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: Enables superoxide-generating NADPH oxidase activator activity. Involved in several processes, including cellular response to glucose stimulus; cellular response to testosterone stimulus; and regulation of respiratory burst involved in inflammatory response. Located in several cellular components, including cytosol; dendrite; and neuronal cell body. Part of NADPH oxidase complex. Used to study rheumatoid arthritis. Human ortholog(s) of this gene implicated in Williams-Beuren syndrome; autosomal recessive chronic granulomatous disease 1; 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
Previously 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 Orthologs
More Info more info ...
Allele / Splice: Ncf1W
Is Marker For: Strains:   LEW/Mol   LEW/Ztm  
Candidate Gene For: Cia12 Pia22 Cia25 Ean6
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81228,121,816 - 28,131,080 (+)NCBIGRCr8
mRatBN7.21222,485,382 - 22,494,647 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1222,485,451 - 22,494,646 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1223,628,473 - 23,637,751 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01224,239,570 - 24,248,848 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01223,305,038 - 23,314,250 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01225,497,104 - 25,506,300 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1225,497,104 - 25,506,300 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01227,505,793 - 27,514,989 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41223,578,097 - 23,587,292 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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)
(S)-nicotine  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
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  (EXP,ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (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-amanitin  (ISO)
alpha-hexachlorocyclohexane  (ISO)
alpha-naphthoflavone  (ISO)
alpha-Zearalanol  (EXP)
ammonium chloride  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP)
apocynin  (EXP,ISO)
arachidonic acid  (ISO)
aristolochic acid A  (ISO)
arsane  (EXP,ISO)
arsenic atom  (EXP,ISO)
arsenic trichloride  (ISO)
arsenous acid  (ISO)
atrazine  (EXP,ISO)
benazepril  (EXP)
benzo[a]pyrene  (ISO)
berberine  (ISO)
beta-naphthoflavone  (ISO)
bezafibrate  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
BQ 123  (ISO)
bucladesine  (ISO)
Butylbenzyl phthalate  (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)
Cuprizon  (EXP)
cyanocob(III)alamin  (ISO)
D-glucose  (EXP,ISO)
daunorubicin  (EXP)
DDE  (ISO)
Deoxycorticosterone acetate  (ISO)
dexamethasone  (ISO)
Di-n-octyl phthalate  (ISO)
diallyl trisulfide  (EXP)
diarsenic trioxide  (ISO)
dibenziodolium  (ISO)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (ISO)
diclofenac  (ISO)
diethyl phthalate  (ISO)
Diisodecyl phthalate  (ISO)
diisononyl phthalate  (ISO)
dimethylarsinic acid  (ISO)
diminazene diaceturate  (ISO)
dioxygen  (EXP,ISO)
dorsomorphin  (EXP)
doxorubicin  (EXP,ISO)
edaravone  (EXP)
elemental carbon  (ISO)
endosulfan  (EXP,ISO)
eplerenone  (EXP)
ethanol  (EXP,ISO)
felodipine  (ISO)
filipin III  (ISO)
folic acid  (ISO)
fructose  (ISO)
gallic acid  (EXP)
ginkgolide B  (EXP)
ginsenoside Re  (ISO)
gliclazide  (EXP)
glucose  (EXP,ISO)
glyburide  (ISO)
glyphosate  (ISO)
Goe 6976  (EXP,ISO)
hexadecanoic acid  (EXP)
homocysteine  (ISO)
Honokiol  (ISO)
hydralazine  (ISO)
hydrogen peroxide  (EXP,ISO)
indirubin  (ISO)
irbesartan  (ISO)
irinotecan  (ISO)
isoprenaline  (EXP)
isorhamnetin  (EXP)
ketoconazole  (EXP)
L-methionine  (ISO)
lanthanum trichloride  (ISO)
lead diacetate  (ISO)
lidocaine  (EXP)
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)
methylarsonic acid  (ISO)
miconazole  (EXP)
minocycline  (ISO)
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  (EXP,ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-methyl-D-aspartic acid  (ISO)
N-nitrosomorpholine  (EXP)
nebivolol  (EXP)
nicotine  (ISO)
nicotinic acid  (EXP)
nitrates  (ISO)
nitroglycerin  (ISO)
oxalic acid  (ISO)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
patulin  (ISO)
phencyclidine  (ISO)
phenformin  (EXP)
phenol  (EXP)
phenylephrine  (EXP,ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
potassium atom  (ISO)
prazosin  (EXP)
puerarin  (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 arsenate  (ISO)
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)
tetrathiomolybdate(2-)  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trandolapril  (EXP)
trichloroethene  (ISO)
triphenyl phosphate  (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
cytoplasm  (IBA,IEA,ISO)
cytoplasmic side of plasma membrane  (IEA,ISO)
cytosol  (IDA,IEA,ISO)
dendrite  (IDA)
membrane  (IEA,ISO)
NADPH oxidase complex  (IBA,IDA,IEA,ISO)
neuronal cell body  (IDA)
plasma membrane  (IDA,IEA,ISO)

