Runx2 (RUNX family transcription factor 2) - Rat Genome Database
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Gene: Runx2 (RUNX family transcription factor 2) Rattus norvegicus
Analyze
Symbol: Runx2
Name: RUNX family transcription factor 2
RGD ID: 2282
Description: Exhibits histone deacetylase binding activity and transcription factor binding activity. Involved in cellular response to fibroblast growth factor stimulus; osteoblast differentiation; and positive regulation of ossification. Localizes to nucleus. Human ortholog(s) of this gene implicated in cleidocranial dysplasia and metaphyseal dysplasia-maxillary hypoplasia-brachydacty syndrome. Orthologous to human RUNX2 (RUNX family transcription factor 2); PARTICIPATES IN fibroblast growth factor signaling pathway; transforming growth factor-beta Smad dependent signaling pathway; INTERACTS WITH (20S)-ginsenoside Rg3; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CBF-alpha-1; Cbfa1; core-binding factor subunit alpha-1; OSF-2; osteoblast-specific transcription factor 2; runt related transcription factor 2; runt-related transcription factor 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
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
Rnor_6.0918,564,743 - 18,773,092 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl918,564,927 - 18,773,092 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0917,448,142 - 17,658,373 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4911,869,234 - 12,025,219 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1911,867,896 - 11,943,304 (+)NCBI
Celera913,904,221 - 14,111,920 (+)NCBICelera
Cytogenetic Map9q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(20S)-ginsenoside Rg3  (EXP)
(R)-camphor  (ISO)
1,4-benzoquinone  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
15-deoxy-Delta(12,14)-prostaglandin J2  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-trans,6-trans,10-trans-geranylgeranyl diphosphate  (ISO)
2-trans,6-trans-farnesyl diphosphate  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
3-chloropropane-1,2-diol  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-(1,4-diazepane-1-sulfonyl)isoquinoline  (ISO)
5-fluorouracil  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (EXP)
acetamide  (EXP)
adenine  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (ISO)
aldehydo-D-glucose  (ISO)
alendronic acid  (EXP)
all-trans-retinoic acid  (ISO)
all-trans-retinol  (ISO)
ammonium chloride  (EXP,ISO)
Anacardic acid  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP,ISO)
apocynin  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (EXP,ISO)
azadirachtin A  (ISO)
bafilomycin A1  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
berberine  (ISO)
beta-D-glucosamine  (ISO)
bezafibrate  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
boric acid  (ISO)
Butylparaben  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (EXP)
calcidiol  (ISO)
calciol  (ISO)
calcitriol  (EXP,ISO)
camphor  (ISO)
captopril  (ISO)
celecoxib  (ISO)
CHIR 99021  (ISO)
chitosan  (ISO)
chloroacetaldehyde  (ISO)
chloroquine  (ISO)
chlorpyrifos  (EXP)
choline  (ISO)
chromium(3+) trichloride  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (ISO)
clodronic acid  (ISO)
cobalt dichloride  (EXP,ISO)
cocaine  (EXP)
colforsin daropate hydrochloride  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
corticosterone  (EXP)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cycloheximide  (ISO)
D-glucose  (ISO)
DDT  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (EXP,ISO)
diclofenac  (EXP)
dioxygen  (ISO)
disodium selenite  (ISO)
disulfiram  (EXP)
dorsomorphin  (ISO)
enalapril  (EXP)
ethanol  (ISO)
Ethylenethiourea  (EXP)
farnesyl diphosphate  (ISO)
fasudil hydrochloride  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
fulvestrant  (EXP,ISO)
gallocatechin  (EXP)
gamma-aminobutyric acid  (EXP)
gamma-Oryzanol (TN)  (EXP)
genistein  (EXP,ISO)
Ginkgoic acid  (ISO)
ginsenoside Rb1  (EXP)
glucose  (ISO)
glycerol 2-phosphate  (EXP,ISO)
glycidol  (EXP)
glycyrrhetinate  (ISO)
glycyrrhetinic acid  (ISO)
hexaconazole  (ISO)
hexadecanoic acid  (EXP)
hydrogen chloride  (ISO)
