Nr1d2 (nuclear receptor subfamily 1, group D, member 2) - Rat Genome Database

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Gene: Nr1d2 (nuclear receptor subfamily 1, group D, member 2) Rattus norvegicus
Analyze
Symbol: Nr1d2
Name: nuclear receptor subfamily 1, group D, member 2
RGD ID: 628828
Description: Predicted to have DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and nuclear receptor activity. Predicted to be involved in several processes, including energy homeostasis; regulation of skeletal muscle cell differentiation; and regulation of transcription by RNA polymerase II. Predicted to localize to cytoplasm and nucleoplasm. Orthologous to human NR1D2 (nuclear receptor subfamily 1 group D member 2); INTERACTS WITH 17alpha-ethynylestradiol; 2,2',4,4'-Tetrabromodiphenyl ether; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: EAR4; HZF-2; nuclear receptor subfamily 1 group D member 2; orphan nuclear receptor HZF-2; orphan receptor; rev-erb-beta; Rev-erb-Beta2; Rev-ErbA-beta
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2157,524,257 - 7,550,553 (+)NCBI
Rnor_6.0 Ensembl158,730,871 - 8,757,165 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0158,730,871 - 8,757,165 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01512,792,652 - 12,819,056 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera157,577,813 - 7,604,107 (+)NCBICelera
Cytogenetic Map15p16NCBI
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-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3-chloropropane-1,2-diol  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4-hydroxynon-2-enal  (ISO)
4-phenylbutyric acid  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
avobenzone  (ISO)
benzene  (EXP)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
beta-naphthoflavone  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
buspirone  (EXP)
butanal  (ISO)
C60 fullerene  (EXP)
calcium atom  (EXP)
calcium(0)  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chenodeoxycholic acid  (ISO)
chloroprene  (EXP)
choline  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
coumarin  (EXP)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
D-gluconic acid  (EXP)
D-glucose  (ISO)
decabromodiphenyl ether  (EXP)
deoxycholic acid  (EXP)
dibenz[a,h]anthracene  (ISO)
dibenzofuran  (EXP)
dibutyl phthalate  (ISO)
dichloroacetic acid  (ISO)
dichloromethane  (ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
flavonoids  (EXP)
fluoranthene  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
gentamycin  (EXP)
geraniol  (ISO)
glucose  (ISO)
L-methionine  (ISO)
leflunomide  (ISO)
manganese(II) chloride  (EXP)
mercury dichloride  (EXP)
methyl methanesulfonate  (ISO)
methylparaben  (ISO)
motexafin gadolinium  (ISO)
N-methylformamide  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosomorpholine  (EXP)
nefazodone  (EXP)
nickel atom  (ISO)
nimesulide  (EXP)
oxaliplatin  (EXP)
paracetamol  (ISO)
paraquat  (ISO)
pentanal  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (EXP)
phenformin  (EXP)
phenobarbital  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
propanal  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
SCH-351591  (EXP)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
styrene  (ISO)
succimer  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tauroursodeoxycholic acid  (EXP)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
titanium dioxide  (EXP,ISO)
topotecan  (EXP)
tributylstannane  (ISO)
trichloroethene  (EXP,ISO)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
tunicamycin  (ISO)
valdecoxib  (EXP)
valproic acid  (EXP,ISO)
zinc acetate  (ISO)
zinc atom  (EXP)
zinc sulfate  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (ISO,ISS)
nucleoplasm  (IEA,ISO)
nucleus  (IEA,ISO,ISS)

References

Additional References at PubMed
PMID:7838156   PMID:7838158   PMID:7914660   PMID:8747539   PMID:11058961   PMID:15623503   PMID:17892483   PMID:17996965   PMID:19682428   PMID:21076970   PMID:23221024   PMID:29508494  
PMID:29533925   PMID:29723273  


