Smad1 (SMAD family member 1) - Rat Genome Database

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Gene: Smad1 (SMAD family member 1) Rattus norvegicus
Analyze
Symbol: Smad1
Name: SMAD family member 1
RGD ID: 3030
Description: Predicted to enable several functions, including SMAD binding activity; enzyme binding activity; and nucleic acid binding activity. Involved in several processes, including BMP signaling pathway; negative regulation of muscle cell apoptotic process; and positive regulation of dendrite morphogenesis. Located in cytoplasm and nucleus. Used to study pulmonary hypertension. Biomarker of glomerulonephritis; male infertility; nephrotic syndrome; and pulmonary hypertension. Orthologous to human SMAD1 (SMAD family member 1); PARTICIPATES IN Bone morphogenetic proteins signaling pathway; the extracellular signal-regulated Raf/Mek/Erk signaling pathway; transforming growth factor-beta superfamily mediated signaling pathway; INTERACTS WITH 2,4-dinitrotoluene; 3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: MAD (mothers against decapentaplegic Drosophila) homolog 1; MAD (mothers against decapentaplegic, Drosophila) homolog 1; MAD homolog 1; MAD homolog 1 (Drosophila); MAD homolog1 (mothers against decapentaplegic Drosophila); MAD homolog1 (mothers against decapentaplegic, Drosophila); Madh1; mothers against decapentaplegic homolog 1; mothers against DPP homolog 1; SMAD 1; SMAD, mothers against DPP homolog 1; SMAD, mothers against DPP homolog 1 (Drosophila)
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
mRatBN7.21928,513,130 - 28,573,665 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1928,513,131 - 28,573,651 (+)Ensembl
Rnor_6.01932,182,942 - 32,248,694 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1932,188,267 - 32,248,684 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01943,079,695 - 43,145,300 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41930,348,886 - 30,409,345 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11930,353,711 - 30,414,170 (+)NCBI
Celera1928,023,055 - 28,083,575 (+)NCBICelera
Cytogenetic Map19q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroperoxycyclophosphamide  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-methoxypsoralen  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (EXP,ISO)
arsenic atom  (EXP,ISO)
arsenous acid  (ISO)
aucubin  (ISO)
azadirachtin A  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
caffeine  (ISO)
calciol  (ISO)
captan  (ISO)
carbon nanotube  (ISO)
casticin  (ISO)
chlordecone  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cytochalasin D  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dichlorine  (EXP)
diclofenac  (ISO)
divanadium pentaoxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
enzyme inhibitor  (ISO)
fluoxetine  (EXP)
folic acid  (ISO)
folpet  (ISO)
galangin  (ISO)
glycerol 2-phosphate  (ISO)
glyphosate  (ISO)
imperatorin  (ISO)
indometacin  (ISO)
isoprenaline  (ISO)
L-ascorbic acid  (ISO)
lead diacetate  (ISO)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
monocrotaline  (EXP)
N-nitrosodiethylamine  (EXP)
nickel dichloride  (ISO)
nicotine  (ISO)
nonanoic acid  (ISO)
oxaliplatin  (EXP)
ozone  (EXP)
paracetamol  (ISO)
paraquat  (ISO)
phenobarbital  (ISO)
picrotoxin  (EXP)
pirinixic acid  (EXP,ISO)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
propiconazole  (ISO)
resveratrol  (ISO)
Salidroside  (ISO)
SB 431542  (ISO)
simvastatin  (ISO)
sirtinol  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
Soman  (EXP)
streptozocin  (EXP)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
toluene 2,4-diisocyanate  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anatomical structure morphogenesis  (IBA)
BMP signaling pathway  (IBA,IEA,IMP,ISO,ISS)
bone development  (IEA,ISO)
cardiac muscle cell proliferation  (IEA,ISO)
cartilage development  (IEA,ISO)
cell differentiation  (IBA)
cellular response to BMP stimulus  (ISO)
cellular response to organic cyclic compound  (IEA,ISO)
embryonic pattern specification  (ISS)
gamete generation  (IEA,ISO)
hindbrain development  (IEA,ISO)
homeostatic process  (IEA,ISO)
inflammatory response  (IEA,ISO)
kidney development  (IEP)
MAPK cascade  (IEA,IMP,ISO)
mesodermal cell fate commitment  (IEA,ISO)
midbrain development  (IEA,ISO)
negative regulation of cell population proliferation  (IEA,ISO)
negative regulation of muscle cell apoptotic process  (IEP)
negative regulation of muscle cell differentiation  (IEA,ISO)
osteoblast differentiation  (ISO)
osteoblast fate commitment  (IEA,ISO)
positive regulation of cartilage development  (IEA,ISO)
positive regulation of cell differentiation  (IDA)
positive regulation of dendrite morphogenesis  (IEP)
positive regulation of gene expression  (IEA,ISO)
positive regulation of osteoblast differentiation  (IEA,ISO)
positive regulation of pri-miRNA transcription by RNA polymerase II  (IEA,ISO)
positive regulation of sprouting angiogenesis  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus  (IEA,ISO)
protein phosphorylation  (IEA,ISO)
regulation of transcription by RNA polymerase II  (ISO)
response to organonitrogen compound  (IEP)
response to xenobiotic stimulus  (IDA)
SMAD protein complex assembly  (IEA,ISO)
SMAD protein signal transduction  (IBA,IEA,ISO)
transforming growth factor beta receptor signaling pathway  (IBA,IEA)
ureteric bud development  (IEA,ISO)
wound healing  (IEP)

