Rora (RAR-related orphan receptor A) - Rat Genome Database

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Gene: Rora (RAR-related orphan receptor A) Rattus norvegicus
Analyze
Symbol: Rora
Name: RAR-related orphan receptor A
RGD ID: 1308419
Description: Predicted to have several functions, including beta-catenin binding activity; nuclear receptor activity; and transcription coregulator binding activity. Involved in circadian rhythm. Predicted to localize to nucleus. Orthologous to human RORA (RAR related orphan receptor A); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC103693129; LOC300807; nuclear receptor ROR-alpha; nuclear receptor ROR-alpha-like; RAR-related orphan receptor alpha
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
mRatBN7.2869,301,635 - 70,034,741 (+)NCBI
Rnor_6.0 Ensembl875,516,904 - 75,607,212 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0875,515,886 - 75,616,477 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0879,195,918 - 79,934,499 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4873,052,282 - 73,817,764 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1873,744,425 - 73,837,420 (+)NCBI
Celera871,690,522 - 71,789,466 (-)NCBICelera
Cytogenetic Map8q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-anisomycin  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
25-hydroxycholesterol  (ISO)
3,4-dichloroaniline  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-phenoxybenzoic acid  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bifenthrin  (ISO)
bisphenol A  (EXP)
cadmium dichloride  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
chenodeoxycholic acid  (ISO)
chloroprene  (EXP,ISO)
choline  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
cortisol  (ISO)
cycloprothrin  (ISO)
cyclosporin A  (ISO)
cyhalothrin  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
dichloromethane  (ISO)
diclofenac  (ISO)
difenoconazole  (ISO)
dioxygen  (ISO)
diuron  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
endrin  (ISO)
enilconazole  (ISO)
ethanol  (ISO)
flucythrinate  (ISO)
fluoranthene  (ISO)
flutamide  (EXP)
fluvalinate  (ISO)
folic acid  (ISO)
hexaconazole  (ISO)
Indeno[1,2,3-cd]pyrene  (ISO)
indole-3-methanol  (EXP)
isotretinoin  (ISO)
ketamine  (EXP)
L-methionine  (ISO)
leflunomide  (EXP)
lipopolysaccharide  (ISO)
melatonin  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-acetyl-L-cysteine  (EXP)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP)
nickel atom  (ISO)
nickel dichloride  (ISO)
ozone  (EXP)
paracetamol  (ISO)
PCB138  (ISO)
phenobarbital  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (ISO)
quercetin  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
styrene  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (ISO)
tetraconazole  (ISO)
thimerosal  (ISO)
trichostatin A  (ISO)
triflumizole  (ISO)
troglitazone  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vincristine  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
zinc dichloride  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,ISO)

References

Additional References at PubMed
PMID:1565842   PMID:7518067   PMID:7838156   PMID:7838158   PMID:7926749   PMID:8996814   PMID:9328355   PMID:9862959   PMID:10478845   PMID:11053433   PMID:11252722   PMID:14687547  
PMID:15199055   PMID:17476214   PMID:17545671   PMID:17666523   PMID:17693386   PMID:18055760   PMID:18164222   PMID:18658046   PMID:18957222   PMID:19039140   PMID:19324970   PMID:19955433  
PMID:19965867   PMID:21292463   PMID:21628546   PMID:22753030   PMID:23172836   PMID:23723244   PMID:29032151   PMID:33669807  


Genomics

Comparative Map Data
Rora
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2869,301,635 - 70,034,741 (+)NCBI
Rnor_6.0 Ensembl875,516,904 - 75,607,212 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0875,515,886 - 75,616,477 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0879,195,918 - 79,934,499 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4873,052,282 - 73,817,764 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1873,744,425 - 73,837,420 (+)NCBI
Celera871,690,522 - 71,789,466 (-)NCBICelera
Cytogenetic Map8q24NCBI
