Cycs (cytochrome c, somatic) - Rat Genome Database

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Gene: Cycs (cytochrome c, somatic) Rattus norvegicus
Analyze
Symbol: Cycs
Name: cytochrome c, somatic
RGD ID: 2451
Description: Enables enzyme binding activity. Involved in several processes, including mitochondrial electron transport, cytochrome c to oxygen; negative regulation of hydrogen peroxide biosynthetic process; and response to ischemia. Located in cytosol and mitochondrion. Human ortholog(s) of this gene implicated in cholangiocarcinoma; lung non-small cell carcinoma; pancreatic cancer; and thrombocytopenia. Orthologous to human CYCS (cytochrome c, somatic); PARTICIPATES IN intrinsic apoptotic pathway; cardiolipin metabolic pathway; ceramide signaling pathway; INTERACTS WITH (+)-taxifolin; (R)-adrenaline; (R)-lipoic acid.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CYCSA; Cytochrome C expressed in somatic tissues; Cytochrome C, expressed in somatic tissues; MGC93634
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
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
mRatBN7.2479,651,894 - 79,653,994 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl479,651,378 - 79,654,054 (-)Ensembl
Rnor_6.0480,331,226 - 80,333,326 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl480,331,227 - 80,333,326 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04145,002,156 - 145,004,256 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4478,825,878 - 78,827,978 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1479,102,008 - 79,104,108 (-)NCBI
Celera474,558,589 - 74,560,689 (-)NCBICelera
Cytogenetic Map4q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(+)-dexrazoxane  (ISO)
(+)-taxifolin  (EXP)
(-)-citrinin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(-)-selegiline  (ISO)
(R)-adrenaline  (EXP)
(R)-lipoic acid  (EXP)
(R)-noradrenaline  (EXP)
(S)-naringenin  (EXP,ISO)
(S)-nicotine  (EXP,ISO)
(Z)-3-butylidenephthalide  (ISO)
(Z)-ligustilide  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dichloropropan-2-ol  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2,4-dinitrotoluene  (EXP)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2,6-dinitrotoluene  (EXP)
2-(4-iodo-2,5-dimethoxyphenyl)-1-methylethylamine  (EXP)
2-amino-2-deoxy-D-galactopyranose  (ISO)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-pyridylethylamine  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3,3'-diindolylmethane  (ISO)
3-chloropropane-1,2-diol  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methyladenine  (ISO)
3-phenylprop-2-enal  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (EXP,ISO)
4-phenylbutyric acid  (ISO)
4-tert-Octylphenol  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
5-Hydroxycapric acid  (EXP)
5-methyl-4-oxido-2-pyrazin-4-iumcarboxylic acid  (ISO)
6-formylpterin  (ISO)
6-propyl-2-thiouracil  (EXP)
7H-xanthine  (EXP)
8-Br-cAMP  (ISO)
9-cis,11-trans-octadecadienoic acid  (EXP)
9H-xanthine  (EXP)
acrolein  (ISO)
acrylamide  (EXP)
actinomycin D  (EXP)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucosamine  (ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (ISO)
all-trans-retinol  (EXP)
alloxan  (EXP)
Allyl chloride  (EXP)
Aloe emodin  (ISO)
alpha-mangostin  (ISO)
alpinumisoflavone  (ISO)
alvocidib  (ISO)
amiloride  (ISO)
