This gene encodes a transcriptional repressor that interacts with specific negative regulatory elements to mediate transcriptional repression of certain nuclear factor kappa B responsive genes. The protein localizes predominantly to the nucleolus with a small fraction found in the nucleoplasm and cytoplasm. Alternate splicing results in multiple transcript variants. [provided b... See more...

Aliases for NKRF Gene

Aliases for NKRF Gene

  • NFKB Repressing Factor 2 3 5
  • ITBA4 2 3 4
  • NRF 2 3 4
  • NF-Kappa-B-Repressing Factor 3 4
  • Transcription Factor NRF 3 4
  • NF-KappaB Repressing Factor 2
  • NFkB-Repressing Factor 4
  • Protein ITBA4 4
  • NKRF 5

External Ids for NKRF Gene

Previous GeneCards Identifiers for NKRF Gene

  • GC0XM118504
  • GC0XM118606
  • GC0XM118722
  • GC0XM108215

Summaries for NKRF Gene

Entrez Gene Summary for NKRF Gene

  • This gene encodes a transcriptional repressor that interacts with specific negative regulatory elements to mediate transcriptional repression of certain nuclear factor kappa B responsive genes. The protein localizes predominantly to the nucleolus with a small fraction found in the nucleoplasm and cytoplasm. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]

GeneCards Summary for NKRF Gene

NKRF (NFKB Repressing Factor) is a Protein Coding gene. Diseases associated with NKRF include Angiokeratoma Of Mibelli and Retinitis Pigmentosa 46. Gene Ontology (GO) annotations related to this gene include nucleic acid binding. An important paralog of this gene is CDKN2AIP.

UniProtKB/Swiss-Prot Summary for NKRF Gene

  • Interacts with a specific negative regulatory element (NRE) 5'-AATTCCTCTGA-3' to mediate transcriptional repression of certain NK-kappa-B responsive genes. Involved in the constitutive silencing of the interferon beta promoter, independently of the virus-induced signals, and in the inhibition of the basal and cytokine-induced iNOS promoter activity. Also involved in the regulation of IL-8 transcription.

Gene Wiki entry for NKRF Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NKRF Gene

Genomics for NKRF Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for NKRF Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ119604 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.7 729 3.4 MYC ZNF600 ZNF580 POLR2A BRCA1 ZBTB10 YY1 SMAD5 CHD2 BHLHE40 HSALNG0139779 RF00005-219 NKRF STEEP1 UBE2A
GH0XJ119674 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 14.5 -78.3 -78268 20.2 BCLAF1 SP1 ZNF654 IKZF1 MYC NCOR1 ZNF600 JUND ZNF580 ZNF592 SEPTIN6 EEF1A1P30 NKAPP1 NKRF MIR766 STEEP1 CUL4B SLC25A5-AS1 NKAP PGRMC1
GH0XJ119638 Enhancer 1 Ensembl ENCODE dbSUPER 13 -34.1 -34058 5 SP1 ZNF207 EBF1 SPI1 BATF IKZF1 MTA3 ATF2 JUNB ZBED1 NKRF STEEP1 lnc-NKRF-1 MIR766 SEPTIN6
GH0XJ119941 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 5.7 -336.9 -336853 3 BCLAF1 NCOR1 ZNF600 SIX5 JUND ZNF580 ZMYM3 ATF2 POLR2A ZNF10 NKAP RHOXF1P3 RHOXF1-AS1 NKRF RHOXF1 AKAP14 RF00017-8033
GH0XJ119635 Enhancer 0.9 Ensembl ENCODE dbSUPER 13 -29.7 -29712 2.2 TARDBP EBF1 IKZF1 SPI1 IKZF2 RAD51 MTA2 EED TCF12 RUNX3 lnc-NKRF-1 NKRF STEEP1 RF00017-8030 SEPTIN6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NKRF on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NKRF

Top Transcription factor binding sites by QIAGEN in the NKRF gene promoter:
  • GCNF
  • GCNF-1
  • GCNF-2
  • NF-kappaB
  • NF-kappaB1
  • STAT1
  • STAT1alpha
  • STAT1beta
  • STAT2
  • STAT5B

Genomic Locations for NKRF Gene

Latest Assembly
chrX:119,588,337-119,606,443
(GRCh38/hg38)
Size:
18,107 bases
Orientation:
Minus strand

Previous Assembly
chrX:118,722,300-118,740,387
(GRCh37/hg19 by Entrez Gene)
Size:
18,088 bases
Orientation:
Minus strand

chrX:118,722,300-118,739,858
(GRCh37/hg19 by Ensembl)
Size:
17,559 bases
Orientation:
Minus strand

Genomic View for NKRF Gene

Genes around NKRF on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NKRF Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NKRF Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NKRF Gene

