Cdc42 (cell division cycle 42) - Rat Genome Database

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Gene: Cdc42 (cell division cycle 42) Rattus norvegicus
Analyze
Symbol: Cdc42
Name: cell division cycle 42
RGD ID: 71043
Description: Exhibits GTP binding activity and mitogen-activated protein kinase kinase kinase binding activity. Involved in several processes, including Cdc42 protein signal transduction; actin filament branching; and regulation of synapse organization. Localizes to several cellular components, including Golgi membrane; Schaffer collateral - CA1 synapse; and secretory granule. Predicted to colocalize with centrosome. Biomarker of temporal lobe epilepsy. Human ortholog(s) of this gene implicated in fibrosarcoma. Orthologous to human CDC42 (cell division cycle 42); PARTICIPATES IN Rho/Rac/Cdc42 mediated signaling pathway; adenosine signaling pathway; c-Jun N-terminal kinases MAPK signaling pathway; INTERACTS WITH 2,4-dinitrotoluene; acrylamide; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cell division control protein 42 homolog; cell division cycle 42 (GTP binding protein); cell division cycle 42 homolog; cell division cycle 42 homolog (S. cerevisiae)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25149,555,069 - 149,593,239 (-)NCBI
Rnor_6.0 Ensembl5155,691,390 - 155,728,300 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.05155,690,267 - 155,728,385 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.05159,446,154 - 159,485,163 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45156,106,123 - 156,143,040 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15156,116,164 - 156,153,079 (-)NCBI
Celera5147,953,334 - 147,989,998 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
1,4-dichlorobenzene  (ISO)
1,8-cineole  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
2-amino-14,16-dimethyloctadecan-3-ol  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
acetylsalicylic acid  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
bazedoxifene  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP)
bortezomib  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
carbon nanotube  (ISO)
carboplatin  (EXP)
casticin  (ISO)
cefaloridine  (EXP)
chrysene  (ISO)
cisplatin  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
CU-O LINKAGE  (ISO)
D-glucose  (ISO)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (ISO)
disodium selenite  (ISO)
ethanol  (EXP,ISO)
flusilazole  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fumonisin B1  (ISO)
gallic acid  (ISO)
gamma-hexachlorocyclohexane  (EXP)
gentamycin  (EXP)
glucose  (ISO)
glyphosate  (EXP)
GTP  (EXP,ISO)
haloperidol  (EXP)
hexaconazole  (ISO)
hydralazine  (ISO)
hypochlorous acid  (ISO)
indometacin  (EXP)
kainic acid  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
lovastatin  (ISO)
mercury dichloride  (EXP)
metformin  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (EXP)
methylseleninic acid  (ISO)
microcystin-LR  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodimethylamine  (EXP)
niclosamide  (ISO)
nicotine  (ISO)
NSC 23766  (ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
phenobarbital  (ISO)
pioglitazone  (ISO)
piroxicam  (ISO)
Propiverine  (EXP)
quercetin  (ISO)
resveratrol  (ISO)
Risedronate sodium  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
simvastatin  (ISO)
sodium arsenite  (EXP)
sodium dichromate  (EXP)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
titanium dioxide  (ISO)
tremolite asbestos  (ISO)
triadimefon  (ISO)
Triptolide  (EXP)
valproic acid  (ISO)
warfarin  (ISO)
zinc oxide  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
actin cytoskeleton organization  (ISO)
actin filament branching  (IMP)
actin filament organization  (IMP,ISO,ISS)
adherens junction organization  (ISO)
cardiac conduction system development  (ISO)
Cdc42 protein signal transduction  (IBA,IDA)
cell division  (IEA)
cell junction assembly  (ISO,ISS)
cell migration  (IBA)
cell projection assembly  (IBA)
cellular protein localization  (ISO)
cellular response to interferon-gamma  (ISO)
dendritic cell migration  (ISO)
dendritic spine morphogenesis  (ISO,ISS)
