Ncf1 (neutrophil cytosolic factor 1) - Rat Genome Database

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Gene: Ncf1 (neutrophil cytosolic factor 1) Rattus norvegicus
Analyze
Symbol: Ncf1
Name: neutrophil cytosolic factor 1
RGD ID: 61307
Description: Contributes to superoxide-generating NAD(P)H oxidase activity. Involved in apoptotic process and respiratory burst. Localizes to several cellular components, including NADPH oxidase complex; neuronal cell body; and rough endoplasmic reticulum. Human ortholog(s) of this gene implicated in Williams-Beuren syndrome; autosomal recessive chronic granulomatous disease cytochrome b-positive type I; and chronic granulomatous disease. Orthologous to several human genes including NCF1 (neutrophil cytosolic factor 1); PARTICIPATES IN chemokine mediated signaling pathway; Fc gamma receptor mediated signaling pathway; Leishmaniasis pathway; INTERACTS WITH (+)-catechin; (R)-lipoic acid; 11-deoxycorticosterone.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC100912379; Ncf-1; neutrophil cytosol factor 1; neutrophil cytosol factor 1-like; neutrophil cytosolic factor 1-like; p47phox; phagocyte oxidase 47 kDa; phagocyte oxidase, 47 kDa
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Ncf1W  
Is Marker For: Strains:   LEW/Mol   LEW/Ztm  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21222,485,382 - 22,494,647 (+)NCBI
Rnor_6.0 Ensembl1225,497,104 - 25,506,300 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01225,497,104 - 25,506,300 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01227,505,793 - 27,514,989 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41223,578,097 - 23,587,292 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11223,441,312 - 23,450,507 (+)NCBI
Celera1224,246,402 - 24,255,599 (+)NCBICelera
Cytogenetic Map12q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (EXP,ISO)
(R)-lipoic acid  (EXP)
1,1-bis(2-aminoethyl)-2-hydroxy-3-oxotriazane  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
11-deoxycorticosterone  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (EXP,ISO)
3-chloropropane-1,2-diol  (EXP)
3-methylcholanthrene  (ISO)
3-phenylprop-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-phenylbutyric acid  (EXP)
6-propyl-2-thiouracil  (EXP)
8-OH-DPAT  (ISO)
acetamide  (EXP)
acetylcholine  (ISO)
acetylsalicylic acid  (ISO)
acrolein  (ISO)
actinomycin D  (ISO)
Adiponectin  (ISO)
AICA ribonucleotide  (EXP)
aldehydo-D-glucose  (EXP,ISO)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
alpha-hexachlorocyclohexane  (ISO)
alpha-naphthoflavone  (ISO)
ammonium chloride  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP)
apocynin  (EXP,ISO)
arachidonic acid  (ISO)
arsane  (EXP,ISO)
arsenic atom  (EXP,ISO)
arsenic trichloride  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benazepril  (EXP)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bezafibrate  (ISO)
bisphenol A  (EXP,ISO)
BQ 123  (ISO)
bucladesine  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
calcium atom  (ISO)
calcium dichloride  (ISO)
calcium(0)  (ISO)
carbon atom  (ISO)
carbon nanotube  (EXP,ISO)
carbonyl sulfide  (EXP)
cerium trichloride  (ISO)
chelerythrine  (EXP)
cholesterol  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
cocaine  (EXP,ISO)
D-glucose  (EXP,ISO)
daunorubicin  (EXP)
DDE  (ISO)
Deoxycorticosterone acetate  (ISO)
dexamethasone  (ISO)
diallyl trisulfide  (EXP)
diarsenic trioxide  (ISO)
dibenziodolium  (ISO)
diclofenac  (ISO)
diminazene diaceturate  (ISO)
dioxygen  (EXP,ISO)
dorsomorphin  (EXP)
doxorubicin  (EXP)
edaravone  (EXP)
elemental carbon  (ISO)
endosulfan  (EXP,ISO)
eplerenone  (EXP)
ethanol  (EXP,ISO)
felodipine  (ISO)
filipin III  (ISO)
folic acid  (ISO)
gallic acid  (EXP)
ginkgolide B  (EXP)
ginsenoside Re  (ISO)
gliclazide  (EXP)
glucose  (EXP,ISO)
glyburide  (ISO)
Goe 6976  (EXP,ISO)
hexadecanoic acid  (EXP)
homocysteine  (ISO)
Honokiol  (ISO)
hydralazine  (ISO)
hydrogen peroxide  (EXP,ISO)
irbesartan  (ISO)
isoprenaline  (EXP)
isorhamnetin  (EXP)
ketoconazole  (EXP)
L-methionine  (ISO)
lead diacetate  (ISO)
linoleic acid  (ISO)
lipoic acid  (EXP)
