Cdkn1b (cyclin-dependent kinase inhibitor 1B) - Rat Genome Database

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Gene: Cdkn1b (cyclin-dependent kinase inhibitor 1B) Rattus norvegicus
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Symbol: Cdkn1b
Name: cyclin-dependent kinase inhibitor 1B
RGD ID: 69062
Description: Enables Hsp70 protein binding activity and chaperone binding activity. Involved in several processes, including regulation of cyclin-dependent protein serine/threonine kinase activity; response to estradiol; and response to glucose. Located in cytoplasm and nucleus. Part of protein-containing complex. Used to study cataract; endocrine organ benign neoplasm (multiple); infertility; multiple endocrine neoplasia; and myocardial infarction. Biomarker of several diseases, including acute kidney failure; glomerulonephritis (multiple); obesity; pulmonary hypertension; and sciatic neuropathy. Human ortholog(s) of this gene implicated in acute myeloid leukemia; breast cancer; multiple endocrine neoplasia type 4; and myelodysplastic syndrome. Orthologous to human CDKN1B (cyclin dependent kinase inhibitor 1B); PARTICIPATES IN forkhead class A signaling pathway; G1/S transition pathway; phosphatidylinositol 3-kinase-Akt signaling pathway; INTERACTS WITH (+)-pilocarpine; (Z)-3-butylidenephthalide; 1,2-dimethylhydrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Cdki1b; CDKN4; Cyclin-dependent kinase inhibitor 1B (p27 Kip1); Cyclin-dependent kinase inhibitor 1B (p27); Cyclin-dependent kinase inhibitor 1B (p27, Kip1); cyclin-dependent kinase inhibitor p27; cyclin-dependent kinase inhibitor p27/Kip1; Kip1; p27; P27KIP1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Cdkn1bwe   Cdkn1bem1Musc   Cdkn1bem4Musc  
Genetic Models: SD-Cdkn1bwe ACI.Cg.-Cdkn1bem4Musc ACI.Cg.-Cdkn1bem1Musc
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24167,760,067 - 167,765,177 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl4167,760,181 - 167,764,982 (+)Ensembl
Rnor_6.04168,689,043 - 168,694,159 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4168,689,163 - 168,693,964 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04232,962,218 - 232,967,323 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44171,841,705 - 171,846,506 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14172,086,631 - 172,091,508 (+)NCBI
Celera4156,357,827 - 156,362,628 (+)NCBICelera
Cytogenetic Map4q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acute kidney failure  (IEP)
acute myeloid leukemia  (ISO)
autosomal dominant non-syndromic intellectual disability 6  (ISO)
Brain Injuries  (IEP)
breast cancer  (ISO)
Breast Neoplasms  (ISO)
cataract  (IAGP,IMP)
cervix uteri carcinoma in situ  (ISO)
Chloracne  (ISO)
chronic myeloid leukemia  (ISO)
Diabetic Nephropathies  (IEP)
Endometrial Neoplasms  (ISO)
Endometrioid Carcinomas  (ISO)
Fallopian Tube Neoplasms  (ISO)
Familial Prostate Cancer  (ISO)
Fibrosis  (IEP)
glaucoma  (IEP)
Helicobacter Infections  (ISO)
hepatocellular adenoma  (ISO)
hepatocellular carcinoma  (ISO)
Hereditary Neoplastic Syndromes  (ISO)
infertility  (IMP)
Intestinal Neoplasms  (ISO)
Kidney Neoplasms  (ISO)
Left Ventricular Hypertrophy  (IEP)
Leukoencephalopathies  (IDA)
Leydig cell tumor  (ISO)
Liver Neoplasms  (ISO)
Lung Neoplasms  (ISO)
lung non-small cell carcinoma  (ISO)
lung small cell carcinoma  (ISO)
Lymphatic Metastasis  (ISO)
macular degeneration  (ISO)
Mammary Neoplasms, Experimental  (IDA,IEP)
membranoproliferative glomerulonephritis  (IEP)
membranous glomerulonephritis  (IEP)
