Pcna (proliferating cell nuclear antigen) - Rat Genome Database

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Gene: Pcna (proliferating cell nuclear antigen) Rattus norvegicus
Analyze
Symbol: Pcna
Name: proliferating cell nuclear antigen
RGD ID: 3269
Description: Enables estrogen receptor binding activity. Involved in several processes, including estrous cycle; liver regeneration; and response to dexamethasone. Located in nucleus. Biomarker of several diseases, including brain ischemia (multiple); mucositis; obstructive jaundice; osteoporosis; and sciatic neuropathy. Human ortholog(s) of this gene implicated in stomach cancer. Orthologous to human PCNA (proliferating cell nuclear antigen); PARTICIPATES IN mismatch repair pathway; nucleotide excision repair pathway; base excision repair pathway; INTERACTS WITH (+)-pilocarpine; (+)-taxifolin; (-)-epigallocatechin 3-gallate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cyclin; Pcna/cyclin; PCNAR
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
mRatBN7.23119,499,039 - 119,502,911 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl3119,498,810 - 119,502,995 (-)Ensembl
Rnor_6.03124,880,698 - 124,884,570 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3124,880,698 - 124,884,570 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03131,376,235 - 131,380,108 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43120,008,715 - 120,012,589 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13119,914,289 - 119,918,243 (-)NCBI
Celera3118,296,567 - 118,300,439 (-)NCBICelera
RH 3.4 Map31023.4RGD
Cytogenetic Map3q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(+)-taxifolin  (EXP)
(-)-epigallocatechin 3-gallate  (EXP)
(-)-quinic acid  (ISO)
(R)-lipoic acid  (EXP)
(R)-mevalonic acid  (ISO)
(R,R,R)-alpha-tocopherol  (EXP)
(S)-nicotine  (ISO)
(Z)-3-butylidenephthalide  (ISO)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichlorobenzene  (EXP)
1,2-dimethylhydrazine  (EXP,ISO)
1,3-thiazolidine-2,4-dione  (ISO)
1,4-dichlorobenzene  (EXP)
1,4-dioxane  (EXP)
1-chloro-2,4-dinitrobenzene  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2,4-D  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2-acetamidofluorene  (EXP)
2-nitrofluorene  (EXP)
2-tert-butylhydroquinone  (EXP)
3,3',5-triiodo-L-thyronine  (ISO)
3-[(4-anilinophenyl)diazenyl]benzene-1-sulfonic acid  (EXP)
3-aminobenzamide  (EXP)
3-BROMO-7-NITROINDAZOLE  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP,ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (EXP,ISO)
4-nonylphenol  (EXP,ISO)
4-vinylcyclohexene dioxide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (EXP)
5-fluorouracil  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP,ISO)
5-methyltetrahydrofolic acid  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (EXP)
6-propyl-2-thiouracil  (ISO)
7,12-dimethyltetraphene  (EXP,ISO)
acetamide  (EXP)
acetic acid  (EXP)
acetylsalicylic acid  (EXP)
acrylamide  (EXP)
actinomycin D  (EXP,ISO)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (ISO)
allethrin  (EXP)
alpha-amanitin  (ISO)
alpha-hexachlorocyclohexane  (EXP)
