Smad3 (SMAD family member 3) - Rat Genome Database

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Gene: Smad3 (SMAD family member 3) Rattus norvegicus
Analyze
Symbol: Smad3
Name: SMAD family member 3
RGD ID: 3032
Description: Exhibits several functions, including DNA-binding transcription factor activity; SMAD binding activity; and beta-catenin binding activity. Involved in several processes, including positive regulation of cellular metabolic process; regulation of gene expression; and transmembrane receptor protein serine/threonine kinase signaling pathway. Localizes to cytoplasm; nucleus; and transcription regulator complex. Used to study pre-malignant neoplasm. Human ortholog(s) of this gene implicated in Loeys-Dietz syndrome 3; Lynch syndrome; and pancreatic cancer. Orthologous to human SMAD3 (SMAD family member 3); PARTICIPATES IN transforming growth factor-beta Smad dependent signaling pathway; altered transforming growth factor-beta Smad dependent signaling pathway; colorectal cancer pathway; INTERACTS WITH (S)-nicotine; 2-acetamidofluorene; 2-amino-2-deoxy-D-galactopyranose.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: MAD (mothers against decapentaplegic Drosophila) homolog 3; MAD (mothers against decapentaplegic, Drosophila) homolog 3; MAD homolog 3; MAD homolog 3 (Drosophila); mad3; Madh3; mothers against decapentaplegic homolog 3; mothers against DPP homolog 3; Smad 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2864,126,829 - 64,236,960 (-)NCBI
Rnor_6.0 Ensembl868,569,530 - 68,678,349 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0868,569,530 - 68,678,349 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0868,290,927 - 68,397,727 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4867,803,909 - 67,952,056 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1867,822,964 - 67,971,110 (-)NCBI
Celera863,537,497 - 63,647,062 (-)NCBICelera
Cytogenetic Map8q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-O-oleoyl-sn-glycero-3-phosphocholine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-acetamidofluorene  (EXP)
2-amino-2-deoxy-D-galactopyranose  (EXP)
2-hydroxypropanoic acid  (ISO)
3,4-dihydroxybenzaldehyde  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-nonylphenol  (ISO)
4-vinylcyclohexene dioxide  (ISO)
5-aza-2'-deoxycytidine  (EXP,ISO)
9-cis-retinoic acid  (ISO)
acetaldehyde  (ISO)
acteoside  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
alpha-naphthoflavone  (ISO)
AM-251  (ISO)
Ammothamnine  (ISO)
amphetamine  (EXP)
andrographolide  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP,ISO)
antirheumatic drug  (ISO)
aripiprazole  (ISO)
arsane  (EXP)
arsenic atom  (EXP)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
benazepril  (EXP)
benzene  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (EXP)
benzo[e]pyrene  (ISO)
benzophenone  (ISO)
betulin  (EXP)
betulinic acid  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (EXP,ISO)
butan-1-ol  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (EXP,ISO)
candesartan  (EXP)
Candesartan cilexetil  (EXP)
cantharidin  (ISO)
carbamazepine  (ISO)
carbofuran  (EXP)
casticin  (ISO)
celastrol  (ISO)
CGS-21680  (EXP)
chlorpyrifos  (ISO)
cholesterol  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
chrysin  (ISO)
cisplatin  (ISO)
cocaine  (EXP)
coenzyme Q10  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
corosolic acid  (ISO)
corticosterone  (EXP)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
curcumin  (EXP)
cyclosporin A  (ISO)
cytochalasin D  (ISO)
D-glucose  (ISO)
Deguelin  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (EXP)
dibenzo[a,l]pyrene  (EXP)
