Socs3 (suppressor of cytokine signaling 3) - Rat Genome Database

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Gene: Socs3 (suppressor of cytokine signaling 3) Rattus norvegicus
Analyze
Symbol: Socs3
Name: suppressor of cytokine signaling 3
RGD ID: 621087
Description: Predicted to have 1-phosphatidylinositol-3-kinase regulator activity and phosphotyrosine residue binding activity. Involved in several processes, including receptor signaling pathway via JAK-STAT; response to estradiol; and response to steroid hormone. Localizes to cytoplasm. Biomarker of obesity; status epilepticus; and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in atopic dermatitis 4. Orthologous to human SOCS3 (suppressor of cytokine signaling 3); PARTICIPATES IN erythropoietin signaling pathway; insulin signaling pathway; interleukin-2 signaling pathway; INTERACTS WITH (S)-nicotine; 1-naphthyl isothiocyanate; 15-deoxy-Delta(12,14)-prostaglandin J2.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Cish3; cytokine inducible SH2-containing protein 3; cytokine-inducible SH2 protein 3; Socs-3; Ssi-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
mRatBN7.210103,193,909 - 103,197,322 (-)NCBI
Rnor_6.0 Ensembl10106,975,178 - 106,976,040 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.010106,973,863 - 106,976,969 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.010106,611,459 - 106,616,694 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410107,958,468 - 107,959,330 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.110107,972,971 - 107,973,834 (-)NCBI
Celera10101,756,900 - 101,757,762 (-)NCBICelera
Cytogenetic Map10q32.2NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
(S)-naringenin  (ISO)
(S)-nicotine  (EXP)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
15-deoxy-Delta(12,14)-prostaglandin J2  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-butoxyethanol  (ISO)
2-hydroxypropanoic acid  (ISO)
3',5'-cyclic AMP  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-methylcholanthrene  (EXP,ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-azacytidine  (ISO)
8-Br-cAMP  (ISO)
AACOCF3  (ISO)
acrylamide  (EXP,ISO)
actinomycin D  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
ammonium hexachloroplatinate  (ISO)
antirheumatic drug  (ISO)
apigenin  (ISO)
arachidonic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atropine  (ISO)
avobenzone  (ISO)
belinostat  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A5  (ISO)
bortezomib  (ISO)
cannabidiol  (ISO)
captan  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
cefaloridine  (EXP)
CGS-21680  (EXP)
chloroethene  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (ISO)
colforsin daropate hydrochloride  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cycloheximide  (ISO)
cyproconazole  (ISO)
D-glucose  (ISO)
delta-tocotrienol  (ISO)
deoxynivalenol  (ISO)
dibutyl phthalate  (ISO)
diclofenac  (ISO)
diethyl maleate  (ISO)
dimercaprol  (ISO)
dioxygen  (EXP,ISO)
divanadium pentaoxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
doxycycline  (ISO)
entinostat  (ISO)
erlotinib hydrochloride  (EXP)
estriol  (ISO)
ethanol  (EXP)
fenofibrate  (EXP)
fenthion  (ISO)
flavone  (ISO)
fluoranthene  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fructose  (EXP)
fulvestrant  (ISO)
gemfibrozil  (ISO)
genistein  (ISO)
ginsenoside Re  (ISO)
glucose  (ISO)
GW 3965  (EXP)
hexachlorobenzene  (EXP)
hexaconazole  (ISO)
hexadecanoic acid  (ISO)
hexamethylene diisocyanate  (ISO)
hydrogen peroxide  (ISO)
ibuprofen  (ISO)
isoeugenol  (ISO)
isoflavones  (ISO)
isoprenaline  (ISO)
ketamine  (ISO)
KT 5720  (ISO)