ammonium chloride  (EXP)
anastrozole  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antimycin A  (ISO)
apigenin  (EXP,ISO)
arachidonic acid  (ISO)
aristolochic acid  (ISO)
arjunolic acid  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (EXP,ISO)
Aspidin  (ISO)
atorvastatin calcium  (EXP)
atrazine  (EXP,ISO)
azadirachtin A  (ISO)
azoxystrobin  (ISO)
baicalein  (ISO)
BAPTA  (ISO)
bathocuproine disulfonic acid  (EXP)
benzo[a]pyrene  (ISO)
berberine  (ISO)
beta-D-glucosamine  (ISO)
bexarotene  (ISO)
bifenthrin  (ISO)
bis(2-chloroethyl) sulfide  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (EXP)
bortezomib  (ISO)
bromobenzene  (EXP)
bufalin  (ISO)
buserelin  (ISO)
Butylparaben  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
cafestol  (ISO)
caffeine  (ISO)
cajanol  (ISO)
calcidiol  (EXP)
calcium atom  (EXP)
calcium(0)  (EXP)
camptothecin  (ISO)
carbamazepine  (ISO)
CARBENOXOLONE  (ISO)
carbon nanotube  (ISO)
carboplatin  (EXP)
carvedilol  (EXP)
casticin  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
chrysazin  (ISO)
cisplatin  (EXP,ISO)
Clivoline  (ISO)
clobetasol  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
cocaine  (EXP,ISO)
codeinone  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) chloride  (EXP)
coumarin  (ISO)
crocidolite asbestos  (ISO)
crocin-1  (EXP)
Cuprizon  (EXP)
curcumin  (ISO)
cycloheximide  (ISO)
cyclosporin A  (EXP,ISO)
cypermethrin  (EXP)
D-glucose  (EXP,ISO)
dapagliflozin  (EXP)
daunorubicin  (ISO)
DDE  (EXP)
deguelin  (ISO)
dehydroascorbic acid  (ISO)
delphinidin  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (EXP,ISO)
diazinon  (EXP,ISO)
diazoxide  (EXP)
dibutyl phthalate  (EXP)
dichlorvos  (EXP)
diclofenac  (ISO)
dicoumarol  (EXP)
dicrotophos  (ISO)
dieldrin  (EXP)
diethyldithiocarbamic acid  (ISO)
diethylstilbestrol  (EXP,ISO)
digitoxin  (ISO)
dioscin  (ISO)
dioxygen  (EXP,ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
Echinocystic acid  (ISO)
edaravone  (EXP)
elemental selenium  (ISO)
enalapril  (EXP)
endrin  (ISO)
entinostat  (ISO)
equol  (ISO)
erdosteine  (ISO)
esculetin  (ISO)
ethanol  (ISO)
ethylbenzene  (EXP)
etoposide  (ISO)
eugenol  (ISO)
fenofibrate  (ISO)
fipronil  (ISO)
flavanone  (ISO)
flavonoids  (ISO)
folic acid  (EXP,ISO)
folpet  (ISO)
formaldehyde  (ISO)
fraxetin  (ISO)
fructose  (EXP,ISO)
fulvestrant  (EXP,ISO)
fumonisin B1  (ISO)
gallic acid  (ISO)
gamma-hexachlorocyclohexane  (EXP)
Garcinol  (ISO)
gefitinib  (ISO)
genistein  (ISO)
gentamycin  (EXP)
Gentiopicrin  (ISO)
ginsenoside Rd  (EXP)
glabridin  (ISO)
glucose  (EXP,ISO)
glutathione  (ISO)
glycochenodeoxycholic acid  (EXP)
glyphosate  (EXP,ISO)
gold atom  (ISO)
gold(0)  (ISO)
Grifolin  (ISO)
heptachlor  (EXP)
hesperetin  (ISO)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
hyperforin  (EXP,ISO)
indole-3-methanol  (ISO)
indometacin  (ISO)
Ioversol  (EXP)
isatin  (ISO)
isoprenaline  (EXP)
ivermectin  (ISO)
kaempferol  (ISO)
kainic acid  (EXP,ISO)
ketoconazole  (EXP)
KN-93  (ISO)
L-ascorbic acid  (ISO)
L-dehydroascorbic acid  (ISO)
letrozole  (ISO)
leuprolide  (EXP,ISO)
limonene  (EXP)
linoleic acid  (ISO)
linsidomine  (ISO)
lipoic acid  (EXP)
lipopolysaccharide  (EXP,ISO)
Longikaurin A  (ISO)
losartan  (EXP)
LY294002  (ISO)
magnesium oxide  (ISO)
mancozeb  (ISO)
manganese atom  (EXP,ISO)
manganese(0)  (EXP,ISO)
manganese(II) chloride  (ISO)