aluminium atom  (ISO)
aluminium(0)  (ISO)
alvocidib  (ISO)
amifostine  (ISO)
amiodarone  (EXP)
ammonium chloride  (EXP)
amphibole asbestos  (ISO)
andrographolide  (ISO)
aniline  (EXP,ISO)
anthocyanin  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP,ISO)
apigenin  (ISO)
apocynin  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite ion  (EXP)
arsenite(3-)  (ISO)
arsenous acid  (EXP,ISO)
artesunate  (EXP)
asiatic acid  (EXP)
atrazine  (ISO)
atropine  (ISO)
avobenzone  (ISO)
azadirachtin A  (ISO)
azathioprine  (ISO)
azoxystrobin  (ISO)
bafilomycin A1  (ISO)
bathocuproine disulfonic acid  (ISO)
benazepril  (EXP)
benzamide  (EXP)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
Besigomsin  (ISO)
beta-aminopropionitrile  (ISO)
beta-naphthoflavone  (EXP)
beta-tocopherol  (EXP)
betulinic acid  (ISO)
bezafibrate  (EXP,ISO)
bicalutamide  (ISO)
biphenyl-4-amine  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (EXP)
boric acid  (EXP)
boron atom  (EXP)
bromocriptine  (EXP)
bromodichloromethane  (EXP,ISO)
bromoform  (ISO)
brucine  (EXP)
budesonide  (ISO)
buspirone  (EXP)
Butylbenzyl phthalate  (ISO)
C.I. Natural Red 20  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (EXP)
calcidiol  (ISO)
calcitriol  (EXP,ISO)
camostat  (ISO)
cannabidiol  (ISO)
captafol  (EXP)
carbamate ester  (ISO)
carbon nanotube  (ISO)
carboplatin  (EXP,ISO)
cefaloridine  (EXP)
celastrol  (ISO)
celecoxib  (ISO)
cerium trichloride  (ISO)
chelerythrine  (EXP)
Chlorodibromomethane  (ISO)
chloroform  (ISO)
chlorogenic acid  (ISO)
chlorpyrifos  (EXP)
cholic acid  (ISO)
chromium(6+)  (EXP)
chrysin  (EXP)
chrysophanol  (ISO)
cilostazol  (ISO)
Cinobufagin  (ISO)
cisplatin  (EXP,ISO)
citral  (EXP)
clofibrate  (EXP)
cobalt dichloride  (EXP,ISO)
coenzyme Q10  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
cortisol  (ISO)
costunolide  (ISO)
coumarin  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
CU-O LINKAGE  (ISO)
Cuprizon  (EXP)
curcumin  (EXP,ISO)
cyanidin cation  (ISO)
cyclohexanols  (EXP)
cycloheximide  (ISO)
cyclophosphamide  (EXP,ISO)
cyclosporin A  (EXP,ISO)
cyhalothrin  (EXP)
cylindrospermopsin  (ISO)
cypermethrin  (EXP,ISO)
cyprodinil  (ISO)
D-aspartic acid  (ISO)
D-glucose  (EXP,ISO)
daidzein  (EXP,ISO)
dapoxetine  (EXP)
decabromodiphenyl ether  (ISO)
delta-tocopherol  (EXP)
deoxynivalenol  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (EXP,ISO)
Diallyl sulfide  (EXP)
diallyl trisulfide  (ISO)
diamminedichloroplatinum  (ISO)
diarsenic trioxide  (EXP,ISO)
diazinon  (ISO)
dibenz[a,h]anthracene  (ISO)
dibenzo[a,l]pyrene  (ISO)
dibutyl phthalate  (ISO)
dichlorine  (EXP)
dichloroacetic acid  (ISO)
diclofenac  (ISO)
dicrotophos  (ISO)
dieckol  (ISO)
dieldrin  (EXP)
diethyl maleate  (ISO)
diethylstilbestrol  (EXP,ISO)
diheptyl phthalate  (EXP)
dihydroxyacetone  (ISO)
dimethylarsinic acid  (EXP)
diosmin  (EXP)
dioxygen  (ISO)
disodium selenite  (ISO)
dodecanoic acid  (ISO)
doxorubicin  (EXP,ISO)
elemental boron  (EXP)
elemental selenium  (ISO)
ellagic acid  (ISO)
embelin  (ISO)
emodin  (EXP)
endosulfan  (ISO)
Enterolactone  (ISO)
entinostat  (ISO)
enzacamene  (ISO)