L-methionine  (ISO)
lipopolysaccharide  (ISO)
LY294002  (ISO)
malathion  (ISO)
methamphetamine  (EXP)
methotrexate  (ISO)
methoxychlor  (EXP)
methylisothiazolinone  (ISO)
methylmercury chloride  (EXP,ISO)
monosodium L-glutamate  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-methyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosomorpholine  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
nicotine  (EXP)
nitrobenzenes  (EXP)
oleic acid  (ISO)
oxaliplatin  (EXP)
ozone  (EXP,ISO)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (EXP,ISO)
poly(I:C)  (ISO)
pravastatin  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (EXP,ISO)
propiconazole  (ISO)
prostaglandin F2alpha  (EXP)
protein kinase inhibitor  (ISO)
quercetin  (EXP,ISO)
rac-lactic acid  (ISO)
resveratrol  (EXP,ISO)
rifampicin  (ISO)
rimonabant  (EXP)
rofecoxib  (ISO)
rolipram  (ISO)
rutin  (EXP)
Salinomycin  (ISO)
SB 431542  (ISO)
selumetinib  (ISO)
silicon dioxide  (EXP,ISO)
simvastatin  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
Soman  (EXP,ISO)
stattic  (ISO)
streptozocin  (EXP)
succimer  (ISO)
sulpiride  (EXP)
sunitinib  (ISO)
tamoxifen  (ISO)
terbufos  (ISO)
testosterone  (EXP,ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
tofacitinib  (ISO)
topotecan  (EXP)
trans-isoeugenol  (ISO)
tremolite asbestos  (ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
tropan-3alpha-yl 3-hydroxy-2-phenylpropanoate  (ISO)
trovafloxacin  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
vorinostat  (ISO)
wortmannin  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aging  (IEP)
animal organ regeneration  (IEP)
branching involved in labyrinthine layer morphogenesis  (IEA,ISO)
cellular response to leukemia inhibitory factor  (IEA,ISO)
intracellular signal transduction  (IDA,IEA)
negative regulation of apoptotic process  (IEA)
negative regulation of inflammatory response  (IEA,ISO)
negative regulation of insulin receptor signaling pathway  (IEA,ISO)
negative regulation of receptor signaling pathway via JAK-STAT  (ISO)
negative regulation of signal transduction  (ISO)
negative regulation of tyrosine phosphorylation of STAT protein  (IEA,ISO)
phosphatidylinositol phosphate biosynthetic process  (IBA)
placenta blood vessel development  (IEA,ISO)
positive regulation of cell differentiation  (IEA,ISO)
protein ubiquitination  (IEA)
receptor signaling pathway via JAK-STAT  (IDA,IEA,TAS)
regulation of cell differentiation  (ISO)
regulation of cell growth  (TAS)
regulation of growth  (IEA)
regulation of phosphatidylinositol 3-kinase activity  (IEA)
regulation of protein phosphorylation  (ISO)
response to bacterium  (IEP)
response to cytokine  (IEP)
response to drug  (IEP)
response to estradiol  (IEP)
response to food  (IEP)
response to gamma radiation  (IEP)
response to glucocorticoid  (IEP)
response to heat  (IEP)
response to hormone  (IEP)
response to hypoxia  (IEP)
response to insulin  (IEP)
response to lipopolysaccharide  (IEP)
response to organic cyclic compound  (IEP)
response to peptide hormone  (IEP)
response to progesterone  (IEP)
signal transduction  (IDA,TAS)
spongiotrophoblast differentiation  (IEA,ISO)
trophoblast giant cell differentiation  (IEA,ISO)

Cellular Component

Molecular Function

References

References - curated
1. Bai L, etal., Respir Physiol Neurobiol. 2006 May;152(1):83-91. Epub 2005 Aug 24.
2. Calegari VC, etal., Endocrinology 2003 Oct;144(10):4586-96. Epub 2003 Jun 26.
3. Cha B, etal., Ann N Y Acad Sci. 2007 Jan;1096:24-8.
4. Curlewis JD, etal., Endocrinology 2002 Oct;143(10):3984-93.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. GOA data from the GO Consortium