methadone  (ISO)
methamphetamine  (EXP)
methotrexate  (ISO)
methoxychlor  (EXP)
methylisothiazolinone  (ISO)
metiram  (ISO)
miconazole  (EXP)
mifepristone  (ISO)
minocycline  (EXP,ISO)
mitomycin C  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
monocrotophos  (EXP)
morin  (EXP)
morphine  (EXP,ISO)
mycophenolic acid  (ISO)
myricetin  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (EXP)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP)
naphthalene  (ISO)
naringin  (ISO)
nelfinavir  (ISO)
neocuproine  (EXP)
nickel subsulfide  (EXP)
nickel sulfate  (EXP)
niclosamide  (ISO)
nicotine  (EXP,ISO)
nimodipine  (EXP)
nitric oxide  (EXP,ISO)
Norethindrone enanthate  (EXP)
nortriptyline  (ISO)
ochratoxin A  (EXP,ISO)
oleanolic acid  (ISO)
oleic acid  (ISO)
oxidopamine  (EXP)
p-tert-Amylphenol  (EXP)
paclitaxel  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
PD 168393  (ISO)
Pentoxifylline  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perifosine  (ISO)
phenethyl caffeate  (EXP)
phenethyl isothiocyanate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosphoramide mustard  (EXP)
piperine  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
potassium iodide  (EXP)
pravastatin  (EXP)
pregnenolone 16alpha-carbonitrile  (EXP)
probucol  (EXP)
procyanidin B2  (ISO)
progesterone  (EXP)
propetamphos  (EXP)
propofol  (ISO)
protoporphyrin  (EXP)
pterostilbene  (ISO)
pyrogallol  (ISO)
pyrrolidine dithiocarbamate  (EXP,ISO)
quercetin  (EXP,ISO)
quercetin 3-O-beta-D-galactopyranoside  (ISO)
resveratrol  (EXP,ISO)
rocaglamide  (ISO)
rotenone  (EXP,ISO)
S-adenosyl-L-methioninate  (ISO)
S-adenosyl-L-methionine  (ISO)
safrole  (ISO)
salubrinal  (ISO)
Salvianolic acid A  (EXP)
saxagliptin  (EXP)
SB 203580  (EXP,ISO)
SB 431542  (ISO)
selenium atom  (ISO)
sevoflurane  (EXP)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (ISO)
sodium fluoride  (ISO)
Soman  (EXP)
sorafenib  (ISO)
streptozocin  (EXP)
sulforaphane  (ISO)
sulfur dioxide  (EXP)
surfactin  (ISO)
surfactin C  (ISO)
T-2 toxin  (ISO)
tamoxifen  (EXP,ISO)
taurine  (EXP)
tebufenpyrad  (ISO)
telmisartan  (EXP)
temozolomide  (ISO)
TEMPO  (EXP)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP)
thalidomide  (ISO)
thapsigargin  (ISO)
thymoquinone  (ISO)
tigecycline  (EXP)
tipifarnib  (ISO)
titanium dioxide  (ISO)
torcetrapib  (ISO)
tributylstannane  (ISO)
Tributyltin oxide  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
trimethylenediamine  (ISO)
trimethyltin  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
tunicamycin  (ISO)
ursolic acid  (ISO)
valinomycin  (ISO)
valproic acid  (ISO)
vitamin E  (EXP,ISO)
vorinostat  (ISO)
wortmannin  (EXP)
xestospongin C  (EXP)
xylitol  (ISO)
zearalenone  (ISO)
zinc pyrithione  (ISO)
ziram  (ISO)

References

References - curated
1. Atlante A, etal., J Biol Chem. 2000 Nov 24;275(47):37159-66.
2. Bhattacharjee M, etal., Int Immunol. 2008 Dec;20(12):1489-505. Epub 2008 Oct 17.
3. Cao LQ, etal., Hepatol Res. 2009 Dec;39(12):1190-7. Epub 2009 Sep 25.
4. De Rocco D, etal., Biochim Biophys Acta. 2014 Feb;1842(2):269-74. doi: 10.1016/j.bbadis.2013.12.002. Epub 2013 Dec 8.
5. Garber EA and Margoliash E, Biochim Biophys Acta. 1994 Sep 27;1187(3):289-95.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. Gillick K and Crompton M, J Cell Sci. 2008 Mar 1;121(Pt 5):618-26. Epub 2008 Feb 5.
