S100b (S100 calcium binding protein B) - Rat Genome Database

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Gene: S100b (S100 calcium binding protein B) Rattus norvegicus
Analyze
Symbol: S100b
Name: S100 calcium binding protein B
RGD ID: 3615
Description: Enables RAGE receptor binding activity; identical protein binding activity; and metal ion binding activity. Involved in several processes, including long-term synaptic potentiation; negative regulation of skeletal muscle cell differentiation; and positive regulation of myelination. Located in cytoplasm and extracellular space. Used to study demyelinating disease. Biomarker of several diseases, including bipolar disorder; borna disease; brain disease (multiple); mental depression; and sleep apnea. Human ortholog(s) of this gene implicated in Alzheimer's disease; Parkinson's disease; aspergillosis; and schizophrenia. Orthologous to human S100B (S100 calcium binding protein B); PARTICIPATES IN calcium/calcium-mediated signaling pathway; INTERACTS WITH (+)-pilocarpine; (R)-lipoic acid; 1,2-dimethylhydrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: MGC93559; protein S100-B; S-100 protein beta chain; S-100 protein subunit beta; S100 calcium-binding protein B; S100 calcium-binding protein beta (neural); S100 calcium-binding protein, beta (neural); S100 protein, beta polypeptide; S100 protein, beta polypeptide, neural; S100P
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
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
mRatBN7.22012,372,866 - 12,381,619 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl2012,372,881 - 12,394,743 (-)Ensembl
Rnor_6.02013,130,633 - 13,142,856 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2013,130,636 - 13,142,856 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02015,287,745 - 15,296,485 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42012,791,440 - 12,824,508 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12012,791,666 - 12,824,735 (-)NCBI
Celera2013,867,276 - 13,875,895 (-)NCBICelera
Cytogenetic Map20p12NCBI
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
(+)-catechin  (ISO)
(+)-pilocarpine  (EXP)
(R)-lipoic acid  (EXP)
(R)-noradrenaline  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17beta-estradiol  (ISO)
2,2,2-tetramine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3',5'-cyclic AMP  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-dihydroxybenzaldehyde  (ISO)
3,7-dihydropurine-6-thione  (EXP)
3-[3-(tert-butylsulfanyl)-1-(4-chlorobenzyl)-5-(propan-2-yl)-1H-indol-2-yl]-2,2-dimethylpropanoic acid  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
6-propyl-2-thiouracil  (EXP)
aconitine  (ISO)
aluminium atom  (EXP)
aluminium(0)  (EXP)
aminoguanidine  (EXP)
ammonia  (EXP)
ammonium chloride  (EXP)
arsenous acid  (ISO)
astemizole  (EXP)
benzo[a]pyrene  (ISO)
bexarotene  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
buspirone  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (EXP)
calcitriol  (ISO)
capsaicin  (EXP)
carbofuran  (EXP)
carbon nanotube  (ISO)
chrysin  (ISO)
cobalt atom  (ISO)