dibutyl phthalate  (ISO)
diminazene diaceturate  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
disulfiram  (ISO)
doxorubicin  (ISO)
ebselen  (ISO)
Enterolactone  (ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
fenofibrate  (ISO)
ferulic acid  (EXP)
fipronil  (EXP)
fluoranthene  (EXP,ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
galangin  (ISO)
gallic acid  (EXP)
genistein  (EXP,ISO)
geraniol  (ISO)
glucose  (ISO)
glyphosate  (ISO)
heptachlor  (ISO)
hexachlorobenzene  (ISO)
Honokiol  (EXP,ISO)
hyaluronic acid  (ISO)
hydrogen peroxide  (ISO)
irbesartan  (EXP)
irinotecan  (ISO)
isorhamnetin  (ISO)
L-methionine  (ISO)
lead diacetate  (EXP)
leptomycin B  (ISO)
linoleic acid  (ISO)
lipopolysaccharide  (ISO)
lithocholic acid  (ISO)
LY 364947  (ISO)
lycopene  (ISO)
melphalan  (ISO)
menadione  (ISO)
methamphetamine  (EXP)
methapyrilene  (ISO)
Methylazoxymethanol acetate  (EXP)
methylmercury chloride  (ISO)
methylparaben  (ISO)
mirtazapine  (ISO)
N-acetyl-L-cysteine  (ISO)
N-nitrosodiethylamine  (EXP)
naringin  (EXP)
niclosamide  (EXP,ISO)
nicotine  (EXP,ISO)
nitric oxide  (EXP)
nitrofen  (ISO)
Nonylphenol  (ISO)
ochratoxin A  (ISO)
oridonin  (ISO)
osthole  (ISO)
ozone  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
perindopril  (EXP)
phenylarsine oxide  (ISO)
phenylmercury acetate  (ISO)
phloroglucinol  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
picrotoxin  (EXP)
pirinixic acid  (ISO)
platycodin D  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
quercetin  (ISO)
quercitrin  (ISO)
rac-lactic acid  (ISO)
reactive oxygen species  (ISO)
resveratrol  (EXP,ISO)
SB 203580  (ISO)
SB 431542  (EXP,ISO)
SCH 23390  (EXP)
serpentine asbestos  (ISO)
sevoflurane  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
silver(1+) nitrate  (ISO)
simvastatin  (EXP,ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium fluoride  (ISO)
sorafenib  (ISO)
streptozocin  (EXP,ISO)
tacrolimus hydrate  (EXP)
tamoxifen  (ISO)
Tanshinone I  (ISO)
tauro-beta-muricholic acid  (ISO)
taurochenodeoxycholic acid  (ISO)
taurolithocholic acid  (ISO)
tauroursodeoxycholic acid  (ISO)
tert-butyl hydroperoxide  (ISO)
Tesaglitazar  (EXP)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP,ISO)
trichostatin A  (ISO)
troglitazone  (EXP,ISO)
tungsten  (ISO)
ursodeoxycholic acid  (EXP)
valproic acid  (ISO)
valsartan  (EXP)
vitamin D  (ISO)
vitamin E  (ISO)
zearalenone  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
ziram  (ISO)
zoledronic acid  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO)
activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway  (IMP)
activin receptor signaling pathway  (ISO)
adrenal gland development  (IDA)
anatomical structure morphogenesis  (IBA)
BMP signaling pathway  (IBA)
cell differentiation  (IBA)
cell-cell junction organization  (ISO)
cellular response to transforming growth factor beta stimulus  (ISO)
developmental growth  (ISO)
embryonic cranial skeleton morphogenesis  (ISO)
embryonic foregut morphogenesis  (ISO)
embryonic pattern specification  (ISO)
endoderm development  (ISO)
extrinsic apoptotic signaling pathway  (ISO)
gastrulation  (ISO)
heart looping  (ISO)
immune response  (ISO)
immune system development  (ISO)
in utero embryonic development  (ISO)
lens fiber cell differentiation  (ISO)
liver development  (ISO)
mesoderm formation  (ISO)
negative regulation of apoptotic process  (IDA)
negative regulation of cardiac muscle hypertrophy in response to stress  (IGI)
negative regulation of cell growth  (ISO)
negative regulation of cell population proliferation  (IDA)
negative regulation of cytosolic calcium ion concentration  (ISO)