enzyme inhibitor  (ISO)
Estragole  (EXP)
ethanol  (EXP,ISO)
eugenol  (EXP,ISO)
famotidine  (EXP)
fenhexamid  (ISO)
fenofibrate  (ISO)
fenvalerate  (EXP)
finasteride  (EXP)
fipronil  (EXP)
fludioxonil  (ISO)
flufenoxuron  (ISO)
flutamide  (EXP)
folic acid  (EXP,ISO)
fulvestrant  (ISO)
furan  (EXP)
gallic acid  (EXP)
gamma-linolenic acid  (ISO)
gamma-tocopherol  (EXP)
gefitinib  (ISO)
gemfibrozil  (EXP)
genistein  (EXP,ISO)
gentamycin  (EXP)
geranial  (EXP)
geraniol  (EXP,ISO)
glucaric acid  (ISO)
glucose  (EXP,ISO)
glycitein  (ISO)
glyphosate  (ISO)
hesperetin  (ISO)
hesperidin  (EXP)
hexachlorobenzene  (EXP,ISO)
histamine  (ISO)
hydralazine  (EXP)
hydrochlorothiazide  (EXP)
hydrogen chloride  (ISO)
hydrogen peroxide  (ISO)
hydroxyurea  (ISO)
indometacin  (EXP,ISO)
irinotecan  (EXP)
iron atom  (EXP)
iron dextran  (EXP)
iron(0)  (EXP)
iron(III) nitrilotriacetate  (EXP)
isoflavones  (EXP)
ivermectin  (ISO)
juglone  (ISO)
kaempferol  (EXP)
kojic acid  (EXP,ISO)
L-ascorbic acid  (EXP,ISO)
L-cysteine  (EXP)
L-glutamine  (ISO)
lapatinib  (ISO)
lead diacetate  (EXP)
leflunomide  (ISO)
limonene  (EXP)
linsidomine  (ISO)
linuron  (EXP)
lipoic acid  (EXP)
lipopolysaccharide  (ISO)
lithium chloride  (ISO)
lupeol  (ISO)
LY 364947  (ISO)
LY294002  (ISO)
lycopene  (EXP)
mabuterol  (EXP)
malachite green cation  (EXP)
malathion  (ISO)
maneb  (ISO)
masoprocol  (ISO)
Mecamylamine  (ISO)
mechlorethamine  (EXP)
melatonin  (EXP,ISO)
meloxicam  (ISO)
menadione  (ISO)
methapyrilene  (EXP)
methimazole  (ISO)
methotrexate  (ISO)
methoxychlor  (ISO)
methyl methanesulfonate  (ISO)
methylarsonic acid  (EXP)
methylseleninic acid  (ISO)
methyltestosterone  (EXP)
miconazole  (ISO)
mitomycin C  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
monocrotaline  (ISO)
myricitrin  (ISO)
N'-Nitrosonornicotine  (ISO)
N,N-bis(2-hydroxypropyl)nitrosamine  (EXP)
N-acetyl-L-cysteine  (ISO)
N-ethyl-N-nitrosourea  (EXP,ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (EXP,ISO)
N-methyl-N-nitrosourea  (EXP,ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP,ISO)
nefazodone  (ISO)
nelfinavir  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
nicotine  (ISO)
nimesulide  (EXP)
nitrofen  (EXP,ISO)
nitrogen dioxide  (ISO)
Nutlin-3  (ISO)
ochratoxin A  (EXP,ISO)
okadaic acid  (ISO)
oleanolic acid  (EXP,ISO)
omeprazole  (EXP,ISO)
orlistat  (ISO)
ouabain  (ISO)
ozone  (EXP)
paclitaxel  (ISO)
palbociclib  (ISO)
pantoprazole  (EXP)
paracetamol  (EXP,ISO)
paraquat  (EXP,ISO)
parathion  (ISO)
PD 0325901  (ISO)
pentachlorophenol  (ISO)
perfluorobutyric acid  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (EXP,ISO)
phenylephrine  (EXP)
PhIP  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
piclamilast  (EXP)
picoxystrobin  (ISO)
pinosylvin  (ISO)
piperonyl butoxide  (EXP,ISO)
pirinixic acid  (EXP,ISO)
piroxicam  (ISO)
poly(propylene imine) macromolecule  (ISO)
potassium dichromate  (EXP)
potassium iodide  (EXP)
potassium nitrate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
probucol  (ISO)
progesterone  (EXP,ISO)
propiconazole  (ISO)
pterostilbene  (EXP)
pyrithione  (ISO)
pyrogallol  (ISO)