Mesothelioma  (ISO)
multiple endocrine neoplasia  (IAGP,ISO)
multiple endocrine neoplasia type 4  (ISO)
myelodysplastic syndrome  (ISO)
myocardial infarction  (IMP,ISO)
nephroblastoma  (ISO)
neuroendocrine tumor  (ISO)
obesity  (IEP)
Ovarian Neoplasms  (ISO)
paraganglioma  (IAGP)
pheochromocytoma  (IAGP)
pituitary adenoma  (IAGP)
Pituitary Neoplasms  (ISO)
primary hyperparathyroidism  (ISO)
prostate carcinoma in situ  (ISO)
Prostatic Neoplasms  (ISO)
pulmonary hypertension  (IEP)
rectal benign neoplasm  (ISO)
renal cell carcinoma  (ISO)
Reperfusion Injury  (IEP)
sciatic neuropathy  (IEP)
senile cataract  (ISO)
Sezary's disease  (ISO)
Spinal Cord Injuries  (IDA)
Stomach Neoplasms  (ISO)
Testicular Neoplasms  (ISO)
transitional cell carcinoma  (ISO)
urinary bladder cancer  (ISO)
Uterine Cervical Neoplasms  (ISO)
Uterine Neoplasms  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(+)-Tetrandrine  (ISO)
(-)-citrinin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(S)-(-)-perillyl alcohol  (ISO)
(S)-nicotine  (ISO)
(Z)-3-butylidenephthalide  (EXP)
1,2-dimethylhydrazine  (EXP,ISO)
1,3-thiazolidine-2,4-dione  (ISO)
1-naphthyl isothiocyanate  (EXP)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
15-deoxy-Delta(12,14)-prostaglandin J2  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-acetamidofluorene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (EXP)
2-cyclopenten-1-one  (ISO)
2-hydroxypropanoic acid  (ISO)
2-methoxy-17beta-estradiol  (ISO)
2-methoxyethanol  (EXP)
25-hydroxycholesterol  (EXP)
3',5'-cyclic AMP  (EXP,ISO)
3,3',5-triiodo-L-thyronine  (EXP,ISO)
3,3'-diindolylmethane  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-nitroquinoline N-oxide  (ISO)
4-nonylphenol  (EXP,ISO)
4-vinylcyclohexene dioxide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
5-iodotubercidin  (EXP)
6-propyl-2-thiouracil  (ISO)
9-cis-retinoic acid  (ISO)
acetylsalicylic acid  (ISO)
acrolein  (EXP)
acrylamide  (ISO)
acrylonitrile  (ISO)
acteoside  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (EXP)
aldehydo-D-glucose  (EXP)
all-trans-retinoic acid  (EXP,ISO)
allose  (ISO)
alpha-naphthoflavone  (ISO)
alvocidib  (ISO)
ammonium chloride  (EXP)
anilines  (ISO)
anthocyanin  (ISO)
aristolochic acid  (ISO)
arotinoid acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
aspartame  (ISO)
atorvastatin calcium  (ISO)
atrazine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (EXP,ISO)
berberine  (ISO)
beta-D-glucosamine  (EXP)
beta-hexachlorocyclohexane  (ISO)
bicalutamide  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bortezomib  (ISO)
bosutinib  (ISO)
BQ 123  (ISO)
brassinolide  (ISO)
Brodifacoum  (EXP)
bucladesine  (EXP)
budesonide  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
calciol  (ISO)
calcitriol  (ISO)
calcium dichloride  (EXP)
Calpeptin  (ISO)
capsaicin  (ISO)
captan  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carbonyl cyanide p-trifluoromethoxyphenylhydrazone  (ISO)
carbonyl sulfide  (EXP)
carnosic acid  (ISO)
casticin  (ISO)
cefaloridine  (EXP)
celecoxib  (ISO)
chenodeoxycholic acid  (ISO)
chloropicrin  (ISO)
choline  (ISO)
chromium(6+)  (EXP,ISO)
ciglitazone  (EXP)
cisplatin  (ISO)
clobenpropit  (ISO)
clofibric acid  (EXP)
clotrimazole  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) chloride  (ISO)
corticosterone  (EXP)
CU-O LINKAGE  (ISO)
cudraflavone B  (ISO)
curcumin  (EXP,ISO)
cyclophosphamide  (ISO)
cyclosporin A  (EXP,ISO)
cytochalasin B  (ISO)
D-glucose  (EXP)
daunorubicin  (EXP)
decabromodiphenyl ether  (ISO)
