Socs1 (suppressor of cytokine signaling 1) - Rat Genome Database

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Gene: Socs1 (suppressor of cytokine signaling 1) Rattus norvegicus
Analyze
Symbol: Socs1
Name: suppressor of cytokine signaling 1
RGD ID: 69272
Description: Predicted to enable insulin-like growth factor receptor binding activity; kinase regulator activity; and protein kinase binding activity. Involved in several processes, including response to estradiol; response to lipopolysaccharide; and response to progesterone. Acts upstream of or within cellular response to cytokine stimulus and cellular response to organic cyclic compound. Predicted to be located in cytoplasmic ribonucleoprotein granule and nucleoplasm. Predicted to be part of phosphatidylinositol 3-kinase complex. Biomarker of myocardial infarction and obesity. Human ortholog(s) of this gene implicated in ovarian carcinoma; prostate cancer; and urinary bladder cancer. Orthologous to human SOCS1 (suppressor of cytokine signaling 1); PARTICIPATES IN insulin signaling pathway; interleukin-12 signaling pathway; interleukin-2 signaling pathway; INTERACTS WITH 15-deoxy-Delta(12,14)-prostaglandin J2; 17beta-estradiol; 2,2',5,5'-tetrachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Cish1; cytokine inducible SH2-containing protein 1; Socs-1
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
mRatBN7.2104,882,651 - 4,884,342 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl104,882,560 - 4,884,383 (+)Ensembl
Rnor_6.0104,956,795 - 4,958,472 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl104,957,326 - 4,958,461 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0103,782,936 - 3,783,574 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4104,819,971 - 4,820,609 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1104,819,970 - 4,820,609 (+)NCBI
Celera103,904,246 - 3,905,811 (+)NCBICelera
Cytogenetic Map10q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
15-deoxy-Delta(12,14)-prostaglandin J2  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-acetamidofluorene  (EXP)
2-hydroxypropanoic acid  (ISO)
4-hydroxy-TEMPO  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
9-cis-retinoic acid  (ISO)
acetamide  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antigen  (ISO)
aripiprazole  (ISO)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP)
bleomycin A2  (ISO)
buta-1,3-diene  (ISO)
butanal  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
choline  (ISO)
cisplatin  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
cycloheximide  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
diethylstilbestrol  (ISO)
divanadium pentaoxide  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
fenvalerate  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
hexadecanoic acid  (ISO)
isotretinoin  (ISO)
L-methionine  (ISO)
lead nitrate  (ISO)
Licochalcone B  (ISO)
lipopolysaccharide  (ISO)
lomustine  (ISO)
manganese(II) chloride  (EXP)
muramyl dipeptide  (ISO)
nickel atom  (ISO)
ochratoxin A  (ISO)
oleic acid  (ISO)
ozone  (ISO)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
pentanal  (ISO)
phosphane  (EXP)
poly(I:C)  (ISO)
progesterone  (EXP,ISO)
propanal  (ISO)
prostaglandin F2alpha  (EXP)
protein kinase inhibitor  (ISO)
pyridaben  (ISO)
rac-lactic acid  (ISO)
reactive oxygen species  (ISO)
resveratrol  (ISO)
rimonabant  (EXP)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sulpiride  (EXP)
T-2 toxin  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
titanium dioxide  (ISO)
torcetrapib  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
Triptolide  (EXP)
urethane  (ISO)
valproic acid  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
animal organ regeneration  (IEP)
cellular response to amino acid stimulus  (IEA,ISO)
cellular response to cytokine stimulus  (IDA)
cellular response to interferon-gamma  (IEP)
cellular response to lipopolysaccharide  (IEP)
cellular response to organic cyclic compound  (IDA)
cellular response to thyrotropin-releasing hormone  (IEP)
cellular response to vascular endothelial growth factor stimulus  (IEP)
cytokine-mediated signaling pathway  (IEA,ISO)
fat cell differentiation  (IEA,ISO)
intracellular signal transduction  (IEA)
negative regulation of catalytic activity  (IEA)
negative regulation of CD8-positive, alpha-beta T cell differentiation  (IEA,ISO,ISS)
negative regulation of hepatic stellate cell proliferation  (IMP)
negative regulation of insulin receptor signaling pathway  (IEA,ISO)
negative regulation of receptor signaling pathway via JAK-STAT  (ISO)
negative regulation of tyrosine phosphorylation of STAT protein  (IEA,ISO)
phosphatidylinositol phosphate biosynthetic process  (IBA)
positive regulation of CD4-positive, alpha-beta T cell differentiation  (IEA,ISO,ISS)
positive regulation of fibroblast apoptotic process  (IMP)
positive regulation of regulatory T cell differentiation  (IEA,ISO)
protein ubiquitination  (IEA)
receptor signaling pathway via JAK-STAT  (IEA,ISO)
regulation of activation of Janus kinase activity  (IEA,ISO)
regulation of cytokine production  (IEA,ISO)
regulation of growth  (IEA)
regulation of interferon-gamma-mediated signaling pathway  (IEA)
regulation of phosphatidylinositol 3-kinase activity  (IEA)
regulation of protein phosphorylation  (ISO)
regulation of receptor signaling pathway via JAK-STAT  (ISO)
regulation of tyrosine phosphorylation of STAT protein  (ISO)
response to cytokine  (IEP)
response to erythropoietin  (IEP)
response to estradiol  (IEP)
response to lipopolysaccharide  (IEP)
response to peptide hormone  (IEP)
response to progesterone  (IEP)
response to xenobiotic stimulus  (IEP)

