Rarb (retinoic acid receptor, beta) - Rat Genome Database

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Gene: Rarb (retinoic acid receptor, beta) Rattus norvegicus
Analyze
Symbol: Rarb
Name: retinoic acid receptor, beta
RGD ID: 3535
Description: Exhibits retinoid X receptor binding activity. Involved in neural precursor cell proliferation and regulation of myelination. Localizes to nucleus. Human ortholog(s) of this gene implicated in asbestos-related lung carcinoma; lung adenocarcinoma; lung non-small cell carcinoma; lung small cell carcinoma; and syndromic microphthalmia 12. Orthologous to human RARB (retinoic acid receptor beta); PARTICIPATES IN retinoic acid signaling pathway; non-small cell lung carcinoma pathway; small cell lung carcinoma pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC684994; retinoic acid receptor beta
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2158,700,533 - 9,051,288 (+)NCBI
Rnor_6.0 Ensembl1510,120,206 - 10,262,599 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0159,915,223 - 10,262,599 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01513,963,567 - 14,307,996 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera158,949,068 - 9,094,754 (+)NCBICelera
Cytogenetic Map15p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(-)-anisomycin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
15-deoxy-Delta(12,14)-prostaglandin J2  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2-(2-Chlorophenyl-4'-chlorophenyl)-1,1-dichloroethene  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-bromohexadecanoic acid  (ISO)
3,3',5-triiodo-L-thyronine  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
8'-apo-beta,psi-caroten-8'-al  (ISO)
9-cis-retinoic acid  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
aldrin  (ISO)
all-trans-4-hydroxyretinoic acid  (ISO)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (EXP,ISO)
amsacrine  (ISO)
antirheumatic drug  (ISO)
arotinoid acid  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
beta-carotene  (ISO)
bexarotene  (ISO)
bezafibrate  (EXP)
bicalutamide  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol A diglycidyl ether  (ISO)
bisphenol F  (ISO)
buspirone  (EXP)
butanal  (ISO)
carbon nanotube  (ISO)
ciglitazone  (ISO)
cisplatin  (EXP,ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
cycloheximide  (EXP)
cyclosporin A  (ISO)
cyproconazole  (ISO)
diarsenic trioxide  (ISO)
dichloroacetic acid  (ISO)
dieldrin  (ISO)
difenoconazole  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
emodin  (ISO)
endosulfan  (EXP,ISO)
endrin  (ISO)
entinostat  (ISO)
ethanol  (EXP,ISO)
fenarimol  (EXP)
fenhexamid  (ISO)
fenofibrate  (EXP)
fludioxonil  (ISO)
flusilazole  (EXP)
flutamide  (EXP)
folic acid  (ISO)
genistein  (ISO)
griseofulvin  (ISO)
haloperidol  (EXP)
hexaconazole  (ISO)
hydralazine  (ISO)
isotretinoin  (EXP,ISO)
ketoconazole  (EXP)
kojic acid  (EXP)
lipopolysaccharide  (ISO)
melphalan  (ISO)
mercury dibromide  (ISO)
methapyrilene  (ISO)
mitoxantrone  (ISO)
Monobutylphthalate  (EXP)
monosodium L-glutamate  (ISO)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP)
nickel subsulfide  (EXP)
nimesulide  (EXP)
nitrofen  (EXP)
nobiletin  (ISO)
Nonylphenol  (ISO)
Oxadiazon  (ISO)
paclitaxel  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
pentanal  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
pirinixic acid  (ISO)
propiconazole  (EXP,ISO)
quercetin  (ISO)
Ro 41-5253  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tamibarotene  (EXP,ISO)
tangeretin  (ISO)
Tanshinone I  (ISO)
tazarotene  (ISO)
tazarotenic acid  (ISO)
tert-butyl hydroperoxide  (ISO)
Tesaglitazar  (EXP)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
triadimefon  (EXP)
tributylstannane  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (ISO)
troglitazone  (EXP)
trovafloxacin  (EXP)
valdecoxib  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
vinyl carbamate  (ISO)
vorinostat  (ISO)
zearalenone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleoplasm  (IEA,ISO)
nucleus  (IDA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Feng Q, etal., Cancer Epidemiol Biomarkers Prev. 2008 Mar;17(3):645-54. doi: 10.1158/1055-9965.EPI-07-2518.
2. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Germain P, etal., Pharmacol Rev. 2006 Dec;58(4):712-25.
4. GOA data from the GO Consortium
5. Goncalves MB, etal., Dev Biol. 2009 Feb 15;326(2):305-13. Epub 2008 Dec 7.
6. Kettunen E, etal., Int J Cancer. 2017 Nov 15;141(10):2014-2029. doi: 10.1002/ijc.30897. Epub 2017 Aug 2.
7. Latasa MJ, etal., Glia. 2010 Sep;58(12):1451-64.
8. Mattei MG, etal., Genomics 1991 Aug;10(4):1061-9.
9. McGrane MM J Nutr Biochem. 2007 Aug;18(8):497-508. Epub 2007 Feb 22.
10. MGD data from the GO Consortium
11. NCBI rat LocusLink and RefSeq merged data July 26, 2002
12. OMIM Disease Annotation Pipeline
13. Pipeline to import KEGG annotations from KEGG into RGD
14. Prins GS, etal., Endocrinology 2002 Sep;143(9):3628-40.
15. Reboul P, etal., Biochem Mol Biol Int. 1995 Aug;36(5):1097-105.
16. RGD automated data pipeline
17. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. RGD automated import pipeline for gene-chemical interactions
19. Rochette-Egly C and Germain P, Nucl Recept Signal. 2009 May 8;7:e005.
20. Walter RFH, etal., PLoS One. 2018 May 31;13(5):e0195716. doi: 10.1371/journal.pone.0195716. eCollection 2018.
21. Wang L, etal., Arch Biochem Biophys. 2004 Aug 1;428(1):92-8.
22. Wu H, etal., Eur J Cancer Prev. 2016 Nov;25(6):508-17. doi: 10.1097/CEJ.0000000000000214.
23. Zhao Y, etal., Oncol Lett. 2013 Apr;5(4):1211-1218. doi: 10.3892/ol.2013.1161. Epub 2013 Jan 29.
Additional References at PubMed
PMID:1313565   PMID:1655807   PMID:7607067   PMID:7823919   PMID:8152920   PMID:8681798   PMID:9428411   PMID:9659935   PMID:10075839   PMID:10684250   PMID:12195422   PMID:15766748  
PMID:16207763   PMID:18254374   PMID:18443282   PMID:18845237   PMID:19389355   PMID:19443732   PMID:21292463   PMID:24389816   PMID:26609164   PMID:26923513   PMID:33130074  