deguelin  (ISO)
dexamethasone  (ISO)
diacetylmonoxime  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
dibenzofuran  (EXP)
diclofenac  (ISO)
diethanolamine  (EXP,ISO)
diethylstilbestrol  (EXP)
digitoxin  (ISO)
dimethyldithiocarbamate  (ISO)
dioscin  (ISO)
dioxygen  (ISO)
disodium selenite  (EXP)
disulfiram  (ISO)
divanadium pentaoxide  (ISO)
doxorubicin  (ISO)
ellipticine  (ISO)
entinostat  (ISO)
enzalutamide  (ISO)
esculetin  (ISO)
etoposide  (ISO)
eugenol  (ISO)
farnesol  (ISO)
fasudil  (EXP)
fenofibrate  (EXP,ISO)
fenvalerate  (ISO)
ferric oxide  (EXP)
flavanone  (ISO)
fluoxetine  (ISO)
flutamide  (EXP)
folic acid  (ISO)
folpet  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
furan  (EXP)
gallic acid  (ISO)
gamma-tocopherol  (ISO)
ganglioside GM1  (EXP)
gefitinib  (ISO)
gemcitabine  (ISO)
genistein  (ISO)
geraniol  (ISO)
gingerol  (ISO)
glafenine  (EXP)
glucose  (EXP)
glycyrrhetinate  (ISO)
glycyrrhetinic acid  (ISO)
glyphosate  (EXP,ISO)
gold atom  (ISO)
gold(0)  (ISO)
guggulsterone  (ISO)
harmine  (EXP)
hemin  (ISO)
heparin  (ISO)
hesperetin  (ISO)
hexachlorobenzene  (EXP,ISO)
hexadecanoic acid  (ISO)
histamine  (ISO)
hydralazine  (EXP)
hydrochlorothiazide  (EXP)
hydrogen chloride  (ISO)
hydroxyurea  (ISO)
indole-3-methanol  (ISO)
indometacin  (ISO)
isoeugenol  (ISO)
isoflavones  (ISO)
isoliquiritigenin  (ISO)
isoprene  (ISO)
ivermectin  (ISO)
ketoconazole  (EXP)
kojic acid  (EXP)
L-ascorbic acid  (EXP)
L-cysteine  (ISO)
L-methionine  (ISO)
L-mimosine  (ISO)
lactacystin  (ISO)
lamivudine  (ISO)
lapatinib  (ISO)
lidocaine  (ISO)
linalool  (ISO)
lipopolysaccharide  (ISO)
lithium atom  (EXP)
lithium chloride  (ISO)
lithium hydride  (EXP)
lovastatin  (EXP,ISO)
luteolin  (ISO)
LY294002  (ISO)
Maxacalcitol  (ISO)
medroxyprogesterone acetate  (ISO)
menadione  (ISO)
metformin  (ISO)
methotrexate  (ISO)
methoxsalen  (ISO)
methylseleninic acid  (EXP,ISO)
mifepristone  (ISO)
minocycline  (ISO)
mitomycin C  (ISO)
ML-7  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
monobenzyl phthalate  (ISO)
monoethyl phthalate  (ISO)
monosodium L-glutamate  (ISO)
motexafin gadolinium  (ISO)
mycophenolic acid  (ISO)
myo-inositol hexakisphosphate  (ISO)
N-(6-acetamidohexyl)acetamide  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
NAD zwitterion  (EXP)
NAD(+)  (EXP)
naphthalene  (ISO)
nickel dichloride  (EXP,ISO)
nickel subsulfide  (EXP)
nicotinamide  (EXP)
nicotine  (ISO)
nilutamide  (ISO)
nimesulide  (ISO)
nitroglycerin  (EXP)
NS-398  (ISO)
ochratoxin A  (ISO)
orlistat  (ISO)
oxaliplatin  (EXP,ISO)
paclitaxel  (ISO)
palbociclib  (ISO)
Panduratin A  (ISO)
panobinostat  (ISO)
paracetamol  (EXP)
Pentoxifylline  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
perillyl alcohol  (ISO)
phenethyl caffeate  (EXP,ISO)
phenobarbital  (ISO)
phenylephrine  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
phosphatidylcholine  (ISO)
picoxystrobin  (ISO)
pioglitazone  (EXP,ISO)
piroxicam  (EXP)
platycodin D  (ISO)
potassium chromate  (ISO)
potassium dichromate  (EXP)
prednisone  (ISO)
progesterone  (ISO)
pterostilbene  (ISO)
pyrimidines  (ISO)
pyrrolidine dithiocarbamate  (EXP)
quercetin  (ISO)
quinazolines  (ISO)
rac-lactic acid  (ISO)
raloxifene  (ISO)
reserpine  (EXP)
resveratrol  (EXP,ISO)
rimonabant  (ISO)
ritonavir  (ISO)
Ro 41-5253  (ISO)
rubitecan  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP)
SB 203580  (ISO)
Se-methyl-L-selenocysteine  (EXP)
Se-methylselenocysteine  (EXP)
serpentine asbestos  (ISO)
silibinin  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP,ISO)
