Map Data
Rara
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81084,379,780 - 84,424,371 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1084,389,622 - 84,425,160 (+)EnsemblGRCr8
mRatBN7.21083,883,490 - 83,928,932 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1083,893,384 - 83,928,142 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1088,859,187 - 88,872,075 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01088,357,291 - 88,370,179 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01083,749,813 - 83,762,723 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01086,838,819 - 86,884,224 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1086,860,685 - 86,884,210 (+)Ensemblrn6Rnor6.0
Rnor_5.01086,663,856 - 86,681,847 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41087,740,479 - 87,753,265 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1082,656,708 - 82,669,574 (+)NCBICelera
RGSC_v3.11087,754,841 - 87,767,635 (+)NCBI
Cytogenetic Map10q31NCBI
RARA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381740,309,180 - 40,357,643 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1740,309,180 - 40,357,643 (+)Ensemblhg38GRCh38
GRCh371738,465,432 - 38,513,895 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361735,718,972 - 35,767,420 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341735,740,895 - 35,767,420NCBI
Celera1735,125,565 - 35,174,038 (+)NCBICelera
Cytogenetic Map17q21.2NCBI
HuRef1734,258,584 - 34,307,018 (+)NCBIHuRef
CHM1_11738,700,731 - 38,749,203 (+)NCBICHM1_1
T2T-CHM13v2.01741,172,682 - 41,221,155 (+)NCBIT2T-CHM13v2.0
Rara
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391198,818,626 - 98,865,768 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1198,818,644 - 98,865,768 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381198,927,800 - 98,974,942 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1198,927,818 - 98,974,942 (+)Ensemblmm10GRCm38
MGSCv371198,799,010 - 98,836,256 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361198,753,943 - 98,788,760 (+)NCBIMGSCv36mm8
Celera11108,602,792 - 108,640,796 (+)NCBICelera
Cytogenetic Map11DNCBI
cM Map1162.76NCBI
Rara
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545114,897,726 - 14,917,134 (+)Ensembl
ChiLan1.0NW_00495545114,876,663 - 14,917,134 (+)NCBIChiLan1.0ChiLan1.0
RARA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21924,598,318 - 24,646,791 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11726,493,204 - 26,541,701 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01716,932,485 - 16,980,958 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11717,156,923 - 17,205,451 (-)NCBIPanPan1.1PanPan1.1panPan2
RARA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1922,254,803 - 22,298,614 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl922,254,806 - 22,289,459 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha921,727,250 - 21,761,701 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0923,046,731 - 23,091,126 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl923,046,740 - 23,081,981 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1921,821,642 - 21,856,078 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0922,080,340 - 22,114,785 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0922,205,221 - 22,239,665 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Rara
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560221,654,499 - 21,698,923 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649015,376,205 - 15,421,611 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493649015,376,217 - 15,420,638 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RARA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1222,047,443 - 22,085,673 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11222,047,449 - 22,085,759 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21222,356,038 - 22,403,796 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RARA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11665,817,849 - 65,866,862 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1665,817,757 - 65,866,878 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366607736,718,924 - 36,759,030 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rara
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247952,934,731 - 2,967,232 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247952,935,432 - 2,975,226 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Rara
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1955,468,152 - 55,513,456 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Rara
615 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:313
Count of miRNA genes:174
Interacting mature miRNAs:199
Transcripts:ENSRNOT00000008659
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105107189796071897Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102702353598502431Rat
8657410Bp374Blood pressure QTL 374heart left ventricle size trait (VT:0002753)heart left ventricle end-diastolic diameter (CMO:0000982)1067476608107713808Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063719161107713808Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103550938391417879Rat
631555Bp134Blood pressure QTL 1340.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)108101207791729860Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042546145107713808Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1058073360103073360Rat
12903252Cm113Cardiac mass QTL 1130.047heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1066817119107713808Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105429633699451733Rat
4889948Bss91Bone structure and strength QTL 914tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)108306123692869129Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1064939013107713808Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104183127886831278Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076951790107713808Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105046480295464802Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)1079272424102982300Rat
70168Eae12Experimental allergic encephalomyelitis QTL 120.0009nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1073599825107713808Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104552916496099749Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104493935989939359Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1054296227107713808Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107674313395464802Rat
12903269Am15Aortic mass QTL 150.042aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1066817119107713808Rat
10450493Bp382Blood pressure QTL 3820.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105086028895860288Rat
12903266Cm114Cardiac mass QTL 1140.02heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1066817119107713808Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107395035396620293Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101499153586964295Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062556066107556066Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14282327487823274Rat
724516Uae17Urinary albumin excretion QTL 173.6urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)107870758585720738Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072724423107713808Rat
12880372Am12Aortic mass QTL 120.003aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1066817119107713808Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062556066107556066Rat
12880375Kidm66Kidney mass QTL 660.009kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1066817119107713808Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106724133498502431Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104493935989939359Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat
12880370Cm105Cardiac mass QTL 1050.008heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1066817119107713808Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104282327487823274Rat
12880371Cm106Cardiac mass QTL 1060.007heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1066817119107713808Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106184349698710773Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)107369533997272278Rat
11565453Kidm58Kidney mass QTL 580.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1066817119107713808Rat
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1065390777107713808Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1081012077101828297Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102293137391127454Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107304965694495280Rat
2306792Ean4Experimental allergic neuritis QTL 44nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)104949549294495492Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1052269185107713808Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068920187107713808Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)1065307813107713808Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1061843496106843496Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)102980091091417879Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070698731107713808Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)102758722696099902Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105530797293608131Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)1061843496100198886Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104360879388608793Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040535708107713808Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)104994371094943710Rat
2325836Bp346Blood pressure QTL 3460.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107674313384503487Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1066108888107555881Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104493935989939359Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1061843496100198886Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104786912992869129Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107674313395604677Rat
2292436Bp310Blood pressure QTL 310arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105060467795604677Rat
12880050Am10Aortic mass QTL 100.016aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)103950348784503487Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072724423107713808Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)103550938388177745Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1076128947107713808Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107395035396620293Rat
634354Rends3Renal damage susceptibility QTL 30.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)1061997479106997479Rat
2301405Cm69Cardiac mass QTL 690.031heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1066817119107713808Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102702353599451848Rat