Cellular Component

References

References - curated
1. Angley C, etal., J Neurosci 2003 Jan 1;23(1):260-8.
2. Bucelli RC, etal., J Pharmacol Exp Ther. 2007 Dec 13;.
3. Chen Y, etal., Proc Natl Acad Sci U S A 1996 Nov 12;93(23):12992-7.
4. Fan J, etal., J Cell Physiol. 2006 May;207(2):499-505.
5. Fukada T, etal., PLoS One. 2008;3(11):e3642. doi: 10.1371/journal.pone.0003642. Epub 2008 Nov 5.
6. Fuller ML, etal., Ann Neurol. 2007 Sep;62(3):288-300.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. GOA data from the GO Consortium
9. Izumi M, etal., J Biol Chem. 2001 Aug 17;276(33):31133-41. Epub 2001 Jun 14.
10. Izumi M, etal., J Mol Cell Cardiol. 2006 Feb;40(2):224-33. Epub 2006 Jan 19.
11. Kim IJ, etal., J Neurosci. 2004 Mar 31;24(13):3304-12.
12. Li P, etal., Nephrology (Carlton). 2007 Oct;12(5):466-73.
13. Ma J, etal., Zhonghua Nan Ke Xue. 2005 Jan;11(1):17-21.
14. Maire M, etal., Endocrinology. 2005 Dec;146(12):5135-43. Epub 2005 Sep 15.
15. Masaki M, etal., Circulation. 2005 May 31;111(21):2752-9. Epub 2005 May 23.
16. Matsubara T, etal., Lab Invest. 2006 Apr;86(4):357-68.
17. MGD data from the GO Consortium
18. Morty RE, etal., Arterioscler Thromb Vasc Biol. 2007 May;27(5):1072-8. Epub 2007 Mar 8.
19. NCBI rat LocusLink and RefSeq merged data July 26, 2002
20. Okuyama N, etal., Brain Res. 2007 Feb 9;1132(1):36-41. Epub 2006 Dec 12.
21. OMIM Disease Annotation Pipeline
22. Oxburgh L and Robertson EJ, Mech Dev. 2002 Mar;112(1-2):207-11.
23. Paez-Pereda M, etal., Proc Natl Acad Sci U S A 2003 Feb 4;100(3):1034-9.
24. Pangas SA, etal., Mol Cell Biol. 2008 Jan;28(1):248-57. Epub 2007 Oct 29.
25. Pipeline to import KEGG annotations from KEGG into RGD
26. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
27. Ramos MF, etal., Toxicol Pathol. 2008 Feb;36(2):311-20. doi: 10.1177/0192623307311402. Epub 2008 Mar 26.
28. RGD automated data pipeline
29. RGD automated import pipeline for gene-chemical interactions
30. Shen H, etal., J Cell Physiol. 2007 Sep;212(3):764-70.
31. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
32. Takahashi H, etal., Am J Physiol Lung Cell Mol Physiol. 2006 Mar;290(3):L450-8. Epub 2005 Dec 16.
33. Takahashi T, etal., J Biol Chem. 2005 Feb 25;280(8):7100-6. Epub 2004 Dec 9.
34. Yew KH, etal., J Biol Chem. 2005 Sep 16;280(37):32209-17. Epub 2005 Jul 14.
35. Yu Y, etal., J Biomed Mater Res 2002 Jun 5;60(3):392-7.
36. Yue J, etal., J Cell Physiol 1999 Mar;178(3):387-96.
Additional References at PubMed
PMID:8653785   PMID:9111321   PMID:9389648   PMID:9436979   PMID:11160896   PMID:11779505   PMID:12151307   PMID:12270938   PMID:12647004   PMID:12874272   PMID:14633973   PMID:14656760  
PMID:15150273   PMID:15198985   PMID:15231748   PMID:15557274   PMID:15647271   PMID:15899870   PMID:16556916   PMID:16604073   PMID:16767106   PMID:16801560   PMID:17350578   PMID:17530186  
PMID:18184649   PMID:18285555   PMID:18548003   PMID:18622394   PMID:18692037   PMID:18776146   PMID:18842318   PMID:18997172   PMID:19103752   PMID:19224984   PMID:19251704   PMID:19252488  
PMID:19664780   PMID:19793887   PMID:19796622   PMID:19834880   PMID:20147459   PMID:20522807   PMID:20843790   PMID:20926379   PMID:21145505   PMID:21515935   PMID:21724602   PMID:21737358  
PMID:21804025   PMID:21986617   PMID:22051847   PMID:22500633   PMID:23169531   PMID:23610558   PMID:24042587   PMID:24047927   PMID:24211589   PMID:25010525   PMID:25100727   PMID:26352281  
PMID:26687945   PMID:27035233   PMID:27618520   PMID:28457943   PMID:28697500   PMID:29328402   PMID:30729278   PMID:30894415  


