Rxrb (retinoid X receptor beta) - Rat Genome Database

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Gene: Rxrb (retinoid X receptor beta) Rattus norvegicus
Analyze
Symbol: Rxrb
Name: retinoid X receptor beta
RGD ID: 3611
Description: Enables nuclear receptor activity; nuclear receptor binding activity; and nuclear receptor coactivator activity. Involved in regulation of myelination. Predicted to be located in nucleoplasm. Predicted to be part of RNA polymerase II transcription regulator complex. Orthologous to human RXRB (retinoid X receptor beta); PARTICIPATES IN retinoic acid signaling pathway; eicosanoid signaling pathway via peroxisome proliferator-activated receptor gamma; non-small cell lung carcinoma pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 3,3',5-triiodo-L-thyronine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: nuclear receptor co-regulator 1; nuclear receptor coregulator 1; nuclear receptor subfamily 2 group B member 2; Retinoic acid receptor beta; retinoic acid receptor RXR-beta; retinoic acid receptor, beta; RXR-beta
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,816,813 - 4,823,267 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl204,816,815 - 4,828,773 (-)Ensembl
Rnor_6.0203,822,673 - 3,829,138 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,823,042 - 3,829,140 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,901,997 - 5,908,469 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,954,336 - 4,960,880 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1204,955,307 - 4,960,928 (-)NCBI
Celera206,417,001 - 6,422,951 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
2,2-(2-Chlorophenyl-4'-chlorophenyl)-1,1-dichloroethene  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trichlorophenol  (ISO)
2,4-dichlorophenol  (ISO)
2,4-dinitrotoluene  (EXP)
2-hydroxyphytanic acid  (ISO)
2-isopropylphenol  (ISO)
2-tert-Butylphenol  (ISO)
3,3',5-triiodo-L-thyronine  (EXP)
3,4-Dichlorophenol  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-tert-Octylphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
8-Br-cAMP  (ISO)
9-cis-retinoic acid  (EXP,ISO)
acrylamide  (ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
bexarotene  (ISO)
bezafibrate  (ISO)
bicalutamide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
Butylbenzyl phthalate  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (EXP)
calciol  (ISO)
capsaicin  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
cholesterol  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cyclosporin A  (ISO)
DDE  (ISO)
DDT  (ISO)
Di-n-decyl phthalate  (ISO)
Di-n-hexyl phthalate  (ISO)
diazinon  (ISO)
dibutyl phthalate  (ISO)
diethyl phthalate  (ISO)
diheptyl phthalate  (ISO)
Diisodecyl phthalate  (ISO)
diisononyl phthalate  (ISO)
Dimethyl phthalate  (ISO)
dipentyl phthalate  (ISO)
dipropyl phthalate  (ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
ethanol  (ISO)
fenthion  (ISO)
fentin hydroxide  (ISO)
fludioxonil  (ISO)
folic acid  (ISO)
gamma-hexachlorocyclohexane  (ISO)
hexachlorobenzene  (ISO)
isotretinoin  (EXP)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
lithocholic acid  (ISO)
methidathion  (ISO)
methoprene  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
nickel sulfate  (ISO)
p-tert-Amylphenol  (ISO)
paracetamol  (EXP)
paraquat  (EXP)
parathion  (ISO)
pentanal  (ISO)
phthalic acid  (ISO)
phytanic acid  (ISO)
pirinixic acid  (EXP)
potassium dichromate  (ISO)
raloxifene  (ISO)
rimonabant  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone enanthate  (ISO)
Tetrachlorobisphenol A  (ISO)
tributylstannane  (EXP)
trichloroethene  (EXP)
urethane  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. 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.
2. International Union of Pharmacology. LXIII. Retinoid X receptors. Germain P, etal., Pharmacol Rev. 2006 Dec;58(4):760-72.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Retinoic acid regulates myelin formation in the peripheral nervous system. Latasa MJ, etal., Glia. 2010 Sep;58(12):1451-64.
5. 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.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
8. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
9. GOA pipeline RGD automated data pipeline
10. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. RXR beta: a coregulator that enhances binding of retinoic acid, thyroid hormone, and vitamin D receptors to their cognate response elements. Yu VC, etal., Cell 1991 Dec 20;67(6):1251-66.
Additional References at PubMed
PMID:1312497   PMID:2554307   PMID:7823919   PMID:7831303   PMID:7990953   PMID:9428411   PMID:9892670   PMID:12477932   PMID:12767074   PMID:17182792   PMID:18922886   PMID:19100254  
PMID:23017197   PMID:23318218   PMID:23327965   PMID:28267642  