sirolimus  (EXP,ISO)
sirtinol  (ISO)
sodium arsenate  (EXP)
sodium arsenite  (ISO)
sorafenib  (EXP,ISO)
staurosporine  (ISO)
sterigmatocystin  (EXP)
stilbenoid  (ISO)
sulindac  (EXP)
sulindac sulfone  (ISO)
tacrolimus hydrate  (EXP)
tamoxifen  (ISO)
Tanshinone I  (ISO)
temozolomide  (ISO)
terazosin  (ISO)
Terfenadine  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
theophylline  (EXP,ISO)
thioacetamide  (EXP)
thiophenes  (ISO)
tipifarnib  (ISO)
tolbutamide  (EXP)
toluene 2,4-diisocyanate  (ISO)
Tomentosin  (ISO)
topotecan  (EXP)
trans-isoeugenol  (ISO)
tributylstannane  (EXP)
Tributyltin oxide  (EXP)
trichostatin A  (ISO)
Triptolide  (EXP)
troglitazone  (EXP,ISO)
urethane  (ISO)
ursolic acid  (ISO)
valproic acid  (ISO)
valsartan  (ISO)
vemurafenib  (ISO)
vinyl carbamate  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
wogonin  (EXP,ISO)
wortmannin  (ISO)
Y-27632  (EXP)
zidovudine  (ISO)
zinc acetate  (ISO)
zinc dichloride  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
autophagic cell death  (ISO)
cell death  (IMP)
cellular response to antibiotic  (ISO)
cellular response to lithium ion  (ISO)
cellular response to organic cyclic compound  (ISO)
G1/S transition of mitotic cell cycle  (IBA,ISO)
heart development  (ISO)
inner ear development  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of cardiac muscle tissue regeneration  (ISO)
negative regulation of cell cycle G1/S phase transition  (ISO)
negative regulation of cell growth  (ISO)
negative regulation of cell population proliferation  (IBA,IMP,ISO)
negative regulation of cellular component movement  (ISO)
negative regulation of cyclin-dependent protein kinase activity  (ISO)
negative regulation of cyclin-dependent protein serine/threonine kinase activity  (IBA,IMP,ISO)
negative regulation of epithelial cell proliferation  (ISO)
negative regulation of epithelial cell proliferation involved in prostate gland development  (ISO)
negative regulation of kinase activity  (ISO)
negative regulation of mitotic cell cycle  (IBA)
negative regulation of phosphorylation  (ISO)
negative regulation of transcription, DNA-templated  (ISO)
negative regulation of vascular associated smooth muscle cell proliferation  (ISO)
Notch signaling pathway  (ISO)
phosphorylation  (IEA)
placenta development  (ISO)
positive regulation of cell death  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of cyclin-dependent protein serine/threonine kinase activity  (IMP)
positive regulation of microtubule polymerization  (ISO)
positive regulation of protein catabolic process  (ISO)
potassium ion transport  (ISO)
regulation of cell cycle  (ISO)
regulation of cell cycle G1/S phase transition  (ISO)
regulation of cyclin-dependent protein serine/threonine kinase activity  (ISO)
regulation of exit from mitosis  (ISO)
regulation of G1/S transition of mitotic cell cycle  (ISO)
regulation of lens fiber cell differentiation  (ISO)
regulation of mitotic cell cycle  (ISO)
response to amino acid  (IEP)
response to cadmium ion  (IEP)
response to estradiol  (IEP)
response to glucose  (IEP)
response to hypoxia  (IEP)
response to organic cyclic compound  (IEP)
response to peptide hormone  (IEP)
response to xenobiotic stimulus  (IEP)
sensory perception of sound  (ISO)

Cellular Component

References

References - curated
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22. GOA data from the GO Consortium
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45. Nakamura S, etal., Biochem Biophys Res Commun. 1999 Apr 13;257(2):340-3.