RORA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1560,488,284 - 61,229,302 (-)EnsemblGRCh38hg38GRCh38
GRCh381560,488,284 - 61,229,302 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371560,780,483 - 61,521,501 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361558,576,755 - 59,308,794 (-)NCBINCBI36hg18NCBI36
Build 341558,576,754 - 58,671,999NCBI
Celera1537,669,158 - 37,859,340 (-)NCBI
Cytogenetic Map15q22.2NCBI
HuRef1537,602,935 - 37,793,081 (-)NCBIHuRef
CHM1_11560,900,085 - 61,640,967 (-)NCBICHM1_1
Rora
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39968,560,627 - 69,295,528 (+)NCBIGRCm39mm39
GRCm39 Ensembl968,561,068 - 69,295,528 (+)Ensembl
GRCm38968,653,404 - 69,388,246 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl968,653,786 - 69,388,246 (+)EnsemblGRCm38mm10GRCm38
MGSCv37968,501,609 - 69,226,838 (+)NCBIGRCm37mm9NCBIm37
MGSCv36968,452,966 - 69,178,195 (+)NCBImm8
Celera965,876,634 - 66,600,643 (+)NCBICelera
Cytogenetic Map9CNCBI
cM Map937.45NCBI
Rora
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545014,262,190 - 14,425,233 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545014,262,199 - 14,434,611 (+)NCBIChiLan1.0ChiLan1.0
RORA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11557,763,345 - 57,901,854 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1557,771,735 - 57,980,460 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01539,461,553 - 40,200,118 (-)NCBIMhudiblu_PPA_v0panPan3
RORA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13025,315,974 - 26,026,708 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3025,325,275 - 26,026,623 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3025,391,427 - 25,943,891 (-)NCBI
Rora
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640103,544,814 - 104,221,651 (-)NCBI
SpeTri2.0NW_00493647121,402,056 - 21,567,908 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RORA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1110,719,190 - 111,477,703 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11110,719,004 - 111,482,807 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21123,140,609 - 123,247,974 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RORA
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12622,263,889 - 23,002,224 (+)NCBI
ChlSab1.1 Ensembl2622,812,445 - 22,993,021 (+)Ensembl
Rora
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478111,014,185 - 11,688,558 (+)NCBI

Position Markers
D8Mgh17  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,349,194 - 69,349,344 (+)MAPPER
mRatBN7.2869,349,194 - 69,349,344 (-)MAPPER
Rnor_6.0880,839,918 - 80,840,067NCBIRnor6.0
Rnor_6.0874,917,593 - 74,917,742NCBIRnor6.0
Rnor_5.0879,244,914 - 79,245,063UniSTSRnor5.0
Rnor_5.0876,889,142 - 76,889,291UniSTSRnor5.0
RGSC_v3.4873,102,006 - 73,102,155UniSTSRGSC3.4
RGSC_v3.4873,102,005 - 73,102,155RGDRGSC3.4
RGSC_v3.1873,121,059 - 73,121,209RGD
Celera872,371,421 - 72,371,570UniSTS
Cytogenetic Map8q24UniSTS
D8Rat33  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,910,240 - 69,910,402 (+)MAPPER
Rnor_6.0875,491,856 - 75,492,017NCBIRnor6.0
Rnor_5.0879,818,765 - 79,818,926UniSTSRnor5.0
RGSC_v3.4873,700,766 - 73,700,927UniSTSRGSC3.4
RGSC_v3.4873,700,765 - 73,701,128RGDRGSC3.4
RGSC_v3.1873,719,820 - 73,719,981RGD
Celera871,813,307 - 71,813,468UniSTS
RH 3.4 Map8871.79RGD
RH 3.4 Map8871.79UniSTS
RH 2.0 Map8646.7RGD
SHRSP x BN Map844.82RGD
FHH x ACI Map851.31RGD
Cytogenetic Map8q24UniSTS
D8Rat146  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,352,596 - 69,352,742 (+)MAPPER
mRatBN7.2869,352,596 - 69,352,742 (-)MAPPER
Rnor_6.0874,920,991 - 74,921,134NCBIRnor6.0
Rnor_6.0880,836,277 - 80,836,420NCBIRnor6.0
Rnor_5.0879,248,312 - 79,248,455UniSTSRnor5.0
Rnor_5.0876,885,501 - 76,885,644UniSTSRnor5.0
RGSC_v3.4873,105,404 - 73,105,547UniSTSRGSC3.4
RGSC_v3.4873,105,403 - 73,105,547RGDRGSC3.4
RGSC_v3.1873,124,457 - 73,124,601RGD
Celera872,368,036 - 72,368,173UniSTS
SHRSP x BN Map844.82RGD
SHRSP x BN Map844.82UniSTS
Cytogenetic Map8q24UniSTS
D8Rat234  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,582,277 - 69,582,478 (+)MAPPER
Rnor_6.0875,151,013 - 75,151,213NCBIRnor6.0
Rnor_6.0874,609,451 - 74,609,651NCBIRnor6.0