negative regulation of fat cell differentiation  (ISO)
negative regulation of inflammatory response  (ISO)
negative regulation of lung blood pressure  (IGI)
negative regulation of mitotic cell cycle  (ISO)
negative regulation of osteoblast differentiation  (ISO)
negative regulation of osteoblast proliferation  (ISO)
negative regulation of protein catabolic process  (IDA,IMP)
negative regulation of transcription by RNA polymerase II  (IMP,ISO)
negative regulation of wound healing  (ISO)
nodal signaling pathway  (ISO)
osteoblast development  (ISO)
osteoblast differentiation  (ISO)
paraxial mesoderm morphogenesis  (ISO)
pericardium development  (ISO)
positive regulation of alkaline phosphatase activity  (IDA)
positive regulation of bone mineralization  (IDA)
positive regulation of canonical Wnt signaling pathway  (IMP)
positive regulation of cell migration  (IMP)
positive regulation of chondrocyte differentiation  (ISO)
positive regulation of epithelial to mesenchymal transition  (ISO)
positive regulation of extracellular matrix assembly  (ISO)
positive regulation of focal adhesion assembly  (IDA)
positive regulation of gene expression  (ISO)
positive regulation of interleukin-1 beta production  (IMP)
positive regulation of nitric oxide biosynthetic process  (IGI,ISO)
positive regulation of positive chemotaxis  (IDA)
positive regulation of pri-miRNA transcription by RNA polymerase II  (ISO)
positive regulation of stress fiber assembly  (IDA)
positive regulation of transcription by RNA polymerase II  (IDA,IMP,ISO)
positive regulation of transcription, DNA-templated  (ISO)
positive regulation of transforming growth factor beta3 production  (IMP)
protein stabilization  (IMP)
regulation of binding  (ISO)
regulation of cell cycle  (ISO)
regulation of epithelial cell proliferation  (ISO)
regulation of immune response  (ISO)
regulation of striated muscle tissue development  (ISO)
regulation of transcription by RNA polymerase II  (ISO)
regulation of transforming growth factor beta receptor signaling pathway  (ISO)
regulation of transforming growth factor beta2 production  (ISO)
response to hypoxia  (ISO)
signal transduction involved in regulation of gene expression  (IMP)
skeletal system development  (ISO)
SMAD protein complex assembly  (IPI,ISO)
SMAD protein signal transduction  (IBA,ISO)
somitogenesis  (ISO)
T cell activation  (ISO)
thyroid gland development  (ISO)
transdifferentiation  (IDA)
transforming growth factor beta receptor signaling pathway  (IBA,IMP,ISO)
ureteric bud development  (ISO)

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
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21. MGD data from the GO Consortium
22. NCBI rat LocusLink and RefSeq merged data July 26, 2002
23. Okuyama N, etal., Brain Res. 2007 Feb 9;1132(1):36-41. Epub 2006 Dec 12.
24. OMIM Disease Annotation Pipeline
25. Piestrzeniewicz-Ulanska D, etal., Oncol Rep. 2003 Sep-Oct;10(5):1539-44.
26. Pipeline to import KEGG annotations from KEGG into RGD
27. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
28. RGD automated data pipeline
29. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
30. RGD automated import pipeline for gene-chemical interactions
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38. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
39. Uemura M, etal., Mol Biol Cell. 2005 Sep;16(9):4214-24. Epub 2005 Jun 29.
40. Wang EY, etal., J Endocrinol 2003 Jul;178(1):137-48.
41. Wei XH, etal., Microcirculation. 2013 Jan;20(1):17-29. doi: 10.1111/micc.12002.
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44. Zhang M, etal., J Biol Chem. 2010 Mar 19;285(12):8703-10. doi: 10.1074/jbc.M109.093526. Epub 2010 Jan 22.