pyrrolidine dithiocarbamate  (ISO)
quercetin  (EXP,ISO)
raloxifene  (EXP,ISO)
Rebamipide  (EXP)
reparixin  (ISO)
reserpine  (EXP)
resveratrol  (EXP,ISO)
ribavirin  (ISO)
royal jelly  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP,ISO)
SB 203580  (ISO)
scutellarin  (ISO)
selenium atom  (ISO)
selenomethionine  (ISO)
serpentine asbestos  (EXP)
shikimic acid  (ISO)
Shikonin  (EXP)
silibinin  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
silver(1+) nitrate  (ISO)
simvastatin  (ISO)
sirolimus  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP,ISO)
sodium fluoride  (EXP)
Soman  (EXP)
stattic  (ISO)
stavudine  (EXP,ISO)
sterigmatocystin  (EXP)
streptozocin  (EXP)
sulfasalazine  (ISO)
sulforaphane  (ISO)
sulindac  (EXP,ISO)
sulindac sulfone  (ISO)
sunitinib  (ISO)
Swertiamarin  (EXP)
T-2 toxin  (EXP)
tacrolimus hydrate  (ISO)
tamibarotene  (ISO)
tamoxifen  (EXP,ISO)
taurine  (EXP)
terephthalic acid  (EXP)
testosterone  (EXP,ISO)
tetrachlorohydroquinone  (ISO)
tetrachloromethane  (EXP,ISO)
tetrathiomolybdate(2-)  (ISO)
thapsigargin  (ISO)
thioacetamide  (EXP,ISO)
thymoquinone  (EXP)
thyroxine  (ISO)
titanium dioxide  (ISO)
tocopherol  (EXP)
tolcapone  (EXP)
toluene 2,4-diisocyanate  (ISO)
Tomentosin  (ISO)
topotecan  (ISO)
trans-pinosylvin  (ISO)
transplatin  (ISO)
trichloroacetic acid  (ISO)
trichloroethene  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
trimethylarsine oxide  (EXP)
troglitazone  (EXP,ISO)
tropan-3alpha-yl 3-hydroxy-2-phenylpropanoate  (ISO)
tungsten  (ISO)
tunicamycin  (ISO)
tyrphostin AG 1478  (ISO)
urethane  (ISO)
ursodeoxycholic acid  (ISO)
valproic acid  (EXP)
vanadium atom  (EXP)
vanadium(0)  (EXP)
vancomycin  (ISO)
vinyl carbamate  (ISO)
vitamin E  (ISO)
Y-27632  (ISO)
zerumbone  (EXP)
zidovudine  (ISO)
zinc atom  (ISO)
zinc dichloride  (EXP)
zinc sulfate  (EXP)
zinc(0)  (ISO)
zingerone  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Amare Kadam PS, etal., Cancer Genet Cytogenet. 2001 Mar;125(2):139-46.
2. Arnaiz MR, etal., J Parasitol. 2002 Oct;88(5):919-25.
3. Cayli S, etal., Acta Histochem 2002;104(3):271-7.
4. Czykier E and Dzieciol J, Rocz Akad Med Bialymst. 2004;49 Suppl 1:172-4.
5. Deng X, etal., J Mol Histol. 2012 Dec;43(6):669-79. doi: 10.1007/s10735-012-9450-y. Epub 2012 Sep 27.
6. Frierson HF Jr Mod Pathol. 1993 May;6(3):290-4.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Gerzanich V, etal., Arterioscler Thromb Vasc Biol. 2003 Nov 1;23(11):2048-54. Epub 2003 Sep 11.
9. GOA data from the GO Consortium
10. Hassan MH, etal., Hum Reprod. 2011 Nov;26(11):3008-18. doi: 10.1093/humrep/der280. Epub 2011 Sep 6.
11. Hedglin M, etal., Cold Spring Harb Perspect Biol. 2013 Apr 1;5(4):a010165. doi: 10.1101/cshperspect.a010165.
12. Holmes EW, etal., Exp Mol Pathol 2002 Dec;73(3):209-19.
13. Hori K, etal., Pathol Int. 1997 May;47(5):282-7.
14. Imai H, etal., Eur J Neurosci 2002 Jun;15(12):1929-36.
15. Johnson M, etal., Hippocampus. 2011 Oct;21(10):1126-36. doi: 10.1002/hipo.20826. Epub 2010 Jul 21.
16. Johnson M, etal., Int J Biochem Cell Biol. 2011 Jan;43(1):65-73. doi: 10.1016/j.biocel.2010.09.014. Epub 2010 Sep 29.
