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Aliases for NR2E3 Gene

Aliases for NR2E3 Gene

  • Nuclear Receptor Subfamily 2 Group E Member 3 2 3 4 5
  • Retina-Specific Nuclear Receptor 3 4
  • PNR 3 4
  • RNR 3 4
  • Nuclear Receptor Subfamily 2, Group E, Member 3 2
  • Photoreceptor-Specific Nuclear Receptor 3
  • ESCS 3
  • RP37 3
  • Rd7 3

External Ids for NR2E3 Gene

Previous GeneCards Identifiers for NR2E3 Gene

  • GC15P067898
  • GC15P065200
  • GC15P069660
  • GC15P069818
  • GC15P069889
  • GC15P072102
  • GC15P048933
  • GC15P072084

Summaries for NR2E3 Gene

Entrez Gene Summary for NR2E3 Gene

  • 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]

GeneCards Summary for NR2E3 Gene

NR2E3 (Nuclear Receptor Subfamily 2 Group E Member 3) is a Protein Coding gene. Diseases associated with NR2E3 include Enhanced S-Cone Syndrome and Retinitis Pigmentosa 37. Among its related pathways are Gene Expression and Nuclear Receptor transcription pathway. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and steroid hormone receptor activity. An important paralog of this gene is NR2E1.

UniProtKB/Swiss-Prot for NR2E3 Gene

  • Orphan nuclear receptor of retinal photoreceptor cells. Transcriptional factor that is an activator of rod development and repressor of cone development. Binds the promoter region of a number of rod- and cone-specific genes, including rhodopsin, M- and S-opsin and rod-specific phosphodiesterase beta subunit. Enhances rhodopsin expression. Represses M- and S-cone opsin expression.

Gene Wiki entry for NR2E3 Gene

Additional gene information for NR2E3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NR2E3 Gene

Genomics for NR2E3 Gene

GeneHancer (GH) Regulatory Elements for NR2E3 Gene

Promoters and enhancers for NR2E3 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
GH15I071788 Enhancer 0.9 Ensembl ENCODE 550.8 -1.9 -1876 4.3 JUN ZSCAN4 MAX KLF17 PAX8 CEBPG ZBTB40 ZFHX2 CTBP1 GATA3 NR2E3 PARP6 MYO9A THSD4-AS2
GH15I071810 Promoter 0.8 EPDnew 550.4 +17.9 17899 0.1 RFX1 ZFP64 ZNF600 ZIC2 ZBTB20 ZNF423 NR2E3 ENSG00000260037
GH15I071808 Enhancer 0.3 FANTOM5 53.9 +16.2 16231 0.2 NR2E3 ENSG00000260037
GH15I071745 Enhancer 1.2 Ensembl ENCODE 11.6 -45.2 -45222 3.5 PKNOX1 CLOCK FOXA2 MLX NEUROD1 SIN3A FEZF1 ZNF2 ZNF143 FOS ENSG00000261187 PARP6 BBS4 LRRC49 CELF6 NR2E3 TMEM202-AS1 ARIH1 ENSG00000260672 HMGB1P6
GH15I071751 Enhancer 1 Ensembl ENCODE 11.9 -39.8 -39796 2.3 CTCF MXI1 CLOCK ZNF449 JUN MAX SIN3A RAD21 ZNF335 GATA3 NR2E3 THSD4-AS2 THSD4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NR2E3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NR2E3 gene promoter:

Genomic Locations for NR2E3 Gene

Genomic Locations for NR2E3 Gene
chr15:71,792,638-71,818,666
(GRCh38/hg38)
Size:
26,029 bases
Orientation:
Plus strand
chr15:72,084,977-72,110,600
(GRCh37/hg19)

Genomic View for NR2E3 Gene

Genes around NR2E3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NR2E3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NR2E3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NR2E3 Gene

Proteins for NR2E3 Gene

  • Protein details for NR2E3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5X4-NR2E3_HUMAN
    Recommended name:
    Photoreceptor-specific nuclear receptor
    Protein Accession:
    Q9Y5X4
    Secondary Accessions:
    • B6ZGU0
    • Q9UHM4

    Protein attributes for NR2E3 Gene

    Size:
    410 amino acids
    Molecular mass:
    44692 Da
    Quaternary structure:
    • Homodimer. Interacts with PIAS3; the interaction sumoylates NR2E3 and promotes repression of cone-specific gene transcription and activation of rod-specific genes (By similarity). Component of a complex that includes NR2E3, PIAS3, NRL, CRX and/or NR1D1. Binds NR1D1. Binds direcly in the complex with CRX, PIAS3 and NR1D1 (By similarity). Interacts (via the DNA-binding domain) with CRX (via its DNA binding domain); the interaction represses S- and M-cone opsin expression.

