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NKRF NFKB repressing factor [ Homo sapiens (human) ]

Gene ID: 55922, updated on 3-Nov-2024

Summary

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Official Symbol
NKRFprovided by HGNC
Official Full Name
NFKB repressing factorprovided by HGNC
Primary source
HGNC:HGNC:19374
See related
Ensembl:ENSG00000186416 MIM:300440; AllianceGenome:HGNC:19374
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NRF; ITBA4
Summary
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]
Annotation information
Annotation category: suggests misassembly
Expression
Ubiquitous expression in brain (RPKM 6.5), lymph node (RPKM 4.2) and 25 other tissues See more
Orthologs
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Genomic context

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See NKRF in Genome Data Viewer
Location:
Xq24
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (119588337..119606424, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (117966055..117984174, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (118722300..118740387, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905208 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:118708298-118708798 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:118708799-118709299 Neighboring gene ubiquitin conjugating enzyme E2 A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29882 Neighboring gene septin 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29883 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29886 Neighboring gene microRNA 766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29887 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:118811626-118812126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29889 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29891 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29892 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29893 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29895 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20965 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20966 Neighboring gene sosondowah ankyrin repeat domain family member D

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The transcriptional silencer protein NRF: a repressor of NF-kappa B enhancers. Nourbakhsh M, et al. Immunobiology, 1997 Dec. PMID 9442378
  2. Cloning of the correct full length cDNA of NF-kappaB-repressing factor. Jianfeng D, et al. Mol Cells, 2003 Dec 31. PMID 14744032
  3. Nucleolar localization and mobility analysis of the NF-kappaB repressing factor NRF. Niedick I, et al. J Cell Sci, 2004 Jul 15. PMID 15226370
  4. Human NF-κB repressing factor acts as a stress-regulated switch for ribosomal RNA processing and nucleolar homeostasis surveillance. Coccia M, et al. Proc Natl Acad Sci U S A, 2017 Jan 31. PMID 28096332, Free PMC Article
  5. NF-kappaB-repressing factor inhibits elongation of human immunodeficiency virus type 1 transcription by DRB sensitivity-inducing factor. Dreikhausen U, et al. Mol Cell Biol, 2005 Sep. PMID 16107696, Free PMC Article