Markers in Region
RH141071  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,927,801 - 83,928,007 (+)MAPPERmRatBN7.2
Rnor_6.01086,883,094 - 86,883,299NCBIRnor6.0
Rnor_5.01086,681,507 - 86,681,712UniSTSRnor5.0
RGSC_v3.41087,752,925 - 87,753,130UniSTSRGSC3.4
Celera1082,669,234 - 82,669,439UniSTS
RH 3.4 Map10860.1UniSTS
Cytogenetic Map10q31UniSTS


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 67 160 91 90 59 92 59 6 356 192 11 139 81 92 31 17 17

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001429976 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001429977 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001429978 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_031528 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767945 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597011 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085214 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063268421 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063268422 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063268423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063268424 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC141969 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ002940 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ002941 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC099830 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226387 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U15211 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000008659   ⟹   ENSRNOP00000008659
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1084,411,186 - 84,425,159 (+)Ensembl
mRatBN7.2 Ensembl1083,914,976 - 83,928,103 (+)Ensembl
Rnor_6.0 Ensembl1086,870,523 - 86,883,434 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000084644   ⟹   ENSRNOP00000069776
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1084,389,622 - 84,425,160 (+)Ensembl
mRatBN7.2 Ensembl1083,893,384 - 83,928,142 (+)Ensembl
Rnor_6.0 Ensembl1086,860,685 - 86,884,210 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000168609   ⟹   ENSRNOP00000098789
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1084,410,402 - 84,425,160 (+)Ensembl
RefSeq Acc Id: NM_031528   ⟹   NP_113716
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81084,411,467 - 84,424,371 (+)NCBI
mRatBN7.21083,915,238 - 83,928,142 (+)NCBI
Rnor_6.01086,870,530 - 86,883,434 (+)NCBI
Rnor_5.01086,663,856 - 86,681,847 (+)NCBI
RGSC_v3.41087,740,479 - 87,753,265 (+)RGD
Celera1082,656,708 - 82,669,574 (+)RGD
Sequence:
RefSeq Acc Id: XM_017597011   ⟹   XP_017452500
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81084,389,476 - 84,424,367 (+)NCBI
mRatBN7.21083,893,380 - 83,928,932 (+)NCBI
Rnor_6.01086,848,661 - 86,884,224 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039085214   ⟹   XP_038941142
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81084,394,751 - 84,424,367 (+)NCBI
mRatBN7.21083,902,720 - 83,928,932 (+)NCBI
RefSeq Acc Id: XM_039085219   ⟹   XP_038941147
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81084,400,282 - 84,424,367 (+)NCBI
mRatBN7.21083,904,427 - 83,928,932 (+)NCBI
RefSeq Acc Id: XM_063268421   ⟹   XP_063124491
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81084,379,780 - 84,424,367 (+)NCBI
RefSeq Acc Id: XM_063268422   ⟹   XP_063124492
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81084,389,611 - 84,424,367 (+)NCBI
RefSeq Acc Id: XM_063268423   ⟹   XP_063124493
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81084,393,761 - 84,424,367 (+)NCBI
RefSeq Acc Id: XM_063268424   ⟹   XP_063124494
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81084,394,766 - 84,424,367 (+)NCBI
RefSeq Acc Id: NP_113716   ⟸   NM_031528
- UniProtKB: Q499N1 (UniProtKB/TrEMBL),   A6HIV9 (UniProtKB/TrEMBL),   Q9QWJ1 (UniProtKB/TrEMBL),   F7EXR0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017452500   ⟸   XM_017597011
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000069776   ⟸   ENSRNOT00000084644
Ensembl Acc Id: ENSRNOP00000008659   ⟸   ENSRNOT00000008659
RefSeq Acc Id: XP_038941142   ⟸   XM_039085214
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038941147   ⟸   XM_039085219
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JW78 (UniProtKB/TrEMBL),   A6HIV8 (UniProtKB/TrEMBL),   Q9QWJ1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063124491   ⟸   XM_063268421
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JW78 (UniProtKB/TrEMBL),   A6HIV8 (UniProtKB/TrEMBL),   Q9QWJ1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063124492   ⟸   XM_063268422
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JW78 (UniProtKB/TrEMBL),   A6HIV8 (UniProtKB/TrEMBL),   Q9QWJ1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063124493   ⟸   XM_063268423
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JW78 (UniProtKB/TrEMBL),   A6HIV8 (UniProtKB/TrEMBL),   Q9QWJ1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063124494   ⟸   XM_063268424
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JW78 (UniProtKB/TrEMBL),   A6HIV8 (UniProtKB/TrEMBL),   Q9QWJ1 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000098789   ⟸   ENSRNOT00000168609
Protein Domains
NR LBD   Nuclear receptor