Rnor_5.0879,478,996 - 79,479,196UniSTSRnor5.0
Rnor_5.0878,936,283 - 78,936,483UniSTSRnor5.0
RGSC_v3.4873,363,441 - 73,363,641UniSTSRGSC3.4
Celera872,140,085 - 72,140,285UniSTS
SHRSP x BN Map844.83RGD
SHRSP x BN Map844.83UniSTS
Cytogenetic Map8q24UniSTS
D8Got108  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,892,209 - 69,892,462 (+)MAPPER
Rnor_6.0875,473,828 - 75,474,078NCBIRnor6.0
Rnor_5.0879,800,737 - 79,800,987UniSTSRnor5.0
RGSC_v3.4873,682,736 - 73,682,987RGDRGSC3.4
RGSC_v3.4873,682,737 - 73,682,987UniSTSRGSC3.4
RGSC_v3.1873,701,791 - 73,702,041RGD
Celera871,831,207 - 71,831,457UniSTS
RH 3.4 Map8871.2UniSTS
RH 3.4 Map8871.2RGD
RH 2.0 Map8645.0RGD
Cytogenetic Map8q24UniSTS
D8Got306  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,827,011 - 69,827,150 (+)MAPPER
Rnor_6.0877,887,470 - 77,887,608NCBIRnor6.0
Rnor_6.0875,408,639 - 75,408,777NCBIRnor6.0
Rnor_5.0875,197,421 - 75,197,559UniSTSRnor5.0
Rnor_5.0879,735,020 - 79,735,158UniSTSRnor5.0
RGSC_v3.4873,616,925 - 73,617,063UniSTSRGSC3.4
Celera871,896,467 - 71,896,620UniSTS
Cytogenetic Map8q24UniSTS
D8Got305  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,361,077 - 69,361,219 (+)MAPPER
mRatBN7.2869,361,077 - 69,361,219 (-)MAPPER
Rnor_6.0874,929,559 - 74,929,698NCBIRnor6.0
Rnor_6.0880,827,806 - 80,827,945NCBIRnor6.0
Rnor_5.0879,256,880 - 79,257,019UniSTSRnor5.0
Rnor_5.0876,877,030 - 76,877,169UniSTSRnor5.0
RGSC_v3.4873,113,972 - 73,114,111UniSTSRGSC3.4
Celera872,359,545 - 72,359,684UniSTS
Cytogenetic Map8q24UniSTS
SGC33753  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,595,724 - 69,595,850 (+)MAPPER
Rnor_6.0874,622,896 - 74,623,021NCBIRnor6.0
Rnor_6.0875,164,458 - 75,164,583NCBIRnor6.0
Rnor_5.0879,492,441 - 79,492,566UniSTSRnor5.0
Rnor_5.0878,949,728 - 78,949,853UniSTSRnor5.0
RGSC_v3.4873,376,886 - 73,377,011UniSTSRGSC3.4
Cytogenetic Map8q24UniSTS
RH138861  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,885,046 - 69,885,170 (+)MAPPER
Rnor_6.0875,466,666 - 75,466,789NCBIRnor6.0
Rnor_5.0879,793,575 - 79,793,698UniSTSRnor5.0
RGSC_v3.4873,675,574 - 73,675,697UniSTSRGSC3.4
Celera871,838,500 - 71,838,623UniSTS
RH 3.4 Map8871.59UniSTS
Cytogenetic Map8q24UniSTS
AU049942  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,872,924 - 69,873,091 (+)MAPPER
Rnor_6.0875,454,546 - 75,454,710NCBIRnor6.0
Rnor_5.0879,781,455 - 79,781,619UniSTSRnor5.0
RGSC_v3.4873,663,454 - 73,663,618UniSTSRGSC3.4
Celera871,850,572 - 71,850,736UniSTS
Cytogenetic Map8q24UniSTS
RH142618  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,995,939 - 69,996,045 (+)MAPPER
Rnor_6.0875,577,518 - 75,577,623NCBIRnor6.0
Rnor_5.0879,904,774 - 79,904,879UniSTSRnor5.0
RGSC_v3.4873,788,039 - 73,788,144UniSTSRGSC3.4
Celera871,727,721 - 71,727,826UniSTS
Cytogenetic Map8q24UniSTS
RH144170  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,604,533 - 69,604,633 (+)MAPPER
Rnor_6.0875,173,272 - 75,173,371NCBIRnor6.0
Rnor_6.0874,631,641 - 74,631,740NCBIRnor6.0
Rnor_5.0879,501,255 - 79,501,354UniSTSRnor5.0
Rnor_5.0878,958,473 - 78,958,572UniSTSRnor5.0
RGSC_v3.4873,385,700 - 73,385,799UniSTSRGSC3.4
Celera872,117,947 - 72,118,046UniSTS
RH 3.4 Map8872.89UniSTS
Cytogenetic Map8q24UniSTS
BE101994  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,303,682 - 69,303,868 (+)MAPPER
Rnor_6.0874,870,631 - 74,870,816NCBIRnor6.0
Rnor_6.0874,494,016 - 74,494,201NCBIRnor6.0
Rnor_5.0879,197,873 - 79,198,058UniSTSRnor5.0
Rnor_5.0878,820,848 - 78,821,033UniSTSRnor5.0
RGSC_v3.4873,054,237 - 73,054,422UniSTSRGSC3.4
Celera872,416,614 - 72,416,799UniSTS
RH 3.4 Map8872.19UniSTS
Cytogenetic Map8q24UniSTS
BF400829  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,619,522 - 69,619,660 (+)MAPPER
Rnor_6.0875,188,241 - 75,188,378NCBIRnor6.0
Rnor_6.0874,646,614 - 74,646,751NCBIRnor6.0
Rnor_5.0879,516,224 - 79,516,361UniSTSRnor5.0
Rnor_5.0878,973,446 - 78,973,583UniSTSRnor5.0
RGSC_v3.4873,400,459 - 73,400,596UniSTSRGSC3.4
Celera872,102,940 - 72,103,077UniSTS
RH 3.4 Map8871.79UniSTS
Cytogenetic Map8q24UniSTS
RH137194  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,343,930 - 69,344,138 (+)MAPPER
mRatBN7.2869,343,930 - 69,344,138 (-)MAPPER
Rnor_6.0874,912,244 - 74,912,451NCBIRnor6.0
