Human Gene NCF1C (uc003ubv.3)
  Description: Homo sapiens neutrophil cytosolic factor 1C pseudogene (NCF1C), non-coding RNA.
RefSeq Summary (NR_003187): 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].
Transcript (Including UTRs)
   Position: hg19 chr7:74,572,384-74,587,816 Size: 15,433 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr7:74,572,600-74,587,677 Size: 15,078 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:74,572,384-74,587,816)mRNA (may differ from genome)Protein (366 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMalacardsMGIneXtProtPubMed
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: NCF1C_HUMAN
DESCRIPTION: RecName: Full=Putative neutrophil cytosol factor 1C; Short=NCF-1C; AltName: Full=Putative SH3 and PX domain-containing protein 1C;
FUNCTION: May be required for activation of the latent NADPH oxidase (necessary for superoxide production) (By similarity).
SUBCELLULAR LOCATION: Cytoplasm (By similarity).
SIMILARITY: Contains 1 PX (phox homology) domain.
SIMILARITY: Contains 2 SH3 domains.
CAUTION: Could be the product of a pseudogene.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NCF1C
CDC HuGE Published Literature: NCF1C

-  MalaCards Disease Associations
  MalaCards Gene Search: NCF1C
Diseases sorted by gene-association score: chronic granulomatous disease (4)

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 41.39 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 125.42 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -49.30139-0.355 Picture PostScript Text
3' UTR -84.20216-0.390 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR015039 - NADPH_oxidase_p47Phox_C
IPR001655 - P47PHOX
IPR001683 - Phox
IPR001452 - SH3_domain

Pfam Domains:
PF00018 - SH3 domain
PF00787 - PX domain
PF07653 - Variant SH3 domain
PF08944 - NADPH oxidase subunit p47Phox, C terminal domain
PF14604 - Variant SH3 domain
PF16621 - SH3 terminal domain of 2nd SH3 on Neutrophil cytosol factor 1

SCOP Domains:
50044 - SH3-domain
64268 - PX domain

ModBase Predicted Comparative 3D Structure on A8MVU1
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0016175 superoxide-generating NADPH oxidase activity
GO:0016176 superoxide-generating NADPH oxidase activator activity
GO:0035091 phosphatidylinositol binding

Biological Process:
GO:0006801 superoxide metabolic process
GO:0043085 positive regulation of catalytic activity
GO:0055114 oxidation-reduction process
GO:0071800 podosome assembly

Cellular Component:
GO:0002102 podosome
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  BC071711 - Homo sapiens cDNA clone IMAGE:5500254, containing frame-shift errors.
AF330627 - Homo sapiens adaptor protein p47phox (NCF1) mRNA, complete cds.
BC094845 - Homo sapiens cDNA clone IMAGE:5093319, containing frame-shift errors.
M25665 - Human neutrophil cytosol factor 1 (NCF-47k) protein, complete cds.
M55067 - Human 47-kD autosomal chronic granulomatous disease protein mRNA, complete cds.
AF330626 - Homo sapiens adaptor protein p47phox (NCF1) mRNA, partial cds.
AF330625 - Homo sapiens ECV-304 adaptor protein p47phox (NCF1) mRNA, partial cds.
AK301397 - Homo sapiens cDNA FLJ54892 complete cds, moderately similar to Neutrophil cytosol factor 1.
AK298739 - Homo sapiens cDNA FLJ59954 complete cds, moderately similar to Neutrophil cytosol factor 1.
AK316329 - Homo sapiens cDNA, FLJ79228 complete cds, highly similar to Neutrophil cytosol factor 1.
JD022805 - Sequence 3829 from Patent EP1572962.
JD189424 - Sequence 170448 from Patent EP1572962.
JD547019 - Sequence 528043 from Patent EP1572962.
JD494107 - Sequence 475131 from Patent EP1572962.
JD143596 - Sequence 124620 from Patent EP1572962.
GU215077 - Homo sapiens neutrophil cytosolic factor 1 (NCF1) pseudogene mRNA, partial sequence.
U25793 - Human neutrophil oxidase factor mRNA, partial cds.
JD455521 - Sequence 436545 from Patent EP1572962.
JD215784 - Sequence 196808 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_fMLPpathway - fMLP induced chemokine gene expression in HMC-1 cells

-  Other Names for This Gene
  Alternate Gene Symbols: A8MVU1, NCF1C_HUMAN, NR_003187, SH3PXD1C
UCSC ID: uc003ubv.3
RefSeq Accession: NR_003187
Protein: A8MVU1 (aka NCF1C_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NR_003187.2
exon count: 11CDS single in 3' UTR: no RNA size: 1456
ORF size: 1101CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2332.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.