hydrogen peroxide  (EXP,ISO)
hydroquinone  (ISO)
hydroxyurea  (ISO)
icariin  (EXP,ISO)
Indeno[1,2,3-cd]pyrene  (ISO)
indole-3-methanol  (EXP)
ionomycin  (ISO)
isonicotinamide  (ISO)
kaempferol  (ISO)
ketoconazole  (ISO)
L-ascorbic acid  (EXP,ISO)
L-methionine  (ISO)
lead nitrate  (ISO)
lead(0)  (EXP,ISO)
lead(2+)  (EXP,ISO)
linalool  (EXP)
losartan  (EXP)
manganese(II) chloride  (EXP)
melatonin  (ISO)
menaquinone  (EXP)
mercury dibromide  (ISO)
metformin  (EXP)
methotrexate  (ISO)
methoxychlor  (EXP)
methylmercury chloride  (EXP)
methylparaben  (ISO)
mifepristone  (EXP)
modafinil  (EXP)
mono(2-ethylhexyl) phthalate  (ISO)
Monobutylphthalate  (ISO)
montelukast  (ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-nitrosodiethylamine  (EXP,ISO)
naringin  (EXP,ISO)
neoeriocitrin  (ISO)
Niclosamide  (ISO)
nicotinamide  (EXP,ISO)
notoginsenoside R1  (ISO)
NS-398  (ISO)
ochratoxin A  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
PCB138  (EXP,ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenethyl caffeate  (EXP)
phenylmercury acetate  (ISO)
phylloquinone  (EXP)
picene  (ISO)
polaprezinc  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
prostaglandin E2  (ISO)
prostaglandin F2alpha  (ISO)
quercetin  (EXP,ISO)
quercetin 3-O-beta-D-glucofuranoside  (EXP)
quercetin 3-O-beta-D-glucopyranoside  (EXP)
raloxifene  (ISO)
resveratrol  (EXP,ISO)
riboflavin  (ISO)
rotenone  (ISO)
rottlerin  (ISO)
Salidroside  (ISO)
SB 203580  (EXP)
SB 431542  (ISO)
silicon dioxide  (ISO)
simvastatin  (ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (EXP,ISO)
streptozocin  (EXP)
succimer  (ISO)
tacrolimus hydrate  (EXP)
tamibarotene  (ISO)
Tanshinone I  (ISO)
tebuconazole  (ISO)
tetrachloromethane  (EXP,ISO)
thromboxane A2  (ISO)
tremolite asbestos  (ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
triflumizole  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
tyrphostin AG 1478  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin K  (EXP)
warfarin  (EXP,ISO)
zinc atom  (EXP)
zinc dichloride  (ISO)
zinc sulfate  (ISO)
zinc(0)  (EXP)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
BMP signaling pathway  (IEA,ISO)
cell maturation  (IEA,ISO)
cellular response to BMP stimulus  (ISO)
cellular response to fibroblast growth factor stimulus  (IEP)
chondrocyte development  (IEA,ISO)
chondrocyte differentiation  (IBA,ISO)
embryonic cranial skeleton morphogenesis  (IEA,ISO)
embryonic forelimb morphogenesis  (IEA,ISO)
endochondral ossification  (IEA,ISO)
hemopoiesis  (IBA)
negative regulation of smoothened signaling pathway  (IEA,ISO)
negative regulation of transcription, DNA-templated  (IEA,ISO)
neuron differentiation  (IBA)
odontogenesis of dentin-containing tooth  (IEA,ISO)
ossification  (IBA)
osteoblast development  (IEA,ISO)
osteoblast differentiation  (IMP,ISO)
osteoblast fate commitment  (IEA,ISO)
positive regulation of cell population proliferation  (IEA,ISO)
positive regulation of chondrocyte differentiation  (IEA,ISO)
positive regulation of gene expression  (ISO)
positive regulation of ossification  (IMP)
positive regulation of osteoblast differentiation  (IEA,ISO,ISS)
positive regulation of transcription by RNA polymerase II  (ISO,ISS)
positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus  (IEA,ISO)
positive regulation of transcription, DNA-templated  (ISO)
regulation of cell differentiation  (IBA)
regulation of fibroblast growth factor receptor signaling pathway  (IEA,ISO)
regulation of gene expression  (ISO)
regulation of odontogenesis of dentin-containing tooth  (IEA,ISO)
regulation of ossification  (IEA,ISO)
regulation of osteoblast differentiation  (ISO,TAS)
regulation of transcription by RNA polymerase II  (IBA)
skeletal system development  (ISO)
skeletal system morphogenesis  (ISO)
stem cell differentiation  (IEA,ISO)
T cell differentiation  (IEA,ISO)

Cellular Component
chromatin  (IBA,IEA,ISO)
cytoplasm  (IEA,ISO)
nucleoplasm  (ISO,TAS)
nucleus  (IDA,ISO,ISS)
transcription regulator complex  (IEA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Fu Y, etal., Int J Biochem Cell Biol. 2014 Sep;54:68-77. doi: 10.1016/j.biocel.2014.07.003. Epub 2014 Jul 11.
2. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. GOA data from the GO Consortium
4. Joshi S, etal., Biochim Biophys Acta. 2015 Sep;1852(9):2000-12. doi: 10.1016/j.bbadis.2015.06.020. Epub 2015 Jun 27.
5. Kim HJ, etal., J Biol Chem. 2003 Jan 3;278(1):319-26. Epub 2002 Oct 25.
6. Massagué J, etal., Genes Dev. 2005 Dec 1;19(23):2783-810.
7. MGD data from the GO Consortium
8. Mundlos S, etal., Cell. 1997 May 30;89(5):773-9.
9. NCBI rat LocusLink and RefSeq merged data July 26, 2002
10. OMIM Disease Annotation Pipeline
11. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
12. RGD automated data pipeline
13. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14. RGD automated import pipeline for gene-chemical interactions
15. Ross S and Hill CS, Int J Biochem Cell Biol. 2008;40(3):383-408. Epub 2007 Oct 7.
16. Shi N, etal., Arterioscler Thromb Vasc Biol. 2017 Mar;37(3):446-454. doi: 10.1161/ATVBAHA.116.308606. Epub 2017 Jan 5.
17. Shimizu E, etal., J Biol Chem. 2010 Mar 26;285(13):9616-26. doi: 10.1074/jbc.M109.094862. Epub 2010 Jan 22.
18. Shintaku Y, etal., Cells Tissues Organs. 2011;194(1):38-48. doi: 10.1159/000322557. Epub 2011 Jan 22.
19. Sierra J, etal., Mol Cell Biol. 2003 May;23(9):3339-51.
20. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
21. Wang FS, etal., J Biol Chem. 2002 Mar 29;277(13):10931-7. Epub 2002 Jan 9.
22. Xiao ZS, etal., Gene 1998 Jul 3;214(1-2):187-97.
23. Xue T, etal., Gene Ther. 2010 Mar;17(3):370-9. doi: 10.1038/gt.2009.154. Epub 2009 Nov 26.
24. Young DW, etal., Nature. 2007 Jan 25;445(7126):442-6.
25. Yu S, etal., J Biol Chem. 2008 Feb 29;283(9):5542-53. doi: 10.1074/jbc.M705653200. Epub 2008 Jan 2.
Additional References at PubMed
PMID:7862157   PMID:9182762   PMID:9632804   PMID:10072783   PMID:10213384   PMID:11965546   PMID:12112009   PMID:12369786   PMID:12434156   PMID:12551949   PMID:12807883   PMID:12815054  
PMID:12951324   PMID:14688224   PMID:14982932   PMID:15013103   PMID:15030764   PMID:15050892   PMID:15051730   PMID:15107406   PMID:15107836   PMID:15136142   PMID:15150273   PMID:15175325  
PMID:15225881   PMID:15389629   PMID:15456860   PMID:15537544   PMID:15537653   PMID:15565649   PMID:15668330   PMID:15668335   PMID:15990875   PMID:16099986   PMID:16115867   PMID:16443755  
PMID:16476422   PMID:16543677   PMID:16610234   PMID:16751105   PMID:17182356   PMID:17265428   PMID:17334410   PMID:17352693   PMID:17693062   PMID:17708712   PMID:17950631   PMID:18432284  
PMID:18487609   PMID:18701816   PMID:18804520   PMID:18986983   PMID:19075196   PMID:19121369   PMID:19124839   PMID:19144722   PMID:19170063   PMID:19423655   PMID:19739101   PMID:19822991  
PMID:19893245   PMID:20019778   PMID:20093419   PMID:20128911   PMID:20197312   PMID:20568992   PMID:20628571   PMID:20818503   PMID:20843790   PMID:21221986   PMID:21302441   PMID:21324897  
PMID:21412826   PMID:21628588   PMID:21893222   PMID:22008669   PMID:22009963   PMID:22407386   PMID:22547067   PMID:22713854   PMID:22827283   PMID:22873791   PMID:22906827   PMID:22916278  
PMID:23517179   PMID:24042587   PMID:24349534   PMID:24391920   PMID:24505141   PMID:24520423   PMID:24535991   PMID:24854956   PMID:25159845   PMID:25205373   PMID:25409708   PMID:25823394  
PMID:26345541   PMID:26617945   PMID:26666855   PMID:26743583   PMID:27178636   PMID:27184949   PMID:27216774   PMID:27281956   PMID:27321958   PMID:27503378   PMID:27748856   PMID:28125630  
PMID:28290608   PMID:28419442   PMID:28462510   PMID:28505335   PMID:28703881   PMID:28738062   PMID:30203400   PMID:30320897   PMID:30374602   PMID:30411113   PMID:30430007   PMID:31666602  
PMID:31715615   PMID:33187585  


Genomics

Comparative Map Data
Runx2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0918,564,743 - 18,773,092 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl918,564,927 - 18,773,092 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0917,448,142 - 17,658,373 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4911,869,234 - 12,025,219 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1911,867,896 - 11,943,304 (+)NCBI
Celera913,904,221 - 14,111,920 (+)NCBICelera
Cytogenetic Map9q13NCBI
RUNX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl645,328,157 - 45,664,349 (+)EnsemblGRCh38hg38GRCh38
GRCh38645,328,330 - 45,551,082 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37645,296,054 - 45,518,819 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36645,404,032 - 45,626,797 (+)NCBINCBI36hg18NCBI36
Build 34645,498,291 - 45,623,020NCBI
Celera646,849,063 - 47,071,816 (+)NCBI
Cytogenetic Map6p21.1NCBI
HuRef645,018,738 - 45,241,794 (+)NCBIHuRef
CHM1_1645,298,649 - 45,521,390 (+)NCBICHM1_1
Runx2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391744,806,874 - 45,125,684 (-)NCBIGRCm39mm39
GRCm381744,495,987 - 44,814,797 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1744,495,987 - 44,814,797 (-)EnsemblGRCm38mm10GRCm38
MGSCv371744,740,950 - 44,951,746 (-)NCBIGRCm37mm9NCBIm37
MGSCv361744,067,056 - 44,277,682 (-)NCBImm8
Celera1748,040,272 - 48,252,046 (-)NCBICelera
Cytogenetic Map17B3NCBI
cM Map1721.33NCBI
Runx2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543710,598,145 - 10,800,560 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543710,598,145 - 10,885,858 (+)NCBIChiLan1.0ChiLan1.0
RUNX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1646,189,426 - 46,411,889 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl646,189,432 - 46,524,389 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0645,003,962 - 45,133,148 (+)NCBIMhudiblu_PPA_v0panPan3