17. Kayisli UA, etal., Reprod Sci. 2007 Oct;14(7):678-86.
18. Koike E, etal., Toxicol Sci 2002 Jun;67(2):241-6.
19. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
20. Lai MD, etal., J Endocrinol. 2000 Jul;166(1):87-93.
21. Levavasseur F, etal., FEBS Lett. 1995 Apr 17;363(1-2):132-6.
22. Li GM Cell Res. 2008 Jan;18(1):85-98.
23. Liu FS, etal., Zhonghua Yi Xue Za Zhi (Taipei). 1999 Oct;62(10):695-702.
24. Liu YC and Bambara RA, Biochem Biophys Res Commun. 1989 Jun 15;161(2):873-82.
25. Marino TA, etal., Anat Rec. 1996 Aug;245(4):677-84.
26. Matsumoto K, etal., EMBO J 1987 Mar;6(3):637-42.
27. MGD data from the GO Consortium
28. Moldovan GL, etal., Cell. 2007 May 18;129(4):665-79.
29. Morishita R, etal., Proc Natl Acad Sci U S A. 1993 Sep 15;90(18):8474-8.
30. NCBI rat LocusLink and RefSeq merged data July 26, 2002
31. Niu Y, etal., Zhonghua Bing Li Xue Za Zhi. 1997 Dec;26(6):337-9.
32. Ohyama C, etal., Nippon Hinyokika Gakkai Zasshi. 1995 Oct;86(10):1543-51.
33. Okada M, etal., Neuroreport. 1996 Jul 29;7(11):1770-2.
34. Pathak S, etal., Mol Cell Endocrinol. 2010 Jan 15;314(1):110-7. doi: 10.1016/j.mce.2009.08.005. Epub 2009 Aug 14.
35. Pipeline to import KEGG annotations from KEGG into RGD
36. Pipeline to import SMPDB annotations from SMPDB into RGD
37. RGD automated data pipeline
38. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
39. RGD automated import pipeline for gene-chemical interactions
40. Seomun Y, etal., Mol Vis. 2005 Sep 16;11:764-74.
41. Sheen-Chen SM, etal., World J Surg. 2003 Oct;27(10):1161-4. Epub 2003 Aug 18.
42. Skotnicka-Klonowicz G, etal., Eur J Surg Oncol. 2002 Feb;28(1):67-71.
43. Solanas M, etal., Carcinogenesis. 2009 Oct 13.
44. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
45. Stubbe J, etal., Am J Physiol Renal Physiol. 2006 Oct;291(4):F812-22. Epub 2006 Apr 25.
46. Tahan SR, etal., Cancer. 1993 Jun 1;71(11):3552-9.
47. Tazuke Y, etal., Pediatr Surg Int. 2011 Feb;27(2):151-8. doi: 10.1007/s00383-010-2798-8.
48. Theocharis SE, etal., Dig Dis Sci. 1994 Feb;39(2):245-52.
49. Tomasevic G, etal., Brain Res Mol Brain Res. 1998 Oct 1;60(2):168-76.
50. Tousson E, etal., Reprod Sci. 2011 Jul;18(7):679-86. doi: 10.1177/1933719110395401. Epub 2011 Jan 27.
51. Ye Y, etal., Tumour Biol. 2016 Mar;37(3):3185-95. doi: 10.1007/s13277-015-4100-0. Epub 2015 Oct 2.
52. Yu SJ, etal., Exp Biol Med (Maywood). 2012 Apr;237(4):395-406. doi: 10.1258/ebm.2011.011217.
53. Zafar H and Ali S, Arch Biochem Biophys. 2013 Jan 15;529(2):66-74. doi: 10.1016/j.abb.2012.11.008. Epub 2012 Dec 3.
54. Zhou J, etal., J Exp Zoolog A Comp Exp Biol 2005 Mar 1;303(3):227-40.
Additional References at PubMed
PMID:9774970   PMID:10079221   PMID:10888872   PMID:11005803   PMID:11595739   PMID:11934988   PMID:11942627   PMID:11981756   PMID:12040017   PMID:12203718   PMID:12638230   PMID:12857463  
PMID:12970760   PMID:14703996   PMID:15177179   PMID:15489334   PMID:15494374   PMID:15543136   PMID:15569628   PMID:15606305   PMID:15805117   PMID:15818741   PMID:15982757   PMID:16099430  
PMID:16489008   PMID:17031671   PMID:17115032   PMID:17456401   PMID:18331714   PMID:18377963   PMID:18390212   PMID:18467674   PMID:18664354   PMID:18692037   PMID:18704299   PMID:18794347  
PMID:19016366   PMID:19023449   PMID:19032457   PMID:19135898   PMID:19443450   PMID:19734146   PMID:19995904   PMID:20129063   PMID:20458337   PMID:20529819   PMID:20531390   PMID:20605140  
PMID:20972911   PMID:21383955   PMID:21492153   PMID:22330348   PMID:22477723   PMID:23277426   PMID:23284756   PMID:23976951   PMID:24115439   PMID:24625528   PMID:24726645   PMID:24939902  
PMID:25416956   PMID:25596037   PMID:26030842   PMID:26130252   PMID:26677001   PMID:27665784   PMID:29333769   PMID:29476059   PMID:29569173   PMID:29748930   PMID:31515488   PMID:33450132  
PMID:33510839  


Genomics

Comparative Map Data
Pcna
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23119,499,039 - 119,502,911 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl3119,498,810 - 119,502,995 (-)Ensembl
Rnor_6.03124,880,698 - 124,884,570 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3124,880,698 - 124,884,570 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03131,376,235 - 131,380,108 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43120,008,715 - 120,012,589 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13119,914,289 - 119,918,243 (-)NCBI