Genomics

Comparative Map Data
Rarb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2158,700,533 - 9,051,288 (+)NCBI
Rnor_6.0 Ensembl1510,120,206 - 10,262,599 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0159,915,223 - 10,262,599 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01513,963,567 - 14,307,996 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera158,949,068 - 9,094,754 (+)NCBICelera
Cytogenetic Map15p16NCBI
RARB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl325,174,332 - 25,597,932 (+)EnsemblGRCh38hg38GRCh38
GRCh38324,829,321 - 25,597,932 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37324,870,812 - 25,639,423 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36325,444,758 - 25,614,424 (+)NCBINCBI36hg18NCBI36
Build 34325,444,757 - 25,614,424NCBI
Celera325,406,007 - 25,576,301 (+)NCBI
Cytogenetic Map3p24.2NCBI
HuRef325,415,219 - 25,584,899 (+)NCBIHuRef
CHM1_1324,822,263 - 25,589,413 (+)NCBICHM1_1
Rarb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39145,387,365 - 6,038,924 (+)NCBIGRCm39mm39
GRCm39 Ensembl145,650,540 - 6,038,924 (+)Ensembl
GRCm381416,430,839 - 17,082,331 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1416,430,839 - 16,819,156 (-)EnsemblGRCm38mm10GRCm38
MGSCv371417,263,353 - 17,407,724 (-)NCBIGRCm37mm9NCBIm37
MGSCv361415,224,106 - 15,368,477 (-)NCBImm8
Celera1412,125,158 - 12,276,529 (-)NCBICelera
Cytogenetic Map14A1NCBI
cM Map147.08NCBI
Rarb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543017,295,174 - 17,460,045 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543017,067,536 - 17,457,558 (+)NCBIChiLan1.0ChiLan1.0
RARB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1325,660,850 - 25,830,372 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl325,660,922 - 25,833,297 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0324,729,220 - 25,499,187 (+)NCBIMhudiblu_PPA_v0panPan3
RARB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12318,207,253 - 18,931,128 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2318,207,760 - 18,482,652 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2318,204,235 - 18,714,201 (-)NCBI
ROS_Cfam_1.02318,509,719 - 19,020,664 (-)NCBI
UMICH_Zoey_3.12318,328,357 - 18,839,472 (-)NCBI
UNSW_CanFamBas_1.02318,431,214 - 18,948,405 (-)NCBI
UU_Cfam_GSD_1.02318,545,126 - 19,056,015 (-)NCBI
Rarb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118183,488,653 - 184,007,944 (+)NCBI
SpeTri2.0NW_00493647316,983,829 - 17,146,517 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RARB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11312,336,387 - 12,507,688 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21313,948,616 - 14,119,377 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RARB
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11569,851,447 - 70,266,215 (+)NCBI
ChlSab1.1 Ensembl1570,096,117 - 70,264,905 (+)Ensembl
Rarb
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247882,738,341 - 3,493,140 (+)NCBI

Position Markers
D15Got21  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01510,236,706 - 10,236,976NCBIRnor6.0
Rnor_5.01514,282,103 - 14,282,373UniSTSRnor5.0
Celera159,067,929 - 9,068,199UniSTS
RH 3.4 Map1582.5UniSTS
RH 3.4 Map1582.5RGD
RH 2.0 Map1544.5RGD
PMC113761P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01510,120,290 - 10,120,905NCBIRnor6.0
Rnor_5.01514,166,367 - 14,166,982UniSTSRnor5.0
RGSC_v3.41510,517,448 - 10,518,063UniSTSRGSC3.4
Celera158,949,152 - 8,949,767UniSTS
RH133722  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01510,262,223 - 10,262,405NCBIRnor6.0
Rnor_5.01514,307,620 - 14,307,802UniSTSRnor5.0
Celera159,094,378 - 9,094,560UniSTS
RH 3.4 Map1590.8UniSTS
AW531034  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01510,185,731 - 10,185,908NCBIRnor6.0
Rnor_5.01514,231,379 - 14,231,556UniSTSRnor5.0
Celera159,014,827 - 9,015,004UniSTS
RH 3.4 Map1590.8UniSTS
PMC134698P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01510,120,147 - 10,120,313NCBIRnor6.0