Runx2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647614,695,965 - 14,818,246 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RUNX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl740,106,513 - 40,459,686 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1740,106,581 - 40,353,304 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2746,278,416 - 46,417,291 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RUNX2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11726,679,386 - 26,807,812 (-)NCBI
ChlSab1.1 Ensembl1726,683,175 - 26,807,319 (-)Ensembl
Runx2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475414,601,574 - 14,868,469 (-)NCBI

Position Markers
BE116846  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0918,761,793 - 18,761,946NCBIRnor6.0
Rnor_5.0917,647,074 - 17,647,227UniSTSRnor5.0
RGSC_v3.4912,013,930 - 12,014,083UniSTSRGSC3.4
Celera914,100,624 - 14,100,777UniSTS
Cytogenetic Map9q12UniSTS
RH 3.4 Map988.5UniSTS
PMC150810P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0918,769,113 - 18,769,215NCBIRnor6.0
Rnor_5.0917,654,394 - 17,654,496UniSTSRnor5.0
RGSC_v3.4912,021,250 - 12,021,352UniSTSRGSC3.4
Celera914,107,941 - 14,108,043UniSTS
Cytogenetic Map9q12UniSTS
Runx2  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0918,565,038 - 18,565,346NCBIRnor6.0
Rnor_5.0917,451,099 - 17,451,407UniSTSRnor5.0
RGSC_v3.4911,792,215 - 11,792,523UniSTSRGSC3.4
Celera913,904,332 - 13,904,640UniSTS
Cytogenetic Map9q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9129467098Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9140383872Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9140383872Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9140383872Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9145029794Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9235572247355722Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9235572247355722Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9288097747375681Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9288097747880977Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9498609549986095Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9498609549986095Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9572425425692342Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)91221677157216771Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)91242546357425463Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)91242546357425463Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91555490147249201Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1025
Count of miRNA genes:318
Interacting mature miRNAs:458
Transcripts:ENSRNOT00000061014
Prediction methods:Microtar, 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 2
Low 3 10 28 12 19 12 2 2 56 34 37 11 2
Below cutoff 33 29 29 29 6 9 18 1 2 6

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001278483 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001278484 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244549 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244550 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244551 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244554 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596547 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596548 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596549 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596551 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596552 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07066834 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07066835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07066836 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07066837 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07066838 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01058361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01058362 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01058363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01058364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01058365 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01058366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01058367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01058368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01058369 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01058370 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01058371 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB025797 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB115745 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB115746 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB573881 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB573882 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF053950 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF053953 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF325502 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473987 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000061014   ⟹   ENSRNOP00000057733
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl918,564,927 - 18,773,092 (+)Ensembl
RefSeq Acc Id: NM_001278483   ⟹   NP_001265412
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0918,564,927 - 18,773,092 (+)NCBI
Rnor_5.0917,448,142 - 17,658,373 (+)NCBI
Celera913,904,221 - 14,111,920 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001278484   ⟹   NP_001265413
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0918,643,570 - 18,773,092 (+)NCBI
Rnor_5.0917,448,142 - 17,658,373 (+)NCBI
Celera913,982,280 - 14,111,920 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244549   ⟹   XP_006244611
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0918,565,007 - 18,773,083 (+)NCBI
Rnor_5.0917,448,142 - 17,658,373 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244550   ⟹   XP_006244612