Proteins for NKRF Gene

  • Protein details for NKRF Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15226-NKRF_HUMAN
    Recommended name:
    NF-kappa-B-repressing factor
    Protein Accession:
    O15226
    Secondary Accessions:
    • G3V1N1
    • Q4VC41
    • Q9UJ91

    Protein attributes for NKRF Gene

    Size:
    690 amino acids
    Molecular mass:
    77673 Da
    Quaternary structure:
    • Interacts with NF-kappa-B. Interacts with XRN2 (PubMed:24462208).
    SequenceCaution:
    • Sequence=AL539002; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305}; Sequence=CAB56459.1; Type=Frameshift; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NKRF Gene

    Alternative splice isoforms for NKRF Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NKRF Gene

Post-translational modifications for NKRF Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NKRF Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NKRF Gene

Domains & Families for NKRF Gene

Gene Families for NKRF Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for NKRF Gene

InterPro:
Blocks:
  • D111/G-patch domain
  • Single-stranded nucleic acid binding R3H

Suggested Antigen Peptide Sequences for NKRF Gene

GenScript: Design optimal peptide antigens:
  • NF-kappaB repressing factor (A1Z1A7_HUMAN)
  • NF-kappaB repressing factor (A2I827_HUMAN)
  • NF-kappaB repressing factor (A2I828_HUMAN)
  • NF-kappaB repressing factor (A2I829_HUMAN)
  • NF-kappaB repressing factor (A2I830_HUMAN)
genes like me logo Genes that share domains with NKRF: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for NKRF Gene

Function for NKRF Gene

Molecular function for NKRF Gene

UniProtKB/Swiss-Prot Function:
Interacts with a specific negative regulatory element (NRE) 5'-AATTCCTCTGA-3' to mediate transcriptional repression of certain NK-kappa-B responsive genes. Involved in the constitutive silencing of the interferon beta promoter, independently of the virus-induced signals, and in the inhibition of the basal and cytokine-induced iNOS promoter activity. Also involved in the regulation of IL-8 transcription.

Phenotypes From GWAS Catalog for NKRF Gene

Gene Ontology (GO) - Molecular Function for NKRF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 10562553
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IDA 10562553
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding HDA 22658674
genes like me logo Genes that share ontologies with NKRF: view
genes like me logo Genes that share phenotypes with NKRF: view

Animal Models for NKRF Gene

MGI Knock Outs for NKRF:
  • Nkrf Nkrf<tm1.1Hjh>

miRNA for NKRF Gene

miRTarBase miRNAs that target NKRF

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NKRF

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NKRF Gene

Localization for NKRF Gene

Subcellular locations from UniProtKB/Swiss-Prot for NKRF Gene

Nucleus, nucleolus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NKRF gene
Compartment Confidence
nucleus 5
endoplasmic reticulum 3
cytosol 3
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 2
peroxisome 2
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NKRF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 10562553
GO:0005654 nucleoplasm IBA,IDA --
GO:0005730 nucleolus IBA,IDA --
genes like me logo Genes that share ontologies with NKRF: view

Pathways & Interactions for NKRF Gene

PathCards logo

SuperPathways for NKRF Gene

No Data Available

Gene Ontology (GO) - Biological Process for NKRF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0045892 negative regulation of transcription, DNA-templated IDA 10562553
GO:0045944 positive regulation of transcription by RNA polymerase II IDA 10562553
genes like me logo Genes that share ontologies with NKRF: view

No data available for Pathways by source and SIGNOR curated interactions for NKRF Gene

Drugs & Compounds for NKRF Gene

No Compound Related Data Available

Transcripts for NKRF Gene

mRNA/cDNA for NKRF Gene

3 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NKRF

Alternative Splicing Database (ASD) splice patterns (SP) for NKRF Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c
SP1: -
SP2: - -
SP3:

Relevant External Links for NKRF Gene

GeneLoc Exon Structure for
NKRF

Expression for NKRF Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NKRF Gene

Protein differential expression in normal tissues from HIPED for NKRF Gene

This gene is overexpressed in Lung (24.2), Monocytes (15.6), Saliva (8.5), Esophagus (7.5), and Peripheral blood mononuclear cells (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NKRF Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NKRF

SOURCE GeneReport for Unigene cluster for NKRF Gene:

Hs.437084

mRNA Expression by UniProt/SwissProt for NKRF Gene:

O15226-NKRF_HUMAN
Tissue specificity: Widely and constitutively expressed. Expressed at lower level in colon, peripheral blood lymphocytes, lung and kidney.