lipopolysaccharide  (EXP,ISO)
losartan  (EXP,ISO)
maneb  (ISO)
medroxyprogesterone acetate  (ISO)
menadione  (ISO)
metformin  (EXP)
methamphetamine  (EXP)
methimazole  (EXP)
methyl beta-cyclodextrin  (ISO)
miconazole  (EXP)
ML-7  (ISO)
monascin  (ISO)
N,N-dimethylformamide  (ISO)
N-[2-[4-(2-methoxyphenyl)-1-piperazinyl]ethyl]-N-(2-pyridinyl)cyclohexanecarboxamide  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-formyl-L-methionyl-L-leucyl-L-phenylalanine  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosomorpholine  (EXP)
nebivolol  (EXP)
nicotinic acid  (EXP)
nitroglycerin  (ISO)
oxalic acid  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
phencyclidine  (ISO)
phenformin  (EXP)
phenol  (EXP)
phenylephrine  (EXP,ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
potassium atom  (ISO)
prazosin  (EXP)
quercetin  (EXP,ISO)
reactive oxygen species  (EXP,ISO)
reserpine  (EXP)
resveratrol  (EXP,ISO)
rotenone  (ISO)
rottlerin  (ISO)
salvianolic acid B  (EXP)
SB 203580  (ISO)
silicon dioxide  (EXP)
sirolimus  (EXP)
sodium arsenite  (EXP,ISO)
streptozocin  (EXP,ISO)
succimer  (ISO)
sulforaphane  (ISO)
superoxide  (EXP)
tamibarotene  (ISO)
taurine  (ISO)
telmisartan  (EXP,ISO)
tert-butyl hydroperoxide  (EXP,ISO)
testosterone  (EXP,ISO)
tetrachloromethane  (EXP,ISO)
tetrahydrocurcumin  (ISO)
trandolapril  (EXP)
trichloroethene  (ISO)
triphenylstannane  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
Y-27632  (ISO)
zinc atom  (ISO)
zinc dichloride  (ISO)
zinc protoporphyrin  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Del Campo M, etal., Am J Hum Genet. 2006 Apr;78(4):533-42. Epub 2006 Jan 31.
2. Espinosa A, etal., J Cell Physiol. 2006 Nov;209(2):379-88.
3. Francke U, etal., Am J Hum Genet. 1990 Sep;47(3):483-92.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Glass MJ, etal., Exp Neurol. 2007 Jun;205(2):383-95. Epub 2007 Mar 3.
6. Glass MJ, etal., Neuroscience. 2006 Dec 1;143(2):547-64. Epub 2006 Oct 4.
7. Griffiths MM, etal., Arthritis Rheum 2000 Jun;43(6):1278-89
8. Hultqvist M, etal., Antioxid Redox Signal. 2011 Jun 15;14(12):2373-83. doi: 10.1089/ars.2010.3440. Epub 2011 Mar 31.
9. Kim MJ, etal., Brain Res. 2005 Apr 8;1040(1-2):178-86.
10. Meng HC,etal., Arthritis Rheum. 2004 Aug;50(8):2695-705.
11. MGD data from the GO Consortium
12. NCBI rat LocusLink and RefSeq merged data July 26, 2002
13. Olofsson P, etal., Genomics 2004 May;83(5):765-71.
14. Olofsson P, etal., Nat Genet 2003 Jan;33(1):25-32.
15. OMIM Disease Annotation Pipeline
16. Pipeline to import KEGG annotations from KEGG into RGD
17. Pithon-Curi TC, etal., Clin Sci (Lond). 2002 Oct;103(4):403-8.
18. Reinehr R, etal., Gastroenterology. 2005 Dec;129(6):2009-31.
19. RGD automated data pipeline
20. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
21. RGD automated import pipeline for gene-chemical interactions
22. Serezani CH, etal., Blood. 2005 Aug 1;106(3):1067-75. Epub 2005 Feb 17.
23. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
24. Tanabe M, etal., DNA Seq. 2005 Feb;16(1):65-8.
25. Tyagi N, etal., J Mol Neurosci. 2012 May;47(1):128-38. doi: 10.1007/s12031-011-9695-z. Epub 2012 Jan 3.
26. Volpp BD and Lin Y, J Clin Invest. 1993 Jan;91(1):201-7.
Additional References at PubMed
PMID:2547247   PMID:2550933   PMID:7650482   PMID:7938008   PMID:8119734   PMID:8280052   PMID:9116268   PMID:10678931   PMID:10714686   PMID:10725280   PMID:10987289   PMID:11156938  
PMID:11867678   PMID:11907569   PMID:12356722   PMID:14717343   PMID:15258578   PMID:15626477   PMID:15850784   PMID:15936744   PMID:16041040   PMID:16085178   PMID:16670314   PMID:17310103  
PMID:17490473   PMID:17526748   PMID:17698723   PMID:18045865   PMID:19052348   PMID:19180494   PMID:19292057   PMID:19299744   PMID:20185631   PMID:20399741   PMID:21228337   PMID:21691064  
PMID:21739151   PMID:21792922   PMID:21859816   PMID:21911753   PMID:22107602   PMID:22566500   PMID:22661470   PMID:22798525   PMID:22801596   PMID:22832955   PMID:23846495   PMID:23922819  
PMID:24633549   PMID:24852886   PMID:25220477   PMID:25224032   PMID:26021615   PMID:26058943   PMID:26514550   PMID:26514923   PMID:26989452   PMID:28751934  


