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: Exhibits 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. Localizes to 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2479,651,894 - 79,653,994 (-)NCBI
Rnor_6.0 Ensembl480,331,227 - 80,333,326 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0480,331,226 - 80,333,326 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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-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)
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)
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)
curcumin  (ISO)
cycloheximide  (ISO)
cyclosporin A  (EXP,ISO)
cypermethrin  (EXP)
D-glucose  (EXP,ISO)
daunorubicin  (ISO)
DDE  (EXP)
dehydroascorbic acid  (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)
fipronil  (ISO)
flavanone  (ISO)
flavonoids  (ISO)
folic acid  (EXP,ISO)
folpet  (ISO)
formaldehyde  (ISO)
fraxetin  (ISO)
fructose  (EXP)
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)
gold atom  (ISO)
gold(0)  (ISO)
heptachlor  (EXP)
hesperetin  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
hyperforin  (EXP,ISO)
indole-3-methanol  (ISO)
indometacin  (ISO)
Ioversol  (EXP)
isatin  (ISO)
isoprenaline  (EXP)
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)
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)
nitric oxide  (EXP,ISO)
Norethindrone enanthate  (EXP)
nortriptyline  (ISO)
ochratoxin A  (EXP,ISO)
oleic acid  (ISO)
oxidopamine  (EXP)
p-tert-Amylphenol  (EXP)
paclitaxel  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
PD 168393  (ISO)
Pentoxifylline  (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)
salvianolic acid B  (ISO)
saxagliptin  (EXP)
SB 203580  (EXP,ISO)
SB 431542  (ISO)
selenium atom  (ISO)
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)
telmisartan  (EXP)
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  


Genomics

Comparative Map Data
Cycs
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2479,651,894 - 79,653,994 (-)NCBI
Rnor_6.0 Ensembl480,331,227 - 80,333,326 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0480,331,226 - 80,333,326 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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 Ensembl725,120,091 - 25,125,361 (-)EnsemblGRCh38hg38GRCh38
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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12133,251,825 - 33,253,298 (+)NCBI
LOC101718508
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247395,411,192 - 5,413,995 (+)NCBI

Position Markers
PMC195978P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
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 (Rnor_6.0)
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)43043231145254791Rat
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)4734240492484039Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47850904182171018Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)423850384169318094Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42665474981874227Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)429549895112807890Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43182556083531021Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43182556083531021Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43182556083531021Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)43427793299067150Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)436615599145611886Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)437703272115372927Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)43920822284208222Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)43920824784208247Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44241577787415777Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)443414605155469929Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)443414792146942075Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)443414792146942075Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)446898276145611886Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)449906054145611886Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)455324953148360954Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)455375865125671711Rat
634311Sach7Saccharin preference QTL 7taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)45579156482134846Rat
631546Bp86Blood pressure QTL 863.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45579156492484312Rat
1578657Bss12Bone structure and strength QTL 128.9femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)456092756101092756Rat
1578658Bss13Bone structure and strength QTL 138femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)456092756101092756Rat
1558651Swd3Spike wave discharge measurement QTL 34.620.000024brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)45710107792990863Rat
1358363Sradr3Stress Responsive Adrenal Weight QTL 36.19adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)458166424103166424Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)458640017154427984Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)458640017154427984Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)458640017154427984Rat
1549843Bw53Body weight QTL 530.0001body mass (VT:0001259)body weight gain (CMO:0000420)46043912799066957Rat
1549839Bw52Body weight QTL 520.0001body mass (VT:0001259)body weight gain (CMO:0000420)460439127113416139Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)461038901127777403Rat
7394826Bw126Body weight QTL 1260.002body mass (VT:0001259)body weight gain (CMO:0000420)46170810388565113Rat
8552807Vie4Viral induced encephalitis QTL 47.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)46170834183531021Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in pulse pressure (CMO:0001882)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in systolic blood pressure (CMO:0000747)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in mean arterial blood pressure (CMO:0002035)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)461708341113100992Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)461708341113100992Rat
2300179Bmd50Bone mineral density QTL 505.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)461975371106975371Rat
1641919Alc22Alcohol consumption QTL 220.0005drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)462947687125671711Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)463537179157286626Rat
6478684Anxrr30Anxiety related response QTL 300.00087defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)463812687108812687Rat
6478743Anxrr40Anxiety related response QTL 400.83076defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)463812687108812687Rat
6478772Anxrr49Anxiety related response QTL 490.15488defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)463812687108812687Rat
631651Bp124Blood pressure QTL 1243arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)463938412108938412Rat
2312569Pur19Proteinuria QTL 193.40.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)46598924397759057Rat
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)470773471132455556Rat
634344Hcar7Hepatocarcinoma resistance QTL 77.8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)471476518116476518Rat
634344Hcar7Hepatocarcinoma resistance QTL 77.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)471476518116476518Rat
631646Stl4Serum triglyceride level QTL 46.50.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)473786419132455556Rat
724522Bp146Blood pressure QTL 1462.20.0021arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)475258970120258970Rat
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)475258970120258970Rat
738015Pia9Pristane induced arthritis QTL 94.50.048joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)476567036121567036Rat
70167Bw22Body weight QTL 223.1body mass (VT:0001259)body weight (CMO:0000012)477307388116916073Rat
1357342Bw40Body weight QTL 400.001body mass (VT:0001259)body weight (CMO:0000012)477307388116916073Rat
631662Hcar2Hepatocarcinoma resistance QTL 23.10.0003liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)479555067124555067Rat
631556Bp135Blood pressure QTL 1350.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)479557856116916073Rat
2317586Eae25Experimental allergic encephalomyelitis QTL 259.300000190734863nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)47955938084053053Rat
2317586Eae25Experimental allergic encephalomyelitis QTL 259.300000190734863nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)47955938084053053Rat
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)47955938084053053Rat
2317586Eae25Experimental allergic encephalomyelitis QTL 259.300000190734863nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)47955938084053053Rat
61364Iddm2Insulin dependent diabetes mellitus QTL 2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47956245198542106Rat

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
Rnor_6.0 Ensembl480,331,227 - 80,333,326 (-)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

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 (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (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
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)
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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
SBN/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: SBN/Ygl sequenced by MCW
SBN/Ygl (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/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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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/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
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/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
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2451 AgrOrtholog
Ensembl Genes ENSRNOG00000010452 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00000032885 UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000014058 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000041521 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000014058 ENTREZGENE, 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
  rno:25309 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105497 IMAGE-MGC_LOAD
  MGC:93634 IMAGE-MGC_LOAD
NCBI Gene 25309 ENTREZGENE
PANTHER PTHR11961 UniProtKB/Swiss-Prot
Pfam Cytochrom_C UniProtKB/Swiss-Prot
PhenoGen Cycs PhenoGen
PRINTS CYTCHRMECIAB UniProtKB/Swiss-Prot
PROSITE CYTC UniProtKB/Swiss-Prot
Superfamily-SCOP SSF46626 UniProtKB/Swiss-Prot
UniProt CYC_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary P00009 UniProtKB/Swiss-Prot
  Q8C2S2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Cycs  cytochrome c, somatic      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_physical_interaction associates with cardiolipin 70241
gene_regulation release from brain mitochondria is inhibited by enrichment with cardiolipin 727631