Nr2c1 (nuclear receptor subfamily 2, group C, member 1) - Rat Genome Database
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Gene: Nr2c1 (nuclear receptor subfamily 2, group C, member 1) Rattus norvegicus
Analyze
Symbol: Nr2c1
Name: nuclear receptor subfamily 2, group C, member 1
RGD ID: 3200
Description: Predicted to have several functions, including DNA-binding transcription factor activity, RNA polymerase II-specific; histone deacetylase binding activity; and protein homodimerization activity. Predicted to be involved in several processes, including cell differentiation; negative regulation of transcription by RNA polymerase II; and positive regulation of retinoic acid receptor signaling pathway. Predicted to localize to PML body and nuclear chromatin. Orthologous to human NR2C1 (nuclear receptor subfamily 2 group C member 1); INTERACTS WITH ammonium chloride; bisphenol A; decabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: nuclear receptor subfamily 2 group C member 1; nuclear receptor subfamily 2, group H, member 1; orphan nuclear receptor TR2; orphan receptor; orphan receptor, TR2-11; pregnancy specific beta-1-glycoprotein 4; Psg4; testicular receptor 2; Tr2; TR2-11
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
mRatBN7.2728,715,347 - 28,768,624 (+)NCBI
Rnor_6.0 Ensembl735,069,814 - 35,122,796 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0735,069,807 - 35,122,810 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0735,137,598 - 35,189,641 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4731,293,180 - 31,345,189 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1731,313,973 - 31,365,460 (+)NCBI
Celera725,816,321 - 25,858,083 (+)NCBICelera
Cytogenetic Map7q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:7794280   PMID:8858600   PMID:9071982   PMID:9369481   PMID:9774688   PMID:9795341   PMID:11463856   PMID:12477932   PMID:16130175   PMID:17974920   PMID:18682553  


Genomics

Comparative Map Data
Nr2c1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2728,715,347 - 28,768,624 (+)NCBI
Rnor_6.0 Ensembl735,069,814 - 35,122,796 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0735,069,807 - 35,122,810 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0735,137,598 - 35,189,641 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4731,293,180 - 31,345,189 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1731,313,973 - 31,365,460 (+)NCBI
Celera725,816,321 - 25,858,083 (+)NCBICelera
Cytogenetic Map7q13NCBI
NR2C1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1295,020,229 - 95,073,628 (-)EnsemblGRCh38hg38GRCh38
GRCh381295,020,229 - 95,073,618 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371295,414,005 - 95,467,394 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh371295,414,005 - 95,467,404 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361293,939,802 - 93,991,487 (-)NCBINCBI36hg18NCBI36
Build 341293,918,138 - 93,969,676NCBI
Celera1295,085,340 - 95,138,686 (-)NCBI
Cytogenetic Map12q22NCBI
HuRef1292,481,137 - 92,534,428 (-)NCBIHuRef
CHM1_11295,378,558 - 95,432,374 (-)NCBICHM1_1
Nr2c1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391093,983,491 - 94,033,078 (+)NCBIGRCm39mm39
GRCm381094,147,542 - 94,197,216 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1094,148,023 - 94,197,211 (+)EnsemblGRCm38mm10GRCm38
MGSCv371093,610,676 - 93,659,959 (+)NCBIGRCm37mm9NCBIm37
MGSCv361093,586,085 - 93,625,150 (+)NCBImm8
Celera1096,123,279 - 96,172,755 (+)NCBICelera
Cytogenetic Map10C2NCBI
cM Map1048.81NCBI
Nr2c1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540531,635,113 - 31,691,465 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540531,637,832 - 31,693,621 (-)NCBIChiLan1.0ChiLan1.0
NR2C1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11296,007,293 - 96,060,878 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1296,007,293 - 96,060,878 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01292,611,459 - 92,664,405 (-)NCBIMhudiblu_PPA_v0panPan3
NR2C1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1535,005,066 - 35,038,968 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11535,003,658 - 35,049,812 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Nr2c1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493650711,266,408 - 11,319,642 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NR2C1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl588,231,264 - 88,277,997 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1588,231,180 - 88,278,803 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2592,480,138 - 92,527,231 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NR2C1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11190,430,307 - 90,481,269 (-)NCBI
ChlSab1.1 Ensembl1190,430,194 - 90,481,493 (-)Ensembl
Nr2c1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475011,972,826 - 12,022,603 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7137009673Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7138119654Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7591147750911477Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7595196950951969Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7975804554758045Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)71164710256647102Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71232846767193263Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)712328467106995532Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71268785067801690Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71395217958952179Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)71444568559445685Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)72021558344668493Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)72021558344668493Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)72021558344668493Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)72216841267168412Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)72473146569731465Rat
61369Mcs2Mammary carcinoma susceptibility QTL 23.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72473868040433335Rat
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)72536563357064364Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)72536563357064364Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)72536563360317612Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)72536563393155402Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)72650888736346595Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72820465373204653Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)73138152976381529Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)73203505377035053Rat
61439Cia8Collagen induced arthritis QTL 85.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)73257294277572942Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)73304444971352127Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:26
Count of miRNA genes:21
Interacting mature miRNAs:25
Transcripts:ENSRNOT00000009578
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 1 22 10 6 6 6 66 20 40 11
Low 2 21 47 35 13 35 8 11 8 15 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009578   ⟹   ENSRNOP00000009578
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl735,070,284 - 35,121,346 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089228   ⟹   ENSRNOP00000071901
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl735,069,814 - 35,122,796 (+)Ensembl
RefSeq Acc Id: NM_145780   ⟹   NP_665723
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2728,715,616 - 28,767,162 (+)NCBI
Rnor_6.0735,069,807 - 35,121,348 (+)NCBI
Rnor_5.0735,137,598 - 35,189,641 (+)NCBI
RGSC_v3.4731,293,180 - 31,345,189 (+)RGD
Celera725,816,321 - 25,858,083 (+)RGD
Sequence:
RefSeq Acc Id: XM_008765216   ⟹   XP_008763438
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2728,715,990 - 28,768,624 (+)NCBI
Rnor_6.0735,069,973 - 35,122,810 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594671   ⟹   XP_017450160
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2728,715,802 - 28,768,624 (+)NCBI
Rnor_6.0735,069,973 - 35,122,810 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594672   ⟹   XP_017450161
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0735,069,885 - 35,122,810 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039078458   ⟹   XP_038934386
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2728,715,347 - 28,768,624 (+)NCBI
RefSeq Acc Id: XM_039078459   ⟹   XP_038934387
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2728,715,990 - 28,768,624 (+)NCBI
RefSeq Acc Id: XR_005486547
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2728,715,347 - 28,761,249 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_665723   ⟸   NM_145780
- UniProtKB: Q8VIJ4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008763438   ⟸   XM_008765216
- Peptide Label: isoform X1
- UniProtKB: Q8VIJ4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017450161   ⟸   XM_017594672
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017450160   ⟸   XM_017594671
- Peptide Label: isoform X1
- UniProtKB: Q8VIJ4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071901   ⟸   ENSRNOT00000089228
RefSeq Acc Id: ENSRNOP00000009578   ⟸   ENSRNOT00000009578
RefSeq Acc Id: XP_038934386   ⟸   XM_039078458
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934387   ⟸   XM_039078459
- Peptide Label: isoform X1
Protein Domains
NR LBD

