Ccnd3 (cyclin D3) - Rat Genome Database

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Gene: Ccnd3 (cyclin D3) Rattus norvegicus
Analyze
Symbol: Ccnd3
Name: cyclin D3
RGD ID: 2293
Description: Enables protein kinase binding activity. Involved in several processes, including G1/S transition of mitotic cell cycle; hyaluronan biosynthetic process; and response to glucose. Predicted to be located in nucleoplasm. Predicted to be part of cyclin-dependent protein kinase holoenzyme complex. Predicted to be active in cytoplasm and nucleus. Orthologous to human CCND3 (cyclin D3); PARTICIPATES IN G1/S transition pathway; cell cycle pathway, mitotic; Jak-Stat signaling pathway; INTERACTS WITH 17beta-estradiol; 2-methoxyethanol; 3,3',5,5'-tetrabromobisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: G1/S-specific cyclin-D3; MGC108760; MGC93643
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
mRatBN7.2913,394,161 - 13,400,341 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl913,394,169 - 13,489,371 (-)Ensembl
Rnor_6.0915,404,816 - 15,410,905 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl915,404,822 - 15,410,943 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0914,326,227 - 14,332,267 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera911,145,441 - 11,151,481 (-)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(aminomethyl)phosphonic acid  (ISO)
(S)-amphetamine  (ISO)
1,2-dimethylhydrazine  (ISO)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
15-deoxy-Delta(12,14)-prostaglandin J2  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2-methoxy-17beta-estradiol  (ISO)
2-methoxyethanol  (EXP)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3,3'-diindolylmethane  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
5-fluorouracil  (ISO)
9-cis-retinoic acid  (ISO)
acetylleucyl-leucyl-norleucinal  (ISO)
acetylsalicylic acid  (ISO)
acteoside  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (EXP,ISO)
ammonium chloride  (EXP)
aniline  (EXP)
aristolochic acid  (ISO)
arotinoid acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
atropine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzoates  (ISO)
biphenyl-4-amine  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (ISO)
bosutinib  (ISO)
bucladesine  (EXP)
butan-1-ol  (ISO)
Butylparaben  (ISO)
butyric acid  (EXP)
cadmium atom  (EXP)
cadmium dichloride  (EXP,ISO)
calycosin  (ISO)
camostat  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chlorohydrocarbon  (ISO)
chloroprene  (ISO)
chlorpromazine  (ISO)
chromium(6+)  (EXP)
cisplatin  (ISO)
clofibrate  (EXP,ISO)
clozapine  (EXP)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
curcumin  (ISO)
cycloheximide  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
daunorubicin  (ISO)
Deguelin  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dichlorine  (EXP)
diclofenac  (ISO)
diethylstilbestrol  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
dronedarone  (ISO)
ethyl methanesulfonate  (ISO)
everolimus  (ISO)
fenamidone  (ISO)
fluoxetine  (ISO)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (EXP,ISO)
furazolidone  (ISO)
gamma-tocopherol  (ISO)
gefitinib  (ISO)
haloperidol  (EXP)
hydroxyurea  (ISO)
hypochlorous acid  (ISO)
isoprenaline  (ISO)
juglone  (ISO)
kinamycin F  (ISO)
L-ascorbic acid  (EXP,ISO)
lithium chloride  (ISO)
lovastatin  (ISO)
LY294002  (ISO)
lycorine  (ISO)
methoxyacetic acid  (ISO)
methyl methanesulfonate  (ISO)
methylazoxymethanol  (ISO)
methylmercury chloride  (EXP,ISO)
mono(2-ethylhexyl) phthalate  (ISO)
monobenzyl phthalate  (ISO)
monoethyl phthalate  (ISO)
monosodium L-glutamate  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-N-nitrosourea  (EXP)
nelfinavir  (ISO)
nickel atom  (ISO)
niclosamide  (ISO)
ozone  (EXP)
palbociclib  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
parathion  (ISO)
PD 0325901  (ISO)
pentobarbital  (EXP)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (EXP)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
picrotoxin  (EXP)
pioglitazone  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
potassium dichromate  (EXP)
progesterone  (EXP)
quercetin  (ISO)
resveratrol  (EXP,ISO)
Ro 41-5253  (ISO)
rotenone  (ISO)
rottlerin  (ISO)
SB 203580  (ISO)
SB 431542  (ISO)
silibinin  (ISO)
silicon dioxide  (ISO)
sirolimus  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP)
sorafenib  (ISO)
sulforaphane  (ISO)
tamoxifen  (ISO)
Tesaglitazar  (EXP)
tetrachloromethane  (EXP)
thymoquinone  (ISO)
titanium dioxide  (ISO)
tocopherol  (ISO)
tolbutamide  (EXP)
Tributyltin oxide  (EXP,ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
tropan-3alpha-yl 3-hydroxy-2-phenylpropanoate  (ISO)
Tryptanthrine  (ISO)
urethane  (ISO)
ursodeoxycholic acid  (ISO)
ursolic acid  (ISO)
usnic acid  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin E  (EXP)
wortmannin  (ISO)
XAV939  (ISO)
Y-27632  (ISO)
ziram  (EXP)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cyclin-dependent protein kinase holoenzyme complex  (IBA,IEA,ISO)
cytoplasm  (IBA,IEA,ISO)
membrane  (IEA)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Bergsagel PL, etal., Blood. 2005 Jul 1;106(1):296-303. Epub 2005 Mar 8.
2. Boylan JM and Gruppuso PA, Biochem Biophys Res Commun. 2005 May 13;330(3):722-30.
3. Gattringer B Nervenarzt 1977 Jun;48(6):326-30.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Grundschober C, etal., J Biol Chem 2001 Dec 14;276(50):46751-8.
7. Hosokawa Y, etal., Gene 1994 Sep 30;147(2):249-52.
8. Ji Y, etal., Mol Cell Biochem. 2008 Feb;309(1-2):49-60. Epub 2007 Nov 16.
9. Justenhoven C, etal., Int J Cancer. 2009 May 1;124(9):2077-81.
10. Levidou G, etal., Int J Gynecol Pathol. 2007 Oct;26(4):410-7.
11. Lopez-Beltran A, etal., J Pathol. 2006 May;209(1):106-13.
12. MGD data from the GO Consortium
13. Motti ML, etal., Oncogene. 2003 Oct 23;22(48):7576-86.
14. NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. Nikoleishvili D, etal., Int Urol Nephrol. 2008;40(4):953-9. Epub 2008 Mar 4.
16. O'Loinsigh ED, etal., J Neurochem. 2004 Jan;88(2):370-9.
17. Pertia A, etal., Int Urol Nephrol. 2009;41(2):243-9. Epub 2008 Aug 5.
18. Pipeline to import KEGG annotations from KEGG into RGD
19. Pirkmaier A, etal., Oncogene. 2003 Jul 10;22(28):4425-33.
20. Ren J, etal., J Biol Chem. 2009 Jun 12;284(24):16621-32. Epub 2009 Mar 9.
21. RGD automated data pipeline
22. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
23. RGD automated import pipeline for gene-chemical interactions
24. Rickheim DG, etal., Hepatology 2002 Jul;36(1):30-8.
25. Sherr CJ Cancer Res. 2000 Jul 15;60(14):3689-95.
26. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
27. Van de Putte G, etal., Gynecol Oncol. 2004 Jan;92(1):40-6.
28. Weroha SJ, etal., Carcinogenesis. 2006 Mar;27(3):491-8. Epub 2005 Nov 25.
29. Wong SC, etal., J Pathol. 2001 May;194(1):35-42.
30. Yang M, etal., Gene 1996 Nov 28;181(1-2):153-9.
Additional References at PubMed
PMID:8114739   PMID:8822197   PMID:11809706   PMID:12130539   PMID:12477932   PMID:14706337   PMID:16412096   PMID:19550149   PMID:19672123   PMID:20066559   PMID:21539824   PMID:23109711  
PMID:25596037   PMID:26657864  