Cellular Component

Molecular Function

References

References - curated
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6. Cheng MX, etal., Transpl Immunol. 2019 Jun;54:59-64. doi: 10.1016/j.trim.2019.02.004. Epub 2019 Feb 13.
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10. Friedrich MG, etal., Urologe A. 2007 Jul;46(7):761-8.
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13. Hanada T, etal., Immunity. 2003 Sep;19(3):437-50. doi: 10.1016/s1074-7613(03)00240-1.
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15. Hashimoto M, etal., Cancer Sci. 2009 Apr;100(4):730-6. doi: 10.1111/j.1349-7006.2009.01098.x.
16. Hong-Brown LQ, etal., Am J Physiol Endocrinol Metab. 2003 Jul;285(1):E63-72. Epub 2003 Mar 18.
17. Howard JK and Flier JS, Trends Endocrinol Metab. 2006 Nov;17(9):365-71. Epub 2006 Sep 28.
18. Hussain S, etal., J Recept Signal Transduct Res. 2011 Apr;31(2):147-56. doi: 10.3109/10799893.2011.553836.
19. Jiang S, etal., Cancer Res. 2010 Apr 15;70(8):3119-27. doi: 10.1158/0008-5472.CAN-09-4250. Epub 2010 Mar 30.
20. Johnson TS, etal., J Endocrinol 2001 May;169(2):409-15.
21. Kang XC, etal., Biomed Pharmacother. 2016 May;80:23-29. doi: 10.1016/j.biopha.2016.02.011. Epub 2016 Mar 14.
22. Kisseleva T, etal., Gene 2002 Feb 20;285(1-2):1-24.
23. Li F, etal., Cancer Biother Radiopharm. 2020 Feb;35(1):72-76. doi: 10.1089/cbr.2019.2898. Epub 2020 Jan 7.
24. Liu D, etal., Front Pharmacol. 2020 Apr 7;11:270. doi: 10.3389/fphar.2020.00270. eCollection 2020.
25. Liu L, etal., Gene Ther. 2013 Jan;20(1):84-92. doi: 10.1038/gt.2012.4. Epub 2012 Feb 9.
26. Liu SZ, etal., Dig Dis Sci. 2017 Jan;62(1):105-114. doi: 10.1007/s10620-016-4277-0. Epub 2016 Aug 18.
27. Liu Y, etal., J Immunol. 2008 May 1;180(9):6270-8.
28. Lv N, etal., Exp Cell Res. 2009 Jul 15;315(12):2064-71. doi: 10.1016/j.yexcr.2009.04.021. Epub 2009 May 3.
29. Mafanda EK, etal., Cytokine. 2019 Dec;124:154501. doi: 10.1016/j.cyto.2018.07.032. Epub 2018 Aug 8.
30. MGD data from the GO Consortium
31. Miki T, etal., J Pharmacol Exp Ther. 2006 Apr;317(1):68-75. Epub 2005 Dec 23.
32. Miyoshi H, etal., J Gastroenterol. 2004 Jun;39(6):563-9. doi: 10.1007/s00535-003-1343-0.
33. NCBI rat LocusLink and RefSeq merged data July 26, 2002
34. Nicol AF, etal., Exp Mol Pathol. 2006 Aug;81(1):42-7.
35. Okochi O, etal., Clin Cancer Res. 2003 Nov 1;9(14):5295-8.
36. Park EJ, etal., J Biol Chem 2003 Apr 25;278(17):14747-52. Epub 2003 Feb 12.
37. Park ES, etal., Mol Endocrinol. 2000 Mar;14(3):440-8. doi: 10.1210/mend.14.3.0433.