45. Zhao M, etal., Virol J. 2017 Jan 13;14(1):5. doi: 10.1186/s12985-016-0670-8.
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Additional References at PubMed
PMID:8774881   PMID:9111321   PMID:9311995   PMID:9679056   PMID:9702197   PMID:9732876   PMID:9759503   PMID:10064594   PMID:10559937   PMID:10647776   PMID:10708948   PMID:10708949  
PMID:10823886   PMID:11160896   PMID:11278251   PMID:11585338   PMID:11711431   PMID:11937490   PMID:12411310   PMID:12446380   PMID:12543979   PMID:12686552   PMID:12845704   PMID:12874272  
PMID:12876289   PMID:12902338   PMID:12943993   PMID:14555988   PMID:14559231   PMID:14617288   PMID:14623893   PMID:14656760   PMID:14754879   PMID:15084457   PMID:15107418   PMID:15150273  
PMID:15150278   PMID:15183723   PMID:15239668   PMID:15282343   PMID:15326485   PMID:15334054   PMID:15464984   PMID:15489334   PMID:15647271   PMID:15761025   PMID:15799969   PMID:16007207  
PMID:16224064   PMID:16266486   PMID:16696323   PMID:16751101   PMID:16777850   PMID:16785237   PMID:16807527   PMID:16824956   PMID:16886151   PMID:16931807   PMID:16980030   PMID:17038494  
PMID:17159989   PMID:17215516   PMID:17251190   PMID:17392319   PMID:17541159   PMID:17723189   PMID:18022758   PMID:18057996   PMID:18395914   PMID:18466073   PMID:18505915   PMID:18548003  
PMID:18679024   PMID:18729074   PMID:18794808   PMID:18832382   PMID:19122240   PMID:19197123   PMID:19525370   PMID:19555739   PMID:19667256   PMID:19816956   PMID:19834880   PMID:19959709  
PMID:20129061   PMID:20182310   PMID:20226149   PMID:20375011   PMID:20404057   PMID:20423827   PMID:20739403   PMID:20874717   PMID:20943464   PMID:21035443   PMID:21158069   PMID:21307346  
PMID:21354414   PMID:21429339   PMID:21468608   PMID:21498085   PMID:21560355   PMID:21724602   PMID:21749980   PMID:21828274   PMID:21852586   PMID:21937600   PMID:21947082   PMID:22045334  
PMID:22338217   PMID:22384127   PMID:22447946   PMID:22674034   PMID:22926646   PMID:23056222   PMID:23064763   PMID:23176567   PMID:23291610   PMID:23390484   PMID:23403244   PMID:23690627  
PMID:24086569   PMID:24290497   PMID:24356887   PMID:24500776   PMID:24718260   PMID:24914373   PMID:24964035   PMID:25010983   PMID:25065622   PMID:25245272   PMID:25416030   PMID:25422985  
PMID:25538336   PMID:25867402   PMID:25893292   PMID:26138247   PMID:26153982   PMID:26253398   PMID:26276823   PMID:26311719   PMID:26483344   PMID:26738448   PMID:26945889   PMID:26946943  
PMID:26954391   PMID:27155082   PMID:27217701   PMID:27239849   PMID:27282665   PMID:27340942   PMID:27422367   PMID:27453280   PMID:27530924   PMID:27633729   PMID:28035691   PMID:28041981  
PMID:28125630   PMID:28193525   PMID:28230313   PMID:28539652   PMID:28552397   PMID:28586069   PMID:28623783   PMID:28647476   PMID:28943431   PMID:29102631   PMID:29104873   PMID:29215718  
PMID:29309309   PMID:29505748   PMID:29704604   PMID:30053527   PMID:30055965   PMID:30066831   PMID:30317638   PMID:30549198   PMID:31521890   PMID:31582430   PMID:31813251   PMID:31917288  
PMID:31960436   PMID:32169420   PMID:32274619   PMID:32949699  


Genomics

Comparative Map Data
Smad3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2864,126,829 - 64,236,960 (-)NCBI
Rnor_6.0 Ensembl868,569,530 - 68,678,349 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0868,569,530 - 68,678,349 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0868,290,927 - 68,397,727 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4867,803,909 - 67,952,056 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1867,822,964 - 67,971,110 (-)NCBI
Celera863,537,497 - 63,647,062 (-)NCBICelera
Cytogenetic Map8q24NCBI
SMAD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1567,063,763 - 67,195,173 (+)EnsemblGRCh38hg38GRCh38
GRCh381567,065,602 - 67,195,195 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371567,357,940 - 67,487,507 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361565,145,249 - 65,274,587 (+)NCBINCBI36hg18NCBI36
Build 341565,145,248 - 65,274,586NCBI
Celera1544,246,635 - 44,375,039 (+)NCBI
Cytogenetic Map15q22.33NCBI
HuRef1544,193,465 - 44,321,904 (+)NCBIHuRef
CHM1_11567,476,260 - 67,605,488 (+)NCBICHM1_1
Smad3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39963,554,048 - 63,665,276 (-)NCBIGRCm39mm39
GRCm39 Ensembl963,554,049 - 63,665,276 (-)Ensembl
GRCm38963,646,766 - 63,757,994 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl963,646,767 - 63,757,994 (-)EnsemblGRCm38mm10GRCm38
MGSCv37963,494,574 - 63,605,801 (-)NCBIGRCm37mm9NCBIm37
