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    NRBF2 nuclear receptor binding factor 2 [ Homo sapiens (human) ]

    Gene ID: 29982, updated on 28-Oct-2024

    Summary

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    Official Symbol
    NRBF2provided by HGNC
    Official Full Name
    nuclear receptor binding factor 2provided by HGNC
    Primary source
    HGNC:HGNC:19692
    See related
    Ensembl:ENSG00000148572 MIM:616477; AllianceGenome:HGNC:19692
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    COPR; COPR1; COPR2; NRBF-2
    Summary
    Involved in autophagy. Located in cytoplasm and phosphatidylinositol 3-kinase complex, class III. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in appendix (RPKM 10.9), placenta (RPKM 10.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NRBF2 in Genome Data Viewer
    Location:
    10q21.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (63133328..63155024)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (63991431..64013145)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (64893088..64914784)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378328 Neighboring gene RNA, U6 small nuclear 543, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3435 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:64940417-64940613 Neighboring gene NANOG hESC enhancer GRCh37_chr10:64959364-64959900 Neighboring gene jumonji domain containing 1C Neighboring gene MPRA-validated peak963 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr10:65000486-65001022 Neighboring gene TatD DNase domain containing 1 pseudogene 1 Neighboring gene uncharacterized LOC124900287

    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. NRBF2-mediated autophagy contributes to metabolite replenishment and radioresistance in glioblastoma. Kim J, et al. Exp Mol Med, 2022 Nov. PMID 36333468, Free PMC Article
    2. Polymorphisms in a Putative Enhancer at the 10q21.2 Breast Cancer Risk Locus Regulate NRBF2 Expression. Darabi H, et al. Am J Hum Genet, 2015 Jul 2. PMID 26073781, Free PMC Article
    3. Isolation and functional analysis of a keratinocyte-derived, ligand-regulated nuclear receptor comodulator. Flores AM, et al. J Invest Dermatol, 2004 Dec. PMID 15610520
    4. Dynamics and architecture of the NRBF2-containing phosphatidylinositol 3-kinase complex I of autophagy. Young LN, et al. Proc Natl Acad Sci U S A, 2016 Jul 19. PMID 27385829, Free PMC Article
    5. NRBF2 is involved in the autophagic degradation process of APP-CTFs in Alzheimer disease models. Yang C, et al. Autophagy, 2017. PMID 28980867, Free PMC Article

    See all (53) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NRBF2-mediated autophagy contributes to metabolite replenishment and radioresistance in glioblastoma.
      Title: NRBF2-mediated autophagy contributes to metabolite replenishment and radioresistance in glioblastoma.
    2. PI3KC3 complex subunit NRBF2 is required for apoptotic cell clearance to restrict intestinal inflammation.
      Title: PI3KC3 complex subunit NRBF2 is required for apoptotic cell clearance to restrict intestinal inflammation.
    3. implicates NRBF2 deficiency as a risk factor for cognitive impairment associated with AD, but also support the idea of NRBF2 as a potential therapeutic target for Alzheimer's Disease
      Title: Autophagy protein NRBF2 has reduced expression in Alzheimer's brains and modulates memory and amyloid-beta homeostasis in mice.
    4. NRBF2 plays an important role in regulating degradation of APP-C-terminal fragments through modulating autophagy.
      Title: NRBF2 is involved in the autophagic degradation process of APP-CTFs in Alzheimer disease models.
    5. Here we show that a putative fifth subunit, nuclear receptor binding factor 2 (NRBF2), is a tightly bound component of the class III phosphatidylinositol 3-kinase complex I that profoundly affects its activity and architecture. NRBF2 is a homodimer and drives the dimerization of the larger PI3KC3-C1 complex, with implications for the higher-order organization of the preautophagosomal structure.
      Title: Dynamics and architecture of the NRBF2-containing phosphatidylinositol 3-kinase complex I of autophagy.
    6. This study reveals NRBF2 as a critical molecular switch of PtdIns3K and autophagy activation, and its on/off state is precisely controlled by MTORC1 through phosphorylation.
      Title: MTORC1-mediated NRBF2 phosphorylation functions as a switch for the class III PtdIns3K and autophagy.
    7. Atg38 and its human ortholog NRBF2, accessory components of complex I consisting of Vps15-Vps34-Vps30/Atg6-Atg14 (yeast) and PIK3R4/VPS15-PIK3C3/VPS34-BECN1/Beclin 1-ATG14 (human), were characterized.
      Title: Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34/PIK3C3 complex.
    8. Polymorphisms in a putative enhancer at the 10q21.2 Breast Cancer Risk Locus regulate NRBF2 expression, implicating this gene in the etiology of breast cancer.
      Title: Polymorphisms in a Putative Enhancer at the 10q21.2 Breast Cancer Risk Locus Regulate NRBF2 Expression.
    9. Nrbf2 may interact with the Atg14L-containing Beclin 1-Vps34 protein complex to modulate protein-protein interactions within the complex.
      Title: Nrbf2 protein suppresses autophagy by modulating Atg14L protein-containing Beclin 1-Vps34 complex architecture and reducing intracellular phosphatidylinositol-3 phosphate levels.
    10. NRBF2 regulates macroautophagy as a component of Vps34 Complex I.
      Title: NRBF2 regulates macroautophagy as a component of Vps34 Complex I.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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

    EBI GWAS Catalog

    Description
    A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.
    EBI GWAS Catalog
    Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
    EBI GWAS Catalog
    Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    EBI GWAS Catalog

    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

    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

    Clone Names

    • FLJ30395, DKFZp564C1664

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in autophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in autophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of lipid kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to endoplasmic reticulum stress IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in autophagosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytoplasmic vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    part_of phosphatidylinositol 3-kinase complex, class III IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    nuclear receptor-binding factor 2
    Names
    comodulator of PPAR and RXR 1
    comodulator of PPAR and RXR 2

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001282405.2 → NP_001269334.1  nuclear receptor-binding factor 2 isoform 2

      See identical proteins and their annotated locations for NP_001269334.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region which results in the use of an alternate AUG compared to variant 1. It encodes isoform 2 which is shorter and has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AK301656, BC001345
      Consensus CDS
      CCDS60537.1
      UniProtKB/Swiss-Prot
      Q96F24
      Related
      ENSP00000397502.2, ENST00000435510.6
      Conserved Domains (1) summary
      pfam08961
      Location:36 → 274
      DUF1875; Domain of unknown function (DUF1875)

    2. NM_030759.5 → NP_110386.2  nuclear receptor-binding factor 2 isoform 1

      See identical proteins and their annotated locations for NP_110386.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AU310836, BC001345, BC011707
      Consensus CDS
      CCDS7268.1
      UniProtKB/Swiss-Prot
      A6PW36, B4DWS0, Q86UR2, Q96F24, Q96NP6, Q9H0S9, Q9H2I2
      Related
      ENSP00000277746.6, ENST00000277746.11
      Conserved Domains (2) summary
      pfam08961
      Location:89 → 284
      NRBF2; Nuclear receptor-binding factor 2, autophagy regulator
      pfam17169
      Location:4 → 86
      NRBF2_MIT; MIT domain of nuclear receptor-binding factor 2

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      63133328..63155024
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047425132.1 → XP_047281088.1  nuclear receptor-binding factor 2 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      63991431..64013145
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054365680.1 → XP_054221655.1  nuclear receptor-binding factor 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96F24.1 GenPept UniProtKB/Swiss-Prot:Q96F24

    Gene LinkOut

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

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