Ikbkb (inhibitor of nuclear factor kappa B kinase subunit beta) - Rat Genome Database

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Gene: Ikbkb (inhibitor of nuclear factor kappa B kinase subunit beta) Rattus norvegicus
Analyze
Symbol: Ikbkb
Name: inhibitor of nuclear factor kappa B kinase subunit beta
RGD ID: 621375
Description: Enables ATP binding activity. Contributes to IkappaB kinase activity. Involved in several processes, including positive regulation of NF-kappaB transcription factor activity; response to cholecystokinin; and response to lipopolysaccharide. Located in cytosol and intracellular membrane-bounded organelle. Part of IkappaB kinase complex. Used to study muscular atrophy and pneumonia. Biomarker of Alzheimer's disease; colitis; colon cancer; hypertension; and transient cerebral ischemia. Human ortholog(s) of this gene implicated in breast cancer; combined immunodeficiency (multiple); dermatitis; prostate cancer (multiple); and type 2 diabetes mellitus. Orthologous to human IKBKB (inhibitor of nuclear factor kappa B kinase subunit beta); PARTICIPATES IN adenosine signaling pathway; FasL mediated signaling pathway; granulocyte-macrophage colony-stimulating factor signaling pathway; INTERACTS WITH (-)-epigallocatechin 3-gallate; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: AIM-1; I-kappa-B kinase 2; I-kappa-B-kinase beta; IKK-B; IKK-beta; IKK2; inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta; inhibitor of kappaB kinase beta; inhibitor of nuclear factor kappa B kinase beta subunit; inhibitor of nuclear factor kappa-B kinase subunit beta; NFKBIKB; nuclear factor NF-kappa-B inhibitor kinase beta; serine/threonine protein kinase IKBKB
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
mRatBN7.21669,319,487 - 69,373,251 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1669,319,554 - 69,373,250 (+)Ensembl
Rnor_6.01674,177,233 - 74,230,809 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1674,177,215 - 74,230,815 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01673,809,854 - 73,863,636 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41673,804,730 - 73,858,510 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11673,805,346 - 73,858,348 (+)NCBI
Celera1667,214,025 - 67,266,348 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-artemisinin  (ISO)
(-)-epigallocatechin 3-gallate  (EXP,ISO)
(S)-colchicine  (ISO)
1'-acetoxychavicol acetate  (ISO)
1,2-dimethylhydrazine  (ISO)
1,2-naphthoquinone  (ISO)
1,4-dithiothreitol  (ISO)
15-oxo-ETE  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-acetamidofluorene  (ISO)
2-amino-2-deoxy-D-galactopyranose  (EXP)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-tert-butylhydroquinone  (EXP)
3-phenylprop-2-enal  (EXP)
4-vinylcyclohexene dioxide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
[6]-Shogaol  (ISO)
acetylsalicylic acid  (EXP,ISO)
acrolein  (ISO)
afatinib  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (ISO)
aldehydo-D-glucose  (EXP,ISO)
aldehydo-D-ribose  (ISO)
all-trans-retinoic acid  (ISO)
allopurinol  (EXP)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
anethole  (ISO)
aniline  (EXP)
anthocyanin  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP)
apigenin  (EXP,ISO)
aristolochic acid  (ISO)
arjunolic acid  (ISO)