7. Gremy O, etal., World J Gastroenterol. 2006 Aug 21;12(31):4996-5004.
8. Hong-Brown LQ, etal., Am J Physiol Endocrinol Metab. 2003 Jul;285(1):E63-72. Epub 2003 Mar 18.
9. Howard JK and Flier JS, Trends Endocrinol Metab. 2006 Nov;17(9):365-71. Epub 2006 Sep 28.
10. Jeschke MG, etal., Endocrinology. 2004 Sep;145(9):4084-93. Epub 2004 Jun 10.
11. Johnson TS, etal., J Endocrinol 2001 May;169(2):409-15.
12. Kisseleva T, etal., Gene 2002 Feb 20;285(1-2):1-24.
13. Kong F, etal., Shock 2002 Oct;18(4):374-9.
14. Kong SE, etal., Am J Physiol Endocrinol Metab 2002 Oct;283(4):E692-701.
15. Linard C, etal., Int J Radiat Oncol Biol Phys. 2004 Feb 1;58(2):427-34.
16. Liu X, etal., Diabetes. 2008 Jun;57(6):1651-8. Epub 2008 Mar 20.
17. Liu Y, etal., J Immunol. 2008 May 1;180(9):6270-8.
18. Ma C, etal., Pharm Biol. 2017 Dec;55(1):2170-2177. doi: 10.1080/13880209.2017.1396350.
19. MGD data from the GO Consortium
20. Morales O, etal., J Biol Chem 2002 Sep 20;277(38):34879-84.
21. Mori H, etal., Biochem Biophys Res Commun. 2007 Aug 10;359(4):952-8. Epub 2007 Jun 4.
22. Nakagawa T, etal., Oncol Rep. 2008 Jan;19(1):33-9.
23. NCBI rat LocusLink and RefSeq merged data July 26, 2002
24. Nicol AF, etal., Exp Mol Pathol. 2006 Aug;81(1):42-7.
25. O'Connor JC, etal., J Immunol. 2007 Jun 1;178(11):6886-93.
26. Park EJ, etal., J Biol Chem 2003 Apr 25;278(17):14747-52. Epub 2003 Feb 12.
27. Paul C, etal., Eur J Biochem. 2000 Oct;267(19):5849-57.
28. Peiser C, etal., Life Sci. 2000 Nov 3;67(24):2971-81.
29. Peralta S, etal., Biochem Biophys Res Commun 2002 Aug 16;296(2):425-8.
30. Peralta S, etal., Biochem Biophys Res Commun 2002 Aug 16;296(2):425.
31. Pipeline to import KEGG annotations from KEGG into RGD
32. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
33. Raccurt M, etal., Br J Cancer. 2003 Aug 4;89(3):524-32.
34. Raghavendra Rao VL, etal., J Neurochem 2002 Dec;83(5):1072-86.
35. RGD automated data pipeline
36. RGD automated import pipeline for gene-chemical interactions
37. Rieusset J, etal., Diabetes. 2004 Sep;53(9):2232-41.
38. Rosell DR, etal., Neuroscience. 2003;122(2):349-58.
39. Sakuda S, etal., J Hepatol. 2002 Mar;36(3):378-84.
40. Seron K, etal., Biochem Biophys Res Commun. 2006 Oct 6;348(4):1232-8. Epub 2006 Jul 24.
41. Shou J, etal., Arthritis Res Ther. 2006;8(1):R28. Epub 2006 Jan 10.
42. Steyn FJ, etal., Endocrinology. 2008 Jun;149(6):3206-14. Epub 2008 Mar 6.
43. Theiss AL, etal., Gastroenterology. 2005 Jul;129(1):204-19.
44. Torisu T, etal., Genes Cells. 2007 Feb;12(2):143-54.
45. Tureyen K, etal., J Neurochem. 2007 Apr;101(1):41-56.
46. Ueki K, etal., Mol Cell Biol. 2004 Jun;24(12):5434-46.
47. Ueki K, etal., Proc Natl Acad Sci U S A. 2004 Jul 13;101(28):10422-7. Epub 2004 Jul 6.
48. Wang Z, etal., Biochem Biophys Res Commun. 2000 Oct 14;277(1):20-6.
49. Worschech A, etal., Cancer Res. 2008 Apr 1;68(7):2436-46.
Additional References at PubMed
PMID:10579313   PMID:11108838   PMID:11481489   PMID:15118263   PMID:15358627   PMID:15514089   PMID:15578154   PMID:15893771   PMID:15998644   PMID:16185683   PMID:16258063   PMID:16289836  
PMID:16300827   PMID:16302975   PMID:16306356   PMID:16484300   PMID:16956890   PMID:16971535   PMID:17223256   PMID:17986523   PMID:18421861   PMID:18586073   PMID:19080716   PMID:19176113  
PMID:19272793   PMID:19293294   PMID:19386987   PMID:19408656   PMID:19639229   PMID:19643162   PMID:19693688   PMID:19862646   PMID:20185635   PMID:20193756   PMID:20303731   PMID:20439489  
PMID:20530874   PMID:20816823   PMID:20819948   PMID:20848345   PMID:21145973   PMID:21168220   PMID:21255014   PMID:21364493   PMID:21521717   PMID:21545521   PMID:22253420   PMID:22982470  
PMID:23007031   PMID:23222907   PMID:23401297   PMID:23669042   PMID:23948778   PMID:24078776   PMID:24088176   PMID:24091940   PMID:24142708   PMID:24463741   PMID:24660535   PMID:24685947  
PMID:24959867   PMID:25019494   PMID:25086044   PMID:25352752   PMID:25847945   PMID:26384335   PMID:27118613   PMID:28036111   PMID:28111888   PMID:28129651   PMID:28326931   PMID:29550470  
PMID:30763670   PMID:31799684   PMID:31857078   PMID:32030968   PMID:32438059   PMID:32630102   PMID:33255404   PMID:33300076  


Genomics

Candidate Gene Status
Socs3 is a candidate Gene for QTL Slep8
Socs3 is a candidate Gene for QTL Insul15
Comparative Map Data
Socs3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.210103,193,909 - 103,197,322 (-)NCBI