endocytosis  (IBA,ISO)
establishment of cell polarity  (TAS)
establishment of epithelial cell apical/basal polarity  (ISO,ISS)
establishment of Golgi localization  (IMP)
establishment or maintenance of apical/basal cell polarity  (ISO)
filopodium assembly  (ISO)
Golgi organization  (IMP)
heart contraction  (ISO)
integrin-mediated signaling pathway  (ISO)
modification of synaptic structure  (IBA,IMP)
negative regulation of protein-containing complex assembly  (ISO)
neuron fate determination  (ISO)
neuropilin signaling pathway  (ISO)
nuclear migration  (ISO)
nucleus localization  (ISO)
organelle transport along microtubule  (IMP)
phagocytosis, engulfment  (ISO,ISS)
positive regulation of actin cytoskeleton reorganization  (ISO)
positive regulation of catalytic activity  (IMP)
positive regulation of cell growth  (ISO)
positive regulation of cytokinesis  (ISO,ISS)
positive regulation of DNA replication  (IMP)
positive regulation of epithelial cell proliferation involved in lung morphogenesis  (ISO)
positive regulation of filopodium assembly  (ISO,ISS)
positive regulation of intracellular protein transport  (IMP)
positive regulation of JNK cascade  (IDA)
positive regulation of lamellipodium assembly  (ISO)
positive regulation of MAPK cascade  (ISO)
positive regulation of neuron apoptotic process  (IMP)
positive regulation of phosphatidylinositol 3-kinase activity  (ISO)
positive regulation of pinocytosis  (ISO,ISS)
positive regulation of pseudopodium assembly  (ISO)
positive regulation of stress fiber assembly  (ISO)
positive regulation of substrate adhesion-dependent cell spreading  (ISO,ISS)
positive regulation of synapse structural plasticity  (IMP)
protein ubiquitination  (IEA)
regulation of attachment of spindle microtubules to kinetochore  (ISO,ISS)
regulation of exocytosis  (TAS)
regulation of filopodium assembly  (ISO,ISS)
regulation of lamellipodium assembly  (ISO)
regulation of mitotic nuclear division  (ISO)
regulation of modification of postsynaptic structure  (IMP)
regulation of protein binding  (ISO)
regulation of stress fiber assembly  (ISO)
response to glucose  (TAS)
small GTPase mediated signal transduction  (IEA)
sprouting angiogenesis  (IMP)
submandibular salivary gland formation  (IEP)
substantia nigra development  (ISO)
viral RNA genome replication  (ISO)

References

References - curated
1. Auer KL, etal., Mol Biol Cell. 1998 Mar;9(3):561-73.
2. Cardell LO, etal., Allergy. 2009 Sep;64(9):1301-8. Epub 2009 Apr 27.
3. Chen JL, etal., FEBS Lett. 2004 May 21;566(1-3):281-6.
4. Chockalingam PS, etal., Am J Physiol Cell Physiol 2002 Aug;283(2):C500-11.
5. Crema VO, etal., J Mol Histol. 2008 Oct;39(5):519-25. Epub 2008 Sep 11.
6. Cuadrado A and Nebreda AR, Biochem J. 2010 Aug 1;429(3):403-17. doi: 10.1042/BJ20100323.
7. Dovas A, etal., J Biol Chem. 2010 Jul 23;285(30):23296-308. doi: 10.1074/jbc.M109.098129. Epub 2010 May 15.
8. El-Sibai M, etal., J Cell Sci. 2007 Oct 1;120(Pt 19):3465-74. Epub 2007 Sep 12.
9. Erschbamer MK, etal., J Comp Neurol. 2005 Apr 4;484(2):224-33.
10. Etienne-Manneville S and Hall A, Nature 2003 Feb 13;421(6924):753-6.
11. Fanger GR, etal., EMBO J. 1997 Aug 15;16(16):4961-72.
12. Fournes B, etal., Mol Cell Biol 2003 Oct;23(20):7291-304.
13. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
14. Hahn A, etal., Biochem J 2002 Feb 15;362(Pt 1):33-40.
15. Han JS, etal., Exp Mol Med 2000 Sep 30;32(3):115-9.
16. Hehnly H, etal., Traffic. 2010 Aug;11(8):1067-78. doi: 10.1111/j.1600-0854.2010.01082.x. Epub 2010 May 26.
17. Ispanovic E, etal., Am J Physiol Cell Physiol. 2008 Sep;295(3):C600-10. Epub 2008 Jun 18.
18. Khan OM, etal., J Clin Invest. 2011 Feb;121(2):628-39. doi: 10.1172/JCI43758. Epub 2011 Jan 25.
19. Lim KB, etal., J Biol Chem. 2008 Jul 18;283(29):20454-72. doi: 10.1074/jbc.M710185200. Epub 2008 Apr 29.
20. Marques CA, etal., Blood. 2008 Feb 1;111(3):1413-9. Epub 2007 Oct 30.
21. MGD Curation, June 12, 2002
22. MGD data from the GO Consortium
23. Murakoshi H, etal., Nature. 2011 Apr 7;472(7341):100-4. Epub 2011 Mar 20.
24. NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. Nevins AK and Thurmond DC, J Biol Chem. 2005 Jan 21;280(3):1944-52. Epub 2004 Nov 9.