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JW78-F1-model_v2 AlphaFold A0A0G2JW78 1-462 view protein structure

Transcriptome

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

Promoters
RGD ID:13697674
Promoter ID:EPDNEW_R8198
Type:initiation region
Name:Rara_1
Description:retinoic acid receptor, alpha
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_6.01086,870,468 - 86,870,528EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3534 AgrOrtholog
BioCyc Gene G2FUF-23334 BioCyc
Ensembl Genes ENSRNOG00000009972 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008659 ENTREZGENE
  ENSRNOT00000008659.6 UniProtKB/TrEMBL
  ENSRNOT00000084644 ENTREZGENE
  ENSRNOT00000084644.3 UniProtKB/TrEMBL
  ENSRNOT00000168609.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.565.10 UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7933868 IMAGE-MGC_LOAD
InterPro NHR_like_domain UniProtKB/TrEMBL
  NR_DBD_RAR UniProtKB/TrEMBL
  NR_LBD_RAR UniProtKB/TrEMBL
  Nucl_hrmn_rcpt_lig-bd_core UniProtKB/TrEMBL
  Retinoic_acid_rcpt UniProtKB/TrEMBL
  Str_hrmn_rcpt UniProtKB/TrEMBL
  Znf_hrmn_rcpt UniProtKB/TrEMBL
  Znf_NHR/GATA UniProtKB/TrEMBL
KEGG Report rno:24705 UniProtKB/TrEMBL
MGC_CLONE MGC:124599 IMAGE-MGC_LOAD
NCBI Gene 24705 ENTREZGENE
PANTHER NUCLEAR HORMONE RECEPTOR UniProtKB/TrEMBL
  RETINOIC ACID RECEPTOR ALPHA UniProtKB/TrEMBL
Pfam Hormone_recep UniProtKB/TrEMBL
  zf-C4 UniProtKB/TrEMBL
PhenoGen Rara PhenoGen
PRINTS RETNOICACIDR UniProtKB/TrEMBL
  STRDHORMONER UniProtKB/TrEMBL
  STROIDFINGER UniProtKB/TrEMBL
PROSITE NR_LBD UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_1 UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000009972 RatGTEx
SMART HOLI UniProtKB/TrEMBL
  ZnF_C4 UniProtKB/TrEMBL
Superfamily-SCOP Glucocorticoid receptor-like (DNA-binding domain) UniProtKB/TrEMBL
  Str_ncl_receptor UniProtKB/TrEMBL
UniProt A0A0G2JW78 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0L4G2_RAT UniProtKB/TrEMBL
  A6HIV8 ENTREZGENE, UniProtKB/TrEMBL
  A6HIV9 ENTREZGENE, UniProtKB/TrEMBL
  F7EXR0 ENTREZGENE, UniProtKB/TrEMBL
  Q499N1 ENTREZGENE
  Q9QWJ1 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary Q499N1 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Rara  Retinoic acid receptor, alpha      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the perinuclear region of prostatic cells 625676
gene_expression expressed in the periductal stromal cells of 6 day old pups 625676
gene_expression expressed in the perinuclear region of prostatic cells also expressed in the periductal stromal cells of 6 day old pups 625676
gene_pathway required in the RA pathway in developing and adult prostates 625676
gene_regulation exposure to estrogen upregulates expression in prostatic cells 625676