Genomics

Candidate Gene Status
Ncf1 is a candidate Gene for QTL Cia12
Ncf1 is a candidate Gene for QTL Pia22
Ncf1 is a candidate Gene for QTL Cia25
Ncf1 is a candidate Gene for QTL Ean6
Comparative Map Data
Ncf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21222,485,382 - 22,494,647 (+)NCBI
Rnor_6.0 Ensembl1225,497,104 - 25,506,300 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01225,497,104 - 25,506,300 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01227,505,793 - 27,514,989 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41223,578,097 - 23,587,292 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11223,441,312 - 23,450,507 (+)NCBI
Celera1224,246,402 - 24,255,599 (+)NCBICelera
Cytogenetic Map12q12NCBI
NCF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl774,773,962 - 74,789,376 (+)EnsemblGRCh38hg38GRCh38
GRCh38774,774,011 - 74,789,315 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37774,188,309 - 74,203,720 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36773,826,245 - 73,841,595 (+)NCBINCBI36hg18NCBI36
Build 34774,017,096 - 74,032,410NCBI
Cytogenetic Map7q11.23NCBI
CHM1_1774,333,378 - 74,348,792 (+)NCBICHM1_1
CRA_TCAGchr7v2773,521,373 - 73,536,784NCBI
Ncf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395134,248,907 - 134,258,479 (-)NCBIGRCm39mm39
GRCm39 Ensembl5134,248,907 - 134,258,479 (-)Ensembl
GRCm385134,220,053 - 134,229,628 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5134,220,053 - 134,229,625 (-)EnsemblGRCm38mm10GRCm38
MGSCv375134,696,130 - 134,705,495 (-)NCBIGRCm37mm9NCBIm37
MGSCv365134,504,886 - 134,514,206 (-)NCBImm8
Celera5131,223,583 - 131,232,950 (-)NCBICelera
Cytogenetic Map5G2NCBI
cM Map574.47NCBI
Ncf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545613,354,011 - 13,363,891 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545613,353,780 - 13,363,956 (-)NCBIChiLan1.0ChiLan1.0
NCF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1781,917,167 - 81,932,589 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl781,917,167 - 81,932,589 (+)Ensemblpanpan1.1panPan2
NCF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.165,702,222 - 5,719,515 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl65,605,694 - 5,719,458 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha67,403,701 - 7,421,192 (-)NCBI
ROS_Cfam_1.065,518,899 - 5,536,384 (-)NCBI
UMICH_Zoey_3.165,510,772 - 5,528,223 (-)NCBI
UNSW_CanFamBas_1.065,457,618 - 5,474,840 (-)NCBI
UU_Cfam_GSD_1.065,619,880 - 5,637,152 (-)NCBI
Ncf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344130,406,743 - 130,420,026 (-)NCBI
SpeTri2.0NW_0049365433,617,369 - 3,630,990 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NCF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl311,820,285 - 11,839,426 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1311,820,367 - 11,834,394 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2311,538,926 - 11,552,955 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NCF1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1288,334,172 - 8,349,828 (-)NCBI
ChlSab1.1 Ensembl288,332,772 - 8,349,804 (-)Ensembl
Ncf1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474013,428,375 - 13,439,915 (-)NCBI