Aroclor 1254  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenic trichloride  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atorvastatin calcium  (ISO)
azadirachtin A  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
beta-D-glucosamine  (ISO)
beta-D-glucosamine 6-sulfate  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
butylated hydroxyanisole  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (EXP)
calcitriol  (EXP)
carbon atom  (ISO)
carbon nanotube  (ISO)
Carnosol  (ISO)
carvedilol  (EXP)
cerium trichloride  (ISO)
chloroquine  (ISO)
chromium atom  (ISO)
chromium(6+)  (ISO)
chrysin  (ISO)
cisplatin  (EXP,ISO)
cocaine  (EXP)
colforsin daropate hydrochloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
curcumin  (ISO)
cytochalasin D  (ISO)
D-glucose  (EXP,ISO)
D-ribofuranose  (ISO)
deferiprone  (EXP)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
diclofenac  (EXP)
dimercaprol  (ISO)
dimethyl fumarate  (ISO)
dimethylarsinic acid  (EXP)
dioxygen  (ISO)
dipyridamole  (ISO)
doxorubicin  (EXP,ISO)
elemental carbon  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
ethanol  (ISO)
etoposide  (ISO)
eugenol  (EXP)
Evodiamine  (ISO)
febuxostat  (EXP)
filipin III  (EXP)
flavonoids  (EXP)
fluorescein 5-isothiocyanate  (ISO)
folic acid  (ISO)
folpet  (ISO)
fructose  (EXP)
fulvestrant  (ISO)
Fusaric acid  (ISO)
gallic acid  (ISO)
genistein  (EXP,ISO)
gentamycin  (EXP)
ginsenoside Re  (ISO)
glucose  (EXP,ISO)
glutathione  (ISO)
homoeriodictyol  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
ibrutinib  (ISO)
indole-3-methanol  (ISO)
indometacin  (EXP)
iron atom  (EXP)
iron(0)  (EXP)
iron(2+) sulfate (anhydrous)  (EXP)
Isorhapontigenin  (EXP)
L-1,4-dithiothreitol  (ISO)
lipopolysaccharide  (EXP,ISO)
LY294002  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
mangiferin  (EXP,ISO)
melittin  (ISO)
metformin  (ISO)
methapyrilene  (EXP,ISO)
methoxyacetic acid  (EXP)
methylmercury chloride  (EXP)
miquelianin  (ISO)
Monobutylphthalate  (EXP,ISO)
monosodium L-glutamate  (ISO)
monotropein  (ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-[3,5-bis(trifluoromethyl)phenyl]-5-chloro-2-hydroxybenzamide  (ISO)
N-acetyl-L-cysteine  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (EXP)
N-nitrosodiethylamine  (ISO)
neratinib  (ISO)
nickel dichloride  (ISO)
niclosamide  (ISO)
nitroprusside  (ISO)
Nonylphenol  (EXP)
notoginsenoside R1  (ISO)
o-anisidine  (ISO)
ozone  (EXP,ISO)
paclitaxel  (ISO)
Paeonol  (ISO)
paracetamol  (ISO)
parthenolide  (ISO)
phenobarbital  (ISO)
phenylephrine  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
pioglitazone  (ISO)
platycodin D  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
protein kinase inhibitor  (ISO)
quercetin  (EXP,ISO)
reactive oxygen species  (ISO)
resiquimod  (ISO)
resveratrol  (EXP,ISO)
rocaglamide  (ISO)
SB 203580  (EXP,ISO)
selenium atom  (ISO)
selenomethionine  (ISO)
silicon dioxide  (ISO)
simvastatin  (ISO)
sodium arsenite  (EXP,ISO)
sodium aurothiomalate  (ISO)
Sodium salicylate  (ISO)
sulfasalazine  (ISO)
sulfur dioxide  (ISO)
sulindac  (ISO)
sulindac sulfide  (ISO)
sunitinib  (ISO)
taurine  (EXP)
titanium dioxide  (ISO)
trans-anethole  (ISO)
Triptolide  (EXP,ISO)
triptonide  (ISO)
tungsten  (ISO)
umbelliferone  (EXP)
valproic acid  (ISO)
vincaleukoblastine  (ISO)
vorinostat  (ISO)
wedelolactone  (ISO)
zerumbone  (ISO)
zinc atom  (ISO)
zinc dichloride  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

