Gata3 (GATA binding protein 3) - Rat Genome Database

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Gene: Gata3 (GATA binding protein 3) Rattus norvegicus
Analyze
Symbol: Gata3
Name: GATA binding protein 3
RGD ID: 621250
Description: Enables DNA-binding transcription factor activity and sequence-specific DNA binding activity. Involved in several processes, including cochlea development; response to gamma radiation; and type IV hypersensitivity. Located in nucleus. Biomarker of asthma. Human ortholog(s) of this gene implicated in hypoparathyroidism; hypoparathyroidism-deafness-renal disease syndrome; nephrosis; and sensorineural hearing loss. Orthologous to human GATA3 (GATA binding protein 3); PARTICIPATES IN interleukin-27 signaling pathway; Notch signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: GATA-binding protein 3; trans-acting T-cell-specific transcription factor GATA-3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21768,643,760 - 68,666,000 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1768,643,873 - 68,665,391 (+)Ensembl
Rnor_6.01772,419,752 - 72,452,043 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1772,429,618 - 72,450,681 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01774,114,785 - 74,137,119 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41779,991,587 - 80,011,574 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11780,002,419 - 80,022,407 (+)NCBI
Celera1768,131,695 - 68,151,337 (+)NCBICelera
Cytogenetic Map17q12.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,4-benzoquinone  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
13,14-dihydro-15-ketoprostaglandin D2  (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-tert-butylhydroquinone  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
4-hydroxynon-2-enal  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-chloro-7-iodoquinolin-8-ol  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-galactosylceramide  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
belinostat  (ISO)
benzalkonium chloride  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
beta-naphthoflavone  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (ISO)
buta-1,3-diene  (ISO)
calcitriol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chlordecone  (ISO)
chloroprene  (EXP)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (EXP)
coumestrol  (ISO)
cyclophosphamide  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diethylstilbestrol  (ISO)
disodium selenite  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
ethanol  (EXP)
ethyl 3,4-dihydroxybenzoate  (ISO)
flutamide  (ISO)
folic acid  (ISO)
fragrance  (ISO)
gamma-hexachlorocyclohexane  (ISO)
gemfibrozil  (EXP)
gentamycin  (EXP)
hydrogen peroxide  (ISO)
ibuprofen  (ISO)
ionomycin  (ISO)
irinotecan  (ISO)
isotretinoin  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
levamisole  (ISO)
Licochalcone B  (ISO)
Mecamylamine  (ISO)
mercury dibromide  (ISO)
methimazole  (EXP,ISO)
methotrexate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
N'-Nitrosonornicotine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
PCB138  (ISO)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
potassium chloride  (EXP)
resveratrol  (ISO)
rofecoxib  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP,ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
SR 144528  (ISO)
tacrine  (EXP)
tamoxifen  (ISO)
testosterone  (EXP)
thalidomide  (EXP)
titanium dioxide  (EXP,ISO)
toluene  (ISO)
topotecan  (EXP)
Tributyltin oxide  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anatomical structure formation involved in morphogenesis  (ISO,ISS)
aortic valve morphogenesis  (ISO,ISS)
axon guidance  (ISO)
canonical Wnt signaling pathway involved in metanephric kidney development  (ISO,ISS)
cardiac right ventricle morphogenesis  (ISO,ISS)
cell activation  (ISO)
cell fate commitment  (IBA)
cell fate determination  (ISO,ISS)
cell maturation  (ISO)
cell morphogenesis  (ISO)
cellular response to BMP stimulus  (ISO)
cellular response to cytokine stimulus  (ISO)
cellular response to interferon-alpha  (ISO)
cellular response to interleukin-4  (ISO)
cellular response to tumor necrosis factor  (ISO)
chromatin remodeling  (ISO)
cochlea development  (IEP)
developmental growth  (ISO)
ear development  (ISO,ISS)
embryonic hemopoiesis  (ISO)
embryonic organ development  (IBA,ISO)
erythrocyte differentiation  (ISO)
homeostasis of number of cells  (ISO)
humoral immune response  (ISO)
