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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

NCF1C Gene

pseudogene   GIFtS: 36
GCID: GC07M074574

Neutrophil Cytosolic Factor 1C Pseudogene

(Previous name: neutrophil cytosolic factor 1C)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 4

Aliases
Neutrophil Cytosolic Factor 1C Pseudogene1 2
SH3PXD1C2 3
Neutrophil Cytosolic Factor 1C1
NCF-1C3
Putative SH3 And PX Domain-Containing Protein 1C3

External Ids:    HGNC: 325231   Entrez Gene: 6548172   Ensembl: ENSG000001651787   UniProtKB: A8MVU13   
ORGUL members:    fRNAdb10:FR303010      
H-InvDB12:HIT000218777    
NCBI13:U25793    
NONCODE14:n346379 n405915      
RNAdb15:HIV1948    

Export aliases for NCF1C gene to outside databases

Previous GC identifers: GC07U901697 GC07P072273 GC07M074211 GC07M073906


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for NCF1C Gene:
The neutrophil cytosolic factor 1 (NCF1) gene encodes the 47 kDa cytosolic subunit of neutrophil NADPH oxidase,
which produces superoxide anion. The NCF1 gene is located in close proximity to two highly similar, multi-exon
pseudogenes at chromosome 7q11.23, corresponding to this gene record and GeneID:654816. The two pseudogenes
contain a dinucleotide deletion (delta-GT) in exon 2 that results in a frameshift and truncation of the open
reading frame, and neither pseudogene is likely to express a protein. Recombination events between the
pseudogenes and the functional NCF1 gene can inactivate the NCF1 gene and result in chronic granulomatous
disease. (provided by RefSeq, Nov 2009)

GeneCards Summary for NCF1C Gene: 
NCF1C (neutrophil cytosolic factor 1C pseudogene) is a pseudogene, and is affiliated with the lncRNA class. Diseases associated with NCF1C include chronic granulomatous disease, and williams-beuren syndrome. GO annotations related to this gene include phosphatidylinositol binding and superoxide-generating NADPH oxidase activity.

UniProtKB/Swiss-Prot: NCF1C_HUMAN, A8MVU1
Function: May be required for activation of the latent NADPH oxidase (necessary for superoxide production) (By
similarity)

Gene Wiki entry for NCF1C Gene

fRNAdb sequence ontology for NCF1C:
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.

View fRNAdb secondary structures for NCF1C

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000007.13  NC_018918.2  NT_007933.15  NT_079593.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the NCF1C gene promoter:
         TBP   Pbx1a   Cdc5   LCR-F1   Meis-1b   YY1   MEF-2A   MZF-1   aMEF-2   Meis-1   
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat NCF1C


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 7q11.23   Ensembl cytogenetic band:  7q11.23   HGNC cytogenetic band: 7q11.23

NCF1C Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NCF1C gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M074574:  view genomic region     (about GC identifiers)

Start:
74,572,384 bp from pter      End:
74,587,848 bp from pter
Size:
15,465 bases      Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 73,905,448-73,920,880     
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for NCF1C

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: NCF1C_HUMAN, A8MVU1 (See protein sequence)
Recommended Name: Putative neutrophil cytosol factor 1C  
Size: 366 amino acids; 41851 Da
Subcellular location: Cytoplasm (By similarity)
Caution: Could be the product of a pseudogene

Explore the universe of human proteins at neXtProt for NCF1C: NX_A8MVU1

NCF1C Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --

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Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005737cytoplasm IEA--

NCF1C for ontologies           About GeneDecksing



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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
4 InterPro protein domains:
 IPR015039 NADPH_oxidase_p47Phox_C
 IPR001683 Phox
 IPR001452 SH3_domain
 IPR001655 P47PHOX

Graphical View of Domain Structure for InterPro Entry A8MVU1

ProtoNet protein and cluster: A8MVU1

UniProtKB/Swiss-Prot: NCF1C_HUMAN, A8MVU1
Similarity: Contains 1 PX (phox homology) domain
Similarity: Contains 2 SH3 domains