References - curated
1. Azoitei N, etal., J Neurochem. 2005 Jun;93(6):1487-501.
2. Baumann B, etal., J Clin Invest. 2007 Jun;117(6):1502-13. Epub 2007 May 24.
3. Bruno ME, etal., Arch Biochem Biophys. 2002 Oct 15;406(2):153-64.
4. Bu DX, etal., FASEB J. 2005 Aug;19(10):1293-5. Epub 2005 Jun 6.
5. Cai D, etal., Nat Med. 2005 Feb;11(2):183-90. Epub 2005 Jan 30.
6. Chang NS J Biol Chem 2002 Mar 22;277(12):10323-31.
7. Chen X, etal., Am J Nephrol. 2009;30(3):287-94. doi: 10.1159/000225928. Epub 2009 Jun 16.
8. Cheng J, etal., J Pharmacol Exp Ther. 2010 Jan;332(1):57-65. doi: 10.1124/jpet.109.159863. Epub 2009 Oct 19.
9. Daniluk J, etal., J Clin Invest. 2012 Apr;122(4):1519-28. doi: 10.1172/JCI59743. Epub 2012 Mar 12.
10. Dyckman AJ, etal., Bioorg Med Chem Lett. 2011 Jan 1;21(1):383-6. doi: 10.1016/j.bmcl.2010.10.133. Epub 2010 Oct 31.
11. Fillmann H, etal., Toxicology. 2007 Jul 17;236(3):217-26. Epub 2007 Apr 27.
12. Fontan E, etal., FEBS J. 2007 May;274(10):2540-51. Epub 2007 Apr 10.
13. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
14. Gillooly KM, etal., J Pharmacol Exp Ther. 2009 Nov;331(2):349-60. doi: 10.1124/jpet.109.156018. Epub 2009 Aug 3.
15. GOA data from the GO Consortium
16. Gupte AA, etal., Diabetes. 2009 Mar;58(3):567-78. doi: 10.2337/db08-1070. Epub 2008 Dec 10.
17. Gupte AA, etal., J Appl Physiol (1985). 2009 Apr;106(4):1425-34. doi: 10.1152/japplphysiol.91210.2008. Epub 2009 Jan 29.
18. Hayden MS and Ghosh S, Cell. 2008 Feb 8;132(3):344-62.
19. Hayes JD and Dinkova-Kostova AT, Trends Biochem Sci. 2014 Apr;39(4):199-218. doi: 10.1016/j.tibs.2014.02.002. Epub 2014 Mar 16.
20. Herrmann O, etal., Nat Med. 2005 Dec;11(12):1322-9. Epub 2005 Nov 13.
21. Ho RC, etal., Am J Physiol Cell Physiol. 2005 Oct;289(4):C794-801. Epub 2005 May 11.
22. Hu WH, etal., J Biol Chem. 2005 Aug 12;280(32):29233-41. Epub 2005 Jun 10.
23. Jain SS and Bird RP, Int J Cancer. 2010 Nov 1;127(9):2042-50. doi: 10.1002/ijc.25232.
24. Je JH, etal., FEBS Lett. 2004 May 21;566(1-3):183-9.
25. Jia RP, etal., Transplant Proc. 2009 Jan-Feb;41(1):69-72. doi: 10.1016/j.transproceed.2008.11.001.
26. Kang YM, etal., Cardiovasc Res. 2009 Jun 1;82(3):503-12. doi: 10.1093/cvr/cvp073. Epub 2009 Feb 25.
27. Kumar S, etal., J Cell Physiol. 2012 Apr;227(4):1408-19. doi: 10.1002/jcp.22855.
28. Kupfer R and Scheinman RI, J Immunol Methods. 2002 Aug 1;266(1-2):155-64.
29. Ling J, etal., Cancer Cell. 2012 Jan 17;21(1):105-20. doi: 10.1016/j.ccr.2011.12.006.
30. Lu H, etal., PLoS One. 2014 Jan 28;9(1):e87530. doi: 10.1371/journal.pone.0087530. eCollection 2014.
31. Maniati E, etal., J Clin Invest. 2011 Dec;121(12):4685-99. doi: 10.1172/JCI45797. Epub 2011 Nov 7.
32. Meng QH, etal., Pharmazie. 2013 Nov;68(11):904-8.
33. MGD data from the GO Consortium
34. NCBI rat LocusLink and RefSeq merged data July 26, 2002
35. OMIM Disease Annotation Pipeline
36. Ouyang J, etal., Scand J Immunol. 2010 May;71(5):336-44.
37. Page A, etal., J Invest Dermatol. 2010 Jun;130(6):1598-610. doi: 10.1038/jid.2010.28. Epub 2010 Mar 4.
38. Pasparakis M, etal., Nature. 2002 Jun 20;417(6891):861-6.
39. Pipeline to import KEGG annotations from KEGG into RGD
40. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
41. Pipeline to import SMPDB annotations from SMPDB into RGD
42. Qin WY, etal., Zhen Ci Yan Jiu. 2013 Aug;38(4):271-6.
43. Rajendrasozhan S, etal., Pulm Pharmacol Ther. 2010 Jun;23(3):172-81. doi: 10.1016/j.pupt.2010.01.002. Epub 2010 Jan 18.