Genomics

Comparative Map Data
Smad1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21928,513,130 - 28,573,665 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1928,513,131 - 28,573,651 (+)Ensembl
Rnor_6.01932,182,942 - 32,248,694 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1932,188,267 - 32,248,684 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01943,079,695 - 43,145,300 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41930,348,886 - 30,409,345 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11930,353,711 - 30,414,170 (+)NCBI
Celera1928,023,055 - 28,083,575 (+)NCBICelera
Cytogenetic Map19q11NCBI
SMAD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl4145,481,194 - 145,559,176 (+)EnsemblGRCh38hg38GRCh38
GRCh384145,481,306 - 145,559,176 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh374146,402,458 - 146,480,328 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 364146,622,401 - 146,699,778 (+)NCBINCBI36hg18NCBI36
Build 344146,760,555 - 146,837,928NCBI
Celera4143,730,483 - 143,807,862 (+)NCBI
Cytogenetic Map4q31.21NCBI
HuRef4142,134,622 - 142,210,284 (+)NCBIHuRef
CHM1_14146,379,527 - 146,456,909 (+)NCBICHM1_1
Smad1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39880,065,024 - 80,126,057 (-)NCBIGRCm39mm39
GRCm39 Ensembl880,065,024 - 80,126,147 (-)Ensembl
GRCm38879,338,395 - 79,399,428 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl879,338,395 - 79,399,518 (-)EnsemblGRCm38mm10GRCm38
MGSCv37881,862,294 - 81,923,367 (-)NCBIGRCm37mm9NCBIm37
MGSCv36882,234,467 - 82,295,540 (-)NCBImm8
Celera883,615,361 - 83,676,406 (-)NCBICelera
Cytogenetic Map8C1NCBI
Smad1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554281,361,085 - 1,429,948 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554281,357,398 - 1,429,521 (+)NCBIChiLan1.0ChiLan1.0
SMAD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.14149,481,819 - 149,558,135 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4149,481,836 - 149,558,135 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v04137,822,269 - 137,899,700 (+)NCBIMhudiblu_PPA_v0panPan3
SMAD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11544,093,491 - 44,171,177 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1544,095,497 - 44,170,098 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1544,485,533 - 44,563,273 (+)NCBI
ROS_Cfam_1.01544,761,101 - 44,839,209 (+)NCBI
UMICH_Zoey_3.11544,034,585 - 44,112,489 (+)NCBI
UNSW_CanFamBas_1.01544,121,557 - 44,199,409 (+)NCBI
UU_Cfam_GSD_1.01544,386,546 - 44,464,496 (+)NCBI
Smad1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530146,145,177 - 46,219,936 (-)NCBI
SpeTri2.0NW_0049365353,582,512 - 3,626,312 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMAD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl882,908,527 - 82,968,994 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1882,907,557 - 82,987,909 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SMAD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1792,047,273 - 92,123,451 (+)NCBI
ChlSab1.1 Ensembl792,079,914 - 92,123,429 (+)Ensembl
Vero_WHO_p1.0NW_02366603771,693,446 - 71,769,726 (+)NCBI
Smad1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248534,415,816 - 4,503,317 (+)NCBI