Celera3118,296,567 - 118,300,439 (-)NCBICelera
RH 3.4 Map31023.4RGD
Cytogenetic Map3q36NCBI
PCNA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl205,114,953 - 5,126,626 (-)EnsemblGRCh38hg38GRCh38
GRCh38205,114,953 - 5,126,622 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37205,095,599 - 5,107,268 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36205,043,599 - 5,055,268 (-)NCBINCBI36hg18NCBI36
Build 34205,043,598 - 5,048,647NCBI
Celera205,165,620 - 5,177,289 (-)NCBI
Cytogenetic Map20p12.3NCBI
HuRef205,049,534 - 5,061,197 (-)NCBIHuRef
CHM1_1205,096,983 - 5,108,646 (-)NCBICHM1_1
Pcna
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392132,091,206 - 132,095,100 (-)NCBIGRCm39mm39
GRCm39 Ensembl2132,091,082 - 132,095,234 (-)Ensembl
GRCm382132,249,286 - 132,253,180 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2132,249,162 - 132,253,314 (-)EnsemblGRCm38mm10GRCm38
MGSCv372132,075,022 - 132,078,916 (-)NCBIGRCm37mm9NCBIm37
MGSCv362131,940,727 - 131,944,621 (-)NCBImm8
Celera2133,472,471 - 133,476,365 (-)NCBICelera
Cytogenetic Map2F2NCBI
cM Map264.15NCBI
Pcna
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541515,744,601 - 15,749,673 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541515,744,601 - 15,748,910 (-)NCBIChiLan1.0ChiLan1.0
PCNA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1204,927,731 - 4,939,440 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl204,927,731 - 4,939,440 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0205,134,930 - 5,146,603 (-)NCBIMhudiblu_PPA_v0panPan3
PCNA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12416,478,774 - 16,485,992 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2416,478,769 - 16,484,992 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2416,301,671 - 16,308,866 (+)NCBI
ROS_Cfam_1.02416,892,157 - 16,899,336 (+)NCBI
ROS_Cfam_1.0 Ensembl2416,892,161 - 16,899,332 (+)Ensembl
UMICH_Zoey_3.12416,489,199 - 16,496,352 (+)NCBI
UNSW_CanFamBas_1.02416,596,221 - 16,603,283 (+)NCBI
UU_Cfam_GSD_1.02416,929,896 - 16,937,077 (+)NCBI
Pcna
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640165,334,861 - 165,339,851 (+)NCBI
SpeTri2.0NW_00493648513,766,221 - 13,771,215 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCNA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1714,125,814 - 14,185,276 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11714,137,746 - 14,142,584 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21715,127,978 - 15,132,806 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PCNA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1232,936,600 - 32,953,635 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl232,948,196 - 32,953,991 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607111,581,432 - 11,598,250 (-)NCBIVero_WHO_p1.0
Pcna
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247416,143,584 - 6,148,055 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH94484  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23119,499,113 - 119,499,312 (+)MAPPERmRatBN7.2
Rnor_6.03124,880,773 - 124,880,971NCBIRnor6.0
Rnor_5.03131,376,310 - 131,376,508UniSTSRnor5.0
RGSC_v3.43120,008,790 - 120,008,988UniSTSRGSC3.4
Celera3118,296,642 - 118,296,840UniSTS
RH 3.4 Map31023.4UniSTS
Cytogenetic Map3q36UniSTS
RH128612  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2147,465,010 - 7,465,236 (+)MAPPERmRatBN7.2
mRatBN7.23119,499,080 - 119,499,300 (+)MAPPERmRatBN7.2
Rnor_6.03124,880,740 - 124,880,959NCBIRnor6.0
Rnor_6.0149,023,281 - 9,023,506NCBIRnor6.0
Rnor_5.0148,992,219 - 8,992,444UniSTSRnor5.0
Rnor_5.03131,376,277 - 131,376,496UniSTSRnor5.0
RGSC_v3.4148,712,241 - 8,712,466UniSTSRGSC3.4
RGSC_v3.43120,008,757 - 120,008,976UniSTSRGSC3.4
Celera147,588,856 - 7,589,081UniSTS
Celera3118,296,609 - 118,296,828UniSTS
Cytogenetic Map3q36UniSTS
Cytogenetic Map14p22UniSTS
PMC133987P4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23119,503,077 - 119,503,437 (+)MAPPERmRatBN7.2
Rnor_6.03124,884,737 - 124,885,096NCBIRnor6.0
Rnor_5.03131,380,275 - 131,380,634UniSTSRnor5.0
RGSC_v3.43120,012,756 - 120,013,115UniSTSRGSC3.4