44. RGD automated data pipeline
45. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
46. RGD automated import pipeline for gene-chemical interactions
47. Romagnoli M, etal., Free Radic Biol Med. 2010 Jul 15;49(2):171-7. doi: 10.1016/j.freeradbiomed.2010.03.024. Epub 2010 Mar 31.
48. Shukla S, etal., Oncotarget. 2015 Oct 13;6(31):31216-32. doi: 10.18632/oncotarget.5157.
49. Slattery M, etal., Carcinogenesis. 2012 May 4.
50. Stratis A, etal., J Invest Dermatol. 2006 Mar;126(3):614-20.
51. Suzuki K and Verma IM, Cell. 2008 Aug 8;134(3):485-95. doi: 10.1016/j.cell.2008.05.050.
52. Tando Y, etal., Digestion. 2002;66(4):237-45. doi: 10.1159/000068364.
53. Van Gammeren D, etal., FASEB J. 2009 Feb;23(2):362-70. doi: 10.1096/fj.08-114249. Epub 2008 Sep 30.
54. Wajant H, etal., Cell Death Differ. 2003 Jan;10(1):45-65.
55. Watterson SH, etal., Bioorg Med Chem Lett. 2011 Dec 1;21(23):7006-12. doi: 10.1016/j.bmcl.2011.09.111. Epub 2011 Oct 5.
56. Wu L, etal., J Hypertens. 2006 Jan;24(1):123-30.
57. Yang J, etal., Mol Cancer Ther. 2009 Mar;8(3):636-47. doi: 10.1158/1535-7163.MCT-08-0749. Epub 2009 Mar 10.
58. Zhang F, etal., J Pharmacol Exp Ther. 2010 Jun;333(3):822-33. doi: 10.1124/jpet.110.165829. Epub 2010 Feb 26.
59. Zhang Y, etal., Biochem Biophys Res Commun 2001 Apr 6;282(3):844-9.
60. Zhang Y, etal., Mol Cancer Ther. 2016 Jul;15(7):1504-14. doi: 10.1158/1535-7163.MCT-15-0999. Epub 2016 Apr 8.
61. Zhao CY, etal., Zhonghua Gan Zang Bing Za Zhi. 2007 Jun;15(6):450-5.
Additional References at PubMed
PMID:9819420   PMID:12235208   PMID:12492477   PMID:12857501   PMID:14743216   PMID:15084260   PMID:15383541   PMID:15684432   PMID:15790681   PMID:16079148   PMID:16079150   PMID:16319058  
PMID:17009244   PMID:17318081   PMID:17954568   PMID:18981174   PMID:19088076   PMID:19362079   PMID:19386987   PMID:19569009   PMID:20434986   PMID:20614026   PMID:20646420   PMID:20930169  
PMID:21399639   PMID:21423167   PMID:22982470   PMID:23016877   PMID:23091055   PMID:23418625   PMID:23453807   PMID:23563696   PMID:23613522   PMID:23776175   PMID:23776406   PMID:24135021  
PMID:24825147   PMID:25636800   PMID:25816133   PMID:26212789   PMID:26514267   PMID:28060742   PMID:28673900   PMID:29785049   PMID:30337470   PMID:30988283   PMID:31297885   PMID:31549412  
PMID:34073390  


Genomics

Comparative Map Data
Ikbkb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21669,319,487 - 69,373,251 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1669,319,554 - 69,373,250 (+)Ensembl
Rnor_6.01674,177,233 - 74,230,809 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1674,177,215 - 74,230,815 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01673,809,854 - 73,863,636 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41673,804,730 - 73,858,510 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11673,805,346 - 73,858,348 (+)NCBI
Celera1667,214,025 - 67,266,348 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
IKBKB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl842,271,302 - 42,332,460 (+)EnsemblGRCh38hg38GRCh38
GRCh38842,270,727 - 42,332,460 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37842,128,820 - 42,189,978 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36842,247,986 - 42,309,122 (+)NCBINCBI36hg18NCBI36
Build 34842,247,985 - 42,309,122NCBI
Celera841,077,798 - 41,138,835 (+)NCBI
Cytogenetic Map8p11.21NCBI
HuRef840,656,604 - 40,717,697 (+)NCBIHuRef
CHM1_1842,177,451 - 42,238,764 (+)NCBICHM1_1
Ikbkb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39823,149,221 - 23,196,605 (-)NCBIGRCm39mm39
GRCm39 Ensembl823,149,228 - 23,196,605 (-)Ensembl
GRCm38822,659,205 - 22,706,589 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl822,659,212 - 22,706,589 (-)EnsemblGRCm38mm10GRCm38
MGSCv37823,769,677 - 23,817,055 (-)NCBIGRCm37mm9NCBIm37
MGSCv36824,125,308 - 24,172,108 (-)NCBImm8
Celera824,149,472 - 24,196,863 (-)NCBICelera
Cytogenetic Map8A2NCBI
Ikbkb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955536612,774 - 658,647 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955536611,965 - 658,647 (-)NCBIChiLan1.0ChiLan1.0