46. NCBI rat LocusLink and RefSeq merged data July 26, 2002
47. Nomura H, etal., Biochem Biophys Res Commun. 1998 Jul 20;248(2):228-34.
48. Nomura H, etal., Gene 1997 Jun 3;191(2):211-8.
49. Nowee ME, etal., Histopathology. 2007 Nov;51(5):666-73.
50. Obaya AJ, etal., J Biol Chem 2002 Aug 23;277(34):31263-9.
51. OMIM Disease Annotation Pipeline
52. Ozkara SK and Corakci A, Pathol Oncol Res. 2004;10(2):89-97. Epub 2004 Jun 9.
53. Pellegata NS, etal., Proc Natl Acad Sci U S A. 2006 Oct 17;103(42):15558-63. Epub 2006 Oct 9.
54. Pham H, etal., Exp Neurol. 2014 Feb;252:114-23. doi: 10.1016/j.expneurol.2013.11.025. Epub 2013 Dec 7.
55. Pipeline to import KEGG annotations from KEGG into RGD
56. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
57. Pujol MJ, etal., J Hepatol. 2000 Aug;33(2):266-74.
58. Raina K, etal., Cancer Res. 2007 Nov 15;67(22):11083-91.
59. RGD automated data pipeline
60. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
61. RGD automated import pipeline for gene-chemical interactions
62. Rizk DE, etal., Int Urogynecol J Pelvic Floor Dysfunct. 2008 May 22;.
63. Rodier G, etal., EMBO J 2001 Dec 3;20(23):6672-82.
64. Romics I, etal., Pathol Oncol Res. 2008 Apr 16;.
65. Rosen DG, etal., Clin Cancer Res. 2005 Jan 15;11(2 Pt 1):632-7.
66. Sasaki T, etal., Surg Today. 2007;37(12):1073-82. Epub 2007 Nov 26.
67. Shen A, etal., Neurochem Int. 2008 May;52(6):1266-75. Epub 2008 Jan 31.
68. Sherr CJ Cancer Res. 2000 Jul 15;60(14):3689-95.
69. Szentmary N, etal., Histol Histopathol. 2010 Mar;25(3):287-90.
70. Szpirer C, etal., Mamm Genome 2000 Sep;11(9):729-35
71. Tao LJ, etal., Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2004 Feb;29(1):58-60.
72. Tokumoto YM, etal., Dev Biol 2002 May 1;245(1):224-34.
73. Uranbileg B, etal., J Biol Chem. 2012 Feb 24;287(9):6275-83. doi: 10.1074/jbc.M111.318295. Epub 2012 Jan 5.
74. Wu SH, etal., Zhongguo Dang Dai Er Ke Za Zhi. 2006 Jun;8(3):225-30.
75. Wu X, etal., J Mol Neurosci. 2012 Jan;46(1):184-91. doi: 10.1007/s12031-011-9572-9. Epub 2011 Jul 5.
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77. Xu ZG, etal., Kidney Int. 2005 Mar;67(3):944-52.
78. Yao C, etal., Nan Fang Yi Ke Da Xue Xue Bao. 2008 Apr;28(4):642-5.
79. Yatabe Y, etal., Cancer Res. 1998 Mar 1;58(5):1042-7.
80. Yu JY, etal., J Pharmacol Sci. 2008 May;107(1):90-8.
81. Yu S, etal., Exp Eye Res. 2006 Oct;83(4):758-70. Epub 2006 May 16.
82. Zheng T and Lu Y, Curr Eye Res. 2011 May;36(5):449-55. doi: 10.3109/02713683.2011.559301.
Additional References at PubMed
PMID:8033212   PMID:8033213   PMID:8534916   PMID:8684460   PMID:8973354   PMID:9190208   PMID:9264403   PMID:9784491   PMID:9811456   PMID:10079221   PMID:10208428   PMID:10827137  
PMID:10918569   PMID:11751454   PMID:11800646   PMID:12093740   PMID:12130539   PMID:12421491   PMID:12698196   PMID:12759355   PMID:12773549   PMID:12823546   PMID:12891709   PMID:15024385  
PMID:15213258   PMID:15220466   PMID:15355997   PMID:15564458   PMID:15568022   PMID:15647380   PMID:15652749   PMID:15665120   PMID:15701816   PMID:15879300   PMID:15894805   PMID:15964824  
PMID:16014817   PMID:16188652   PMID:16195383   PMID:16288221   PMID:16393152   PMID:16532026   PMID:16790529   PMID:16839413   PMID:16953280   PMID:17031475   PMID:17205219   PMID:17438373  