MGSCv36963,444,773 - 63,556,000 (-)NCBImm8
Celera960,869,117 - 60,980,879 (-)NCBICelera
Cytogenetic Map9CNCBI
Smad3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554508,747,651 - 8,842,136 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554508,747,651 - 8,842,003 (-)NCBIChiLan1.0ChiLan1.0
SMAD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11564,284,949 - 64,414,185 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1564,284,949 - 64,414,185 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01546,013,764 - 46,143,126 (+)NCBIMhudiblu_PPA_v0panPan3
SMAD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13031,246,313 - 31,360,098 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3031,245,657 - 31,363,337 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3031,175,971 - 31,289,442 (+)NCBI
ROS_Cfam_1.03031,444,224 - 31,557,937 (+)NCBI
UMICH_Zoey_3.13031,371,657 - 31,485,227 (+)NCBI
UNSW_CanFamBas_1.03031,431,846 - 31,545,247 (+)NCBI
UU_Cfam_GSD_1.03031,673,713 - 31,787,293 (+)NCBI
Smad3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640109,232,767 - 109,341,735 (+)NCBI
SpeTri2.0NW_00493647127,080,662 - 27,185,861 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMAD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1164,998,083 - 165,124,454 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11164,998,457 - 165,124,455 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21182,902,348 - 182,926,370 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMAD3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12616,319,959 - 16,446,472 (-)NCBI
ChlSab1.1 Ensembl2616,320,933 - 16,446,527 (-)Ensembl
Vero_WHO_p1.0NW_023666048125,021,354 - 125,151,320 (+)NCBI
Smad3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247815,795,652 - 5,890,047 (-)NCBI

Position Markers
Madh3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2864,236,564 - 64,236,759 (+)MAPPER
Rnor_6.0868,677,954 - 68,678,148NCBIRnor6.0
Rnor_5.0868,397,332 - 68,397,526UniSTSRnor5.0
RGSC_v3.4867,951,661 - 67,951,855UniSTSRGSC3.4
Celera863,646,667 - 63,646,861UniSTS
Cytogenetic Map8q24UniSTS
RH130799  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2864,235,228 - 64,235,441 (+)MAPPER
Rnor_6.0868,676,610 - 68,676,822NCBIRnor6.0
Rnor_5.0868,396,418 - 68,396,630UniSTSRnor5.0
RGSC_v3.4867,950,063 - 67,950,275UniSTSRGSC3.4
Celera863,645,365 - 63,645,577UniSTS
RH 3.4 Map8810.0UniSTS
Cytogenetic Map8q24UniSTS
RH143351  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2864,162,995 - 64,163,140 (+)MAPPER
Rnor_6.0868,605,604 - 68,605,748NCBIRnor6.0
Rnor_5.0868,327,124 - 68,327,268UniSTSRnor5.0
RGSC_v3.4867,856,537 - 67,856,681UniSTSRGSC3.4
Celera863,573,666 - 63,573,810UniSTS
RH 3.4 Map8805.0UniSTS
Cytogenetic Map8q24UniSTS
RH143448  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2864,126,996 - 64,127,126 (+)MAPPER
Rnor_6.0868,569,698 - 68,569,827NCBIRnor6.0
Rnor_5.0868,291,095 - 68,291,224UniSTSRnor5.0
RGSC_v3.4867,820,872 - 67,821,001UniSTSRGSC3.4
Celera863,537,665 - 63,537,794UniSTS
RH 3.4 Map8809.9UniSTS
Cytogenetic Map8q24UniSTS
RH138729  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2864,126,876 - 64,127,014 (+)MAPPER
Rnor_6.0868,569,578 - 68,569,715NCBIRnor6.0
Rnor_5.0868,290,975 - 68,291,112UniSTSRnor5.0
RGSC_v3.4867,820,752 - 67,820,889UniSTSRGSC3.4
Celera863,537,545 - 63,537,682UniSTS
RH 3.4 Map8810.0UniSTS
Cytogenetic Map8q24UniSTS
PE5L-LSB  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2864,216,656 - 64,217,035 (+)MAPPER
Rnor_6.0868,658,300 - 68,658,678NCBIRnor6.0
Rnor_5.0868,379,536 - 68,379,914UniSTSRnor5.0
RGSC_v3.4867,931,905 - 67,932,283UniSTSRGSC3.4
Celera863,626,945 - 63,627,323UniSTS
Cytogenetic Map8q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)89531047119211942Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810938911120496129Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)82146491991140553Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)821813070100873963Rat
631842Inf1Infertility severity QTL 14.10.001seminal gland mass (VT:0010524)seminal vesicle wet weight (CMO:0001603)82784149672841496Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)829867983106526740Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)829867983106526740Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)829867983106526740Rat
2303564Gluco43Glucose level QTL 433blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)83014480075144800Rat
2303572Insul13Insulin level QTL 132blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)83014480075144800Rat