IKBKB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1838,960,594 - 39,020,971 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl838,960,594 - 39,020,971 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0841,515,613 - 41,576,229 (+)NCBIMhudiblu_PPA_v0panPan3
IKBKB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11623,359,551 - 23,419,114 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1623,359,813 - 23,419,075 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1623,864,109 - 23,923,669 (-)NCBI
ROS_Cfam_1.01625,108,158 - 25,167,347 (-)NCBI
UMICH_Zoey_3.11623,479,268 - 23,538,442 (-)NCBI
UNSW_CanFamBas_1.01624,042,615 - 24,101,962 (-)NCBI
UU_Cfam_GSD_1.01624,093,332 - 24,152,694 (-)NCBI
Ikbkb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494346,401,726 - 46,450,359 (-)NCBI
SpeTri2.0NW_004936785358,128 - 406,751 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IKBKB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1711,289,690 - 11,348,553 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11711,289,607 - 11,348,557 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21713,063,170 - 13,101,270 (+)NCBISscrofa10.2Sscrofa10.2susScr3
IKBKB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1840,267,532 - 40,325,282 (+)NCBI
ChlSab1.1 Ensembl840,268,079 - 40,326,381 (+)Ensembl
Vero_WHO_p1.0NW_0236660521,461,878 - 1,520,432 (-)NCBI
Ikbkb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624780922,524 - 978,687 (-)NCBI

Position Markers
RH131248  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21669,372,599 - 69,372,802 (+)MAPPERmRatBN7.2
Rnor_6.01674,230,158 - 74,230,360NCBIRnor6.0
Rnor_5.01673,862,985 - 73,863,187UniSTSRnor5.0
RGSC_v3.41673,857,859 - 73,858,061UniSTSRGSC3.4
Celera1667,265,697 - 67,265,899UniSTS
RH 3.4 Map16691.7UniSTS
Cytogenetic Map16q12.5UniSTS
RH138696  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21669,370,092 - 69,370,227 (+)MAPPERmRatBN7.2
Rnor_6.01674,227,651 - 74,227,785NCBIRnor6.0
Rnor_5.01673,860,478 - 73,860,612UniSTSRnor5.0
RGSC_v3.41673,855,352 - 73,855,486UniSTSRGSC3.4
Celera1667,263,190 - 67,263,324UniSTS
RH 3.4 Map16663.21UniSTS
Cytogenetic Map16q12.5UniSTS
RH139961  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21669,372,999 - 69,373,186 (+)MAPPERmRatBN7.2
Rnor_6.01674,230,558 - 74,230,744NCBIRnor6.0
Rnor_5.01673,863,385 - 73,863,571UniSTSRnor5.0
RGSC_v3.41673,858,259 - 73,858,445UniSTSRGSC3.4
Celera1667,266,097 - 67,266,283UniSTS
RH 3.4 Map16691.4UniSTS
Cytogenetic Map16q12.5UniSTS
BF390838  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21669,330,561 - 69,330,719 (+)MAPPERmRatBN7.2
Rnor_6.01674,188,233 - 74,188,390NCBIRnor6.0
Rnor_5.01673,820,854 - 73,821,011UniSTSRnor5.0
RGSC_v3.41673,815,730 - 73,815,887UniSTSRGSC3.4
Celera1667,225,025 - 67,225,182UniSTS
RH 3.4 Map16665.92UniSTS
Cytogenetic Map16q12.5UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)162432551369325513Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162515279370152793Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165571108783402471Rat
1298527Arunc2Aerobic running capacity QTL 22.9exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)166853271675029966Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:468
Count of miRNA genes:251
Interacting mature miRNAs:306
Transcripts:ENSRNOT00000025851
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 35 53 37 19 37 3 66 35 34 11
Low 8 4 4 4 8 8 8 7 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000025851   ⟹   ENSRNOP00000025851
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1669,319,554 - 69,373,250 (+)Ensembl
Rnor_6.0 Ensembl1674,177,215 - 74,230,815 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000097362   ⟹   ENSRNOP00000077348
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1669,319,554 - 69,373,250 (+)Ensembl
RefSeq Acc Id: NM_053355   ⟹   NP_445807
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21669,319,555 - 69,373,251 (+)NCBI
Rnor_6.01674,177,233 - 74,230,809 (+)NCBI
Rnor_5.01673,809,854 - 73,863,636 (+)NCBI
RGSC_v3.41673,804,730 - 73,858,510 (+)RGD
Celera1667,214,025 - 67,266,348 (+)RGD
Sequence:
RefSeq Acc Id: XM_039094867   ⟹   XP_038950795
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21669,319,487 - 69,362,366 (+)NCBI
Protein Sequences
Protein RefSeqs NP_445807 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950795 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF21978 (Get FASTA)   NCBI Sequence Viewer  
  EDM09011 (Get FASTA)   NCBI Sequence Viewer  
  EDM09012 (Get FASTA)   NCBI Sequence Viewer  
  Q9QY78 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_445807   ⟸   NM_053355
- UniProtKB: Q9QY78 (UniProtKB/Swiss-Prot),   G3V8H5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000025851   ⟸   ENSRNOT00000025851
RefSeq Acc Id: XP_038950795   ⟸   XM_039094867
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000077348   ⟸   ENSRNOT00000097362
Protein Domains
Protein kinase

Transcriptome

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

Promoters
RGD ID:13700184
Promoter ID:EPDNEW_R10708
Type:initiation region
Name:Ikbkb_1
Description:inhibitor of nuclear factor kappa B kinase subunit beta
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_6.01674,177,222 - 74,177,282EPDNEW

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)
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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
M520/NRrrcMcwi (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
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)
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)
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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)
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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)
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:621375 AgrOrtholog
Ensembl Genes ENSRNOG00000019073 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000025851 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025851 ENTREZGENE, UniProtKB/TrEMBL
InterPro IKBKB_SDD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IKKbetaNEMObind UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kinase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot_kinase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ser/Thr_kinase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84351 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 84351 ENTREZGENE
Pfam IKBKB_SDD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IKKbetaNEMObind UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pkinase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ikbkb PhenoGen
PROSITE PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_ST UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART IKKbetaNEMObind UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  S_TKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V8H5 ENTREZGENE, UniProtKB/TrEMBL
  IKKB_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-02-01 Ikbkb  inhibitor of nuclear factor kappa B kinase subunit beta  Ikbkb  inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-02-26 Ikbkb  inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta  Ikbkb  inhibitor of kappaB kinase beta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Ikbkb  inhibitor of kappaB kinase beta    inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta  Name updated 1299863 APPROVED
2002-08-07 Ikbkb  inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in megakaryocytes 633167
gene_expression expressed in rat liver and spleen cells 70526
gene_function cytosolic fragment interacts physically with p53 and prevents the nuclear translocation of p53  
gene_physical_interaction cytosolic fragment interacts physically with p53 and prevents the nuclear translocation of p53 70526
gene_process regulates growth 70526
gene_process forms a complex with p53 and the dissociation of this complex results in growth suppression by Tgf-b1, apoptosis, stress, hypoxia, DNA damage and UV radiation  
gene_regulation forms a complex with p53 and the dissociation of this complex results in growth suppression by Tgf-b1, apoptosis, stress, hypoxia, DNA damage and UV radiation 70526