8. Gybina AA and Prohaska JR, J Nutr. 2003 Nov;133(11):3361-8.
9. Inoki Y, etal., Biochem Biophys Res Commun. 2000 Oct 5;276(3):1210-6.
10. Javid J, etal., Tumour Biol. 2015 Jun;36(6):4253-60. doi: 10.1007/s13277-015-3062-6. Epub 2015 Jan 13.
11. KEGG
12. Kiechle T, etal., Neuromolecular Med. 2002;1(3):183-95.
13. La Piana G, etal., Arch Biochem Biophys 2003 Feb 15;410(2):201-11.
14. MGD data from the GO Consortium
15. Morison IM, etal., Nat Genet. 2008 Apr;40(4):387-9. doi: 10.1038/ng.103. Epub 2008 Mar 16.
16. Morrone A, etal., Am J Med Genet 2002 Jul 22;111(1):10-8.
17. Mouria M, etal., Int J Cancer. 2002 Apr 10;98(5):761-9.
18. NCBI rat LocusLink and RefSeq merged data July 26, 2002
19. Ogneva IV, etal., Aviakosm Ekolog Med. 2014;48(6):23-9.
20. OMIM Disease Annotation Pipeline
21. Online Mendelian Inheritance in Man, OMIM (TM).
22. Ott M, etal., Proc Natl Acad Sci U S A 2002 Feb 5;99(3):1259-63.
23. Pasdois P, etal., Biochem J. 2011 Jun 1;436(2):493-505. doi: 10.1042/BJ20101957.
24. Penney DG, etal., J Toxicol Environ Health. 1983 Aug-Sep;12(2-3):395-406.
25. Piccotti L, etal., J Biol Chem 2002 Apr 5;277(14):12075-81.
26. Pipeline to import KEGG annotations from KEGG into RGD
27. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
28. Pipeline to import SMPDB annotations from SMPDB into RGD
29. Ren M, etal., Prog Lipid Res. 2014 Jul;55:1-16. doi: 10.1016/j.plipres.2014.04.001. Epub 2014 Apr 24.
30. RGD automated data pipeline
31. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
32. RGD automated import pipeline for gene-chemical interactions
33. Russell JC, etal., J Neurochem. 2008 Aug;106(3):1357-70. Epub 2008 May 13.
34. Savoia A, etal., Platelets. 2009 Feb;20(1):72-3. doi: 10.1080/09537100802485129.
35. Song Y, etal., Toxicology. 2008 Nov 20;253(1-3):53-61. Epub 2008 Sep 4.
36. Tan Z, etal., Cell Death Differ. 2007 Oct;14(10):1721-32. Epub 2007 Jun 15.
37. Virbasius JV and Scarpulla RC, J Biol Chem 1988 May 15;263(14):6791-6.
Additional References at PubMed
PMID:191069   PMID:6130852   PMID:6263917   PMID:8689682   PMID:10830166   PMID:12107093   PMID:12477932   PMID:14623868   PMID:14651853   PMID:14657025   PMID:14693685   PMID:15271982  
PMID:15475362   PMID:15489334   PMID:15907471   PMID:16103131   PMID:16469926   PMID:16757556   PMID:16854843   PMID:17634366   PMID:17899337   PMID:18070754   PMID:18418843   PMID:18614015  
PMID:18724894   PMID:19166515   PMID:19169378   PMID:19182904   PMID:19393246   PMID:20671748   PMID:20833797   PMID:21630459   PMID:21660956   PMID:22173498   PMID:22437740   PMID:22942730  
PMID:25512382   PMID:25634059   PMID:25848832   PMID:26271974   PMID:26316108   PMID:33710703  


Genomics

Comparative Map Data
Cycs
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2479,651,894 - 79,653,994 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl479,651,378 - 79,654,054 (-)Ensembl
Rnor_6.0480,331,226 - 80,333,326 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl480,331,227 - 80,333,326 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04145,002,156 - 145,004,256 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4478,825,878 - 78,827,978 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1479,102,008 - 79,104,108 (-)NCBI
Celera474,558,589 - 74,560,689 (-)NCBICelera
Cytogenetic Map4q24NCBI
CYCS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl725,118,656 - 25,125,260 (-)EnsemblGRCh38hg38GRCh38
GRCh38725,118,656 - 25,125,260 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37725,158,275 - 25,164,879 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36725,124,800 - 25,131,480 (-)NCBINCBI36hg18NCBI36
Celera725,146,921 - 25,154,374 (-)NCBI
Cytogenetic Map7p15.3NCBI
HuRef725,044,828 - 25,051,539 (-)NCBIHuRef
CHM1_1725,160,181 - 25,166,894 (-)NCBICHM1_1
CRA_TCAGchr7v2725,209,510 - 25,216,457 (-)NCBI
Cycs
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39650,539,543 - 50,543,549 (-)NCBIGRCm39mm39
GRCm39 Ensembl650,539,543 - 50,543,518 (-)Ensembl
GRCm38650,562,563 - 50,566,569 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl650,562,563 - 50,566,538 (-)EnsemblGRCm38mm10GRCm38
MGSCv37650,512,562 - 50,516,473 (-)NCBIGRCm37mm9NCBIm37
MGSCv36650,492,149 - 50,496,060 (-)NCBImm8
Celera651,079,647 - 51,083,558 (-)NCBICelera
Cytogenetic Map6B2.3NCBI
cM Map624.32NCBI
LOC102023786
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541027,086,405 - 27,089,255 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541027,086,405 - 27,089,255 (-)NCBIChiLan1.0ChiLan1.0
LOC100986481
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1725,396,013 - 25,398,549 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl725,396,013 - 25,398,549 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0725,784,900 - 25,791,598 (-)NCBIMhudiblu_PPA_v0panPan3
CYCS
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11438,579,446 - 38,581,983 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1438,579,446 - 38,581,983 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1438,129,129 - 38,131,665 (-)NCBI
ROS_Cfam_1.01438,516,027 - 38,518,562 (-)NCBI
UMICH_Zoey_3.11438,628,462 - 38,630,996 (-)NCBI
UNSW_CanFamBas_1.01438,321,370 - 38,323,910 (-)NCBI
UU_Cfam_GSD_1.01438,663,988 - 38,666,523 (-)NCBI
CYCS
