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: Exhibits nuclear hormone receptor binding activity; nuclear receptor activity; and nuclear receptor coactivator activity. Involved in regulation of myelination. Predicted to localize to RNA polymerase II transcription regulator complex and nucleoplasm. 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 2,4-dinitrotoluene; 3,3',5-triiodo-L-thyronine; 3H-1,2-dithiole-3-thione.
Type: protein-coding
RefSeq Status: VALIDATED
Also 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,816,813 - 4,823,267 (-)NCBI
Rnor_6.0 Ensembl203,823,042 - 3,829,140 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0203,822,673 - 3,829,138 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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  (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)
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)
fentin hydroxide  (ISO)
fludioxonil  (ISO)
folic acid  (ISO)
gamma-hexachlorocyclohexane  (ISO)
hexachlorobenzene  (ISO)
isotretinoin  (EXP)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
lithocholic acid  (ISO)
methoprene  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
nickel sulfate  (ISO)
p-tert-Amylphenol  (ISO)
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)
urethane  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

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 (-)NCBI
Rnor_6.0 Ensembl203,823,042 - 3,829,140 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0203,822,673 - 3,829,138 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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
GRCh38.p13 Ensembl633,193,588 - 33,200,688 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl633,193,588 - 33,200,665 (-)EnsemblGRCh38hg38GRCh38
GRCh38633,193,588 - 33,200,991 (-)NCBIGRCh38GRCh38hg38GRCh38
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 - 33,170,504 (-)NCBICHM1_1
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
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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11738,874,467 - 38,881,527 (+)NCBI
ChlSab1.1 Ensembl1738,874,681 - 38,881,653 (+)Ensembl
Rxrb
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475423,607,046 - 23,613,399 (+)NCBI

Position Markers
Rxrb  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
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
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
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
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
Rnor_6.0203,827,394 - 3,827,941NCBIRnor6.0
Rnor_5.0205,906,725 - 5,907,272UniSTSRnor5.0
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2015192000Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2020187706567419Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2031518156896013Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2031518156896013Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat

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
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: 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
Protein Domains
NR LBD   Nuc_recep-AF1   Nuclear receptor

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 (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (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_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
Ensembl Genes ENSRNOG00000000464 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000040499 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068701 UniProtKB/TrEMBL
  ENSRNOP00000070175 UniProtKB/TrEMBL
  ENSRNOP00000074360 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041613 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000079967 UniProtKB/TrEMBL
  ENSRNOT00000081588 UniProtKB/TrEMBL
  ENSRNOT00000087670 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
  Nuc_recep-AF1 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
  Nuc_recep-AF1 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 A0A0G2JTG2_RAT UniProtKB/TrEMBL
  A0A0G2JX85_RAT UniProtKB/TrEMBL
  A0A0G2K7V3_RAT UniProtKB/TrEMBL
  A0A0G2QBZ5 ENTREZGENE, 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