See all (166) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A1CF Binding to the p65 Interaction Site on NKRF Decreased IFN-beta Expression and p65 Phosphorylation (Ser536) in Renal Carcinoma Cells.
    Title: A1CF Binding to the p65 Interaction Site on NKRF Decreased IFN-β Expression and p65 Phosphorylation (Ser536) in Renal Carcinoma Cells.
  2. WWP2 binds to NKRF, enhances the NF-kappaB signaling, and promotes malignant phenotypes of acute myeloid leukemia cells.
    Title: WWP2 binds to NKRF, enhances the NF-κB signaling, and promotes malignant phenotypes of acute myeloid leukemia cells.
  3. Upregulation of miRNA301a3p promotes tumor progression in gastric cancer by suppressing NKRF and activating NFkappaB signaling.
    Title: Upregulation of miRNA‑301a‑3p promotes tumor progression in gastric cancer by suppressing NKRF and activating NF‑κB signaling.
  4. Low NRF expression is associated with obesity induced nephropathy.
    Title: MiR-802 causes nephropathy by suppressing NF-κB-repressing factor in obese mice and human.
  5. RNA affinity, helicase, and ATPase activity of DHX15 are increased when the G-patch motif of NKRF binds in an extended conformation across the helicase surface
    Title: Structural basis for DEAH-helicase activation by G-patch proteins.
  6. NKRF is a nucleolar HSP essential for nucleolus homeostasis and cell survival under proteotoxic stress. NKRF is a thermosensor translocating from the nucleolus to the nucleoplasm during heat stress; nucleolar pools are replenished upon HSF1-mediated NKRF resynthesis. NKRF is an unconventional HSP crucial for correct rRNA processing. Under stress conditions, NKRF directs XRN2 nucleolus/nucleoplasm trafficking.
    Title: Human NF-κB repressing factor acts as a stress-regulated switch for ribosomal RNA processing and nucleolar homeostasis surveillance.
  7. Data suggest that L protein from LCMV interactions with host proteome, specifically DDX3X, NKRF, and TRIM21. (LCMV = Lymphocytic choriomeningitis mammarenavirus; DDX3X = DEAD-box helicase 3; NKRF = NF-kappa-B-repressing factor; TRIM21 = tripartite motif-containing protein-21)
    Title: Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein.
  8. depletion of NKRF, XRN2 or DHX15 impairs an early pre-rRNA cleavage step.
    Title: The G-patch protein NF-κB-repressing factor mediates the recruitment of the exonuclease XRN2 and activation of the RNA helicase DHX15 in human ribosome biogenesis.
  9. NF-kappaB-repressing factor (NKRF) phosphorylation modulates promoter-proximal transcription elongation of NF-kappaB/NKRF-regulated genes via direct interactions with elongation complex in response to specific stimuli
    Title: NF-κB-repressing factor phosphorylation regulates transcription elongation via its interactions with 5'→3' exoribonuclease 2 and negative elongation factor.
  10. The up-regulated NKRF serves as an endogenous repressor for IP-10 and IL-8 synthesis to hinder host from robust response to MTb infection.
    Title: NF-κB repressing factor downregulates basal expression and mycobacterium tuberculosis induced IP-10 and IL-8 synthesis via interference with NF-κB in monocytes.
Submit: New GeneRIF Correction See all GeneRIFs (22)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify NFKappaB repressing factor (NKRF), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify NFKappaB repressing factor (NKRF), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify NFKappaB repressing factor (NKRF), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify NFKappaB repressing factor (NKRF), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human NFKB repressing factor (NKRF) at amino acid residues 21-22 by the HIV-1 protease PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATPase activator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA binding HDA PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
NF-kappa-B-repressing factor
Names
transcription factor NRF

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_016800.1 RefSeqGene

    Range
    5001..22547
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001417890.1 → NP_001404819.1  NF-kappa-B-repressing factor

    Status: REVIEWED

    Source sequence(s)
    AC004913, NTIA01000131
    UniProtKB/TrEMBL
    A0AAG2UWQ9
    Related
    ENSP00000508667.1, ENST00000688521.1

RNA

  1. NR_163972.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AA845622, AL539002, AY208891, BC047878, LPVO02000272
    Related
    ENST00000542113.3

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    119588337..119606424 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791817.1 Reference GRCh38.p14 PATCHES

    Range
    39338..57458 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333329.1 → XP_054189304.1  NF-kappa-B-repressing factor isoform X1

    UniProtKB/Swiss-Prot
    G3V1N1, O15226, Q4VC41, Q9UJ91
    UniProtKB/TrEMBL
    A3F769

  2. XM_054333330.1 → XP_054189305.1  NF-kappa-B-repressing factor isoform X1

    UniProtKB/Swiss-Prot
    G3V1N1, O15226, Q4VC41, Q9UJ91
    UniProtKB/TrEMBL
    A3F769

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    117966055..117984174 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327401.1 → XP_054183376.1  NF-kappa-B-repressing factor isoform X2

    UniProtKB/Swiss-Prot
    G3V1N1, O15226, Q4VC41, Q9UJ91
    UniProtKB/TrEMBL
    A3F769

  2. XM_054327402.1 → XP_054183377.1  NF-kappa-B-repressing factor isoform X2

    UniProtKB/Swiss-Prot
    G3V1N1, O15226, Q4VC41, Q9UJ91
    UniProtKB/TrEMBL
    A3F769

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001173487.1: Suppressed sequence

    Description
    NM_001173487.1: This RefSeq was removed because currently there is insufficient support for the protein.

  2. NM_001173488.1: Suppressed sequence

    Description
    NM_001173488.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15226.2 GenPept UniProtKB/Swiss-Prot:O15226

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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