Rnor_6.0 Ensembl10106,975,178 - 106,976,040 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.010106,973,863 - 106,976,969 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.010106,611,459 - 106,616,694 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410107,958,468 - 107,959,330 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.110107,972,971 - 107,973,834 (-)NCBI
Celera10101,756,900 - 101,757,762 (-)NCBICelera
Cytogenetic Map10q32.2NCBI
SOCS3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1778,356,778 - 78,360,077 (-)EnsemblGRCh38hg38GRCh38
GRCh381778,356,778 - 78,360,925 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371776,352,859 - 76,357,006 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361773,864,454 - 73,867,753 (-)NCBINCBI36hg18NCBI36
Build 341773,864,458 - 73,867,753NCBI
Celera1772,946,889 - 72,950,188 (-)NCBI
Cytogenetic Map17q25.3NCBI
HuRef1771,775,516 - 71,778,779 (-)NCBIHuRef
CHM1_11776,416,767 - 76,420,069 (-)NCBICHM1_1
Socs3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911117,856,905 - 117,860,192 (-)NCBIGRCm39mm39
GRCm39 Ensembl11117,856,905 - 117,860,873 (-)Ensembl
GRCm3811117,966,079 - 117,970,336 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11117,966,079 - 117,970,047 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711117,827,393 - 117,830,680 (-)NCBIGRCm37mm9NCBIm37
MGSCv3611117,782,169 - 117,785,252 (-)NCBImm8
Celera11129,709,800 - 129,713,087 (-)NCBICelera
Cytogenetic Map11E2NCBI
Socs3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555064,222,455 - 4,225,563 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555064,222,455 - 4,225,563 (+)NCBIChiLan1.0ChiLan1.0
SOCS3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11777,981,752 - 77,985,059 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1777,983,389 - 77,984,066 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01772,433,206 - 72,436,500 (-)NCBIMhudiblu_PPA_v0panPan3
SOCS3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.192,859,267 - 2,859,944 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha93,516,096 - 3,516,773 (+)NCBI
ROS_Cfam_1.093,509,383 - 3,512,579 (+)NCBI
UMICH_Zoey_3.193,533,406 - 3,534,083 (+)NCBI
UNSW_CanFamBas_1.093,657,845 - 3,658,522 (+)NCBI
UU_Cfam_GSD_1.093,738,946 - 3,739,623 (+)NCBI
Socs3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244056023,476,572 - 3,479,692 (+)NCBI
SpeTri2.0NW_0049365942,932,297 - 2,935,358 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SOCS3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl123,643,929 - 3,647,012 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1123,643,832 - 3,647,015 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Pig Cytomap12p15NCBI
SOCS3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11670,353,099 - 70,356,401 (-)NCBI
ChlSab1.1 Ensembl1670,354,746 - 70,355,423 (-)Ensembl
Vero_WHO_p1.0NW_02366607741,479,311 - 41,482,614 (-)NCBI
Socs3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248017,841,230 - 7,843,912 (-)NCBI

Position Markers
PMC148819P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210103,195,568 - 103,196,081 (+)MAPPER
Rnor_6.010106,975,511 - 106,976,023NCBIRnor6.0
Rnor_5.010106,613,107 - 106,613,619UniSTSRnor5.0
RGSC_v3.410107,958,801 - 107,959,313UniSTSRGSC3.4
Celera10101,757,233 - 101,757,745UniSTS
Cytogenetic Map10q32.3UniSTS
PMC148819P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210103,195,944 - 103,196,081 (+)MAPPER
Rnor_6.010106,975,887 - 106,976,023NCBIRnor6.0
Rnor_5.010106,613,483 - 106,613,619UniSTSRnor5.0
RGSC_v3.410107,959,177 - 107,959,313UniSTSRGSC3.4
Celera10101,757,609 - 101,757,745UniSTS
Cytogenetic Map10q32.3UniSTS
PMC22025P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.010106,976,490 - 106,977,356NCBIRnor6.0
Rnor_5.010106,614,086 - 106,614,754UniSTSRnor5.0
RGSC_v3.410107,959,780 - 107,960,863UniSTSRGSC3.4
Celera10101,758,212 - 101,759,056UniSTS
Cytogenetic Map10q32.3UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109841807108540162Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014827894107857673Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014827894110992275Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1023861015112626471Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1043289657108540162Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1053621375112626471Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1053621375112626471Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1055678976112626471Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1062096293107096293Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1065590122110590122Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1065992275110992275Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1065992275110992275Rat
