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    NKRF NFKB repressing factor [ Homo sapiens (human) ]

    Gene ID: 55922, updated on 9-Dec-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
    mouse all
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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
    • 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)

    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
      A0A8I5KX72, 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
      A3F768, A3F769, Q6NUN2

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

      UniProtKB/Swiss-Prot
      G3V1N1, O15226, Q4VC41, Q9UJ91
      UniProtKB/TrEMBL
      A3F768, A3F769, Q6NUN2

    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
      A3F768, A3F769, Q6NUN2

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

      UniProtKB/Swiss-Prot
      G3V1N1, O15226, Q4VC41, Q9UJ91
      UniProtKB/TrEMBL
      A3F768, A3F769, Q6NUN2

    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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