immune system development  (IBA)
in utero embryonic development  (ISO)
inner ear morphogenesis  (ISO)
kidney development  (ISO,ISS)
lens development in camera-type eye  (ISO)
lymphocyte migration  (ISO,ISS)
male gonad development  (ISO,ISS)
mast cell differentiation  (ISO)
mesenchymal to epithelial transition  (ISO,ISS)
mesonephros development  (ISO,ISS)
negative regulation of cell cycle  (ISO,ISS)
negative regulation of cell motility  (ISO,ISS)
negative regulation of cell population proliferation  (ISO,ISS)
negative regulation of cell proliferation involved in mesonephros development  (ISO,ISS)
negative regulation of DNA demethylation  (ISO)
negative regulation of endothelial cell apoptotic process  (ISO,ISS)
negative regulation of epithelial to mesenchymal transition  (ISO)
negative regulation of fat cell differentiation  (ISO,ISS)
negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation  (ISO,ISS)
negative regulation of gene expression  (ISO)
negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation  (ISO,ISS)
negative regulation of inflammatory response  (ISO,ISS)
negative regulation of interferon-gamma production  (ISO)
negative regulation of interleukin-2 production  (ISO)
negative regulation of mammary gland epithelial cell proliferation  (ISO)
negative regulation of transcription by RNA polymerase II  (IBA,ISO)
negative regulation of transcription, DNA-templated  (ISO,ISS)
nephric duct formation  (ISO,ISS)
nephric duct morphogenesis  (ISO,ISS)
nervous system development  (ISO)
neuron differentiation  (ISO)
neuron migration  (ISO)
norepinephrine biosynthetic process  (ISO,ISS)
otic vesicle development  (ISO)
parathyroid gland development  (ISO)
parathyroid hormone secretion  (ISO)
pharyngeal system development  (ISO,ISS)
phosphatidylinositol 3-kinase signaling  (ISO,ISS)
positive regulation of cell differentiation  (ISO)
positive regulation of cytokine production  (ISO)
positive regulation of endothelial cell migration  (ISO,ISS)
positive regulation of gene expression  (ISO)
positive regulation of histone H3-K14 acetylation  (ISO)
positive regulation of histone H3-K9 acetylation  (ISO)
positive regulation of interleukin-13 production  (ISO,ISS)
positive regulation of interleukin-4 production  (ISO,ISS)
positive regulation of interleukin-5 production  (ISO,ISS)
positive regulation of pri-miRNA transcription by RNA polymerase II  (ISO)
positive regulation of protein kinase B signaling  (ISO,ISS)
positive regulation of signal transduction  (ISO,ISS)
positive regulation of T cell differentiation  (ISO,ISS)
positive regulation of T-helper 2 cell cytokine production  (ISO)
positive regulation of thyroid hormone generation  (ISO,ISS)
positive regulation of transcription by RNA polymerase II  (IDA,ISO,ISS)
positive regulation of transcription regulatory region DNA binding  (ISO,ISS)
positive regulation of transcription, DNA-templated  (ISO,ISS)
positive regulation of ureteric bud formation  (ISO,ISS)
post-embryonic development  (ISO)
pro-T cell differentiation  (ISO)
regulation of CD4-positive, alpha-beta T cell differentiation  (ISO)
regulation of cellular response to X-ray  (ISO,ISS)
regulation of cytokine production  (ISO,ISS)
regulation of epithelial cell differentiation  (IBA)
regulation of establishment of cell polarity  (ISO)
regulation of histone H3-K27 methylation  (ISO)
regulation of histone H3-K4 methylation  (ISO)
regulation of nephron tubule epithelial cell differentiation  (ISO,ISS)
regulation of neuron apoptotic process  (ISO)
regulation of neuron projection development  (ISO)
regulation of transcription by RNA polymerase II  (IBA,ISO)
response to estrogen  (ISO)
response to ethanol  (IEP)
response to gamma radiation  (IEP)
response to virus  (ISO)
response to xenobiotic stimulus  (IEP)
signal transduction  (ISO,ISS)
sympathetic nervous system development  (ISO,ISS)
T cell differentiation  (ISO)
T cell differentiation in thymus  (ISO)
T cell receptor signaling pathway  (ISO,ISS)
T-helper 2 cell differentiation  (ISO)
thymic T cell selection  (ISO)
thymus development  (ISO)
TOR signaling  (ISO,ISS)
type IV hypersensitivity  (IEP)
ureter maturation  (ISO)
ureter morphogenesis  (ISO)
ureteric bud formation  (ISO,ISS)
uterus development  (ISO,ISS)
ventricular septum development  (ISO,ISS)

Cellular Component
chromatin  (ISO,ISS)
nucleoplasm  (IEA,ISO)
nucleus  (IC,IDA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Cao L, etal., Am J Physiol Lung Cell Mol Physiol. 2010 Jan 29.