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1847,169,866 - 47,173,866 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11847,169,921 - 47,172,212 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21852,036,068 - 52,038,366 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103226354
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12133,251,825 - 33,253,298 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604271,404,460 - 71,406,988 (-)NCBIVero_WHO_p1.0
LOC101718508
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247395,411,192 - 5,413,995 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
PMC195978P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2479,654,105 - 79,654,448 (+)MAPPERmRatBN7.2
Rnor_6.0480,333,438 - 80,333,780NCBIRnor6.0
Rnor_5.04145,004,368 - 145,004,710UniSTSRnor5.0
RGSC_v3.4478,828,090 - 78,828,432UniSTSRGSC3.4
Celera474,560,801 - 74,561,143UniSTS
Cytogenetic Map4q24UniSTS
RH139613  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map4q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43443048482490359Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)436303261103194984Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)439524264116179656Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44043338885433388Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44043341485433414Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44345797688457976Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)456698790126192555Rat
631546Bp86Blood pressure QTL 863.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711443291360801Rat
634311Sach7Saccharin preference QTL 7taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)457114432102114432Rat
1358363Sradr3Stress Responsive Adrenal Weight QTL 36.19adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)457486946102486946Rat
1558651Swd3Spike wave discharge measurement QTL 34.620.000024brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)45843213392991462Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
1578657Bss12Bone structure and strength QTL 128.9femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)460220938105220938Rat
1578658Bss13Bone structure and strength QTL 138femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)460220938105220938Rat
2300179Bmd50Bone mineral density QTL 505.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)460928534105928534Rat
1549843Bw53Body weight QTL 530.0001body mass (VT:0001259)body weight gain (CMO:0000420)461697658103194791Rat
1549839Bw52Body weight QTL 520.0001body mass (VT:0001259)body weight gain (CMO:0000420)461697658115089733Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)462277855128289560Rat
6478743Anxrr40Anxiety related response QTL 400.83076defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
6478772Anxrr49Anxiety related response QTL 490.15488defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
6478684Anxrr30Anxiety related response QTL 300.00087defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
631651Bp124Blood pressure QTL 1243arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)462879517107879517Rat
7394826Bw126Body weight QTL 1260.002body mass (VT:0001259)body weight gain (CMO:0000420)46293326987483707Rat
8552807Vie4Viral induced encephalitis QTL 47.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)46293350882490359Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in mean arterial blood pressure (CMO:0002035)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in systolic blood pressure (CMO:0000747)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in pulse pressure (CMO:0001882)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)462933508114921294Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
2312569Pur19Proteinuria QTL 193.40.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)46588210796130297Rat
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)470362013132642728Rat
634344Hcar7Hepatocarcinoma resistance QTL 77.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)470808386115808386Rat
634344Hcar7Hepatocarcinoma resistance QTL 77.8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)470808386115808386Rat
631646Stl4Serum triglyceride level QTL 46.50.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)473169846132642728Rat
724522Bp146Blood pressure QTL 1462.20.0021arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)473630210118630210Rat
2302051Pia28Pristane induced arthritis QTL 285.30.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)473630210118630210Rat
70167Bw22Body weight QTL 223.1body mass (VT:0001259)body weight (CMO:0000012)476647384117676292Rat
1357342Bw40Body weight QTL 400.001body mass (VT:0001259)body weight (CMO:0000012)476647384117676292Rat
631662Hcar2Hepatocarcinoma resistance QTL 23.10.0003liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)478878504123878504Rat
631556Bp135Blood pressure QTL 1350.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)478881294117676292Rat
2317586Eae25Experimental allergic encephalomyelitis QTL 259.300000190734863nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)47888281783007655Rat