NCF1C for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Molecular Function:

     UniProtKB/Swiss-Prot Summary: NCF1C_HUMAN, A8MVU1
Function: May be required for activation of the latent NADPH oxidase (necessary for superoxide production) (By
similarity)

     Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016175superoxide-generating NADPH oxidase activity IEA--
GO:0035091phosphatidylinositol binding IEA--
     
NCF1C for ontologies           About GeneDecksing


Phenotypes:
     14 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Ncf1):
 behavior/neurological  cardiovascular system  cellular  endocrine/exocrine gland  growth/size 
 homeostasis/metabolism  immune system  integument  liver/biliary system  mortality/aging 
 muscle  nervous system  respiratory system  skeleton 

NCF1C for phenotypes           About GeneDecksing

Animal Models:
     MGI mouse knock-outs for NCF1C: Ncf1tm1Hbd Ncf1tm1Shl

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miRNA
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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for NCF1C

Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0007154cell communication IEA--

NCF1C for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
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Browse Tocris compounds for NCF1C

1 HMDB Compound for NCF1C    About this table
CompoundSynonyms CAS #PubMed Ids
NADPH2'-(dihydrogen phosphate) 5'-(trihydrogen pyrophosphate) Adenosine 5'-ester with 1,4-dihydro-1-b-D-ribofuranosylnicotinamide (see all 23)53-57-6--

Search CenterWatch for drugs/clinical trials and news about NCF1C

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section
1 fRNAdb Secondary structure:


Unigene Cluster for NCF1C:

Neutrophil cytosolic factor 1C pseudogene
Hs.648940  [show with all ESTs]
Unigene Representative Sequence: AL577485
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000438382(uc003ubv.3) ENST00000297905 ENST00000419670(uc011kfn.2 uc011kfo.2)
ENST00000536284
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Additional mRNA sequence: 

AK298739.1 AK301397.1 

17 DOTS entries:

DT.95329092  DT.92440157  DT.102840657  DT.92440156  DT.121041940  DT.121041970  DT.422643  DT.99981388 
DT.100815093  DT.100815103  DT.101982114  DT.121058223  DT.121058296  DT.40245440  DT.450452  DT.95329095 
DT.97846804 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

NCF1C expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
NCF1C Expression
About this image


Genevestigator expression for NCF1C

SOURCE GeneReport for Unigene cluster: Hs.648940
    SABiosciences Custom PCR Arrays for NCF1C
Primer
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NCF1C

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of human and mouse.

Orthologs for NCF1C gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Ncf15 neutrophil cytosolic factor 1   --   5 (74.47 cM) 134220053 


ENSEMBL Gene Tree for NCF1C (if available)
TreeFam Gene Tree for NCF1C (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for NCF1C gene
6 SIMAP similar genes for NCF1C using alignment to 1 protein entry:     NCF1C_HUMAN:
NCF1B    NCF1    ARHGEF7    ITSN1    SH3PXD2A    SH3PXD2B

NCF1C for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/46 SNPs in NCF1C are shown (see all 46)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 7 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs24290711,2
F--74573171(-) ATCCAC/TCAGCG 1 -- nc-transcript-variant2Minor allele frequency- T:0.33MN NA 186
rs1871443541,2
--74573547(+) CCCGTA/GAGGGT 1 -- int10--------
rs1404542591,2
--74573752(+) GACGGA/GAAGTA 1 -- nc-transcript-variant0--------
rs1920685061,2
--74574818(+) ACAAAA/GGAAAA 1 -- int10--------
rs3677787921,2
C--74576111(+) TCCTGC/TCTGGG 1 -- int10--------
rs1504355701,2
--74578780(+) GTAGTC/TGGCAA 1 -- nc-transcript-variant0--------
rs1381921171,2
C,F--74578781(+) TAGTCG/AGCAAT 1 -- nc-transcript-variant1Minor allele frequency- A:0.02EU 593
rs1496178061,2
--74578797(+) GGTACA/GTCTGC 1 -- nc-transcript-variant0--------
rs3685495581,2
C--74579070(+) AGTGAC/TTGATC 1 -- int10--------
rs1122897181,2
C--74579393(+) TGCAAC/TCTCCA 1 -- int11Minor allele frequency- T:0.00WA 2