2. Fu T, etal., Chin Med J (Engl). 2005 Dec 5;118(23):2000-4.
3. Fu T, etal., Zhonghua Yan Ke Za Zhi 2002 Apr;38(4):213-6.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Gremy O, etal., World J Gastroenterol. 2008 Dec 14;14(46):7075-85.
7. Gross J, etal., Hear Res. 2010 Mar;261(1-2):9-21. doi: 10.1016/j.heares.2009.12.017. Epub 2009 Dec 16.
8. Labastie MC, etal., Genomics 1994 May 1;21(1):1-6.
9. Li J, etal., Inflammation. 2015;38(3):995-1002. doi: 10.1007/s10753-014-0063-3.
10. Marine J and Winoto A, Proc Natl Acad Sci U S A 1991 Aug 15;88(16):7284-8.
11. MGD data from the GO Consortium
12. Nakamura Y, etal., J Allergy Clin Immunol. 1999 Feb;103(2 Pt 1):215-22.
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. OMIM Disease Annotation Pipeline
15. Online Mendelian Inheritance in Man, OMIM (TM).
16. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
17. RGD automated data pipeline
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. Rout UK and Clausen P, Neurosci Res. 2009 Jun;64(2):162-9. Epub 2009 Mar 6.
21. Siegel MD, etal., J Biol Chem 1995 Oct 13;270(41):24548-55.
22. Uchida S, etal., Biochem Biophys Res Commun 1997 Mar 6;232(1):65-8.
23. Van Esch H, etal., Nature 2000 Jul 27;406(6794):419-22.
24. Xiong L, etal., Am J Chin Med. 2007;35(6):1011-20.
Additional References at PubMed
PMID:2017177   PMID:7550312   PMID:7720565   PMID:7956841   PMID:8945476   PMID:9043071   PMID:9576834   PMID:9819382   PMID:10037815   PMID:10447238   PMID:10549629   PMID:10556076  
PMID:10631184   PMID:10835639   PMID:11093124   PMID:11135239   PMID:12127263   PMID:12923059   PMID:14643687   PMID:14670303   PMID:15003631   PMID:15016828   PMID:15087456   PMID:15306564  
PMID:15329349   PMID:15662016   PMID:16319112   PMID:16677481   PMID:17082577   PMID:17357106   PMID:17603486   PMID:17658278   PMID:17658279   PMID:18445004   PMID:18554735   PMID:18621058  
PMID:18776904   PMID:18792410   PMID:18955134   PMID:18997793   PMID:19112489   PMID:19232384   PMID:19248180   PMID:19483726   PMID:19623612   PMID:19666510   PMID:19674970   PMID:19723756  
PMID:19735555   PMID:19796622   PMID:19805038   PMID:19934022   PMID:20176728   PMID:20189993   PMID:20368097   PMID:20398510   PMID:20399120   PMID:20484083   PMID:20484821   PMID:20499358  
PMID:20501701   PMID:20554961   PMID:20583921   PMID:20636338   PMID:20696860   PMID:20702712   PMID:20705609   PMID:20706986   PMID:20818386   PMID:20855495   PMID:20855530   PMID:21217760  
PMID:21344672   PMID:21521737   PMID:21536806   PMID:21553382   PMID:21613615   PMID:21731775   PMID:21761347   PMID:21867929   PMID:22070074   PMID:22384571   PMID:22529382   PMID:22588720  
PMID:23426694   PMID:24802759   PMID:24831988   PMID:25001933   PMID:26451614   PMID:31405951  


Genomics

Comparative Map Data
Gata3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21768,643,760 - 68,666,000 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1768,643,873 - 68,665,391 (+)Ensembl
Rnor_6.01772,419,752 - 72,452,043 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1772,429,618 - 72,450,681 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01774,114,785 - 74,137,119 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41779,991,587 - 80,011,574 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11780,002,419 - 80,022,407 (+)NCBI
Celera1768,131,695 - 68,151,337 (+)NCBICelera
Cytogenetic Map17q12.3NCBI
GATA3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl108,045,378 - 8,075,198 (+)EnsemblGRCh38hg38GRCh38
GRCh38108,045,420 - 8,075,198 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37108,096,651 - 8,117,161 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36108,136,673 - 8,157,170 (+)NCBINCBI36hg18NCBI36
Build 34108,136,672 - 8,157,170NCBI
Celera108,022,059 - 8,042,539 (+)NCBI
Cytogenetic Map10p14NCBI
HuRef108,015,002 - 8,035,471 (+)NCBIHuRef
CHM1_1108,096,969 - 8,117,441 (+)NCBICHM1_1
Gata3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3929,861,889 - 9,892,762 (-)NCBIGRCm39mm39
GRCm39 Ensembl29,861,889 - 9,894,845 (-)Ensembl
GRCm3829,857,078 - 9,887,953 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl29,857,078 - 9,890,034 (-)EnsemblGRCm38mm10GRCm38
MGSCv3729,778,705 - 9,800,227 (-)NCBIGRCm37mm9NCBIm37
MGSCv3629,774,931 - 9,795,629 (-)NCBImm8
Celera29,794,542 - 9,816,062 (-)NCBICelera
Cytogenetic Map2A1NCBI