PMID:17569667   PMID:17647103   PMID:17852410   PMID:17873289   PMID:18076013   PMID:18182390   PMID:18311148   PMID:18513991   PMID:18604603   PMID:18687224   PMID:18787071   PMID:18802749  
PMID:18927218   PMID:19056892   PMID:19088079   PMID:19170105   PMID:19224154   PMID:19266349   PMID:19533683   PMID:19587222   PMID:19838216   PMID:20016102   PMID:20492666   PMID:21141556  
PMID:21182801   PMID:21229311   PMID:21300049   PMID:21452304   PMID:21484444   PMID:21628527   PMID:21693435   PMID:22344541   PMID:22524684   PMID:22930444   PMID:23370976   PMID:23762493  
PMID:23800691   PMID:23939805   PMID:24380855   PMID:24479887   PMID:24772447   PMID:25093615   PMID:25099287   PMID:25535395   PMID:25596037   PMID:25655933   PMID:25932965   PMID:26009842  
PMID:26086369   PMID:26130252   PMID:26151495   PMID:26323483   PMID:26562163   PMID:26917264   PMID:26920732   PMID:27011052   PMID:27434733   PMID:28666995   PMID:29024678   PMID:29436581  
PMID:29742504   PMID:30322885   PMID:30478251   PMID:30578960   PMID:30987681   PMID:32841050   PMID:33216476   PMID:33313941  


Genomics

Candidate Gene Status
Cdkn1b is a candidate Gene for QTL Ept5
Comparative Map Data
Cdkn1b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24167,760,067 - 167,765,177 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl4167,760,181 - 167,764,982 (+)Ensembl
Rnor_6.04168,689,043 - 168,694,159 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4168,689,163 - 168,693,964 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04232,962,218 - 232,967,323 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44171,841,705 - 171,846,506 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14172,086,631 - 172,091,508 (+)NCBI
Celera4156,357,827 - 156,362,628 (+)NCBICelera
Cytogenetic Map4q43NCBI
CDKN1B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1212,685,498 - 12,722,369 (+)EnsemblGRCh38hg38GRCh38
GRCh381212,717,368 - 12,722,369 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371212,870,302 - 12,875,303 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361212,761,576 - 12,766,570 (+)NCBINCBI36hg18NCBI36
Build 341212,761,575 - 12,766,569NCBI
Celera1218,018,828 - 18,023,831 (+)NCBI
Cytogenetic Map12p13.1NCBI
HuRef1212,639,893 - 12,644,900 (+)NCBIHuRef
CHM1_11212,835,677 - 12,840,684 (+)NCBICHM1_1
Cdkn1b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396134,897,364 - 134,902,488 (+)NCBIGRCm39mm39
GRCm39 Ensembl6134,897,364 - 134,902,476 (+)Ensembl
GRCm386134,920,401 - 134,925,525 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6134,920,401 - 134,925,513 (+)EnsemblGRCm38mm10GRCm38
MGSCv376134,870,419 - 134,875,543 (+)NCBIGRCm37mm9NCBIm37
MGSCv366134,886,110 - 134,889,751 (+)NCBImm8
Celera6137,877,174 - 137,882,301 (+)NCBICelera
Cytogenetic Map6G1NCBI
cM Map665.77NCBI
Cdkn1b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554139,615,542 - 9,620,542 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554139,615,542 - 9,620,542 (+)NCBIChiLan1.0ChiLan1.0
CDKN1B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11213,120,306 - 13,125,541 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1213,120,306 - 13,125,541 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01212,742,258 - 12,747,404 (+)NCBIMhudiblu_PPA_v0panPan3