Position Markers
Smad1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21928,539,696 - 28,540,047 (+)MAPPERmRatBN7.2
Rnor_6.01932,214,728 - 32,215,078NCBIRnor6.0
Rnor_5.01943,111,482 - 43,111,832UniSTSRnor5.0
RGSC_v3.41930,375,339 - 30,375,689UniSTSRGSC3.4
Celera1928,049,630 - 28,049,980UniSTS
Cytogenetic Map19q11UniSTS
RH138429  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21928,573,037 - 28,573,176 (+)MAPPERmRatBN7.2
Rnor_6.01932,248,067 - 32,248,205NCBIRnor6.0
Rnor_5.01943,144,673 - 43,144,811UniSTSRnor5.0
RGSC_v3.41930,408,731 - 30,408,869UniSTSRGSC3.4
Celera1928,082,961 - 28,083,099UniSTS
RH 3.4 Map31328.1UniSTS
Cytogenetic Map19q11UniSTS
RH130435  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21928,573,220 - 28,573,440 (+)MAPPERmRatBN7.2
Rnor_6.01932,248,250 - 32,248,469NCBIRnor6.0
Rnor_5.01943,144,856 - 43,145,075UniSTSRnor5.0
RGSC_v3.41930,408,914 - 30,409,133UniSTSRGSC3.4
Celera1928,083,144 - 28,083,363UniSTS
RH 3.4 Map19184.5UniSTS
Cytogenetic Map19q11UniSTS
RH94757  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21928,539,521 - 28,539,681 (+)MAPPERmRatBN7.2
Rnor_6.01932,214,553 - 32,214,712NCBIRnor6.0
Rnor_5.01943,111,307 - 43,111,466UniSTSRnor5.0
RGSC_v3.41930,375,164 - 30,375,323UniSTSRGSC3.4
Celera1928,049,455 - 28,049,614UniSTS
Cytogenetic Map19q11UniSTS
RH142930  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21928,569,488 - 28,569,719 (+)MAPPERmRatBN7.2
Rnor_6.01932,244,518 - 32,244,748NCBIRnor6.0
Rnor_5.01943,141,124 - 43,141,354UniSTSRnor5.0
RGSC_v3.41930,405,182 - 30,405,412UniSTSRGSC3.4
Celera1928,079,412 - 28,079,642UniSTS
RH 3.4 Map19212.5UniSTS
Cytogenetic Map19q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)191392640130303727Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)191511459834521833Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
61328Eae8Experimental allergic encephalomyelitis QTL 84nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)192481604133061905Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192481797839654489Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)192753020737947399Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)192753020737947399Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)192753020737947399Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:609
Count of miRNA genes:269
Interacting mature miRNAs:327
Transcripts:ENSRNOT00000025079
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 35 39 26 17 26 2 2 74 32 34 11 2
Low 8 18 15 2 15 6 9 3 7 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000025079   ⟹   ENSRNOP00000025079
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1928,513,131 - 28,573,651 (+)Ensembl
Rnor_6.0 Ensembl1932,188,267 - 32,248,684 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104934   ⟹   ENSRNOP00000083295
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1928,513,131 - 28,573,651 (+)Ensembl
RefSeq Acc Id: NM_013130   ⟹   NP_037262
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21928,513,240 - 28,573,652 (+)NCBI
Rnor_6.01932,188,275 - 32,248,681 (+)NCBI
Rnor_5.01943,079,695 - 43,145,300 (+)NCBI
RGSC_v3.41930,348,886 - 30,409,345 (+)RGD
Celera1928,023,055 - 28,083,575 (+)RGD
Sequence:
RefSeq Acc Id: XM_006255394   ⟹   XP_006255456
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21928,513,131 - 28,573,665 (+)NCBI
Rnor_6.01932,188,174 - 32,248,694 (+)NCBI
Rnor_5.01943,079,695 - 43,145,300 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006255395   ⟹   XP_006255457
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21928,536,679 - 28,573,665 (+)NCBI
Rnor_6.01932,208,202 - 32,248,694 (+)NCBI
Rnor_5.01943,079,695 - 43,145,300 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006255397   ⟹   XP_006255459
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21928,513,221 - 28,573,658 (+)NCBI
Rnor_6.01932,188,174 - 32,248,694 (+)NCBI
Rnor_5.01943,079,695 - 43,145,300 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039097521   ⟹   XP_038953449
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21928,513,130 - 28,573,665 (+)NCBI
RefSeq Acc Id: XM_039097522   ⟹   XP_038953450
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21928,513,488 - 28,573,665 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_037262   ⟸   NM_013130
- Sequence:
RefSeq Acc Id: XP_006255456   ⟸   XM_006255394
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006255459   ⟸   XM_006255397
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006255457   ⟸   XM_006255395
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000025079   ⟸   ENSRNOT00000025079
RefSeq Acc Id: XP_038953449   ⟸   XM_039097521
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038953450   ⟸   XM_039097522
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000083295   ⟸   ENSRNOT00000104934
Protein Domains
MH1   MH2