cocaine  (EXP)
Cuprizon  (ISO)
cycloheximide  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibenziodolium  (ISO)
dibutyl phthalate  (EXP)
dimethoate  (EXP)
diuron  (EXP)
dorsomorphin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
ethanol  (ISO)
fluoxetine  (EXP,ISO)
folic acid  (ISO)
furosemide  (EXP)
glyphosate  (EXP,ISO)
heparin  (EXP)
hydrogen peroxide  (EXP)
indometacin  (ISO)
ketamine  (EXP)
L-ascorbic acid  (EXP,ISO)
lead diacetate  (EXP)
lipoic acid  (EXP)
manganese(II) chloride  (ISO)
mercaptopurine  (EXP)
mercury atom  (ISO)
mercury(0)  (ISO)
Mesaconitine  (ISO)
methylmercury chloride  (EXP)
monascin  (ISO)
morphine  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
nickel sulfate  (ISO)
nicotine  (ISO)
nitric oxide  (EXP,ISO)
nitroprusside  (EXP)
ouabain  (EXP)
oxidopamine  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
PCB138  (EXP)
perfluorooctane-1-sulfonic acid  (EXP)
phenethyl caffeate  (EXP)
phenylephrine  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (EXP)
purine-6-thiol  (EXP)
quercetin  (ISO)
reactive oxygen species  (EXP,ISO)
resveratrol  (EXP)
risperidone  (EXP)
SB 203580  (ISO)
SB 431542  (ISO)
Soman  (EXP)
streptozocin  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
triptonide  (ISO)
Tungsten carbide  (ISO)
valproic acid  (ISO)
veliparib  (ISO)
vinclozolin  (EXP)
vitamin E  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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20. Gankam Kengne F, etal., J Am Soc Nephrol. 2011 Oct;22(10):1834-45. Epub 2011 Sep 1.
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22. Gazzolo D, etal., Clin Chem. 2004 May;50(5):941-4.
23. Gazzolo D, etal., Crit Care Med. 2004 Jan;32(1):131-6.
24. Ge YL, etal., Acta Anaesthesiol Scand. 2007 Nov;51(10):1331-7.
25. GOA data from the GO Consortium
26. Goncalves D, etal., Neuroreport 2002 Aug 27;13(12):1533-5.
27. Gonzalez-Quevedo A, etal., Clin Biochem. 2011 Feb;44(2-3):154-9. Epub 2010 Dec 1.
28. Hamed SA, etal., Neuropediatrics. 2009 Apr;40(2):66-72. Epub 2009 Oct 6.
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32. Lee SJ, etal., Emerg Med J. 2010 Mar;27(3):209-12.
33. Lin YW and Hsieh CL, J Ethnopharmacol. 2011 May 17;135(2):313-20. Epub 2011 Mar 21.
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35. Liu Y, etal., Mol Pharmacol. 2008 Aug;74(2):371-8. Epub 2008 Apr 29.
36. Machado-Vieira R, etal., Life Sci. 2004 Dec 31;76(7):805-11.
37. Mazzini GS, etal., J Card Fail. 2007 Dec;13(10):850-4.
38. Mbele GO, etal., J Biol Chem 2002 Dec 20;277(51):49998-50007.
39. MGD data from the GO Consortium
40. Mori T, etal., Glia. 2010 Feb;58(3):300-14.
41. Motin VG, etal., Bull Exp Biol Med. 2002 Feb;133(2):110-3.
42. NCBI rat LocusLink and RefSeq merged data July 26, 2002
43. Ohtaki N, etal., J Virol. 2007 Jun;81(11):5940-8. Epub 2007 Mar 21.
44. Oses JP, etal., Brain Res Bull. 2004 Sep 30;64(3):237-42.
45. Pelinka LE, etal., Br J Anaesth. 2003 Oct;91(4):595-7.
46. Petzold A, etal., Brain. 2002 Jul;125(Pt 7):1462-73.
47. Petzold A, etal., Muscle Nerve. 2010 Jan;41(1):42-9.
