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    NR2E3 nuclear receptor subfamily 2 group E member 3 [ Homo sapiens (human) ]

    Gene ID: 10002, updated on 14-Nov-2024

    Summary

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    Official Symbol
    NR2E3provided by HGNC
    Official Full Name
    nuclear receptor subfamily 2 group E member 3provided by HGNC
    Primary source
    HGNC:HGNC:7974
    See related
    Ensembl:ENSG00000278570 MIM:604485; AllianceGenome:HGNC:7974
    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
    PNR; RNR; rd7; ESCS; RP37
    Summary
    This protein is part of a large family of nuclear receptor transcription factors involved in signaling pathways. Nuclear receptors have been shown to regulate pathways involved in embryonic development, as well as in maintenance of proper cell function in adults. Members of this family are characterized by discrete domains that function in DNA and ligand binding. This gene encodes a retinal nuclear receptor that is a ligand-dependent transcription factor. Defects in this gene are a cause of enhanced S cone syndrome. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See NR2E3 in Genome Data Viewer
    Location:
    15q23
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (71810554..71818253)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (69629504..69637203)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (72102894..72110594)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene thrombospondin type 1 domain containing 4 Neighboring gene uncharacterized LOC107984716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6615 Neighboring gene Sharpr-MPRA regulatory region 7020 Neighboring gene Sharpr-MPRA regulatory region 14876 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:71947880-71949079 Neighboring gene THSD4 antisense RNA 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:72053567-72054766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9705 Neighboring gene Sharpr-MPRA regulatory region 1602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9707 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9708 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9709 Neighboring gene RNA, 5S ribosomal pseudogene 399 Neighboring gene myosin IXA Neighboring gene uncharacterized LOC107984713

    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 spectrum of retinal diseases caused by NR2E3 mutations in Israeli and Palestinian patients. Bandah D, et al. Arch Ophthalmol, 2009 Mar. PMID 19273793
    2. Disruption of the human cone photoreceptor mosaic from a defect in NR2E3 transcription factor function in young adults. Park SP, et al. Graefes Arch Clin Exp Ophthalmol, 2013 Oct. PMID 23604511, Free PMC Article
    3. Novel mutations in enhanced S-cone syndrome. Kuniyoshi K, et al. Ophthalmology, 2013 Feb. PMID 23374571
    4. Peculiar fundus abnormalities and pathognomonic electrophysiological findings in a 14-month-old boy with NR2E3 mutations. Cassiman C, et al. Ophthalmic Genet, 2013 Mar-Jun. PMID 23039133
    5. Double concentric autofluorescence ring in NR2E3-p.G56R-linked autosomal dominant retinitis pigmentosa. Escher P, et al. Invest Ophthalmol Vis Sci, 2012 Jul 13. PMID 22661467