Position Markers
Ncf1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21222,492,716 - 22,493,032 (+)MAPPER
mRatBN7.21222,492,716 - 22,493,032 (-)MAPPER
Rnor_6.01225,504,371 - 25,504,686NCBIRnor6.0
Rnor_6.01228,976,675 - 28,976,990NCBIRnor6.0
Rnor_5.01230,927,193 - 30,927,508UniSTSRnor5.0
Rnor_5.01227,513,060 - 27,513,375UniSTSRnor5.0
RGSC_v3.41223,585,363 - 23,585,678UniSTSRGSC3.4
Celera1224,253,670 - 24,253,985UniSTS
Cytogenetic Map12q12UniSTS
RH132543  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map12347.9UniSTS
Cytogenetic Map12q12UniSTS
RH138855  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21222,493,193 - 22,493,410 (+)MAPPER
mRatBN7.21222,493,193 - 22,493,410 (-)MAPPER
Rnor_6.01228,976,297 - 28,976,513NCBIRnor6.0
Rnor_6.01225,504,848 - 25,505,064NCBIRnor6.0
Rnor_5.01227,513,537 - 27,513,753UniSTSRnor5.0
Rnor_5.01230,926,815 - 30,927,031UniSTSRnor5.0
RGSC_v3.41223,585,840 - 23,586,056UniSTSRGSC3.4
Celera1224,254,147 - 24,254,363UniSTS
RH 3.4 Map12355.7UniSTS
Cytogenetic Map12q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12130749723Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12136919844Rat
7387292Kidm42Kidney mass QTL 423.030.0004kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)12138334225Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)1215081045150810Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1215081045150810Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)1249257845492578Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12247568747475687Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12251344247513442Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12251344247513442Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12421005149210051Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12895459327911196Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6922362652716770Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922363052716770Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12978983452716770Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121017588931975590Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)121025689031723732Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)121176499537522089Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121312721127285590Rat
1331755Bp219Blood pressure QTL 2193.041arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121312721131723688Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121312721150320041Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121441977552716770Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)121502198652716770Rat
61416Pia4Pristane induced arthritis QTL 48.4joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)121571460935964508Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121571460941291738Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121590890052716770Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121590890052716770Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121718558044098244Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)121796086538409001Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121834247752716770Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121834247752716770Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121872904352716770Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121875259352716770Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101875259352716770Rat
2306789Ean6Experimental allergic neuritis QTL 64.9nervous system integrity trait (VT:0010566)experimental autoimmune neuritis severity score (CMO:0001528)122265070227190240Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)122265070245946937Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122265070248598906Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)122265070252716770Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122265072141291738Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)122287629743799153Rat
631521Pia12Pristane induced arthritis QTL 128.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122324124626710128Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)122490659052716770Rat