CDKN1B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12733,609,154 - 33,613,558 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2733,611,760 - 33,612,906 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2712,832,036 - 12,833,182 (+)NCBI
ROS_Cfam_1.02733,916,284 - 33,921,570 (-)NCBI
UMICH_Zoey_3.12733,812,098 - 33,813,242 (-)NCBI
UNSW_CanFamBas_1.02733,762,117 - 33,763,263 (-)NCBI
UU_Cfam_GSD_1.02712,566,389 - 12,567,535 (+)NCBI
Cdkn1b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494594,845,531 - 94,850,821 (-)NCBI
SpeTri2.0NW_0049365874,573,166 - 4,578,480 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDKN1B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl559,731,206 - 59,735,831 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1559,731,224 - 59,735,831 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CDKN1B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11112,612,064 - 12,617,228 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1112,612,079 - 12,617,531 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606922,701,998 - 22,707,306 (-)NCBIVero_WHO_p1.0
Cdkn1b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475225,202,474 - 25,207,107 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
PMC140666P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24167,761,026 - 167,761,632 (+)MAPPERmRatBN7.2
Rnor_6.04168,690,009 - 168,690,614NCBIRnor6.0
Rnor_5.04232,963,173 - 232,963,778UniSTSRnor5.0
RGSC_v3.44171,842,551 - 171,843,156UniSTSRGSC3.4
Celera4156,358,673 - 156,359,278UniSTS
Cytogenetic Map4q43UniSTS
AI843786  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24167,764,989 - 167,765,083 (+)MAPPERmRatBN7.2
Rnor_6.04168,693,972 - 168,694,065NCBIRnor6.0
Rnor_5.04232,967,136 - 232,967,229UniSTSRnor5.0
RGSC_v3.44171,846,514 - 171,846,607UniSTSRGSC3.4
Celera4156,362,636 - 156,362,729UniSTS
Cytogenetic Map4q43UniSTS
PMC126040P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24167,759,858 - 167,760,106 (+)MAPPERmRatBN7.2
Rnor_6.04168,688,841 - 168,689,088NCBIRnor6.0
Rnor_5.04232,962,005 - 232,962,252UniSTSRnor5.0
RGSC_v3.44171,841,383 - 171,841,630UniSTSRGSC3.4
Celera4156,357,505 - 156,357,752UniSTS
Cytogenetic Map4q43UniSTS
PMC317217P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24167,760,599 - 167,760,737 (+)MAPPERmRatBN7.2
Rnor_6.04168,689,582 - 168,689,719NCBIRnor6.0
Rnor_5.04232,962,746 - 232,962,883UniSTSRnor5.0
RGSC_v3.44171,842,124 - 171,842,261UniSTSRGSC3.4
Celera4156,358,246 - 156,358,383UniSTS
Cytogenetic Map4q43UniSTS
RH124702  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24167,760,846 - 167,761,003 (+)MAPPERmRatBN7.2
Rnor_6.04168,689,829 - 168,689,985NCBIRnor6.0
Rnor_5.04232,962,993 - 232,963,149UniSTSRnor5.0
RGSC_v3.44171,842,371 - 171,842,527UniSTSRGSC3.4
Celera4156,358,493 - 156,358,649UniSTS
Cytogenetic Map4q43UniSTS
PMC307617P3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24167,760,580 - 167,760,777 (+)MAPPERmRatBN7.2
Rnor_6.04168,689,563 - 168,689,759NCBIRnor6.0
Rnor_5.04232,962,727 - 232,962,923UniSTSRnor5.0
RGSC_v3.44171,842,105 - 171,842,301UniSTSRGSC3.4
Celera4156,358,227 - 156,358,423UniSTS