Genomics

Comparative Map Data
Nr1d2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2157,524,257 - 7,550,553 (+)NCBI
Rnor_6.0 Ensembl158,730,871 - 8,757,165 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0158,730,871 - 8,757,165 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01512,792,652 - 12,819,056 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera157,577,813 - 7,604,107 (+)NCBICelera
Cytogenetic Map15p16NCBI
NR1D2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl323,945,286 - 23,980,617 (+)EnsemblGRCh38hg38GRCh38
GRCh38323,945,286 - 23,980,618 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37323,986,777 - 24,022,108 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36323,961,810 - 23,996,241 (+)NCBINCBI36hg18NCBI36
Build 34323,961,809 - 23,996,240NCBI
Celera323,931,547 - 23,957,664 (+)NCBI
Cytogenetic Map3p24.2NCBI
HuRef323,933,388 - 23,968,134 (+)NCBIHuRef
CHM1_1323,938,552 - 23,973,891 (+)NCBICHM1_1
Nr1d2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39144,230,549 - 4,265,640 (+)NCBIGRCm39mm39
GRCm39 Ensembl144,230,569 - 4,265,642 (+)Ensembl
GRCm381418,204,056 - 18,239,106 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1418,204,054 - 18,239,127 (-)EnsemblGRCm38mm10GRCm38
MGSCv371419,036,570 - 19,071,620 (-)NCBIGRCm37mm9NCBIm37
MGSCv361416,997,184 - 17,032,113 (-)NCBImm8
Celera1413,893,071 - 13,928,619 (-)NCBICelera
Cytogenetic Map14A1NCBI
Nr1d2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543015,812,448 - 15,834,412 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543015,812,449 - 15,834,341 (+)NCBIChiLan1.0ChiLan1.0
NR1D2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1324,189,931 - 24,215,831 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl324,185,798 - 24,215,831 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0323,857,317 - 23,892,533 (+)NCBIMhudiblu_PPA_v0panPan3
NR1D2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12319,758,907 - 19,787,725 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2319,762,052 - 19,787,614 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2319,757,060 - 19,785,724 (-)NCBI
ROS_Cfam_1.02320,065,641 - 20,094,314 (-)NCBI
UMICH_Zoey_3.12319,880,835 - 19,909,714 (-)NCBI
UNSW_CanFamBas_1.02319,990,566 - 20,019,259 (-)NCBI
UU_Cfam_GSD_1.02320,099,576 - 20,128,270 (-)NCBI
Nr1d2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118182,486,589 - 182,508,302 (+)NCBI
SpeTri2.0NW_00493647315,624,597 - 15,646,875 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NR1D2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1310,756,926 - 10,791,210 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11310,756,954 - 10,791,219 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21312,197,595 - 12,222,718 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NR1D2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11568,632,142 - 68,668,467 (+)NCBI
ChlSab1.1 Ensembl1568,632,197 - 68,665,258 (+)Ensembl

Position Markers
RH134269  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0158,756,165 - 8,756,383NCBIRnor6.0
Rnor_5.01512,818,053 - 12,818,271UniSTSRnor5.0
Celera157,603,107 - 7,603,325UniSTS
RH 3.4 Map1573.5UniSTS
Cytogenetic Map15p16UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15137708474Rat
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
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15142844179Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15143521446Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15110589015828368Rat
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
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15232787753535766Rat
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:105
Count of miRNA genes:92
Interacting mature miRNAs:102
Transcripts:ENSRNOT00000071751
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 3 25 34 18 19 18 8 11 35 35 35 11 8
Low 18 23 23 23 39 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000071751   ⟹   ENSRNOP00000065585
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl158,739,589 - 8,754,831 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000081845   ⟹   ENSRNOP00000075553
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl158,730,871 - 8,757,165 (+)Ensembl
RefSeq Acc Id: NM_147210   ⟹   NP_671743
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2157,524,257 - 7,550,553 (+)NCBI
Rnor_6.0158,730,871 - 8,757,165 (+)NCBI
Rnor_5.01512,792,652 - 12,819,056 (+)NCBI
Celera157,577,813 - 7,604,107 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_671743   ⟸   NM_147210
- UniProtKB: Q63504 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075553   ⟸   ENSRNOT00000081845
RefSeq Acc Id: ENSRNOP00000065585   ⟸   ENSRNOT00000071751
Protein Domains
NR LBD   Nuclear receptor

Transcriptome

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

Promoters
RGD ID:13699578
Promoter ID:EPDNEW_R10101
Type:initiation region
Name:Nr1d2_1
Description:nuclear receptor subfamily 1, group D, member 2
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_6.0158,730,913 - 8,730,973EPDNEW

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)
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
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
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)
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
F344/NRrrc (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
FHH/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)
FHH/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
FHL/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)
FHL/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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628828 AgrOrtholog
Ensembl Genes ENSRNOG00000046912 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000065585 UniProtKB/TrEMBL
  ENSRNOP00000075553 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000071751 UniProtKB/TrEMBL
  ENSRNOT00000081845 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.565.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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
  ThyrH_rcpt UniProtKB/TrEMBL
  Znf_hrmn_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_NHR/GATA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:259241 UniProtKB/Swiss-Prot
NCBI Gene 259241 ENTREZGENE
Pfam Hormone_recep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nr1d2 PhenoGen
PRINTS STRDHORMONER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  STROIDFINGER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  THYROIDHORMR 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 A0A0H2UI31_RAT UniProtKB/TrEMBL
  NR1D2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q62756 UniProtKB/Swiss-Prot
  Q63542 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Nr1d2  nuclear receptor subfamily 1, group D, member 2      Symbol and Name status set to approved 625702 APPROVED
2003-02-27 Nr1d2  nuclear receptor subfamily 1, group D, member 2      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expression increases during neonatal brain development and remains elevated in the adult brain 729070