    See all (69) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Loss of an Orphan Nuclear Receptor NR2E3 Augments Wnt/beta-catenin Signaling via Epigenetic Dysregulation that Enhances Sp1-beta catenin-p300 Interactions in Hepatocellular Carcinoma.
      Title: The Loss of an Orphan Nuclear Receptor NR2E3 Augments Wnt/β-catenin Signaling via Epigenetic Dysregulation that Enhances Sp1-β catenin-p300 Interactions in Hepatocellular Carcinoma.
    2. NR2E3 loss disrupts photoreceptor cell maturation and fate in human organoid models of retinal development.
      Title: NR2E3 loss disrupts photoreceptor cell maturation and fate in human organoid models of retinal development.
    3. Clinical and Genetic Features of NR2E3-Associated Retinopathy: A Report of Eight Families with a Longitudinal Study and Literature Review.
      Title: Clinical and Genetic Features of NR2E3-Associated Retinopathy: A Report of Eight Families with a Longitudinal Study and Literature Review.
    4. Nuclear Receptor Subfamily 2 Group E Member 3 (NR2E3): Role in Retinal Development and Disease.
      Title: Nuclear Receptor Subfamily 2 Group E Member 3 (NR2E3): Role in Retinal Development and Disease.
    5. Nr2e3 functional domain ablation by CRISPR-Cas9D10A identifies a new isoform and generates retinitis pigmentosa and enhanced S-cone syndrome models.
      Title: Nr2e3 functional domain ablation by CRISPR-Cas9D10A identifies a new isoform and generates retinitis pigmentosa and enhanced S-cone syndrome models.
    6. Novel Pathogenic Sequence Variants in NR2E3 and Clinical Findings in Three Patients.
      Title: Novel Pathogenic Sequence Variants in NR2E3 and Clinical Findings in Three Patients.
    7. Authors overexpressed wild type (WT) or mutant NR2E3 in RPE-1 cells, followed by AON treatment. Transcript and protein levels of WT and mutant NR2E3 were detected by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and Western blot respectively.
      Title: Antisense Oligonucleotide-Based Downregulation of the G56R Pathogenic Variant Causing NR2E3-Associated Autosomal Dominant Retinitis Pigmentosa.
    8. our work revealed the novel role of NR2E3 as a positive upstream transcriptional regulator of AHR. Loss of NR2E3 caused repression of AHR by epigenetic reprogramming, which altered the active H3K4me2 status by modulating LSD1 distribution and activity.
      Title: Loss of NR2E3 represses AHR by LSD1 reprogramming, is associated with poor prognosis in liver cancer.
    9. Murine proof-of-concept studies suggest that clinical trials of patients with NR2E3 mutations may be forthcoming. Patterns of S-cone hyperfunction across the field would serve as a means to categorize patients as entry criteria or cohort selection in clinical trials.
      Title: Cone Vision Changes in the Enhanced S-Cone Syndrome Caused by NR2E3 Gene Mutations.
    10. Macular involvement was detectable in all the patients, and the abnormal foveal avascular zone (FAZ) supports the role of NR2E3 in retinal development.
      Title: Novel clinical findings in autosomal recessive NR2E3-related retinal dystrophy.
    Submit: New GeneRIF Correction See all GeneRIFs (53)

    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

    Associated conditions

    Description Tests
    Enhanced S-cone syndrome
    MedGen: C1849394 OMIM: 268100 GeneReviews: Not available
    		not available
    Retinitis pigmentosa 37
    MedGen: C1970163 OMIM: 611131 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview
    		not available

    EBI GWAS Catalog

    Description
    Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC49976

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IMP
    Inferred from Mutant Phenotype
    more info
    		 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 nuclear receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nuclear steroid receptor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in eye photoreceptor cell development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in intracellular receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in phototransduction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in retina development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in signal transduction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in steroid hormone receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus TAS
    Traceable Author Statement
    more info
    		 PubMed 
    part_of transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    photoreceptor-specific nuclear receptor
    Names
    retina-specific nuclear receptor

    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_009113.2 RefSeqGene

      Range
      5000..12699
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_014249.4 → NP_055064.1  photoreceptor-specific nuclear receptor isoform b

      See identical proteins and their annotated locations for NP_055064.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (b) contains a longer C-terminus compared to isoform a.
      Source sequence(s)
      AF121129, AL711747, AW080977, BU732726
      Consensus CDS
      CCDS73750.1
      UniProtKB/Swiss-Prot
      B6ZGU0, Q9UHM4, Q9Y5X4
      UniProtKB/TrEMBL
      A0A0F6T557
      Related
      ENSP00000482504.1, ENST00000617575.5
      Conserved Domains (2) summary
      cd06950
      Location:192 → 397
      NR_LBD_Tlx_PNR_like; The ligand binding domain of Tailless-like proteins, orphan nuclear receptors
      cd06970
      Location:39 → 130
      NR_DBD_PNR; DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers

    2. NM_016346.4 → NP_057430.1  photoreceptor-specific nuclear receptor isoform a

      See identical proteins and their annotated locations for NP_057430.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes isoform a.
      Source sequence(s)
      AC104938, AF148128, KF495720
      Consensus CDS
      CCDS73751.1
      UniProtKB/TrEMBL
      A0A0F6T557, F1D8Q9
      Related
      ENSP00000479962.1, ENST00000621098.1
      Conserved Domains (2) summary
      cd06950
      Location:192 → 367
      NR_LBD_Tlx_PNR_like; The ligand binding domain of Tailless-like proteins, orphan nuclear receptors
      cd06970
      Location:39 → 130
      NR_DBD_PNR; DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      71810554..71818253
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      69629504..69637203
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001281446.1: Suppressed sequence

      Description
      NM_001281446.1: This RefSeq was permanently suppressed 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
    Q9Y5X4.1 GenPept UniProtKB/Swiss-Prot:Q9Y5X4

    Gene LinkOut

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

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