Evidence on tissue expression from TISSUES for NKRF Gene

  • Nervous system(4.6)
  • Skin(4.5)
  • Pancreas(4.3)
  • Muscle(2.5)
  • Liver(2.4)
  • Heart(2.4)
  • Kidney(2.4)
  • Blood(2.4)
  • Intestine(2.2)
  • Lung(2.2)
  • Spleen(2.2)
genes like me logo Genes that share expression patterns with NKRF: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for NKRF Gene

Orthologs for NKRF Gene

This gene was present in the common ancestor of animals.

Orthologs for NKRF Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia NKRF 29 30
  • 99.86 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia NKRF 29 30
  • 94.16 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia NKRF 29 30
  • 93.86 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Nkrf 29 16 30
  • 91.16 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 76 (a)
OneToMany
-- 30
  • 69 (a)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia NKRF 30
  • 65 (a)
OneToOne
Chicken
(Gallus gallus)
Aves NKRF 29 30
  • 69.42 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia NKRF 30
  • 61 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia nkrf 29
  • 61.19 (n)
Str.6073 29
Zebrafish
(Danio rerio)
Actinopterygii nkrf 29 30
  • 56.7 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG31301 30
  • 20 (a)
OneToMany
Species where no ortholog for NKRF was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for NKRF Gene

ENSEMBL:
Gene Tree for NKRF (if available)
TreeFam:
Gene Tree for NKRF (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NKRF: view image
Alliance of Genome Resources:
Additional Orthologs for NKRF

Paralogs for NKRF Gene

Paralogs for NKRF Gene

(1) SIMAP similar genes for NKRF Gene using alignment to 9 proteins:

  • NKRF_HUMAN
  • A1Z1A7_HUMAN
  • A2I827_HUMAN
  • A2I828_HUMAN
  • A2I829_HUMAN
  • A2I830_HUMAN
  • A2I831_HUMAN
  • A2I832_HUMAN
  • Q6NUN2_HUMAN
genes like me logo Genes that share paralogs with NKRF: view

Variants for NKRF Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NKRF Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
720644 Benign: not provided 119,589,490(-) A/G
NM_017544.5(NKRF):c.2217T>C (p.Leu739=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
723250 Benign: not provided 119,590,450(-) G/A
NM_017544.5(NKRF):c.1257C>T (p.Ser419=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
736733 Benign: not provided 119,591,248(-) A/G
NM_017544.5(NKRF):c.459T>C (p.Pro153=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for NKRF Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for NKRF Gene

Variant ID Type Subtype PubMed ID
nsv476108 CNV novel sequence insertion 20440878

Variation tolerance for NKRF Gene

Residual Variation Intolerance Score: 14.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.62; 13.35% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NKRF Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NKRF
Leiden Open Variation Database (LOVD)
NKRF

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NKRF Gene

Disorders for NKRF Gene

MalaCards: The human disease database

(8) MalaCards diseases for NKRF Gene - From: COP

Disorder Aliases PubMed IDs
angiokeratoma of mibelli
retinitis pigmentosa 46
  • rp46
posterior cerebral artery infarction
  • infarction, posterior cerebral artery
adhesive otitis media
  • chronic adhesive otitis media
angiokeratoma circumscriptum
- elite association - COSMIC cancer census association via MalaCards
Search NKRF in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NKRF

genes like me logo Genes that share disorders with NKRF: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NKRF Gene

Publications for NKRF Gene

  1. Constitutive silencing of IFN-beta promoter is mediated by NRF (NF-kappaB-repressing factor), a nuclear inhibitor of NF-kappaB. (PMID: 10562553) Nourbakhsh M … Hauser H (The EMBO journal 1999) 2 3 4 22
  2. Identification of a negative response element in the human inducible nitric-oxide synthase (hiNOS) promoter: The role of NF-kappa B-repressing factor (NRF) in basal repression of the hiNOS gene. (PMID: 12381793) Feng X … Geller DA (Proceedings of the National Academy of Sciences of the United States of America 2002) 3 4 22
  3. Neutrophil elastase represses IL-8/CXCL8 synthesis in human airway smooth muscle cells through induction of NF-kappa B repressing factor. (PMID: 19542452) Ho SC … Kuo HP (Journal of immunology (Baltimore, Md. : 1950) 2009) 3 22
  4. NRF IRES activity is mediated by RNA binding protein JKTBP1 and a 14-nt RNA element. (PMID: 17592041) Reboll MR … Nourbakhsh M (RNA (New York, N.Y.) 2007) 3 22
  5. NF-kappaB-repressing factor inhibits elongation of human immunodeficiency virus type 1 transcription by DRB sensitivity-inducing factor. (PMID: 16107696) Dreikhausen U … Nourbakhsh M (Molecular and cellular biology 2005) 3 22

Products for NKRF Gene

Sources for NKRF Gene