26. O'Kane EM, etal., Brain Res Mol Brain Res 2003 May 26;114(1):1-8.
27. OMIM Disease Annotation Pipeline
28. Padmos RC, etal., Arch Gen Psychiatry. 2008 Apr;65(4):395-407.
29. Pipeline to import KEGG annotations from KEGG into RGD
30. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
31. Pipeline to import SMPDB annotations from SMPDB into RGD
32. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
33. RGD automated import pipeline for gene-chemical interactions
34. Sharma AK, etal., Toxicol Pathol. 2009 Oct;37(6):776-89. Epub 2009 Aug 21.
35. Teramoto H, etal., J Biol Chem. 1996 Nov 1;271(44):27225-8.
36. Wang Z and Thurmond DC, J Cell Sci. 2009 Apr 1;122(Pt 7):893-903.
37. Xie C, etal., J Biol Chem. 2011 Oct 14;286(41):35933-42. Epub 2011 Aug 15.
38. Yang D, etal., Dig Dis Sci. 2017 Apr;62(4):958-967. doi: 10.1007/s10620-017-4451-z. Epub 2017 Feb 8.
39. Zhao J, etal., Cell Signal. 2007 Apr;19(4):831-43. Epub 2006 Dec 8.
40. Zhu X, etal., Exp Cell Res. 2011 Oct 1;317(16):2384-9. Epub 2011 Jul 7.
41. Zhu X, etal., Int J Dev Neurosci. 2000 Jul-Aug;18(4-5):433-7.
Additional References at PubMed
PMID:7592896   PMID:8625410   PMID:9748241   PMID:10618719   PMID:10699171   PMID:10724160   PMID:10954424   PMID:11035016   PMID:11260256   PMID:11584266   PMID:11807099   PMID:12477932  
PMID:12612085   PMID:14570905   PMID:14662747   PMID:14978216   PMID:15121898   PMID:15226395   PMID:15249579   PMID:15263019   PMID:15389538   PMID:15489334   PMID:15504731   PMID:15601624  
PMID:15642749   PMID:15723051   PMID:15728722   PMID:15775979   PMID:15797550   PMID:15866890   PMID:15882626   PMID:16195887   PMID:16328953   PMID:16336220   PMID:16380373   PMID:16443932  
PMID:16510873   PMID:16616186   PMID:16621792   PMID:16842757   PMID:16892058   PMID:17081755   PMID:17515837   PMID:17537723   PMID:17634366   PMID:18316075   PMID:18838382   PMID:19039103  
PMID:19056867   PMID:19144319   PMID:19161392   PMID:19199708   PMID:19244314   PMID:19289122   PMID:19376974   PMID:19542631   PMID:19787194   PMID:19796622   PMID:19943951   PMID:19946888  
PMID:20458337   PMID:20530489   PMID:20534521   PMID:20873783   PMID:21048939   PMID:21173111   PMID:21423176   PMID:21435037   PMID:21546274   PMID:21690310   PMID:21828338   PMID:21956892  
PMID:22426478   PMID:22461490   PMID:22494997   PMID:22871113   PMID:22891260   PMID:22926577   PMID:23219958   PMID:23325254   PMID:23358418   PMID:23376485   PMID:23533145   PMID:23620790  
PMID:23750457   PMID:23793062   PMID:24352656   PMID:24792215   PMID:25217619   PMID:25595978   PMID:25753037   PMID:25851601   PMID:26051942   PMID:26204446   PMID:26465210   PMID:27355516  
PMID:27412363   PMID:27482713   PMID:27917469   PMID:28031329   PMID:28161375   PMID:28432079   PMID:28838336   PMID:29321558   PMID:30358011   PMID:31144461   PMID:31397884  


Genomics

Comparative Map Data
Cdc42
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25149,555,069 - 149,593,239 (-)NCBI
Rnor_6.0 Ensembl5155,691,390 - 155,728,300 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.05155,690,267 - 155,728,385 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.05159,446,154 - 159,485,163 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45156,106,123 - 156,143,040 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15156,116,164 - 156,153,079 (-)NCBI
Celera5147,953,334 - 147,989,998 (-)NCBICelera
Cytogenetic Map5q36NCBI
CDC42
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl122,025,511 - 22,101,360 (+)EnsemblGRCh38hg38GRCh38
GRCh38122,052,709 - 22,101,360 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37122,379,202 - 22,427,853 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36122,251,707 - 22,292,023 (+)NCBINCBI36hg18NCBI36
Build 34122,124,487 - 22,164,741NCBI
Celera120,702,109 - 20,742,389 (+)NCBI
Cytogenetic Map1p36.12NCBI
HuRef120,622,960 - 20,663,212 (+)NCBIHuRef
CHM1_1122,491,651 - 22,531,931 (+)NCBICHM1_1
Cdc42
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394137,047,007 - 137,085,070 (-)NCBIGRCm39mm39
GRCm39 Ensembl4137,047,007 - 137,085,031 (-)Ensembl
GRCm384137,319,696 - 137,357,759 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4137,319,696 - 137,357,720 (-)EnsemblGRCm38mm10GRCm38
MGSCv374136,875,611 - 136,913,652 (-)NCBIGRCm37mm9NCBIm37
MGSCv364136,591,779 - 136,608,205 (-)NCBImm8
Celera4135,540,002 - 135,577,854 (-)NCBICelera
Cytogenetic Map4D3NCBI
cM Map469.83NCBI
Cdc42
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554522,255,117 - 2,299,042 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554522,255,940 - 2,299,042 (+)NCBIChiLan1.0ChiLan1.0
CDC42
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1122,188,722 - 22,228,351 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0121,245,970 - 21,286,210 (+)NCBIMhudiblu_PPA_v0panPan3
LOC403934
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1277,153,276 - 77,169,947 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl277,153,095 - 77,199,211 (-)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.044,445,564 - 4,446,293 (+)NCBI
UMICH_Zoey_3.144,457,005 - 4,457,734 (+)NCBI
UNSW_CanFamBas_1.044,574,515 - 4,575,244 (+)NCBI
UU_Cfam_GSD_1.044,796,130 - 4,796,859 (+)NCBI
Cdc42
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505841,731,950 - 41,773,901 (+)NCBI
SpeTri2.0NW_0049364747,556,765 - 7,598,687 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDC42