    Three dimensional structures from OCA and Proteopedia for NR2E3 Gene

    Alternative splice isoforms for NR2E3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NR2E3 Gene

Post-translational modifications for NR2E3 Gene

  • Di- and tri-sumoylated in developing retina. PIAS3-mediated sumoylation promotes repression of cone-specific gene expression and activation of rod-specific genes. Sumoylation on Lys-185 appears to be the main site (By similarity).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NR2E3 Gene

No data available for DME Specific Peptides for NR2E3 Gene

Domains & Families for NR2E3 Gene

Gene Families for NR2E3 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Disease related genes
  • Nuclear receptors
  • Predicted intracellular proteins
  • Transcription factors

Graphical View of Domain Structure for InterPro Entry

Q9Y5X4

UniProtKB/Swiss-Prot:

NR2E3_HUMAN :
  • Belongs to the nuclear hormone receptor family. NR2 subfamily.
Family:
  • Belongs to the nuclear hormone receptor family. NR2 subfamily.
genes like me logo Genes that share domains with NR2E3: view

Function for NR2E3 Gene

Molecular function for NR2E3 Gene

GENATLAS Biochemistry:
nuclear receptor superfamily 2,group E,member 3,homolog to TLX receptor,orphan receptor family
UniProtKB/Swiss-Prot Function:
Orphan nuclear receptor of retinal photoreceptor cells. Transcriptional factor that is an activator of rod development and repressor of cone development. Binds the promoter region of a number of rod- and cone-specific genes, including rhodopsin, M- and S-opsin and rod-specific phosphodiesterase beta subunit. Enhances rhodopsin expression. Represses M- and S-cone opsin expression.

Phenotypes From GWAS Catalog for NR2E3 Gene

Gene Ontology (GO) - Molecular Function for NR2E3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 10220376
GO:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IC --
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IC --
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IEA --
genes like me logo Genes that share ontologies with NR2E3: view
genes like me logo Genes that share phenotypes with NR2E3: view

Human Phenotype Ontology for NR2E3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for NR2E3 Gene

MGI Knock Outs for NR2E3:

Clone Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for NR2E3 Gene

Localization for NR2E3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NR2E3 Gene

Gene Ontology (GO) - Cellular Components for NR2E3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS 10220376
GO:0005654 nucleoplasm TAS --
GO:0005667 transcription factor complex IEA --
genes like me logo Genes that share ontologies with NR2E3: view

No data available for Subcellular locations from COMPARTMENTS and Subcellular locations from the Human Protein Atlas (HPA) for NR2E3 Gene

Pathways & Interactions for NR2E3 Gene

genes like me logo Genes that share pathways with NR2E3: view

Pathways by source for NR2E3 Gene

SIGNOR curated interactions for NR2E3 Gene

Activates:
Is activated by:

Gene Ontology (GO) - Biological Process for NR2E3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II TAS 10220376
GO:0006367 transcription initiation from RNA polymerase II promoter TAS --
genes like me logo Genes that share ontologies with NR2E3: view

Drugs & Compounds for NR2E3 Gene

(13) Drugs for NR2E3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(14) Additional Compounds for NR2E3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with NR2E3: view

Transcripts for NR2E3 Gene

Unigene Clusters for NR2E3 Gene

Nuclear receptor subfamily 2, group E, member 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NR2E3 Gene

No ASD Table

Relevant External Links for NR2E3 Gene

GeneLoc Exon Structure for
NR2E3
ECgene alternative splicing isoforms for
NR2E3

Expression for NR2E3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NR2E3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NR2E3 Gene

This gene is overexpressed in Cervix - Endocervix (x5.9), Prostate (x5.4), and Testis (x4.1).

Protein differential expression in normal tissues from HIPED for NR2E3 Gene

This gene is overexpressed in Lung (56.2) and Retina (12.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NR2E3 Gene



Protein tissue co-expression partners for NR2E3 Gene

NURSA nuclear receptor signaling pathways regulating expression of NR2E3 Gene:

NR2E3

SOURCE GeneReport for Unigene cluster for NR2E3 Gene:

Hs.187354

mRNA Expression by UniProt/SwissProt for NR2E3 Gene:

Q9Y5X4-NR2E3_HUMAN
Tissue specificity: Eye specific; found solely in the outer nuclear layer of the adult neurosensory retina, where the nuclei of cone and rod photoreceptors reside.

Phenotype-based relationships between genes and organs from Gene ORGANizer for NR2E3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • middle ear
  • nose
  • outer ear
  • skull
Pelvis:
  • penis
  • testicle
General:
  • blood
  • blood vessel
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with NR2E3: view

No data available for Evidence on tissue expression from TISSUES for NR2E3 Gene

Orthologs for NR2E3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NR2E3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NR2E3 33
  • 99.34 (n)
cow
(Bos Taurus)
Mammalia NR2E3 33
  • 90.24 (n)
mouse
(Mus musculus)
Mammalia Nr2e3 33 16
  • 84.01 (n)
rat
(Rattus norvegicus)
Mammalia LOC100365683 33
  • 82.59 (n)
chicken
(Gallus gallus)
Aves NR2E3 33
  • 75.36 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia nr2e3 33
  • 68.57 (n)
zebrafish
(Danio rerio)
Actinopterygii nr2e3 33
  • 66.11 (n)
fruit fly
(Drosophila melanogaster)
Insecta Hr51 33
  • 63.73 (n)
dsf 35
  • 50 (a)
CG16801 35
  • 45 (a)
worm
(Caenorhabditis elegans)
Secernentea fax-1 35
  • 38 (a)
Species where no ortholog for NR2E3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • dog (Canis familiaris)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (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)