cM Map26.69NCBI
Gata3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542124,457,496 - 24,478,744 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542124,448,446 - 24,477,885 (+)NCBIChiLan1.0ChiLan1.0
GATA3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1108,055,853 - 8,086,271 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl108,064,207 - 8,086,272 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0108,075,951 - 8,105,573 (+)NCBIMhudiblu_PPA_v0panPan3
GATA3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1228,068,143 - 28,098,445 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl228,069,051 - 28,087,760 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha225,104,703 - 25,134,953 (-)NCBI
ROS_Cfam_1.0228,443,699 - 28,464,623 (-)NCBI
UMICH_Zoey_3.1225,552,826 - 25,583,058 (-)NCBI
UNSW_CanFamBas_1.0226,396,168 - 26,425,115 (-)NCBI
UU_Cfam_GSD_1.0227,112,635 - 27,142,926 (-)NCBI
Gata3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934430,614,585 - 30,645,254 (-)NCBI
SpeTri2.0NW_0049364846,780,692 - 6,800,883 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GATA3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1063,367,660 - 63,388,859 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11063,367,684 - 63,397,977 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21069,582,743 - 69,601,480 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GATA3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.198,101,404 - 8,122,762 (+)NCBI
ChlSab1.1 Ensembl98,101,432 - 8,123,064 (+)Ensembl
Vero_WHO_p1.0NW_02366605113,489,149 - 13,518,902 (+)NCBI
Gata3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247752,985,077 - 3,014,567 (+)NCBI


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172365318468653184Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172365318468653184Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172365318468653184Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172365318468653184Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318468653184Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172365318470974005Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172459934069599340Rat
8552928Pigfal9Plasma insulin-like growth factor 1 level QTL 99blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)172840914773409147Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)172840914773409147Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173136839173951021Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173199078476990784Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173199078481292925Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173455084373951021Rat
724528Uae4Urinary albumin excretion QTL 44.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)173583708569599340Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)173747984782479847Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)173828150983281509Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)173828150983281509Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174054004180387013Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174099000585990005Rat
1354635Bp245Blood pressure QTL 2456arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)174207316069599340Rat
1354635Bp245Blood pressure QTL 2456arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)174207316069599340Rat
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)174992015486533673Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175004027186533673Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175090909986022412Rat
1354588Bvd4Brain ventricular dilatation QTL 45.310.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)175349882882479847Rat
70210Cm15Cardiac mass QTL 156.5heart right ventricle mass (VT:0007033)heart right ventricle wet weight (CMO:0000072)175724672370156904Rat
1600398Edcs5Endometrial carcinoma susceptibility QTL 52.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)175724672370852846Rat
2302365Gluco40Glucose level QTL 404.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)175724684382046127Rat
7488963Bp369Blood pressure QTL 3690.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)175900564977910000Rat
2317045Aia11Adjuvant induced arthritis QTL 114.06joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)176078142686533673Rat