48. Pustylnyak VO, etal., Brain Res. 2011 Jun 7;1394:33-9. Epub 2011 Apr 20.
49. Qi LY, etal., Neurosci Lett. 2009 Sep 22;462(2):113-7. Epub 2009 Jun 17.
50. RGD automated data pipeline
51. RGD automated import pipeline for gene-chemical interactions
52. Rodrigues L, etal., J Neural Transm. 2010 Nov;117(11):1295-305. Epub 2010 Oct 16.
53. Roltsch E, etal., J Neuroinflammation. 2010 Nov 16;7:78.
54. Sbai O, etal., J Cell Sci. 2010 Dec 15;123(Pt 24):4332-9. Epub 2010 Nov 23.
55. Schaub MC and Heizmann CW, Biochem Biophys Res Commun. 2008 Apr 25;369(1):247-64. Epub 2007 Oct 25.
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57. Sorci G, etal., PLoS Pathog. 2011 Mar;7(3):e1001315. Epub 2011 Mar 10.
58. Steinacker P, etal., Sci Rep. 2016 Dec 8;6:38737. doi: 10.1038/srep38737.
59. Tanaka Y, etal., Life Sci. 2007 Aug 2;81(8):657-63. Epub 2007 Jul 21.
60. Tramontina F, etal., Cell Mol Neurobiol 2002 Jun;22(3):373-8.
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62. Tsoporis JN, etal., Circ Res. 2010 Jan 8;106(1):93-101. Epub 2009 Nov 12.
63. Tubaro C, etal., J Cell Physiol. 2010 Apr;223(1):270-82.
64. Wilder PT, etal., Biochemistry. 2005 Apr 19;44(15):5690-702.
65. Wright NT, etal., J Biomol NMR. 2008 Dec;42(4):279-86. Epub 2008 Oct 24.
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67. Ye Y, etal., Neurosci Lett. 2011 Sep 26;503(1):15-9. Epub 2011 Aug 6.
68. Yilmaz N, etal., Cell Mol Neurobiol. 2011 May;31(4):579-85. Epub 2011 Feb 4.
69. Zhai J, etal., Behav Brain Res. 2011 Mar 1;217(2):363-8. Epub 2010 Nov 9.
70. Zhou J, etal., Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2011 Jun;36(6):504-10.
71. Zurek J and Fedora M, Acta Neurochir (Wien). 2011 Oct 7.
Additional References at PubMed
PMID:1653388   PMID:3818655   PMID:6093041   PMID:8794737   PMID:9485423   PMID:9519411   PMID:10211826   PMID:10913138   PMID:11891290   PMID:12042313   PMID:12045670   PMID:12118070  
PMID:12470955   PMID:12477932   PMID:12744484   PMID:12941779   PMID:14736868   PMID:15033494   PMID:15076760   PMID:15248193   PMID:15489334   PMID:15566955   PMID:15567475   PMID:15572370  
PMID:15584905   PMID:15782413   PMID:15809219   PMID:15882069   PMID:15921704   PMID:16194580   PMID:16524173   PMID:16600520   PMID:16633903   PMID:17234709   PMID:17350141   PMID:17403138  
PMID:17499767   PMID:17660747   PMID:17729158   PMID:17880365   PMID:18472341   PMID:18602402   PMID:18621038   PMID:19027832   PMID:19137572   PMID:19559073   PMID:19726345   PMID:19823932  
PMID:20027335   PMID:20437086   PMID:20728493   PMID:21130124   PMID:21614209   PMID:21830043   PMID:21892662   PMID:21970823   PMID:22052576   PMID:22627026   PMID:23561481   PMID:24239092  
PMID:24582971   PMID:24766228   PMID:24770897   PMID:24842050   PMID:25129106   PMID:25416956   PMID:25433207   PMID:25682687   PMID:25898931   PMID:26246400   PMID:26773687   PMID:26782580  
PMID:26871637   PMID:27107012   PMID:27301641   PMID:27488079   PMID:27660208   PMID:27695124   PMID:27928847   PMID:28693920   PMID:28713206   PMID:29050939   PMID:29130118   PMID:29664924  
PMID:29684040   PMID:31038022   PMID:32491925  