1300146Rf17Renal function QTL 172.9renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)83091811275918112Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)830918112107206309Rat
724514Uae15Urinary albumin excretion QTL 152.9urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)83220198175971421Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)832888352101374135Rat
2313046Bss78Bone structure and strength QTL 783.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)83355866089058369Rat
2313057Bss76Bone structure and strength QTL 7630.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)83355866089058369Rat
2313067Bss77Bone structure and strength QTL 773.10.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)83355866089058369Rat
2313088Bss75Bone structure and strength QTL 753.10.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)83355866089058369Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)833558660109028082Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)833558660109028082Rat
1578755Pur5Proteinuria QTL 53.30.0001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)833558660109028082Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)833558764113580387Rat
1298065Scl16Serum cholesterol level QTL 163.8blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)83504141480041414Rat
1582222Epfw2Epididymal fat weight QTL 23.20.0005epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)83592559480925594Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)839230130106506973Rat
61358Bp39Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83992790184927901Rat
61464Niddm11Non-insulin dependent diabetes mellitus QTL 113.10.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83995802284958022Rat
737824Hcar10Hepatocarcinoma resistance QTL 102.9liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)84421919789542960Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)844219197100873963Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)844458129118087517Rat
1331769Rf39Renal function QTL 393.871urine output (VT:0003620)timed urine volume (CMO:0000260)84571234480003418Rat
1298079Activ2Activity QTL 29.50.000001voluntary movement trait (VT:0003491)rearing measurement (CMO:0001515)84571234490712344Rat
631216Stl9Serum triglyceride level QTL 94.710.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)84571247575971259Rat
70161Bp62Blood pressure QTL 622.90.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)84658843796998640Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)847200750106394378Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)847200750106394378Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)847200750106394378Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)847200750106394378Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)847200750106394378Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)847200750106394378Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)850529480128036471Rat
1331837Bw23Body weight QTL 234.190.00007body mass (VT:0001259)body weight (CMO:0000012)850529563106506973Rat
2313086Bss60Bone structure and strength QTL 604.10.0001tibia length (VT:0004357)tibia length (CMO:0000450)85406504489058369Rat
4889938Bss89Bone structure and strength QTL 893.8tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)85406504489058369Rat
5684973Bss100Bone structure and strength QTL 1004.7tibia area (VT:1000281)tibia area measurement (CMO:0001382)85406504489058369Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)855435004115812386Rat
2303570Gluco48Glucose level QTL 482blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)855659105100659105Rat
2293697Bmd39Bone mineral density QTL 39femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)858230766106394378Rat
1582243Bw66Body weight QTL 663.40.0048body mass (VT:0001259)body weight (CMO:0000012)85842551091990535Rat
1582254Kidm31Kidney mass QTL 313kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)85842551091990535Rat
631664Hcar3Hepatocarcinoma resistance QTL 32.90.0005liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)858425510106526740Rat
1300177Cm2Cardiac mass QTL 23.65heart mass (VT:0007028)heart weight (CMO:0000017)859234112108068306Rat
2301402Bp316Blood pressure QTL 3160.005arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)861394378106394378Rat
10402857Bp380Blood pressure QTL 3800.95arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)861394378106394378Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)865717449128033050Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:512