Genomics

Comparative Map Data
Rxrb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,816,813 - 4,823,267 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl204,816,815 - 4,828,773 (-)Ensembl
Rnor_6.0203,822,673 - 3,829,138 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,823,042 - 3,829,140 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,901,997 - 5,908,469 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,954,336 - 4,960,880 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1204,955,307 - 4,960,928 (-)NCBI
Celera206,417,001 - 6,422,951 (-)NCBICelera
Cytogenetic Map20p12NCBI
RXRB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38633,193,588 - 33,200,853 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl633,193,588 - 33,200,665 (-)EnsemblGRCh38hg38GRCh38
GRCh37633,161,365 - 33,168,630 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36633,269,343 - 33,276,410 (-)NCBINCBI36hg18NCBI36
Build 34633,269,343 - 33,276,410NCBI
Celera634,715,731 - 34,722,798 (-)NCBI
Cytogenetic Map6p21.32NCBI
HuRef632,903,933 - 32,910,518 (-)NCBIHuRef
CHM1_1633,163,235 - 33,170,347 (-)NCBICHM1_1
T2T-CHM13v2.0633,014,941 - 33,022,206 (-)NCBI
Rxrb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391734,250,786 - 34,257,377 (+)NCBIGRCm39mm39
GRCm39 Ensembl1734,250,786 - 34,257,373 (+)Ensembl
GRCm381734,031,812 - 34,038,403 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1734,031,812 - 34,038,399 (+)EnsemblGRCm38mm10GRCm38
MGSCv371734,168,797 - 34,175,344 (+)NCBIGRCm37mm9NCBIm37
MGSCv361733,642,306 - 33,648,853 (+)NCBImm8
Celera1736,777,982 - 36,784,532 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1717.98NCBI
Rxrb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554371,767,833 - 1,774,401 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554371,767,833 - 1,774,401 (-)NCBIChiLan1.0ChiLan1.0
RXRB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1633,880,758 - 33,887,887 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl633,880,758 - 33,887,820 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0632,765,818 - 32,772,876 (-)NCBIMhudiblu_PPA_v0panPan3
RXRB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1122,657,058 - 2,663,648 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl122,657,792 - 2,663,706 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha122,738,197 - 2,744,918 (-)NCBI
ROS_Cfam_1.0122,987,789 - 2,994,513 (-)NCBI
ROS_Cfam_1.0 Ensembl122,987,789 - 2,994,459 (-)Ensembl
UMICH_Zoey_3.1122,655,982 - 2,662,701 (-)NCBI
UNSW_CanFamBas_1.0122,737,356 - 2,744,070 (-)NCBI
UU_Cfam_GSD_1.0122,811,921 - 2,818,640 (-)NCBI
Rxrb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494638,297,888 - 38,305,050 (-)NCBI
SpeTri2.0NW_00493647625,655,164 - 25,662,369 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RXRB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl725,236,007 - 25,242,875 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1725,236,005 - 25,242,842 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2729,760,855 - 29,767,618 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RXRB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11738,874,467 - 38,881,527 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1738,874,681 - 38,881,653 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604433,027,908 - 33,034,945 (-)NCBIVero_WHO_p1.0
Rxrb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475423,606,955 - 23,613,508 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462475423,607,046 - 23,613,399 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
Rxrb  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,818,881 - 4,820,582 (-)MAPPERmRatBN7.2
Rnor_6.0203,825,372 - 3,827,071NCBIRnor6.0
Rnor_5.0205,904,703 - 5,906,402UniSTSRnor5.0
RGSC_v3.4204,956,996 - 4,958,695UniSTSRGSC3.4
Celera206,419,067 - 6,420,766UniSTS
Cytogenetic Map20p12UniSTS
BM385817  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,824,348 - 4,824,536 (-)MAPPERmRatBN7.2
Rnor_6.0203,821,418 - 3,821,605NCBIRnor6.0
Rnor_5.0205,900,749 - 5,900,936UniSTSRnor5.0
RGSC_v3.4204,962,463 - 4,962,650UniSTSRGSC3.4
Celera206,424,534 - 6,424,721UniSTS
RH 3.4 Map2068.9UniSTS
Cytogenetic Map20p12UniSTS
MARC_6301-6302:997299518:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,817,779 - 4,818,347 (-)MAPPERmRatBN7.2
Rnor_6.0203,827,606 - 3,828,173NCBIRnor6.0
Rnor_5.0205,906,937 - 5,907,504UniSTSRnor5.0
RGSC_v3.4204,955,301 - 4,956,462UniSTSRGSC3.4
RGSC_v3.4204,955,301 - 4,955,869UniSTSRGSC3.4
Celera206,417,966 - 6,418,533UniSTS
Cytogenetic Map20p12UniSTS
UniSTS:237626  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,816,872 - 4,817,110 (-)MAPPERmRatBN7.2
Rnor_6.0203,828,843 - 3,829,080NCBIRnor6.0
Rnor_5.0205,908,174 - 5,908,411UniSTSRnor5.0
RGSC_v3.4204,954,394 - 4,954,631UniSTSRGSC3.4
Celera206,417,059 - 6,417,296UniSTS
Cytogenetic Map20p12UniSTS
Rxrb  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,820,657 - 4,821,131 (-)MAPPERmRatBN7.2
Rnor_6.0203,824,823 - 3,825,296NCBIRnor6.0
Rnor_5.0205,904,154 - 5,904,627UniSTSRnor5.0
RGSC_v3.4204,958,772 - 4,959,245UniSTSRGSC3.4
Celera206,420,843 - 6,421,316UniSTS
Cytogenetic Map20p12UniSTS
MARC_5897-5898:997299407:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,818,011 - 4,818,559 (-)MAPPERmRatBN7.2
Rnor_6.0203,827,394 - 3,827,941NCBIRnor6.0
Rnor_5.0205,906,725 - 5,907,272UniSTSRnor5.0
Cytogenetic Map20p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036216499243559Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2046066076691706Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat
7175096Tcs1T cell selection QTL 1T cell selectionexpression2047270785024580Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:147
Count of miRNA genes:107
Interacting mature miRNAs:131
Transcripts:ENSRNOT00000041613
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 34 22 9 19 9 3 74 28 41 11
Low 9 35 32 32 8 8 7 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041613   ⟹   ENSRNOP00000040499
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,816,815 - 4,828,773 (-)Ensembl
Rnor_6.0 Ensembl203,823,042 - 3,829,140 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079967   ⟹   ENSRNOP00000074360
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,827,367 - 3,827,906 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000081588   ⟹   ENSRNOP00000068701
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,827,086 - 3,828,288 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084638
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,825,928 - 3,829,140 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000086978
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,826,907 - 3,827,589 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087670   ⟹   ENSRNOP00000070175
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,823,596 - 3,824,966 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087895
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,826,729 - 3,827,926 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091182
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,824,176 - 3,825,802 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000118105   ⟹   ENSRNOP00000087218
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,816,819 - 4,828,773 (-)Ensembl
RefSeq Acc Id: NM_206849   ⟹   NP_996731
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,816,815 - 4,822,766 (-)NCBI
Rnor_6.0203,823,188 - 3,829,138 (+)NCBI
Rnor_5.0205,901,997 - 5,908,469 (+)NCBI
RGSC_v3.4204,954,336 - 4,960,880 (-)RGD
Celera206,417,001 - 6,422,951 (-)RGD
Sequence:
RefSeq Acc Id: XM_006255960   ⟹   XP_006256022
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,816,813 - 4,823,267 (-)NCBI
Rnor_6.0203,822,673 - 3,829,138 (+)NCBI
Rnor_5.0205,901,997 - 5,908,469 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006255961   ⟹   XP_006256023
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,816,813 - 4,822,516 (-)NCBI
Rnor_6.0203,823,458 - 3,829,138 (+)NCBI
Rnor_5.0205,901,997 - 5,908,469 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_996731   ⟸   NM_206849
- UniProtKB: A0A0G2QBZ5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256022   ⟸   XM_006255960
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006256023   ⟸   XM_006255961
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000070175   ⟸   ENSRNOT00000087670
RefSeq Acc Id: ENSRNOP00000040499   ⟸   ENSRNOT00000041613
RefSeq Acc Id: ENSRNOP00000074360   ⟸   ENSRNOT00000079967
RefSeq Acc Id: ENSRNOP00000068701   ⟸   ENSRNOT00000081588
RefSeq Acc Id: ENSRNOP00000087218   ⟸   ENSRNOT00000118105
Protein Domains
NR LBD   Nuclear receptor