Transcriptome

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

Promoters
RGD ID:13701052
Promoter ID:EPDNEW_R11575
Type:multiple initiation site
Name:Smad1_1
Description:SMAD family member 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01932,188,256 - 32,188,316EPDNEW

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)
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
M520/NRrrcMcwi (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
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3030 AgrOrtholog
Ensembl Genes ENSRNOG00000018483 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000025079 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025079 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.200.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.90.520.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5599977 IMAGE-MGC_LOAD
InterPro Dwarfin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MAD_homology1_Dwarfin-type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MAD_homology_MH1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMAD-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMAD_dom_Dwarfin-type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMAD_FHA_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMAD_MH1_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25671 UniProtKB/TrEMBL
MGC_CLONE MGC:72530 IMAGE-MGC_LOAD
NCBI Gene 25671 ENTREZGENE
PANTHER PTHR13703 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam MH1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Smad1 PhenoGen
PROSITE MH1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART DWA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DWB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49879 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56366 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JSQ6_RAT UniProtKB/TrEMBL
  P97588 ENTREZGENE
  Q6P7A6_RAT UniProtKB/TrEMBL
  SMAD1_RAT UniProtKB/Swiss-Prot
UniProt Secondary O70520 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Smad1  SMAD family member 1  Smad1  MAD homolog 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-11-17 Smad1  MAD homolog 1 (Drosophila)      Name updated 1299863 APPROVED
2005-01-20 Smad1  SMAD, mothers against DPP homolog 1 (Drosophila)  Madh1  MAD homolog 1 (Drosophila)  Symbol and Name updated 1299863 APPROVED
2002-06-10 Madh1  MAD homolog 1 (Drosophila)      Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to the cytoplasm and translocated to nucleus after activation by BMP4 631793
gene_process involved in regulating postnatal cerebellar differentiation 631793