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

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Angiotensin II induces Fat1 expression/activation and vascular smooth muscle cell migration via Nox1-dependent reactive oxygen species generation. Bruder-Nascimento T, etal., J Mol Cell Cardiol. 2014 Jan;66:18-26. doi: 10.1016/j.yjmcc.2013.10.013.
2. Hemizygosity at the NCF1 gene in patients with Williams-Beuren syndrome decreases their risk of hypertension. Del Campo M, etal., Am J Hum Genet. 2006 Apr;78(4):533-42. Epub 2006 Jan 31.
3. Myotube depolarization generates reactive oxygen species through NAD(P)H oxidase; ROS-elicited Ca2+ stimulates ERK, CREB, early genes. Espinosa A, etal., J Cell Physiol. 2006 Nov;209(2):379-88.
4. Genes for two autosomal recessive forms of chronic granulomatous disease assigned to 1q25 (NCF2) and 7q11.23 (NCF1). Francke U, etal., Am J Hum Genet. 1990 Sep;47(3):483-92.
5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Changes in the subcellular distribution of NADPH oxidase subunit p47phox in dendrites of rat dorsomedial nucleus tractus solitarius neurons in response to chronic administration of hypertensive agents. Glass MJ, etal., Exp Neurol. 2007 Jun;205(2):383-95. Epub 2007 Mar 3.
7. Subcellular localization of nicotinamide adenine dinucleotide phosphate oxidase subunits in neurons and astroglia of the rat medial nucleus tractus solitarius: relationship with tyrosine hydroxylase immunoreactive neurons. Glass MJ, etal., Neuroscience. 2006 Dec 1;143(2):547-64. Epub 2006 Oct 4.
8. Identification of four new quantitative trait loci regulating arthritis severity and one new quantitative trait locus regulating autoantibody production in rats with collagen-induced arthritis. Griffiths MM, etal., Arthritis Rheum 2000 Jun;43(6):1278-89
9. Positioning of a polymorphic quantitative trait nucleotide in the Ncf1 gene controlling oxidative burst response and arthritis severity in rats. Hultqvist M, etal., Antioxid Redox Signal. 2011 Jun 15;14(12):2373-83. doi: 10.1089/ars.2010.3440. Epub 2011 Mar 31.
10. Immunohistochemical study of p47Phox and gp91Phox distributions in rat brain. Kim MJ, etal., Brain Res. 2005 Apr 8;1040(1-2):178-86.
11. Testosterone reduces AGTR1 expression to prevent β-cell and islet apoptosis from glucotoxicity. Kooptiwut S, etal., J Endocrinol. 2015 Mar;224(3):215-24. doi: 10.1530/JOE-14-0397. Epub 2014 Dec 15.
12. Identification of Two Novel Female-Specific Non-MHC Loci Regulating Collagen-Induced Arthritis Severity and Chronicity, and Evidence for Epistasis. Meng HC,etal., Arthritis Rheum. 2004 Aug;50(8):2695-705.
13. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
14. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. Inconsistent susceptibility to autoimmunity in inbred LEW rats is due to genetic crossbreeding involving segregation of the arthritis-regulating gene Ncf1. Olofsson P, etal., Genomics 2004 May;83(5):765-71.
16. Positional identification of Ncf1 as a gene that regulates arthritis severity in rats. Olofsson P, etal., Nat Genet 2003 Jan;33(1):25-32.
17. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
18. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
19. Glutamine plays a role in superoxide production and the expression of p47phox, p22phox and gp91phox in rat neutrophils. Pithon-Curi TC, etal., Clin Sci (Lond). 2002 Oct;103(4):403-8.
20. Bile salt-induced apoptosis involves NADPH oxidase isoform activation. Reinehr R, etal., Gastroenterology. 2005 Dec;129(6):2009-31.
21. GOA pipeline RGD automated data pipeline
22. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
23. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
24. Leukotrienes enhance the bactericidal activity of alveolar macrophages against Klebsiella pneumoniae through the activation of NADPH oxidase. Serezani CH, etal., Blood. 2005 Aug 1;106(3):1067-75. Epub 2005 Feb 17.
25. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
26. Cloning of rat p47phox and comparison with human p47phox. Tanabe M, etal., DNA Seq. 2005 Feb;16(1):65-8.
27. Tetrahydrocurcumin ameliorates homocysteinylated cytochrome-c mediated autophagy in hyperhomocysteinemia mice after cerebral ischemia. Tyagi N, etal., J Mol Neurosci. 2012 May;47(1):128-38. doi: 10.1007/s12031-011-9695-z. Epub 2012 Jan 3.
28. In vitro molecular reconstitution of the respiratory burst in B lymphoblasts from p47-phox-deficient chronic granulomatous disease. 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   PMID:32805334  