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P49743-F1-model_v2 AlphaFold P49743 1-458 view protein structure

Transcriptome

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

Promoters
RGD ID:13701317
Promoter ID:EPDNEW_R11841
Type:multiple initiation site
Name:Rxrb_1
Description:retinoid X 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_6.0203,823,002 - 3,823,062EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 3828188 3828189 A G snv ACI/N (MCW), Buf/N (MCW), F344/NRrrc (MCW), WN/N (MCW), MR/N (MCW), WKY/N (MCW), M520/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3611 AgrOrtholog
BioCyc Gene G2FUF-4543 BioCyc
Ensembl Genes ENSRNOG00000000464 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000040499 ENTREZGENE
  ENSRNOP00000040499.6 UniProtKB/TrEMBL
  ENSRNOP00000087218.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041613 ENTREZGENE
  ENSRNOT00000041613.6 UniProtKB/TrEMBL
  ENSRNOT00000118105.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.565.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7933132 IMAGE-MGC_LOAD
InterPro NHR-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucl_hrmn_rcpt_lig-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nuclear_hrmn_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Retinoid-X_rcpt/HNF4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_hrmn_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_NHR/GATA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:361801 UniProtKB/TrEMBL
MGC_CLONE MGC:124514 IMAGE-MGC_LOAD
NCBI Gene 361801 ENTREZGENE
Pfam Hormone_recep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rxrb PhenoGen
PRINTS RETINOIDXR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  STRDHORMONER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  STROIDFINGER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE NR_LBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOLI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48508 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2QBZ5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A7J9_RAT UniProtKB/TrEMBL
  P49743 ENTREZGENE
  Q499T0_RAT UniProtKB/TrEMBL
  Q6MGB3_RAT UniProtKB/TrEMBL
  RXRB_RAT UniProtKB/Swiss-Prot
UniProt Secondary F1M9P1 UniProtKB/TrEMBL


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