Rnor_6.0880,845,373 - 80,845,580NCBIRnor6.0
Rnor_5.0879,239,565 - 79,239,772UniSTSRnor5.0
Rnor_5.0876,894,597 - 76,894,804UniSTSRnor5.0
RGSC_v3.4873,096,436 - 73,096,643UniSTSRGSC3.4
RH 3.4 Map8871.59UniSTS
Cytogenetic Map8q24UniSTS
RH138143  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,915,386 - 69,915,611 (+)MAPPER
Rnor_6.0875,497,002 - 75,497,226NCBIRnor6.0
Rnor_5.0879,823,911 - 79,824,135UniSTSRnor5.0
RGSC_v3.4873,705,912 - 73,706,136UniSTSRGSC3.4
Celera871,808,098 - 71,808,322UniSTS
Cytogenetic Map8q24UniSTS
RH138260  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0879,592,062 - 79,592,304NCBIRnor5.0
Rnor_5.0876,764,549 - 76,764,791NCBIRnor5.0
RGSC_v3.4873,473,785 - 73,474,026UniSTSRGSC3.4
Celera872,029,655 - 72,029,896UniSTS
RH 3.4 Map8871.0UniSTS
Cytogenetic Map8q24UniSTS
AI406875  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2870,002,382 - 70,002,567 (+)MAPPER
Rnor_6.0875,583,961 - 75,584,145NCBIRnor6.0
Rnor_5.0879,911,217 - 79,911,401UniSTSRnor5.0
RGSC_v3.4873,794,482 - 73,794,666UniSTSRGSC3.4
Celera871,721,199 - 71,721,383UniSTS
RH 3.4 Map8871.99UniSTS
Cytogenetic Map8q24UniSTS
Rora  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2870,025,151 - 70,025,285 (+)MAPPER
Rnor_6.0875,606,890 - 75,607,023NCBIRnor6.0
Rnor_5.0879,934,146 - 79,934,279UniSTSRnor5.0
RGSC_v3.4873,817,411 - 73,817,544UniSTSRGSC3.4
Celera871,699,959 - 71,700,092UniSTS
Cytogenetic Map8q24UniSTS
G64932  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2869,553,775 - 69,554,349 (+)MAPPER
Rnor_6.0877,831,942 - 77,832,515NCBIRnor6.0
Rnor_6.0875,123,678 - 75,124,251NCBIRnor6.0
Rnor_5.0875,251,713 - 75,252,286UniSTSRnor5.0
Rnor_5.0879,451,975 - 79,452,548UniSTSRnor5.0
RGSC_v3.4873,335,777 - 73,336,350UniSTSRGSC3.4
Celera872,167,562 - 72,168,132UniSTS
Cytogenetic Map8q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)89531047119211942Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810938911120496129Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)82146491991140553Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)821813070100873963Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)829867983106526740Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)829867983106526740Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)829867983106526740Rat
1300146Rf17Renal function QTL 172.9renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)83091811275918112Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)830918112107206309Rat
724514Uae15Urinary albumin excretion QTL 152.9urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)83220198175971421Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)832888352101374135Rat
2313046Bss78Bone structure and strength QTL 783.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)83355866089058369Rat
2313057Bss76Bone structure and strength QTL 7630.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)83355866089058369Rat
2313067Bss77Bone structure and strength QTL 773.10.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)83355866089058369Rat
2313088Bss75Bone structure and strength QTL 753.10.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)83355866089058369Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)833558660109028082Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)833558660109028082Rat
1578755Pur5Proteinuria QTL 53.30.0001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)833558660109028082Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)833558764113580387Rat
1298065Scl16Serum cholesterol level QTL 163.8blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)83504141480041414Rat
1582222Epfw2Epididymal fat weight QTL 23.20.0005epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)83592559480925594Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)839230130106506973Rat
61358Bp39Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83992790184927901Rat
61464Niddm11Non-insulin dependent diabetes mellitus QTL 113.10.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83995802284958022Rat
737824Hcar10Hepatocarcinoma resistance QTL 102.9liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)84421919789542960Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)844219197100873963Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)844458129118087517Rat