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1067880046112626471Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1067988218110992091Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1069385595112626471Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1069385595112626471Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1070166960112626471Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1070800069112626471Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1071692298112626471Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1073008136112626471Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1073008136112626471Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1073008136112626471Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1073467158112626471Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1075544754112626471Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1075544754112626471Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1078970279112626471Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1079927661112626471Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1080239190112626471Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1085079943112626471Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1086566908112626471Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1088544136107545372Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1090041957112626471Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1090296897112626471Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1091689348112626471Rat
1579915Bp280Blood pressure QTL 2800.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1093662786112626471Rat
12880395Cm109Cardiac mass QTL 1090.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1093662786112626471Rat
12880396Am13Aortic mass QTL 130.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1093662786112626471Rat
12880398Kidm67Kidney mass QTL 670.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1093662786112626471Rat
12880384Cm107Cardiac mass QTL 1070.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)93662786112626471Rat
12880385Cm108Cardiac mass QTL 1080.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)93662786112626471Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1093886117110992275Rat
724530Bp149Blood pressure QTL 1490.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1093886117112626471Rat
1558652Bw57Body weight QTL 574.20.0008body mass (VT:0001259)body weight (CMO:0000012)1094170766112626471Rat
61436Cia5Collagen induced arthritis QTL 54.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1094486204107857673Rat
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1096520816110992275Rat
2292436Bp310Blood pressure QTL 310arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1098079221112626471Rat
10450493Bp382Blood pressure QTL 3820.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1098079221112626471Rat
1576307Cia28Collagen induced arthritis QTL 28joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1099492217107857673Rat
1576313Pia25Pristane induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1099492217107857673Rat
1578663Bss18Bone structure and strength QTL 183.6femur width (VT:1000666)femoral neck width (CMO:0001695)10100155035110992275Rat
1578672Bmd16Bone mineral density QTL 166.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)10100155035110992275Rat
631539Oia6Oil induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10100460820108540162Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:103
Count of miRNA genes:84
Interacting mature miRNAs:91
Transcripts:ENSRNOT00000003940
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 9 1 18 1 6 1 10 11
Low 1 43 48 40 1 40 8 11 68 34 30 8
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003940   ⟹   ENSRNOP00000003940
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl10106,975,178 - 106,976,040 (-)Ensembl