Related Rat Strains
The following Strains have been annotated to Ncf1

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:272
Count of miRNA genes:189
Interacting mature miRNAs:214
Transcripts:ENSRNOT00000002028
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 23 11 3 19 3 2 2 3 7 11 2
Low 1 20 46 38 38 6 9 72 32 34 6
Below cutoff 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002028   ⟹   ENSRNOP00000002028
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1225,497,104 - 25,506,300 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076916   ⟹   ENSRNOP00000068213
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1225,498,198 - 25,503,920 (+)Ensembl
RefSeq Acc Id: NM_053734   ⟹   NP_446186
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,485,451 - 22,494,647 (+)NCBI
Rnor_6.01225,497,104 - 25,506,300 (+)NCBI
Rnor_5.01227,505,793 - 27,514,989 (+)NCBI
RGSC_v3.41223,578,097 - 23,587,292 (+)RGD
Celera1224,246,402 - 24,255,599 (+)RGD
Sequence:
RefSeq Acc Id: XM_039089020   ⟹   XP_038944948
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21222,485,382 - 22,493,792 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_446186   ⟸   NM_053734
- UniProtKB: Q811Y3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002028   ⟸   ENSRNOT00000002028
RefSeq Acc Id: ENSRNOP00000068213   ⟸   ENSRNOT00000076916
RefSeq Acc Id: XP_038944948   ⟸   XM_039089020
- Peptide Label: isoform X1
Protein Domains
PX   SH3

Transcriptome

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

Promoters
RGD ID:13698573
Promoter ID:EPDNEW_R9098
Type:multiple initiation site
Name:Ncf1_1
Description:neutrophil cytosolic factor 1
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_6.01225,497,094 - 25,497,154EPDNEW

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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61307 AgrOrtholog
Ensembl Genes ENSRNOG00000001480 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002028 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000068213 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002028 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000076916 UniProtKB/TrEMBL
Gene3D-CATH 3.30.1520.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5598653 IMAGE-MGC_LOAD
InterPro NADPH_oxidase_p47Phox_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NCF1_SH3_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NCF1_SH3_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NECFESHC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P47PHOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Phox UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PX_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PX_p47phox UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:114553 UniProtKB/TrEMBL
MGC_CLONE MGC:72350 IMAGE-MGC_LOAD
NCBI Gene 114553 ENTREZGENE
PANTHER PTHR15706:SF6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam NECFESHC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  p47_phox_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00787 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ncf1 PhenoGen
PRINTS P47PHOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PS50195 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00312 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50044 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF64268 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A096MJP6_RAT UniProtKB/TrEMBL
  F1M707 ENTREZGENE, UniProtKB/Swiss-Prot
  Q811Y3 ENTREZGENE, UniProtKB/TrEMBL
  Q99M65_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Ncf1  neutrophil cytosolic factor 1  LOC100912379  neutrophil cytosol factor 1-like  Data Merged 737654 PROVISIONAL
2012-07-05 LOC100912379  neutrophil cytosol factor 1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Ncf1        Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease SNP causing the amino acid substitution at position 153 (DA rats-Met/E3 rats-Thr) is thought to be involved in the alteration of activity causing inflammation susceptibility 1299867
gene_disease DA Ncf1 rats display an expansion of arthritogenic T cells and lead to a systemic induction of the inflammatory response 628543
gene_disease deficiency maybe associated with the rare monogenic chronic granulomatous disease (CGD) in humans 628543
gene_expression expressed in phagocytic cells 628543
gene_mutations_overexpression arthritis-susceptible and resistant SNPs that correlated with variable production of reactive oxygen species was detected; DA/BklArb rats have A allele and ACI/SegHsd have a G allele at nucleotide 316 (codon 106) and DA/BklArb rats have T allele and ACI/SegHsd have a C allele at nucleotide 458 (codon 153) that cause amino acid change 1285224
gene_physical_interaction following phosphorylation, attaches to Ncf2 and translocates to the membrane and associates with the membrane-bound subunit b558 (consisting of Cyba and Cybb) to form the NADPH oxidase complex 628543
gene_process regulates arthritis severity and plays a role in the cellular host-defense system against bacterial infections 628543
gene_process a component of the NADPH (nicotinamide adenine dinucleotide phosphate) oxidase complex 628543
gene_protein 47 kDa 628543