1331769Rf39Renal function QTL 393.871urine output (VT:0003620)timed urine volume (CMO:0000260)84571234480003418Rat
1298079Activ2Activity QTL 29.50.000001voluntary movement trait (VT:0003491)rearing measurement (CMO:0001515)84571234490712344Rat
631216Stl9Serum triglyceride level QTL 94.710.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)84571247575971259Rat
70161Bp62Blood pressure QTL 622.90.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)84658843796998640Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)847200750106394378Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)847200750106394378Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)847200750106394378Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)847200750106394378Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)847200750106394378Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)847200750106394378Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)850529480128036471Rat
1331837Bw23Body weight QTL 234.190.00007body mass (VT:0001259)body weight (CMO:0000012)850529563106506973Rat
2313086Bss60Bone structure and strength QTL 604.10.0001tibia length (VT:0004357)tibia length (CMO:0000450)85406504489058369Rat
4889938Bss89Bone structure and strength QTL 893.8tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)85406504489058369Rat
5684973Bss100Bone structure and strength QTL 1004.7tibia area (VT:1000281)tibia area measurement (CMO:0001382)85406504489058369Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)855435004115812386Rat
2303570Gluco48Glucose level QTL 482blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)855659105100659105Rat
2293697Bmd39Bone mineral density QTL 39femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)858230766106394378Rat
1582243Bw66Body weight QTL 663.40.0048body mass (VT:0001259)body weight (CMO:0000012)85842551091990535Rat
1582254Kidm31Kidney mass QTL 313kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)85842551091990535Rat
631664Hcar3Hepatocarcinoma resistance QTL 32.90.0005liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)858425510106526740Rat
1300177Cm2Cardiac mass QTL 23.65heart mass (VT:0007028)heart weight (CMO:0000017)859234112108068306Rat
2301402Bp316Blood pressure QTL 3160.005arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)861394378106394378Rat
10402857Bp380Blood pressure QTL 3800.95arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)861394378106394378Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)865717449128033050Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)872849686117849686Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight as a percentage of body weight (CMO:0000654)874917593121080545Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:89
Count of miRNA genes:66
Interacting mature miRNAs:82
Transcripts:ENSRNOT00000013142
Prediction methods:Miranda, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 18 8 7 8 8 9 14 9 8 8 8
Low 3 41 39 33 12 33 2 60 26 32 3
Below cutoff 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013142   ⟹   ENSRNOP00000013142
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl875,516,904 - 75,607,212 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000039376   ⟹   ENSRNOP00000033960
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl874,868,681 - 74,877,837 (+)Ensembl
RefSeq Acc Id: XM_008766408   ⟹   XP_008764630
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0875,515,887 - 75,616,477 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008766409   ⟹   XP_008764631
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0875,515,886 - 75,616,477 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008766410   ⟹   XP_008764632
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2869,935,165 - 70,034,741 (+)NCBI
Rnor_6.0875,516,790 - 75,616,477 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008776764   ⟹   XP_008774986
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera871,690,522 - 71,789,466 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039082823   ⟹   XP_038938751