38. Pipeline to import KEGG annotations from KEGG into RGD
39. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
40. Raccurt M, etal., Br J Cancer. 2003 Aug 4;89(3):524-32.
41. RGD automated data pipeline
42. RGD automated import pipeline for gene-chemical interactions
43. RGD comprehensive gene curation
44. Sakuda S, etal., J Hepatol. 2002 Mar;36(3):378-84.
45. Starska K, etal., Folia Histochem Cytobiol. 2009 Jan;47(3):401-10. doi: 10.2478/v10042-009-0075-2.
46. Steyn FJ, etal., Endocrinology. 2008 Jun;149(6):3206-14. Epub 2008 Mar 6.
47. Sugase T, etal., Int J Cancer. 2017 Jun 1;140(11):2608-2621. doi: 10.1002/ijc.30666. Epub 2017 Mar 10.
48. Sun K and Zhang G, Cell Biosci. 2019 Nov 9;9:90. doi: 10.1186/s13578-019-0353-4. eCollection 2019.
49. Sutherland KD, etal., Oncogene. 2004 Oct 7;23(46):7726-33.
50. Suzuki M, etal., Cancer Lett. 2006 Oct 28;242(2):222-30. Epub 2006 Feb 3.
51. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
52. Toba H, etal., Eur J Pharmacol. 2012 Sep 15;691(1-3):190-7. doi: 10.1016/j.ejphar.2012.07.018. Epub 2012 Jul 14.
53. Ueki K, etal., Mol Cell Biol. 2004 Jun;24(12):5434-46.
54. Ueki K, etal., Proc Natl Acad Sci U S A. 2004 Jul 13;101(28):10422-7. Epub 2004 Jul 6.
55. Wang Z, etal., Biochem Biophys Res Commun. 2000 Oct 14;277(1):20-6.
56. Worschech A, etal., Cancer Res. 2008 Apr 1;68(7):2436-46.
57. Wu XY, etal., Eur Rev Med Pharmacol Sci. 2019 Sep;23(18):8068-8074. doi: 10.26355/eurrev_201909_19023.
58. Xia L, etal., J Mol Neurosci. 2016 Jul;59(3):411-20. doi: 10.1007/s12031-016-0748-1. Epub 2016 Apr 8.
59. Yang J, etal., Ann Palliat Med. 2021 Feb;10(2):1370-1379. doi: 10.21037/apm-20-518. Epub 2020 Oct 16.
60. Yu CR, etal., Inflammation. 2015 Apr;38(2):555-65. doi: 10.1007/s10753-014-9962-6.
61. Zhang M, etal., J Immunol. 2011 Aug 15;187(4):1674-83. doi: 10.4049/jimmunol.1001937. Epub 2011 Jul 8.
Additional References at PubMed
PMID:8720108   PMID:9202126   PMID:9202127   PMID:9727029   PMID:9889194   PMID:10679190   PMID:11342531   PMID:11371356   PMID:11606785   PMID:11854514   PMID:14522994   PMID:16127460  
PMID:16956890   PMID:19080716   PMID:19100470   PMID:19135225   PMID:19176113   PMID:19344732   PMID:20185635   PMID:20519071   PMID:20519645   PMID:20548288   PMID:20832564   PMID:21364493  
PMID:21606371   PMID:22302831   PMID:22387553   PMID:22875468   PMID:23222907   PMID:24091940   PMID:24376119   PMID:24660535   PMID:24880459   PMID:25019494   PMID:25488154   PMID:25847945  
PMID:26617805   PMID:28036111   PMID:28331994   PMID:28842621   PMID:29854745   PMID:30972748   PMID:32587662  


