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 Golgi apparatus; neuronal cell body; and rough endoplasmic reticulum. 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 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
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 Genes
More Info more info ...
Allele / Splice: Ncf1W  
Is Marker For: Strains:   LEW/Mol   LEW/Ztm  
Candidate Gene For: Cia12 Pia22 Cia25 Ean6
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01224,239,570 - 24,248,848 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01223,305,038 - 23,314,250 (+)NCBIRnor_WKY
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)
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)
aristolochic acid A  (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)
Cuprizon  (EXP)
D-glucose  (EXP,ISO)
daunorubicin  (EXP)
DDE  (ISO)
Deoxycorticosterone acetate  (ISO)
dexamethasone  (ISO)
diallyl trisulfide  (EXP)
diarsenic trioxide  (ISO)
dibenziodolium  (ISO)
diclofenac  (ISO)
dimethylarsinic acid  (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)
indirubin  (ISO)
irbesartan  (ISO)
irinotecan  (ISO)
isoprenaline  (EXP)
isorhamnetin  (EXP)
ketoconazole  (EXP)
L-methionine  (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)
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-methyl-D-aspartic acid  (ISO)
N-nitrosomorpholine  (EXP)
nebivolol  (EXP)
nicotine  (ISO)
nicotinic acid  (EXP)
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)
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)
thioacetamide  (EXP)
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
# Reference Title Reference Citation
1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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
8. 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.
9. Immunohistochemical study of p47Phox and gp91Phox distributions in rat brain. Kim MJ, etal., Brain Res. 2005 Apr 8;1040(1-2):178-86.
10. 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.
11. 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.
12. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
13. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. 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.
15. Positional identification of Ncf1 as a gene that regulates arthritis severity in rats. Olofsson P, etal., Nat Genet 2003 Jan;33(1):25-32.
16. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
17. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
18. 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.
19. Bile salt-induced apoptosis involves NADPH oxidase isoform activation. Reinehr R, etal., Gastroenterology. 2005 Dec;129(6):2009-31.
20. GOA pipeline RGD automated data pipeline
21. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
22. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
23. 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.
24. 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.
25. Cloning of rat p47phox and comparison with human p47phox. Tanabe M, etal., DNA Seq. 2005 Feb;16(1):65-8.
26. 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.
27. 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
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_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01224,239,570 - 24,248,848 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01223,305,038 - 23,314,250 (+)NCBIRnor_WKY
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.p13 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
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 (+)EnsemblSpeTri2.0
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
34 total Variants
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12122591684Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123297788Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12129333307Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
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)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
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)12556449546669029Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
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)12556449846669029Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12844949028302290Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)12852542328064601Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)12931821632103380Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121047413746669029Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121047413746669029Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121107382524234895Rat
1331755Bp219Blood pressure QTL 2193.041arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382528064557Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382545055165Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121235161946669029Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121281238546669029Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121281238546669029Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121318273646669029Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101318273646669029Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121319815746669029Rat
61416Pia4Pristane induced arthritis QTL 48.4joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)121363552330827399Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121363552335682913Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121555082638478808Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)121587265332974238Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)121914436246669029Rat
2306789Ean6Experimental allergic neuritis QTL 64.9nervous system integrity trait (VT:0010566)experimental autoimmune neuritis severity score (CMO:0001528)121961087024139202Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)121961087040218516Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961087042828880Rat
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)121961087046669029Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961088935682913Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121983578938193007Rat
631521Pia12Pristane induced arthritis QTL 128.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122025941723672083Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122032881946669029Rat

Markers in Region
Ncf1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21222,492,716 - 22,493,032 (+)MAPPERmRatBN7.2
mRatBN7.21222,492,716 - 22,493,032 (-)MAPPERmRatBN7.2
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 (+)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


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
mRatBN7.2 Ensembl1222,485,451 - 22,494,646 (+)Ensembl
Rnor_6.0 Ensembl1225,497,104 - 25,506,300 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076916   ⟹   ENSRNOP00000068213
RefSeq Status:
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
RefSeq Acc Id: ENSRNOT00000092799   ⟹   ENSRNOP00000094686
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1222,486,449 - 22,494,646 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095426   ⟹   ENSRNOP00000084604
RefSeq Status:
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
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
RefSeq Acc Id: ENSRNOP00000094686   ⟸   ENSRNOT00000092799
RefSeq Acc Id: ENSRNOP00000084604   ⟸   ENSRNOT00000095426
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, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002028 ENTREZGENE
  ENSRNOP00000002028.5 UniProtKB/Swiss-Prot
  ENSRNOP00000068213.2 UniProtKB/TrEMBL
  ENSRNOP00000084604.1 UniProtKB/TrEMBL
  ENSRNOP00000094686.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002028 ENTREZGENE
  ENSRNOT00000002028.9 UniProtKB/Swiss-Prot
  ENSRNOT00000076916.2 UniProtKB/TrEMBL
  ENSRNOT00000092799.2 UniProtKB/TrEMBL
  ENSRNOT00000095426.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.1520.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 Domains 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
  SH3 MULTIPLE DOMAIN 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
  A0A8I5ZYB6_RAT UniProtKB/TrEMBL
  A0A8I6ANL5_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 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_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_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