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0918,564,743 - 18,773,083 (+)NCBI
Rnor_5.0917,448,142 - 17,658,373 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244551   ⟹   XP_006244613
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0918,564,743 - 18,773,083 (+)NCBI
Rnor_5.0917,448,142 - 17,658,373 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244554   ⟹   XP_006244616
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0918,643,551 - 18,773,083 (+)NCBI
Rnor_5.0917,448,142 - 17,658,373 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596547   ⟹   XP_017452036
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0918,565,007 - 18,773,083 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596548   ⟹   XP_017452037
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0918,565,007 - 18,773,083 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596549   ⟹   XP_017452038
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0918,565,007 - 18,773,083 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596551   ⟹   XP_017452040
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0918,643,551 - 18,773,083 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596552   ⟹   XP_017452041
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0918,643,551 - 18,773,083 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001265412   ⟸   NM_001278483
- Peptide Label: isoform 1
- UniProtKB: F1M9C5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001265413   ⟸   NM_001278484
- Peptide Label: isoform 2
- Sequence:
RefSeq Acc Id: XP_006244612   ⟸   XM_006244550
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006244613   ⟸   XM_006244551
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006244611   ⟸   XM_006244549
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006244616   ⟸   XM_006244554
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017452036   ⟸   XM_017596547
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017452037   ⟸   XM_017596548
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017452038   ⟸   XM_017596549
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017452040   ⟸   XM_017596551
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017452041   ⟸   XM_017596552
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: ENSRNOP00000057733   ⟸   ENSRNOT00000061014
Protein Domains
Runt

Transcriptome

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


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)
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)
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
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)
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: 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)
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
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)
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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WKY/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
WKY/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
WKY/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
WKY/NHsd (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
WN/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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 17654242 17654243 G A snv SBH/Ygl (KNAW), SBH/Ygl (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 18768961 18768962 G A snv SBH/Ygl (RGD), SBH/Ygl (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2282 AgrOrtholog
Ensembl Genes ENSRNOG00000020193 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000057733 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061014 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.720 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  4.10.770.10 UniProtKB/TrEMBL
InterPro AML1_Runt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  p53-like_TF_DNA-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  p53/RUNT-type_TF_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Runt_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Runx_central_dom UniProtKB/TrEMBL
  RunxI UniProtKB/TrEMBL
  TF_Runt-rel_RUNX UniProtKB/TrEMBL
KEGG Report rno:367218 UniProtKB/TrEMBL
NCBI Gene 367218 ENTREZGENE
PANTHER PTHR11950 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Runt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RunxI UniProtKB/TrEMBL
PhenoGen Runx2 PhenoGen
PIRSF TF_Runt-rel_RUNX UniProtKB/TrEMBL
PRINTS ONCOGENEAML1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE RUNT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49417 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC202826
UniGene Rn.83672 ENTREZGENE
UniProt F1M9C5 ENTREZGENE, UniProtKB/TrEMBL
  Q9Z2J9 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q99NC7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-05 Runx2  RUNX family transcription factor 2  Runx2  runt-related transcription factor 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-17 Runx2  runt-related transcription factor 2  Runx2  runt related transcription factor 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Runx2  runt related transcription factor 2      Symbol and Name status set to approved 70586 APPROVED
2001-10-24 Runx2  runt related transcription factor 2      Symbol updated to reflect Human and Mouse nomenclature 68913 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function osteoblast-specific transcription factor 69800
gene_process involved in regulation of osteoblast differentiation 69800
gene_transcript has multiple splicing variant forms due to alternative use of transcription start sites 69800