HapMap Linkage Disequilibrium report for NCF1C (74572384 - 74587848 bp)

Structural Variations
     Database of Genomic Variants (DGV) 6 variations for NCF1C:    About this table     
Variant IDTypeSubtypePubMed ID
nsv831034CNV Loss17160897
nsv8148CNV Gain18304495
nsv528969CNV Gain19592680
nsv888381CNV Gain21882294
essv21300CNV CNV17122850
dgv2100e1CNV Complex17122850

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
OMIM information: 141400 605635 608512    
4 diseases for NCF1C:    About MalaCards
chronic granulomatous disease    williams-beuren syndrome    endotheliitis    hypertension

1 disease from the University of Copenhagen DISEASES database for NCF1C:
Chronic granulomatous disease

NCF1C for disorders           About GeneDecksing

Genetic Association Database (GAD): NCF1C
Human Genome Epidemiology (HuGE) Navigator: NCF1C (1 document)

Export disorders for NCF1C gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
About This Section

PubMed articles for NCF1C gene, integrated from 9 sources (see all 47):
(articles sorted by number of sources associating them with NCF1C)
    Utopia: connect your pdf to the dynamic
world of online information

  1. NCF1 gene and pseudogene pattern: association with parasitic infection and autoimmunity. (PubMed id 19077231)1, 4 Greve B....Kremsner P.G. (2008)
  2. Activation of the superoxide-producing phagocyte NADPH oxidase requires co-operation between the tandem SH3 domains of p47phox in recognition of a polyproline type II helix and an adjacent alpha-helix of p22phox. (PubMed id 16460309)1 Nobuhisa I....Sumimoto H. (2006)
  3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
  4. Homocysteine stimulates phosphorylation of NADPH oxidase p47phox and p67phox subunits in monocytes via protein kinase Cbeta activation. (PubMed id 16626305)1 Siow Y.L....O K. (2006)
  5. Coronary artery superoxide production and nox isoform expression in human coronary artery disease. (PubMed id 16293794)1 Guzik T.J....Channon K.M. (2006)
  6. C-terminus of p47(phox) is required for interaction with leukocyte type rat 12-lipoxygenase. (PubMed id 15777282)1 Tanabe M....Radmark O. (2005)
  7. Angiotensin II-induced over-activation of p47phox in fibroblasts from hypertensives: which role in the enhanced ERK1/2 responsiveness to angiotensin II? (PubMed id 15775784)1 Papparella I....Semplicini A. (2005)
  8. MAPKAP kinase-2 is a cell cycle checkpoint kinase that regulates the G2/M transition and S phase progression in response to UV irradiation. (PubMed id 15629715)1 Manke I.A....Yaffe M.B. (2005)
  9. p47phox associates with the cytoskeleton through cortactin in human vascular smooth muscle cells: role in NAD(P)H oxidase regulation by angiotensin II. (PubMed id 15618548)1 Touyz R.M....Schiffrin E.L. (2005)
  10. A region C-terminal to the proline-rich core of p47phox regulates activation of the phagocyte NADPH oxidase by interacting with the C-terminal SH3 domain of p67phox. (PubMed id 16297854)1 Mizuki K....Sumimoto H. (2005)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 654817 HGNC: 32523 Ensembl:ENSG00000165178 euGenes: HUgn654817 ECgene: NCF1C
H-InvDB: NCF1C

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for NCF1C Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for NCF1C gene:
Search GeneIP for patents involving NCF1C

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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transforming growth factor, beta 1
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The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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