Genomics

Comparative Map Data
Ccnd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2913,394,161 - 13,400,341 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl913,394,169 - 13,489,371 (-)Ensembl
Rnor_6.0915,404,816 - 15,410,905 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl915,404,822 - 15,410,943 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0914,326,227 - 14,332,267 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera911,145,441 - 11,151,481 (-)NCBICelera
Cytogenetic Map9q12NCBI
CCND3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl641,934,934 - 42,050,357 (-)EnsemblGRCh38hg38GRCh38
GRCh38641,934,933 - 42,048,894 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37641,902,671 - 42,016,632 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36642,010,649 - 42,017,530 (-)NCBINCBI36hg18NCBI36
Build 34642,010,649 - 42,017,530NCBI
Celera643,455,463 - 43,569,077 (-)NCBI
Cytogenetic Map6p21.1NCBI
HuRef641,621,515 - 41,734,566 (-)NCBIHuRef
CHM1_1641,905,431 - 42,019,143 (-)NCBICHM1_1
Ccnd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391747,815,976 - 47,910,614 (+)NCBIGRCm39mm39
GRCm39 Ensembl1747,815,976 - 47,910,616 (+)Ensembl
GRCm381747,505,051 - 47,599,689 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1747,505,051 - 47,599,691 (+)EnsemblGRCm38mm10GRCm38
MGSCv371747,642,000 - 47,736,638 (+)NCBIGRCm37mm9NCBIm37
MGSCv361747,056,739 - 47,062,880 (+)NCBImm8
Celera1750,938,969 - 51,036,715 (+)NCBICelera
Cytogenetic Map17CNCBI
cM Map1723.37NCBI
Ccnd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554378,268,118 - 8,273,855 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554378,266,523 - 8,273,855 (-)NCBIChiLan1.0ChiLan1.0
CCND3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1642,820,569 - 42,932,944 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl642,820,569 - 42,827,498 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0641,518,421 - 41,630,103 (-)NCBIMhudiblu_PPA_v0panPan3
CCND3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11210,593,786 - 10,688,304 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1210,594,712 - 10,600,891 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1210,623,109 - 10,717,215 (-)NCBI
ROS_Cfam_1.01211,074,540 - 11,169,519 (-)NCBI
UMICH_Zoey_3.11210,604,536 - 10,698,641 (-)NCBI
UNSW_CanFamBas_1.01210,688,499 - 10,783,041 (-)NCBI
UU_Cfam_GSD_1.01210,782,466 - 10,877,073 (-)NCBI
Ccnd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494646,073,366 - 46,160,552 (-)NCBI
SpeTri2.0NW_00493647617,799,754 - 17,886,835 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCND3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl737,082,097 - 37,181,366 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1737,087,336 - 37,182,462 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2742,489,107 - 42,493,235 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CCND3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11730,107,236 - 30,228,449 (+)NCBI
ChlSab1.1 Ensembl1730,221,598 - 30,227,452 (+)Ensembl
Vero_WHO_p1.0NW_02366604441,934,657 - 42,061,231 (-)NCBI
Ccnd3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475417,148,108 - 17,194,626 (+)NCBI