2317586Eae25Experimental allergic encephalomyelitis QTL 259.300000190734863nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)47888281783007655Rat
2317586Eae25Experimental allergic encephalomyelitis QTL 259.300000190734863nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)47888281783007655Rat
2317586Eae25Experimental allergic encephalomyelitis QTL 259.300000190734863nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)47888281783007655Rat
61364Iddm2Insulin dependent diabetes mellitus QTL 2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)478885890102684881Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:350
Count of miRNA genes:197
Interacting mature miRNAs:225
Transcripts:ENSRNOT00000014058
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 10 4
Medium 3 39 57 41 19 41 8 11 74 31 41 11 8
Low
Below cutoff 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012839 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC113910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC081849 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC089051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474011 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211631 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212556 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212860 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213464 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214646 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214733 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214738 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214838 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214855 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214908 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215052 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215109 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215113 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215466 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215744 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215858 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215983 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216103 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216217 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216281 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216426 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216512 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216560 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216674 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216679 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217283 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217634 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218428 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218668 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220855 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224710 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224914 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000142 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  K00750 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M20622 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000014058   ⟹   ENSRNOP00000014058
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl479,651,895 - 79,654,017 (-)Ensembl
Rnor_6.0 Ensembl480,331,227 - 80,333,326 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000116426   ⟹   ENSRNOP00000077186
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl479,651,378 - 79,654,054 (-)Ensembl
RefSeq Acc Id: NM_012839   ⟹   NP_036971
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2479,651,894 - 79,653,994 (-)NCBI
Rnor_6.0480,331,226 - 80,333,326 (-)NCBI
Rnor_5.04145,002,156 - 145,004,256 (-)NCBI
RGSC_v3.4478,825,878 - 78,827,978 (-)RGD
Celera474,558,589 - 74,560,689 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036971   ⟸   NM_012839
- UniProtKB: P62898 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000014058   ⟸   ENSRNOT00000014058
RefSeq Acc Id: ENSRNOP00000077186   ⟸   ENSRNOT00000116426

Transcriptome

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

Promoters
RGD ID:13693043
Promoter ID:EPDNEW_R3568
Type:initiation region
Name:Cycs_1
Description:cytochrome c, somatic
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_6.0480,333,363 - 80,333,423EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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 (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
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:2451 AgrOrtholog
Ensembl Genes ENSRNOG00000010452 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00000032885 UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000014058 UniProtKB/Swiss-Prot
  ENSRNOP00000041521 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000014058 UniProtKB/Swiss-Prot
  ENSRNOT00000048429 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.760.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7192255 IMAGE-MGC_LOAD
  IMAGE:7305562 IMAGE-MGC_LOAD
InterPro Cyt_c-like_dom UniProtKB/Swiss-Prot
  Cyt_c-like_dom_sf UniProtKB/Swiss-Prot
  Cyt_c_1A/1B UniProtKB/Swiss-Prot
KEGG Report rno:100363502 UniProtKB/Swiss-Prot