Celera3118,300,606 - 118,300,965UniSTS
Cytogenetic Map3q36UniSTS
GDB:450240  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23119,499,360 - 119,499,598 (+)MAPPERmRatBN7.2
Rnor_6.03124,881,020 - 124,881,257NCBIRnor6.0
Rnor_5.03131,376,557 - 131,376,794UniSTSRnor5.0
RGSC_v3.43120,009,037 - 120,009,274UniSTSRGSC3.4
Celera3118,296,889 - 118,297,126UniSTS
Cytogenetic Map3q36UniSTS
Pcna-ps2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23119,499,612 - 119,501,278 (+)MAPPERmRatBN7.2
Rnor_6.03124,881,272 - 124,882,937NCBIRnor6.0
Rnor_5.03131,376,809 - 131,378,475UniSTSRnor5.0
RGSC_v3.43120,009,289 - 120,010,956UniSTSRGSC3.4
Celera3118,297,141 - 118,298,806UniSTS
Cytogenetic Map3q36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)370348525121056321Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)370653097121056321Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)389772419134772419Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3112287552135181505Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)3115638168135181505Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)3115638168135181505Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:225
Count of miRNA genes:159
Interacting mature miRNAs:169
Transcripts:ENSRNOT00000028887
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_022381 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC103170 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC060570 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219845 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219897 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220101 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220309 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220924 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225495 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225620 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226677 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227500 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227521 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229469 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229972 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230190 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232129 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233125 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233579 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233966 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234183 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234500 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234529 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234547 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235296 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y00047 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000028887   ⟹   ENSRNOP00000028887
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3119,498,810 - 119,502,995 (-)Ensembl
Rnor_6.0 Ensembl3124,880,698 - 124,884,570 (-)Ensembl
RefSeq Acc Id: NM_022381   ⟹   NP_071776
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23119,499,039 - 119,502,911 (-)NCBI
Rnor_6.03124,880,698 - 124,884,570 (-)NCBI
Rnor_5.03131,376,235 - 131,380,108 (-)NCBI
RGSC_v3.43120,008,715 - 120,012,589 (-)RGD
Celera3118,296,567 - 118,300,439 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_071776 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH60570 (Get FASTA)   NCBI Sequence Viewer  
  CAA68261 (Get FASTA)   NCBI Sequence Viewer  
  EDL80259 (Get FASTA)   NCBI Sequence Viewer  
  P04961 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_071776   ⟸   NM_022381
- UniProtKB: P04961 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000028887   ⟸   ENSRNOT00000028887

Transcriptome

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

Promoters
RGD ID:13692454
Promoter ID:EPDNEW_R2978
Type:initiation region
Name:Pcna_1
Description:proliferating cell nuclear antigen
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_6.03124,884,651 - 124,884,711EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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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