Cytogenetic Map4q43UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat


Genetic Models
This gene Cdkn1b is modified in the following models/strains
miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir222rno-miR-222-3pMirtarbaseexternal_infoqRT-PCR//Luciferase reporter assay//Western blotFunctional MTI19150885
Mir221rno-miR-221-3pMirtarbaseexternal_infoqRT-PCR//Luciferase reporter assay//Western blotFunctional MTI19150885

Predicted Target Of
Summary Value
Count of predictions:618
Count of miRNA genes:263
Interacting mature miRNAs:330
Transcripts:ENSRNOT00000049848
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 56 40 19 40 8 10 74 35 36 11 8
Low 1 1 1 1 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000049848   ⟹   ENSRNOP00000050173
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4167,760,181 - 167,764,982 (+)Ensembl
Rnor_6.0 Ensembl4168,689,163 - 168,693,964 (+)Ensembl
RefSeq Acc Id: NM_031762   ⟹   NP_113950
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24167,760,181 - 167,764,982 (+)NCBI
Rnor_6.04168,689,163 - 168,693,964 (+)NCBI
Rnor_5.04232,962,218 - 232,967,323 (+)NCBI
RGSC_v3.44171,841,705 - 171,846,506 (+)RGD
Celera4156,357,827 - 156,362,628 (+)RGD
Sequence:
RefSeq Acc Id: XM_006237539   ⟹   XP_006237601
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24167,760,067 - 167,765,177 (+)NCBI
Rnor_6.04168,689,043 - 168,694,159 (+)NCBI
Rnor_5.04232,962,218 - 232,967,323 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_113950   ⟸   NM_031762
- UniProtKB: O08769 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237601   ⟸   XM_006237539
- Peptide Label: isoform X1
- UniProtKB: O08769 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000050173   ⟸   ENSRNOT00000049848
Protein Domains
CDI

Transcriptome

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

Promoters
RGD ID:13693453
Promoter ID:EPDNEW_R3978
Type:multiple initiation site
Name:Cdkn1b_1
Description:cyclin-dependent kinase inhibitor 1B
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_6.04168,689,071 - 168,689,131EPDNEW

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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (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
BXH2/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (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
F344/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
F344/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
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (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
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (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
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (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
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (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
LEXF1C/Stm (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
LEXF2B/Stm (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
LEXF3/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
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)
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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)