RefSeq Acc Id: NM_053565   ⟹   NP_446017
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210103,195,236 - 103,196,098 (-)NCBI
Rnor_6.010106,975,178 - 106,976,040 (-)NCBI
Rnor_5.010106,611,459 - 106,616,694 (-)NCBI
RGSC_v3.410107,958,468 - 107,959,330 (-)RGD
Celera10101,756,900 - 101,757,762 (-)RGD
Sequence:
RefSeq Acc Id: XM_008768398   ⟹   XP_008766620
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210103,193,909 - 103,197,322 (-)NCBI
Rnor_6.010106,973,863 - 106,976,969 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_446017 (Get FASTA)   NCBI Sequence Viewer  
  XP_008766620 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC26223 (Get FASTA)   NCBI Sequence Viewer  
  CAB56083 (Get FASTA)   NCBI Sequence Viewer  
  EDM06745 (Get FASTA)   NCBI Sequence Viewer  
  O88583 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446017   ⟸   NM_053565
- UniProtKB: O88583 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008766620   ⟸   XM_008768398
- Peptide Label: isoform X1
- UniProtKB: G3V6D2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003940   ⟸   ENSRNOT00000003940
Protein Domains
SH2   SOCS box

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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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)
ACI/EurMcwi (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
ACI/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
BBDP/Wor (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
BN/SsN (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
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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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
F344/NRrrc (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
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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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
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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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)
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:621087 AgrOrtholog
Ensembl Genes ENSRNOG00000002946 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003940 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003940 ENTREZGENE, UniProtKB/TrEMBL
InterPro SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH2_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOCS3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOCS3_SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOCS_box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOCS_box-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:89829 UniProtKB/Swiss-Prot
NCBI Gene 89829 ENTREZGENE
PANTHER PTHR10155:SF11 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Socs3 PhenoGen
PROSITE SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOCS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOCS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOCS_box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF158235 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF55550 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V6D2 ENTREZGENE, UniProtKB/TrEMBL
  O88583 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q9QYV5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Socs3  suppressor of cytokine signaling 3  Cish3  cytokine inducible SH2-containing protein 3  Symbol and Name updated 1299863 APPROVED
2002-08-07 Cish3  cytokine inducible SH2-containing protein 3      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expression increases in the hypothalamus with aging 625538
gene_expression expressed in mammary galnd with increases during the initial stages of mammary gland involution caused by pup withdrawal 625667
gene_process inhibits JAK activity and may mediate hypothalamic leptin resistance in aged Wistar rats. 625538
gene_process may play a role in the initiation of luteolysis via rapid suppression of luteotropic support from placental lactogen (PL) 625667
gene_product member of the suppressor-of-cytokine-signaling family 625538
gene_regulation transcription is induced by 15-deoxy-Delta12,14-prostaglandin J(2) and rosiglitazone 632385
gene_regulation cloprostenol, a PGF2 analog, rapidly increases mRNA level and is also strongly induced by STAT3 625667