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2869,301,635 - 70,034,741 (+)NCBI
RefSeq Acc Id: XM_039082824   ⟹   XP_038938752
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2869,301,635 - 70,034,741 (+)NCBI
Protein Sequences
Protein RefSeqs XP_008764632 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938751 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938752 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL84220 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_008774986   ⟸   XM_008776764
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008764631   ⟸   XM_008766409
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008764630   ⟸   XM_008766408
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008764632   ⟸   XM_008766410
- Peptide Label: isoform X3
- UniProtKB: F1LZZ3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000013142   ⟸   ENSRNOT00000013142
RefSeq Acc Id: XP_038938751   ⟸   XM_039082823
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038938752   ⟸   XM_039082824
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000033960   ⟸   ENSRNOT00000039376
Protein Domains
NR LBD   Nuclear receptor

Transcriptome

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

Promoters
RGD ID:13696103
Promoter ID:EPDNEW_R6622
Type:initiation region
Name:Rora_1
Description:RAR-related orphan receptor A
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_6.0875,516,890 - 75,516,950EPDNEW

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)
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)
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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)
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)
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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)
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
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)
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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
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)
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
SR/JrHsd (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: 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:1308419 AgrOrtholog
Ensembl Genes ENSRNOG00000027145 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000049584 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000013142 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000033960 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013142 UniProtKB/TrEMBL
  ENSRNOT00000039376 UniProtKB/TrEMBL
Gene3D-CATH 1.10.565.10 UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/TrEMBL
InterPro NHR_like_domain UniProtKB/TrEMBL
  NR_DBD_ROR UniProtKB/TrEMBL
  Nucl_hrmn_rcpt_lig-bd UniProtKB/TrEMBL
  Nuclear_hrmn_rcpt UniProtKB/TrEMBL
  ROR_rcpt UniProtKB/TrEMBL
  Znf_hrmn_rcpt UniProtKB/TrEMBL
  Znf_NHR/GATA UniProtKB/TrEMBL
NCBI Gene 300807 ENTREZGENE
Pfam Hormone_recep UniProtKB/TrEMBL
  zf-C4 UniProtKB/TrEMBL
PharmGKB RORA RGD
PhenoGen Rora PhenoGen
PRINTS RORNUCRECPTR UniProtKB/TrEMBL
  STRDHORMONER UniProtKB/TrEMBL
  STROIDFINGER UniProtKB/TrEMBL
PROSITE NR_LBD UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_1 UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_2 UniProtKB/TrEMBL
SMART HOLI UniProtKB/TrEMBL
  ZnF_C4 UniProtKB/TrEMBL
Superfamily-SCOP SSF48508 UniProtKB/TrEMBL
UniProt D4A8Y3_RAT UniProtKB/TrEMBL
  F1LZZ3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Rora  RAR-related orphan receptor A  LOC103693129  nuclear receptor ROR-alpha-like  Data Merged 737654 PROVISIONAL
2014-08-25 LOC103693129  nuclear receptor ROR-alpha-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-05-25 Rora  RAR-related orphan receptor A  Rora  RAR-related orphan receptor alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Rora  RAR-related orphan receptor alpha   Rora_predicted  RAR-related orphan receptor alpha (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Rora_predicted  RAR-related orphan receptor alpha (predicted)      Symbol and Name status set to approved 70820 APPROVED