Genomics

Comparative Map Data
S100b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22012,372,866 - 12,381,619 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl2012,372,881 - 12,394,743 (-)Ensembl
Rnor_6.02013,130,633 - 13,142,856 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2013,130,636 - 13,142,856 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02015,287,745 - 15,296,485 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42012,791,440 - 12,824,508 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12012,791,666 - 12,824,735 (-)NCBI
Celera2013,867,276 - 13,875,895 (-)NCBICelera
Cytogenetic Map20p12NCBI
S100B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2146,598,604 - 46,605,208 (-)EnsemblGRCh38hg38GRCh38
GRCh382146,598,604 - 46,605,243 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372148,018,517 - 48,024,995 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362146,842,959 - 46,849,463 (-)NCBINCBI36hg18NCBI36
Build 342146,842,958 - 46,849,424NCBI
Celera2133,131,698 - 33,138,202 (-)NCBI
Cytogenetic Map21q22.3NCBI
HuRef2133,398,429 - 33,404,960 (-)NCBIHuRef
CHM1_12147,579,370 - 47,585,892 (-)NCBICHM1_1
S100b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391076,089,670 - 76,097,153 (+)NCBIGRCm39mm39
GRCm39 Ensembl1076,089,687 - 76,096,993 (+)Ensembl
GRCm381076,253,836 - 76,261,319 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1076,253,853 - 76,261,159 (+)EnsemblGRCm38mm10GRCm38
MGSCv371075,716,581 - 75,724,064 (+)NCBIGRCm37mm9NCBIm37
MGSCv361075,697,569 - 75,703,813 (+)NCBImm8
Celera1077,297,763 - 77,305,246 (+)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1038.76NCBI
S100b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540742,972,584 - 42,980,510 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540742,972,584 - 42,980,510 (-)NCBIChiLan1.0ChiLan1.0
S100B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12146,197,750 - 46,203,953 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2146,197,750 - 46,203,953 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02133,063,845 - 33,070,073 (-)NCBIMhudiblu_PPA_v0panPan3
S100B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13139,783,990 - 39,788,289 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3139,784,506 - 39,788,183 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3139,014,186 - 39,018,506 (-)NCBI
ROS_Cfam_1.03139,427,666 - 39,431,986 (-)NCBI
UMICH_Zoey_3.13139,288,949 - 39,293,268 (-)NCBI
UNSW_CanFamBas_1.03139,249,760 - 39,254,080 (-)NCBI
UU_Cfam_GSD_1.03139,768,041 - 39,772,361 (-)NCBI
S100B
(Sus scrofa - pig)
No map positions available.
S100B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1290,188,820 - 90,194,986 (-)NCBI
ChlSab1.1 Ensembl290,188,639 - 90,195,023 (-)Ensembl
Vero_WHO_p1.0NW_02366605418,611,924 - 18,618,244 (-)NCBI
S100b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474531,645,927 - 31,652,846 (-)NCBI

Position Markers
D20Wox6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22012,374,046 - 12,374,191 (+)MAPPERmRatBN7.2
Rnor_6.02013,131,801 - 13,131,945NCBIRnor6.0
Rnor_5.02015,288,913 - 15,289,057UniSTSRnor5.0
RGSC_v3.42012,792,605 - 12,792,749UniSTSRGSC3.4
Celera2013,868,441 - 13,868,585UniSTS
Cytogenetic Map20p12UniSTS
RH94706  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22012,373,324 - 12,373,504 (+)MAPPERmRatBN7.2
Rnor_6.02013,131,079 - 13,131,258NCBIRnor6.0
Rnor_5.02015,288,191 - 15,288,370UniSTSRnor5.0
RGSC_v3.42012,791,883 - 12,792,062UniSTSRGSC3.4
Celera2013,867,719 - 13,867,898UniSTS
Cytogenetic Map20p12UniSTS
AA945753  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22012,420,339 - 12,420,435 (+)MAPPERmRatBN7.2
Rnor_6.02013,212,310 - 13,212,405NCBIRnor6.0
Rnor_5.02015,366,644 - 15,366,739UniSTSRnor5.0
RGSC_v3.42012,816,715 - 12,816,810UniSTSRGSC3.4
Celera2013,914,039 - 13,914,134UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20669170617489458Rat
1581577Pur15Proteinuria QTL 154.380.0002total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20804241017617956Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20903971913461775Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:102
Count of miRNA genes:86
Interacting mature miRNAs:92
Transcripts:ENSRNOT00000001743
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 11
Medium 3 10 3 7 7 35 25 5 7
Low 32 24 18 16 18 1 4 18 31 9 6 1
Below cutoff 7 21 21 21 4 4 4