Genomics

Comparative Map Data
Ncf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81228,121,816 - 28,131,080 (+)NCBIGRCr8
mRatBN7.21222,485,382 - 22,494,647 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1222,485,451 - 22,494,646 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1223,628,473 - 23,637,751 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01224,239,570 - 24,248,848 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01223,305,038 - 23,314,250 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01225,497,104 - 25,506,300 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1225,497,104 - 25,506,300 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01227,505,793 - 27,514,989 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41223,578,097 - 23,587,292 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh38774,774,011 - 74,789,315 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl774,774,011 - 74,789,315 (+)EnsemblGRCh38hg38GRCh38
GRCh37774,188,358 - 74,203,659 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36773,826,245 - 73,841,595 (+)NCBINCBI36Build 36hg18NCBI36
Build 34774,017,096 - 74,032,410NCBI
Cytogenetic Map7q11.23NCBI
CHM1_1774,333,378 - 74,348,792 (+)NCBICHM1_1
T2T-CHM13v2.0775,976,304 - 75,991,631 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2773,521,373 - 73,536,784NCBI
Ncf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395134,248,907 - 134,258,479 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5134,248,907 - 134,258,479 (-)EnsemblGRCm39 Ensembl
GRCm385134,220,053 - 134,229,628 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5134,220,053 - 134,229,625 (-)EnsemblGRCm38mm10GRCm38
MGSCv375134,696,130 - 134,705,495 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365134,504,886 - 134,514,206 (-)NCBIMGSCv36mm8
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
NHGRI_mPanPan1-v2690,107,213 - 90,128,059 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan17138,371,836 - 138,392,363 (-)NCBINHGRI_mPanPan1
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.065,518,899 - 5,536,384 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl65,518,899 - 5,540,134 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.165,510,772 - 5,528,223 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.065,457,618 - 5,474,840 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.065,619,880 - 5,637,152 (-)NCBIUU_Cfam_GSD_1.0
Ncf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344130,406,743 - 130,420,026 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365433,617,372 - 3,630,997 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365433,617,369 - 3,630,990 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NCF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl311,820,266 - 11,839,354 (+)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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1288,334,172 - 8,349,828 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl288,332,772 - 8,349,804 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660708,253,552 - 8,269,564 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ncf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474013,429,476 - 13,439,807 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474013,428,375 - 13,439,915 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ncf1
107 total Variants
miRNA Target Status (No longer updated)

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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)122480502252308831Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121120049452308831Rat
2306789Ean6Experimental allergic neuritis QTL 64.9nervous system integrity trait (VT:0010566)experimental autoimmune neuritis severity score (CMO:0001528)12129775522Rat
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)121120049452308831Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122598935552308831Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12348941648489416Rat
1331739Hrtrt14Heart rate QTL 143.56232heart pumping trait (VT:2000009)heart rate (CMO:0000002)12138687564Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121847304152308831Rat
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)121120049752308831Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)121526424852308831Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)12133700600Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)121174352852308831Rat
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)121120049452308831Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)12138635130Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12128133365Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)121223300030490641Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121746497946784661Rat
1300174Bw15Body weight QTL 152.93body mass (VT:0001259)body weight loss (CMO:0001399)12128606299Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121618743852308831Rat
1331787Rf41Renal function QTL 412.998kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)12133700556Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121613502952308831Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121618743851213550Rat
1331763Wbc2White blood cell count QTL 23.162leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)121120049452308831Rat
61416Pia4Pristane induced arthritis QTL 48.4joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)121874946936488809Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)61120049452308831Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121874946934312613Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12274769447747694Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121847304152308831Rat
2303568Bw88Body weight QTL 883body mass (VT:0001259)body weight (CMO:0000012)12128606299Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12308718048087180Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat
7243862Mcs30Mammary carcinoma susceptibility QTL 308.62mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)12563330650633306Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121613502952308831Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12790162533938215Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat
1331755Bp219Blood pressure QTL 2193.041arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121618743833700556Rat

Markers in Region
Ncf1  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81228,129,150 - 28,129,466 (+)Marker Load Pipeline
mRatBN7.21222,492,716 - 22,493,032 (+)MAPPERmRatBN7.2
mRatBN7.21222,492,716 - 22,493,032 (-)MAPPERmRatBN7.2
Rnor_6.01228,976,675 - 28,976,990NCBIRnor6.0
Rnor_6.01225,504,371 - 25,504,686NCBIRnor6.0
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 (+)MAPPERmRatBN7.2
mRatBN7.21222,493,193 - 22,493,410 (-)MAPPERmRatBN7.2
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