Count of miRNA genes:253
Interacting mature miRNAs:337
Transcripts:ENSRNOT00000039730
Prediction methods:Miranda, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 26 28 12 19 12 8 11 65 35 40 11 8
Low 17 29 29 29 9 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000039730   ⟹   ENSRNOP00000037346
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl868,569,530 - 68,678,349 (-)Ensembl
RefSeq Acc Id: NM_013095   ⟹   NP_037227
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2864,126,829 - 64,236,960 (-)NCBI
Rnor_6.0868,569,530 - 68,678,349 (-)NCBI
Rnor_5.0868,290,927 - 68,397,727 (-)NCBI
RGSC_v3.4867,803,909 - 67,952,056 (-)RGD
Celera863,537,497 - 63,647,062 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008766216   ⟹   XP_008764438
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2864,126,829 - 64,146,730 (-)NCBI
Rnor_6.0868,569,530 - 68,589,751 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039080896   ⟹   XP_038936824
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2864,126,829 - 64,183,523 (-)NCBI
RefSeq Acc Id: XM_039080897   ⟹   XP_038936825
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2864,126,829 - 64,191,240 (-)NCBI
RefSeq Acc Id: XM_039080898   ⟹   XP_038936826
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2864,126,829 - 64,146,304 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_037227   ⟸   NM_013095
- UniProtKB: P84025 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008764438   ⟸   XM_008766216
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000037346   ⟸   ENSRNOT00000039730
RefSeq Acc Id: XP_038936825   ⟸   XM_039080897
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038936824   ⟸   XM_039080896
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038936826   ⟸   XM_039080898
- Peptide Label: isoform X3
Protein Domains
MH1   MH2

Transcriptome

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

Promoters
RGD ID:13696062
Promoter ID:EPDNEW_R6587
Type:multiple initiation site
Name:Smad3_1
Description:SMAD family member 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_6.0868,678,414 - 68,678,474EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3032 AgrOrtholog
Ensembl Genes ENSRNOG00000008620 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000037346 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000039730 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.200.10 UniProtKB/Swiss-Prot
  3.90.520.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5599910 IMAGE-MGC_LOAD
InterPro Dwarfin UniProtKB/Swiss-Prot
  MAD_homology1_Dwarfin-type UniProtKB/Swiss-Prot
  MAD_homology_MH1 UniProtKB/Swiss-Prot
  SMAD-like_dom_sf UniProtKB/Swiss-Prot
  SMAD_dom_Dwarfin-type UniProtKB/Swiss-Prot
  SMAD_FHA_dom_sf UniProtKB/Swiss-Prot
  SMAD_MH1_sf UniProtKB/Swiss-Prot
KEGG Report rno:25631 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72529 IMAGE-MGC_LOAD
NCBI Gene 25631 ENTREZGENE
PANTHER PTHR13703 UniProtKB/Swiss-Prot
Pfam MH1 UniProtKB/Swiss-Prot
  MH2 UniProtKB/Swiss-Prot
PhenoGen Smad3 PhenoGen
PROSITE MH1 UniProtKB/Swiss-Prot
  MH2 UniProtKB/Swiss-Prot
SMART DWA UniProtKB/Swiss-Prot
  DWB UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49879 UniProtKB/Swiss-Prot
  SSF56366 UniProtKB/Swiss-Prot
TIGR TC221903
UniProt P84025 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary O09064 UniProtKB/Swiss-Prot
  O09144 UniProtKB/Swiss-Prot
  O14510 UniProtKB/Swiss-Prot
  O35273 UniProtKB/Swiss-Prot
  Q92940 UniProtKB/Swiss-Prot
  Q93002 UniProtKB/Swiss-Prot
  Q9GKR4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Smad3  SMAD family member 3  Smad3  MAD homolog 3 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-11-17 Smad3  MAD homolog 3 (Drosophila)  Madh3    Symbol updated 1299863 APPROVED
2002-06-10 Madh3  MAD homolog 3 (Drosophila)      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization translocated to the nucleus 727374
gene_disease may be involved in pulmonary fibrosis 625421
gene_drugs bleomycin at a dose of 9U/kg body weight causes down regulation of mRNA 625421
gene_process an essential downstream intracellular target of the TGF-beta receptor signaling pathway 625421
gene_process plays an important role in osteoblastic bone formation 727387
gene_process involved in folliculogenesis 727374
gene_product member of the family of Smad proteins 625421
gene_regulation phosphorylated by activated TGF-beta type 1 receptor which induces the translocation of the protein from the cytoplasm to the nucleus 625421