Rnor_5.01514,166,224 - 14,166,390UniSTSRnor5.0
RGSC_v3.41510,518,040 - 10,518,206UniSTSRGSC3.4
Celera158,949,009 - 8,949,175UniSTS
PMC134698P3  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01510,120,436 - 10,120,901NCBIRnor6.0
Rnor_5.01514,166,513 - 14,166,978UniSTSRnor5.0
RGSC_v3.41510,517,452 - 10,517,917UniSTSRGSC3.4
Celera158,949,298 - 8,949,763UniSTS
BE119548  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01510,116,591 - 10,116,766NCBIRnor6.0
Rnor_5.01514,162,668 - 14,162,843UniSTSRnor5.0
RGSC_v3.41510,521,587 - 10,521,762UniSTSRGSC3.4
Celera158,945,453 - 8,945,628UniSTS
RH 3.4 Map1590.4UniSTS
AW529852  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01510,132,912 - 10,133,090NCBIRnor6.0
Rnor_5.01514,178,989 - 14,179,167UniSTSRnor5.0
RGSC_v3.41510,505,262 - 10,505,440UniSTSRGSC3.4
Celera158,961,766 - 8,961,944UniSTS
RH 3.4 Map1594.3UniSTS
Rarb  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01510,261,240 - 10,261,605NCBIRnor6.0
Rnor_5.01514,306,637 - 14,307,002UniSTSRnor5.0
Celera159,093,395 - 9,093,760UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15143521446Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15142844179Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15232787753535766Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)colorectal tumor number (CMO:0001794)15232787726288802Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15232787726288802Rat
1300142Bp191Blood pressure QTL 1913.14arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)15112800829Rat
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15130597196Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15110589015828368Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15137708474Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15137708474Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15137708474Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15388113148881131Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:173
Count of miRNA genes:77
Interacting mature miRNAs:86
Transcripts:ENSRNOT00000033048, ENSRNOT00000036872, ENSRNOT00000065435
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 18 22 22 22 12 31 17 11
Low 3 25 35 19 19 19 8 11 62 4 19 8
Below cutoff 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000033048   ⟹   ENSRNOP00000036692
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1510,120,206 - 10,262,599 (+)Ensembl
RefSeq Acc Id: NM_031529   ⟹   NP_113717
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2158,905,623 - 9,051,288 (+)NCBI
Rnor_6.01510,120,206 - 10,262,599 (+)NCBI
Rnor_5.01513,963,567 - 14,307,996 (+)NCBI
Celera158,949,068 - 9,094,754 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599578   ⟹   XP_017455067
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2158,700,533 - 9,051,288 (+)NCBI
Rnor_6.0159,915,223 - 10,262,599 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599579   ⟹   XP_017455068
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2158,920,856 - 9,051,288 (+)NCBI
Rnor_6.01510,141,119 - 10,262,599 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039092993   ⟹   XP_038948921
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2158,905,571 - 9,051,288 (+)NCBI
Protein Sequences
Protein RefSeqs NP_113717 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455067 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455068 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948921 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA05769 (Get FASTA)   NCBI Sequence Viewer  
  EDL94092 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_113717   ⟸   NM_031529
- UniProtKB: D3ZFD9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455067   ⟸   XM_017599578
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017455068   ⟸   XM_017599579
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000036692   ⟸   ENSRNOT00000033048
RefSeq Acc Id: XP_038948921   ⟸   XM_039092993
- Peptide Label: isoform X2
Protein Domains
NR LBD   Nuclear receptor