Evolution for NR2E3 Gene

ENSEMBL:
Gene Tree for NR2E3 (if available)
TreeFam:
Gene Tree for NR2E3 (if available)

Paralogs for NR2E3 Gene

Paralogs for NR2E3 Gene

(20) SIMAP similar genes for NR2E3 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with NR2E3: view

Variants for NR2E3 Gene

Sequence variations from dbSNP and Humsavar for NR2E3 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs1023704577 uncertain-significance, Retinitis Pigmentosa, Recessive, Enhanced s-cone syndrome 71,818,137(+) G/T 3_prime_UTR_variant, genic_downstream_transcript_variant
rs104894492 pathogenic, Enhanced s-cone syndrome, Enhanced S cone syndrome (ESCS) [MIM:268100] 71,811,590(+) C/A/T coding_sequence_variant, missense_variant, synonymous_variant
rs104894493 pathogenic, uncertain-significance, Enhanced s-cone syndrome, NR2E3-Related Disorders, Enhanced S cone syndrome (ESCS) [MIM:268100] 71,811,591(+) G/A coding_sequence_variant, missense_variant
rs112520386 uncertain-significance, Retinitis Pigmentosa, Recessive, Enhanced s-cone syndrome 71,811,877(+) G/A intron_variant
rs121912631 conflicting-interpretations-of-pathogenicity, pathogenic, Retinitis pigmentosa 37, not provided, Retinitis pigmentosa 37 (RP37) [MIM:611131] 71,811,530(+) G/A/T coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for NR2E3 Gene

Variant ID Type Subtype PubMed ID
esv3892712 CNV loss 25118596
nsv1036938 CNV gain 25217958
nsv827383 CNV loss 20364138

Additional Variant Information for NR2E3 Gene

Human Gene Mutation Database (HGMD)
NR2E3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NR2E3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for NR2E3 Gene

Disorders for NR2E3 Gene

MalaCards: The human disease database

(7) MalaCards diseases for NR2E3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
enhanced s-cone syndrome
  • escs
retinitis pigmentosa 37
  • rp37
goldmann-favre syndrome
  • enhanced s-cone syndrome
retinitis pigmentosa
  • rp
vasoproliferative tumor of the retina
  • retinal vasoproliferative tumor
- elite association - COSMIC cancer census association via MalaCards
Search NR2E3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NR2E3_HUMAN
  • Enhanced S cone syndrome (ESCS) [MIM:268100]: Autosomal recessive retinopathy in which patients have increased sensitivity to blue light; perception of blue light is mediated by what is normally the least populous cone photoreceptor subtype, the S (short wavelength, blue) cones. ESCS is also associated with visual loss, with night blindness occurring from early in life, varying degrees of L (long, red)- and M (middle, green)-cone vision, and retinal degeneration. {ECO:0000269 PubMed:10655056, ECO:0000269 PubMed:11071390, ECO:0000269 PubMed:12963616, ECO:0000269 PubMed:15459973, ECO:0000269 PubMed:16225923, ECO:0000269 PubMed:18294254, ECO:0000269 PubMed:19006237, ECO:0000269 PubMed:24069298}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Retinitis pigmentosa 37 (RP37) [MIM:611131]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269 PubMed:17564971, ECO:0000269 PubMed:19006237}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for NR2E3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with NR2E3: view

No data available for Genatlas for NR2E3 Gene

Publications for NR2E3 Gene

  1. Identification of a photoreceptor cell-specific nuclear receptor. (PMID: 10220376) Kobayashi M … Umesono K (Proceedings of the National Academy of Sciences of the United States of America 1999) 2 3 4 22 58
  2. Association of NR2E3 but not NRL mutations with retinitis pigmentosa in the Chinese population. (PMID: 19933183) Yang Y … Pang CP (Investigative ophthalmology & visual science 2010) 3 22 44 58
  3. Mutations in NR2E3 can cause dominant or recessive retinal degenerations in the same family. (PMID: 19006237) Escher P … Schorderet DF (Human mutation 2009) 3 4 22 58
  4. Analysis of the involvement of the NR2E3 gene in autosomal recessive retinal dystrophies. (PMID: 18294254) Bernal S … Baiget M (Clinical genetics 2008) 3 4 22 58
  5. The photoreceptor-specific nuclear receptor Nr2e3 interacts with Crx and exerts opposing effects on the transcription of rod versus cone genes. (PMID: 15689355) Peng GH … Chen S (Human molecular genetics 2005) 3 4 22 58

Products for NR2E3 Gene

Sources for NR2E3 Gene

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