Genomics

Comparative Map Data
Socs1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2104,882,651 - 4,884,342 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl104,882,560 - 4,884,383 (+)Ensembl
Rnor_6.0104,956,795 - 4,958,472 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl104,957,326 - 4,958,461 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0103,782,936 - 3,783,574 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4104,819,971 - 4,820,609 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1104,819,970 - 4,820,609 (+)NCBI
Celera103,904,246 - 3,905,811 (+)NCBICelera
Cytogenetic Map10q11NCBI
SOCS1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1611,254,417 - 11,256,204 (-)EnsemblGRCh38hg38GRCh38
GRCh381611,254,417 - 11,256,204 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371611,348,274 - 11,350,039 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361611,255,775 - 11,257,540 (-)NCBINCBI36hg18NCBI36
Build 341611,255,774 - 11,257,540NCBI
Celera1611,517,679 - 11,519,444 (-)NCBI
Cytogenetic Map16p13.13NCBI
HuRef1611,266,017 - 11,267,782 (-)NCBIHuRef
CHM1_11611,348,201 - 11,349,966 (-)NCBICHM1_1
Socs1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391610,601,672 - 10,603,400 (-)NCBIGRCm39mm39
GRCm39 Ensembl1610,600,104 - 10,603,400 (-)Ensembl
GRCm381610,783,808 - 10,785,536 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1610,782,240 - 10,785,536 (-)EnsemblGRCm38mm10GRCm38
MGSCv371610,783,901 - 10,785,629 (-)NCBIGRCm37mm9NCBIm37
MGSCv361610,697,386 - 10,699,114 (-)NCBImm8
Celera1611,411,246 - 11,412,974 (-)NCBICelera
Cytogenetic Map16A1NCBI
cM Map165.81NCBI
Socs1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554427,321,337 - 7,323,109 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554427,321,337 - 7,323,109 (+)NCBIChiLan1.0ChiLan1.0
SOCS1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Mhudiblu_PPA_v01610,196,432 - 10,198,205 (-)NCBIMhudiblu_PPA_v0panPan3
SOCS1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1631,511,003 - 31,511,995 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl631,509,268 - 31,511,557 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha632,893,176 - 32,894,903 (+)NCBI
ROS_Cfam_1.0631,692,882 - 31,694,609 (+)NCBI
UMICH_Zoey_3.1631,506,103 - 31,507,841 (+)NCBI
UNSW_CanFamBas_1.0631,380,389 - 31,382,114 (+)NCBI
UU_Cfam_GSD_1.0631,804,768 - 31,806,494 (+)NCBI
Socs1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344111,469,049 - 111,470,661 (-)NCBI
SpeTri2.0NW_0049365309,312,965 - 9,315,593 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SOCS1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl331,881,225 - 31,884,969 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1331,879,143 - 31,883,041 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2332,670,021 - 32,674,785 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SOCS1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1510,731,866 - 10,733,745 (-)NCBIChlSab1.1chlSab2
ChlSab1.1510,731,866 - 10,733,745 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl510,732,350 - 10,732,991 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606819,430,111 - 19,432,041 (+)NCBIVero_WHO_p1.0
Socs1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248248,444,877 - 8,446,628 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
U88325  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2104,884,050 - 4,884,151 (+)MAPPERmRatBN7.2
Rnor_6.0104,958,181 - 4,958,281NCBIRnor6.0
Rnor_5.0103,783,702 - 3,783,802UniSTSRnor5.0
RGSC_v3.4104,820,737 - 4,820,837UniSTSRGSC3.4
Celera103,905,520 - 3,905,620UniSTS
Cytogenetic Map10q11UniSTS
RH143234  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2104,883,872 - 4,884,157 (+)MAPPERmRatBN7.2
Rnor_6.0104,958,003 - 4,958,287NCBIRnor6.0
Rnor_5.0103,783,524 - 3,783,808UniSTSRnor5.0
RGSC_v3.4104,820,559 - 4,820,843UniSTSRGSC3.4
Celera103,905,342 - 3,905,626UniSTS
Cytogenetic Map10q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
1549898Neuinf3Neuroinflammation QTL 326.4nervous system integrity trait (VT:0010566)MHC Class II RT1A-positive spinal cord ventral horn area to total spinal cord ventral horn area ratio (CMO:0001980)1034063205387112Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:137
Count of miRNA genes:111
Interacting mature miRNAs:117
Transcripts:ENSRNOT00000003458
Prediction methods:Microtar, 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 1 7 9 13
Low 2 43 30 21 10 21 6 9 74 35 28 11 6
Below cutoff 20 20 20 2 2 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003458   ⟹   ENSRNOP00000003458
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl104,882,560 - 4,884,383 (+)Ensembl
Rnor_6.0 Ensembl104,957,326 - 4,958,461 (+)Ensembl
RefSeq Acc Id: NM_145879   ⟹   NP_665886
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2104,882,651 - 4,884,342 (+)NCBI
Rnor_6.0104,956,795 - 4,958,472 (+)NCBI
Rnor_5.0103,782,936 - 3,783,574 (+)NCBI
RGSC_v3.4104,819,971 - 4,820,609 (+)RGD
Celera103,904,246 - 3,905,811 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_665886 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAB64204 (Get FASTA)   NCBI Sequence Viewer  
  EDL96211 (Get FASTA)   NCBI Sequence Viewer  
  Q9QX78 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_665886   ⟸   NM_145879
- UniProtKB: G3V6B4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003458   ⟸   ENSRNOT00000003458
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 (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
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)
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
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (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
PVG/Seac (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
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (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
SHRSP/A3NCrl (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
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69272 AgrOrtholog
Ensembl Genes ENSRNOG00000002568 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003458 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003458 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.30.505.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH2_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOCS1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOCS1_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:252971 UniProtKB/TrEMBL
NCBI Gene 252971 ENTREZGENE
PANTHER PTHR10155:SF4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOCS_box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Socs1 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
TIGR TC217532
UniProt G3V6B4 ENTREZGENE, UniProtKB/TrEMBL
  Q9QX78 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-04-22 Socs1  suppressor of cytokine signaling 1  Cish1  cytokine inducible SH2-containing protein 1  Symbol and Name updated to reflect Human and Mouse nomenclature 625702 APPROVED
2002-06-10 Cish1  cytokine inducible SH2-containing protein 1      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_product member of a family of negative regulators of cytokine signalling 634751