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_013191 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772868 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601568 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC087026 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212122 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213381 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213687 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213774 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213840 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214218 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214292 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214486 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214554 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M15705 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M54919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X01090 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000001743   ⟹   ENSRNOP00000001743
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2012,372,881 - 12,381,781 (-)Ensembl
Rnor_6.0 Ensembl2013,130,636 - 13,142,856 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096333   ⟹   ENSRNOP00000085085
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2012,373,163 - 12,394,743 (-)Ensembl
RefSeq Acc Id: NM_013191   ⟹   NP_037323
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,372,882 - 12,381,619 (-)NCBI
Rnor_6.02013,130,636 - 13,142,856 (-)NCBI
Rnor_5.02015,287,745 - 15,296,485 (-)NCBI
RGSC_v3.42012,791,440 - 12,824,508 (-)RGD
Celera2013,867,276 - 13,875,895 (-)RGD
Sequence:
RefSeq Acc Id: XM_008772868   ⟹   XP_008771090
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,372,866 - 12,381,538 (-)NCBI
Rnor_6.02013,130,633 - 13,137,526 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601568   ⟹   XP_017457057
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22012,372,866 - 12,381,473 (-)NCBI
Rnor_6.02013,130,633 - 13,142,854 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_037323   ⟸   NM_013191
- UniProtKB: P04631 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008771090   ⟸   XM_008772868
- Peptide Label: isoform X1
- UniProtKB: P04631 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017457057   ⟸   XM_017601568
- Peptide Label: isoform X1
- UniProtKB: P04631 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001743   ⟸   ENSRNOT00000001743
RefSeq Acc Id: ENSRNOP00000085085   ⟸   ENSRNOT00000096333
Protein Domains
EF-hand

Transcriptome

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

Promoters
RGD ID:13701520
Promoter ID:EPDNEW_R12044
Type:multiple initiation site
Name:S100b_1
Description:S100 calcium binding protein B
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_6.02013,142,798 - 13,142,858EPDNEW

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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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
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:3615 AgrOrtholog
Ensembl Genes ENSRNOG00000001295 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000001743 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000001743 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7193740 IMAGE-MGC_LOAD
InterPro EF-hand-dom_pair UniProtKB/Swiss-Prot
  EF_Hand_1_Ca_BS UniProtKB/Swiss-Prot
  EF_hand_dom UniProtKB/Swiss-Prot
  S100-B UniProtKB/Swiss-Prot
  S100/CaBP-9k_CS UniProtKB/Swiss-Prot
  S100_Ca-bd_sub UniProtKB/Swiss-Prot
KEGG Report rno:25742 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93559 IMAGE-MGC_LOAD
NCBI Gene 25742 ENTREZGENE
Pfam EF-hand_1 UniProtKB/Swiss-Prot
  S_100 UniProtKB/Swiss-Prot
PhenoGen S100b PhenoGen
PROSITE EF_HAND_1 UniProtKB/Swiss-Prot
  EF_HAND_2 UniProtKB/Swiss-Prot
  S100_CABP UniProtKB/Swiss-Prot
SMART EFh UniProtKB/Swiss-Prot
  S_100 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot
UniProt P04631 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-18 S100b  S100 calcium binding protein B  S100b  S100 protein, beta polypeptide, neural  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-18 S100b  S100 protein, beta polypeptide, neural  S100b  S100 protein, beta polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 S100b  S100 calcium-binding protein, beta (neural)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization colocalizes to membrane ruffles with GTPase activating protein IQGAP 727451
gene_expression expressed in the brain astrocytes and mRNA was detected in the rat heart after coronary artery ligation 628549
gene_process inhibits postinfarct myocardial hypertrophic response 628549
gene_protein 20 kDa calcium binding homodimer 628549
gene_regulation activation of the promoter is mediated through the PKC signalling pathway 628549