Transcriptome

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

Promoters
RGD ID:13695154
Promoter ID:EPDNEW_R5678
Type:initiation region
Name:Nr2c1_1
Description:nuclear receptor subfamily 2, group C, member 1
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_6.0735,069,816 - 35,069,876EPDNEW

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)
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
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 35162444 35162445 C T snv SBH/Ygl (MCW), SBN/Ygl (MCW), SBH/Ygl (KNAW), BUF/MNa (KyushuU), BUF/N (KNAW), WN/N (KNAW), SBN/Ygl (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 35094720 35094721 C T snv SBH/Ygl (MCW), SBH/Ygl (RGD), SBN/Ygl (MCW), Buf/N (MCW), SBN/Ygl (RGD), WN/N (MCW)
7 35095654 35095655 C G snv SBN/Ygl (RGD), SBH/Ygl (RGD), Buf/N (MCW), WN/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 31318562 31318563 C T snv BUF/N (KNAW), WN/N (KNAW), SBH/Ygl (ICL), LCR/2Mco (UMich), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), SBN/Ygl (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3200 AgrOrtholog
Ensembl Genes ENSRNOG00000006983 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000009578 UniProtKB/Swiss-Prot
  ENSRNOP00000071901 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000009578 UniProtKB/Swiss-Prot
  ENSRNOT00000089228 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.565.10 UniProtKB/Swiss-Prot
  3.30.50.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5599041 IMAGE-MGC_LOAD
InterPro NHR-like_dom_sf UniProtKB/Swiss-Prot
  Nucl_hrmn_rcpt_lig-bd UniProtKB/Swiss-Prot
  Nuclear_hrmn_rcpt UniProtKB/Swiss-Prot
  Znf_hrmn_rcpt UniProtKB/Swiss-Prot
  Znf_NHR/GATA UniProtKB/Swiss-Prot
KEGG Report rno:252924 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72289 IMAGE-MGC_LOAD
NCBI Gene 252924 ENTREZGENE
Pfam Hormone_recep UniProtKB/Swiss-Prot
  zf-C4 UniProtKB/Swiss-Prot
PhenoGen Nr2c1 PhenoGen
PRINTS STRDHORMONER UniProtKB/Swiss-Prot
  STROIDFINGER UniProtKB/Swiss-Prot
PROSITE NR_LBD UniProtKB/Swiss-Prot
  NUCLEAR_REC_DBD_1 UniProtKB/Swiss-Prot
  NUCLEAR_REC_DBD_2 UniProtKB/Swiss-Prot
SMART HOLI UniProtKB/Swiss-Prot
  ZnF_C4 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48508 UniProtKB/Swiss-Prot
UniProt NR2C1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-05-06 Nr2c1  nuclear receptor subfamily 2, group C, member 1  Psg4  pregnancy specific beta-1-glycoprotein 4  Data Merged 737654 APPROVED
2003-02-27 Psg4  pregnancy specific beta-1-glycoprotein 4      Symbol and Name status set to provisional 70820 PROVISIONAL
2001-06-20 Tr2  Orphan receptor, TR2-11      Symbol withdrawn, duplicate of Nr2c1 (RGD:3200) 67952 WITHDRAWN
2001-06-20 Nr2c1  Nuclear receptor subfamily 2, group C, member 1      Name updated 67952 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_homology mouse Nr2c1 exhibits transcription factor, subtilase, ligand-dependent nuclear receptor and steroid hormone activities 704405