Related Rat Strains
The following Strains have been annotated to Ncf1
LEW/Mol     LEW/Ztm    


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000002028   ⟹   ENSRNOP00000002028
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1222,485,451 - 22,494,646 (+)Ensembl
Rnor_6.0 Ensembl1225,497,104 - 25,506,300 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000076916   ⟹   ENSRNOP00000068213
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1222,485,451 - 22,492,872 (+)Ensembl
Rnor_6.0 Ensembl1225,498,198 - 25,503,920 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000092799   ⟹   ENSRNOP00000094686
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1222,486,449 - 22,494,646 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000095426   ⟹   ENSRNOP00000084604
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1222,485,451 - 22,494,646 (+)Ensembl
RefSeq Acc Id: NM_053734   ⟹   NP_446186
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81228,121,885 - 28,131,080 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81228,121,816 - 28,131,080 (+)NCBI
mRatBN7.21222,485,382 - 22,493,792 (+)NCBI
RefSeq Acc Id: XM_063270990   ⟹   XP_063127060
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81228,121,953 - 28,131,080 (+)NCBI
RefSeq Acc Id: NP_446186   ⟸   NM_053734
- UniProtKB: F1M707 (UniProtKB/Swiss-Prot),   Q811Y3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000002028   ⟸   ENSRNOT00000002028
Ensembl Acc Id: ENSRNOP00000068213   ⟸   ENSRNOT00000076916
RefSeq Acc Id: XP_038944948   ⟸   XM_039089020
- Peptide Label: isoform X1
- UniProtKB: F1M707 (UniProtKB/Swiss-Prot),   Q99M65 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000094686   ⟸   ENSRNOT00000092799
Ensembl Acc Id: ENSRNOP00000084604   ⟸   ENSRNOT00000095426
RefSeq Acc Id: XP_063127060   ⟸   XM_063270990
- Peptide Label: isoform X2
Protein Domains
PX   SH3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M707-F1-model_v2 AlphaFold F1M707 1-389 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61307 AgrOrtholog
BioCyc Gene G2FUF-19569 BioCyc
Ensembl Genes ENSRNOG00000001480 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000002028 ENTREZGENE
  ENSRNOT00000002028.9 UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.1520.10 UniProtKB/Swiss-Prot
  SH3 Domains UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5598653 IMAGE-MGC_LOAD
InterPro NADPH_Oxidase/PX-Domain UniProtKB/Swiss-Prot
  NADPH_oxidase_p47Phox_C UniProtKB/Swiss-Prot
  NCF1_SH3_1 UniProtKB/Swiss-Prot
  NCF1_SH3_2 UniProtKB/Swiss-Prot
  NECFESHC UniProtKB/Swiss-Prot
  P47PHOX UniProtKB/Swiss-Prot
  Phox UniProtKB/Swiss-Prot
  PX_dom_sf UniProtKB/Swiss-Prot
  PX_p47phox UniProtKB/Swiss-Prot
  SH3-like_dom_sf UniProtKB/Swiss-Prot
  SH3_domain UniProtKB/Swiss-Prot
MGC_CLONE MGC:72350 IMAGE-MGC_LOAD
NCBI Gene 114553 ENTREZGENE
PANTHER PTHR15706:SF6 UniProtKB/Swiss-Prot
  SH3 MULTIPLE DOMAIN UniProtKB/Swiss-Prot
Pfam NECFESHC UniProtKB/Swiss-Prot
  p47_phox_C UniProtKB/Swiss-Prot
  PF00787 UniProtKB/Swiss-Prot
  SH3_1 UniProtKB/Swiss-Prot
PhenoGen Ncf1 PhenoGen
PRINTS P47PHOX UniProtKB/Swiss-Prot
  SH3DOMAIN UniProtKB/Swiss-Prot
PROSITE PS50195 UniProtKB/Swiss-Prot
  SH3 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000001480 RatGTEx
SMART SH3 UniProtKB/Swiss-Prot
  SM00312 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50044 UniProtKB/Swiss-Prot
  SSF64268 UniProtKB/Swiss-Prot
UniProt A0A096MJP6_RAT UniProtKB/TrEMBL
  A0A8I5ZYB6_RAT UniProtKB/TrEMBL
  A0A8I6ANL5_RAT UniProtKB/TrEMBL
  F1M707 ENTREZGENE, UniProtKB/Swiss-Prot
  Q811Y3 ENTREZGENE, UniProtKB/TrEMBL
  Q99M65 ENTREZGENE, 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 from RGD:6487394 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