7411577Bw141Body weight QTL 1410.001body mass (VT:0001259)body weight gain (CMO:0000420)176261951686533673Rat
1300131Bp193Blood pressure QTL 1933.3arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)176364000973951021Rat
631502Cm26Cardiac mass QTL 263.71heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)176570358081153923Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:25
Count of miRNA genes:25
Interacting mature miRNAs:25
Transcripts:ENSRNOT00000026187
Prediction methods:Miranda, Rnahybrid
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 6 7 17 28 13 3
Low 3 26 20 10 12 10 30 7 20 8
Below cutoff 17 28 28 28 7 10 25 8 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026187   ⟹   ENSRNOP00000026187
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1768,643,873 - 68,665,391 (+)Ensembl
Rnor_6.0 Ensembl1772,429,618 - 72,450,681 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101466   ⟹   ENSRNOP00000088644
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1768,643,873 - 68,664,097 (+)Ensembl
RefSeq Acc Id: NM_133293   ⟹   NP_579827
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21768,644,913 - 68,664,097 (+)NCBI
Rnor_6.01772,430,817 - 72,450,140 (+)NCBI
Rnor_5.01774,114,785 - 74,137,119 (+)NCBI
RGSC_v3.41779,991,587 - 80,011,574 (+)RGD
Celera1768,131,695 - 68,151,337 (+)RGD
Sequence:
RefSeq Acc Id: XM_006254253   ⟹   XP_006254315
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21768,643,761 - 68,666,000 (+)NCBI
Rnor_6.01772,429,632 - 72,452,043 (+)NCBI
Rnor_5.01774,114,785 - 74,137,119 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008771893   ⟹   XP_008770115
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21768,644,133 - 68,666,000 (+)NCBI
Rnor_6.01772,430,004 - 72,452,043 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600667   ⟹   XP_017456156
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21768,643,760 - 68,666,000 (+)NCBI
Rnor_6.01772,430,004 - 72,452,043 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_579827 (Get FASTA)   NCBI Sequence Viewer  
  XP_006254315 (Get FASTA)   NCBI Sequence Viewer  
  XP_008770115 (Get FASTA)   NCBI Sequence Viewer  
  XP_017456156 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK00586 (Get FASTA)   NCBI Sequence Viewer  
  EDL78630 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_579827   ⟸   NM_133293
- UniProtKB: Q99NH5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006254315   ⟸   XM_006254253
- Peptide Label: isoform X1
- UniProtKB: Q99NH5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008770115   ⟸   XM_008771893
- Peptide Label: isoform X1
- UniProtKB: Q99NH5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456156   ⟸   XM_017600667
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000026187   ⟸   ENSRNOT00000026187
RefSeq Acc Id: ENSRNOP00000088644   ⟸   ENSRNOT00000101466
Protein Domains
GATA-type

Transcriptome

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

Promoters
RGD ID:13700562
Promoter ID:EPDNEW_R11085
Type:initiation region
Name:Gata3_1
Description:GATA binding protein 3
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_6.01772,430,514 - 72,430,574EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:621250 AgrOrtholog
Ensembl Genes ENSRNOG00000019336 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000026187 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026187 UniProtKB/TrEMBL
Gene3D-CATH 3.30.50.10 UniProtKB/TrEMBL
InterPro GATA-3 UniProtKB/TrEMBL
  TF_GATA-1/2/3 UniProtKB/TrEMBL
  Transcription_factor_GATA UniProtKB/TrEMBL
  Znf_GATA UniProtKB/TrEMBL
  Znf_NHR/GATA UniProtKB/TrEMBL
KEGG Report rno:85471 UniProtKB/TrEMBL
NCBI Gene 85471 ENTREZGENE
PANTHER PTHR10071 UniProtKB/TrEMBL
  PTHR10071:SF106 UniProtKB/TrEMBL
Pfam GATA UniProtKB/TrEMBL
PhenoGen Gata3 PhenoGen
PIRSF TF_GATA-1/2/3 UniProtKB/TrEMBL
PRINTS GATAZNFINGER UniProtKB/TrEMBL
PROSITE GATA_ZN_FINGER_1 UniProtKB/TrEMBL
  GATA_ZN_FINGER_2 UniProtKB/TrEMBL
SMART ZnF_GATA UniProtKB/TrEMBL
UniProt Q99NH5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Gata3  GATA binding protein 3    GATA-binding protein 3  Name updated 1299863 APPROVED
2002-08-07 Gata3  GATA-binding protein 3      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expression increases at 5, 7, 14, 21 days after anterior chamber inoculation 632697