Position Markers
D8Mgh14  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map8q24UniSTS
D2Mit27   No map positions available.
D9Wox28  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2913,401,258 - 13,401,435 (+)MAPPERmRatBN7.2
Rnor_6.0915,411,905 - 15,412,081NCBIRnor6.0
Rnor_5.0914,333,257 - 14,333,433UniSTSRnor5.0
Celera911,152,425 - 11,152,591UniSTS
Cytogenetic Map8q24UniSTS
D9Wox44  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2913,400,793 - 13,400,943 (+)MAPPERmRatBN7.2
Rnor_6.0915,411,440 - 15,411,589NCBIRnor6.0
Rnor_5.0914,332,792 - 14,332,941UniSTSRnor5.0
Celera911,151,957 - 11,152,109UniSTS
Cytogenetic Map8q24UniSTS
RH124354  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2913,394,166 - 13,394,439 (+)MAPPERmRatBN7.2
Rnor_6.0915,404,822 - 15,405,094NCBIRnor6.0
Rnor_5.0914,326,184 - 14,326,456UniSTSRnor5.0
Celera911,145,398 - 11,145,670UniSTS
Cytogenetic Map8q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
1578675Bss17Bone structure and strength QTL 173.8femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)9336865213533896Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9795472022071169Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:73
Count of miRNA genes:64
Interacting mature miRNAs:65
Transcripts:ENSRNOT00000074217
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 51 35 19 35 4 7 71 35 36 11 4
Low 6 6 6 4 4 3 5 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000074217   ⟹   ENSRNOP00000064704
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl913,394,169 - 13,489,371 (-)Ensembl
Rnor_6.0 Ensembl915,404,822 - 15,410,943 (-)Ensembl
RefSeq Acc Id: NM_012766   ⟹   NP_036898
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2913,394,161 - 13,400,341 (-)NCBI
Rnor_6.0915,404,865 - 15,410,905 (-)NCBI
Rnor_5.0914,326,227 - 14,332,267 (-)NCBI
Celera911,145,441 - 11,151,481 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039083034   ⟹   XP_038938962
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2913,394,161 - 13,399,448 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_036898   ⟸   NM_012766
- Sequence:
RefSeq Acc Id: ENSRNOP00000064704   ⟸   ENSRNOT00000074217
RefSeq Acc Id: XP_038938962   ⟸   XM_039083034
- Peptide Label: isoform X1
Protein Domains
Cyclin N-terminal

Transcriptome

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

Promoters
RGD ID:13696499
Promoter ID:EPDNEW_R7022
Type:initiation region
Name:Ccnd3_1
Description:cyclin D3
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_6.0915,410,992 - 15,411,052EPDNEW

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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (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
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/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
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2293 AgrOrtholog
Ensembl Genes ENSRNOG00000050258 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000064704 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074217 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7189593 IMAGE-MGC_LOAD
  IMAGE:7384331 IMAGE-MGC_LOAD
InterPro Cyclin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyclin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyclin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyclin_C-dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyclin_D UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyclin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25193 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108760 IMAGE-MGC_LOAD
  MGC:93643 IMAGE-MGC_LOAD
NCBI Gene 25193 ENTREZGENE
PANTHER PTHR10177 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10177:SF65 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Cyclin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyclin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ccnd3 PhenoGen
PROSITE CYCLINS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CYCLIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyclin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47954 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC228844
UniProt CCND3_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q5U321_RAT UniProtKB/TrEMBL
UniProt Secondary Q63628 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Ccnd3  Cyclin D3      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function binds both cdk4 and cdk6 in hepatocytes 1298736
gene_physical_interaction interacts with Cdk4 70761
gene_process plays a key role in the G1/S transition in cell cycle 70761
gene_regulation protein amount is regulated at the transcription level and protein half-life is 25 minutes 70761