Transcriptome

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

Promoters
RGD ID:13699579
Promoter ID:EPDNEW_R10102
Type:multiple initiation site
Name:Rarb_1
Description:retinoic acid receptor, beta
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_6.01510,120,283 - 10,120,343EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
15 14193445 14193446 G C snv HWY/Slc (KyushuU)


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
15 10147307 10147308 T C snv Buf/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3535 AgrOrtholog
Ensembl Genes ENSRNOG00000024061 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000036692 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000033048 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.565.10 UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/TrEMBL
InterPro NHR_like_domain 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:24706 UniProtKB/TrEMBL
NCBI Gene 24706 ENTREZGENE
Pfam Hormone_recep UniProtKB/TrEMBL
  zf-C4 UniProtKB/TrEMBL
PhenoGen Rarb 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
SMART HOLI UniProtKB/TrEMBL
  ZnF_C4 UniProtKB/TrEMBL
Superfamily-SCOP Str_ncl_receptor UniProtKB/TrEMBL
UniProt D3ZFD9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-29 Rarb  retinoic acid receptor, beta  LOC684994  similar to retinoic acid receptor, beta  Data Merged 737654 PROVISIONAL
2006-11-19 LOC684994  similar to retinoic acid receptor, beta      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Rarb  Retinoic acid receptor, beta      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the nuclei of basally located epithelial cells of six day old pups and reduce in number as they grow; in an adult prostrate mRNA expression is nearly undetectable 625676
gene_mapping maps to chromosome 15 704353
gene_pathway required in the RA pathway in developing and adult prostates 625676
gene_regulation exposure to estrogen upregulated expression in prostatic cells 625676