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl680,035,122 - 80,089,233 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1680,035,034 - 80,089,243 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2674,057,184 - 74,116,824 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CDC42
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120110,568,004 - 110,608,318 (-)NCBI
ChlSab1.1 Ensembl20110,569,352 - 110,582,562 (-)Ensembl
Vero_WHO_p1.0NW_0236660335,689,907 - 5,730,175 (+)NCBI
Cdc42
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247646,874,453 - 6,891,952 (+)NCBI

Position Markers
Cdc42  
Rat AssemblyChrPosition (strand)SourceJBrowse
RGSC_v3.45156,117,344 - 156,117,531UniSTSRGSC3.4
RGSC_v3.45156,105,066 - 156,105,248UniSTSRGSC3.4
Celera5147,964,527 - 147,964,714UniSTS
Celera5147,952,277 - 147,952,459UniSTS
RH137463  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25149,555,701 - 149,555,890 (+)MAPPER
Rnor_6.05155,690,900 - 155,691,088NCBIRnor6.0
Rnor_5.05159,446,787 - 159,446,975UniSTSRnor5.0
RGSC_v3.45156,105,638 - 156,105,826UniSTSRGSC3.4
Celera5147,952,849 - 147,953,037UniSTS
Cytogenetic Map5q36UniSTS
UniSTS:224478  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25149,557,684 - 149,557,838 (+)MAPPER
Rnor_6.05155,692,883 - 155,693,036NCBIRnor6.0
Rnor_5.05159,448,770 - 159,448,923UniSTSRnor5.0
RGSC_v3.45156,107,621 - 156,107,774UniSTSRGSC3.4
Celera5147,954,832 - 147,954,985UniSTS
Cytogenetic Map5q36UniSTS
Cdc42  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.05159,458,806 - 159,458,993UniSTSRnor5.0
RGSC_v3.45156,117,344 - 156,117,531UniSTSRGSC3.4
Celera5147,964,527 - 147,964,714UniSTS
Cytogenetic Map5q36UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)547745646167946134Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)561612600168109659Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)571552569157225114Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)584963058173504662Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5111278451156278451Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5112279412157279412Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5112279412157279412Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5112279412157279412Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5112279412157279412Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5112279412157279412Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5114140832159140832Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5114140832159140832Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5116767924161767924Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5116767924161767924Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5116767924161767924Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5116767924161767924Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5125455818157225114Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5128687766173687766Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5131077716173707219Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132551937173707219Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133943857173707219Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133943857173707219Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5134197905173707219Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5134502140157212422Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5134712342173707219Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5134712342173707219Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5136354114173707219Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136640731173707219Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5138154677172402610Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5142307322173707219Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5142309061173707219Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5149029982173687766Rat
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5149568588167739697Rat
631263Cm24Cardiac mass QTL 243.5heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)5149832180164807402Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5150340838164298744Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5150360936167946134Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:236
Count of miRNA genes:167
Interacting mature miRNAs:190
Transcripts:ENSRNOT00000018118, ENSRNOT00000029025
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_171994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764286 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764287 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110709 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110710 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC132705 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF205635 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF491841 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC060535 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213007 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225541 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225902 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226943 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227167 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227499 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227894 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228149 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231089 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231482 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231846 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232179 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232295 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232459 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233586 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234217 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234623 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234639 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234830 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000018118   ⟹   ENSRNOP00000018118
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl5155,693,116 - 155,709,215 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000029025   ⟹   ENSRNOP00000030928
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl5155,691,390 - 155,728,300 (-)Ensembl
RefSeq Acc Id: NM_171994   ⟹   NP_741991
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25149,556,187 - 149,593,108 (-)NCBI
Rnor_6.05155,691,385 - 155,728,300 (-)NCBI
Rnor_5.05159,446,154 - 159,485,163 (-)NCBI
RGSC_v3.45156,106,123 - 156,143,040 (-)RGD
Celera5147,953,334 - 147,989,998 (-)RGD
Sequence:
RefSeq Acc Id: XM_008764286   ⟹   XP_008762508
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25149,555,069 - 149,589,791 (-)NCBI
Rnor_6.05155,690,267 - 155,725,368 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764287   ⟹   XP_008762509
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25149,557,145 - 149,593,239 (-)NCBI
Rnor_6.05155,692,343 - 155,728,385 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039110709   ⟹   XP_038966637
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25149,555,069 - 149,588,827 (-)NCBI
RefSeq Acc Id: XM_039110710   ⟹   XP_038966638
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25149,555,069 - 149,592,180 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_741991   ⟸   NM_171994
- UniProtKB: Q8CFN2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008762508   ⟸   XM_008764286
- Peptide Label: isoform X1
- UniProtKB: Q8CFN2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008762509   ⟸   XM_008764287
- Peptide Label: isoform X2
- UniProtKB: Q8CFN2 (UniProtKB/Swiss-Prot),   A0A0G2JSM8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018118   ⟸   ENSRNOT00000018118
RefSeq Acc Id: ENSRNOP00000030928   ⟸   ENSRNOT00000029025
RefSeq Acc Id: XP_038966638   ⟸   XM_039110710
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038966637   ⟸   XM_039110709
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13694177
Promoter ID:EPDNEW_R4702
Type:initiation region
Name:Cdc42_1
Description:cell division cycle 42
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_6.05155,728,312 - 155,728,372EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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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)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/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
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 (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
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
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
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
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
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 (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
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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 (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 (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
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 (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 (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:71043 AgrOrtholog
Ensembl Genes ENSRNOG00000013536 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000018118 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000030928 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000018118 UniProtKB/TrEMBL
  ENSRNOT00000029025 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6920523 IMAGE-MGC_LOAD
InterPro Cdc42 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Small_GTP-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Small_GTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Small_GTPase_Rho UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:64465 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72646 IMAGE-MGC_LOAD
NCBI Gene 64465 ENTREZGENE
Pfam Ras UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cdc42 PhenoGen
PROSITE RHO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs small_GTP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JSM8 ENTREZGENE, UniProtKB/TrEMBL
  CDC42_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q6P9Y3 UniProtKB/Swiss-Prot
  Q71TW5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-01-14 Cdc42  cell division cycle 42  Cdc42  cell division cycle 42 (GTP binding protein)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-26 Cdc42  cell division cycle 42 (GTP binding protein)  Cdc42  cell division cycle 42 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-07-09 Cdc42  cell division cycle 42 homolog (S. cerevisiae)      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_process regulates cell polarity through the spatial regulation of GSK-3beta and Apc 632398
gene_process involved in reduction of the expression of dystrophin-glycoprotein complex (DGC) in muscle atrophy 625642