Human Gene NR2E3 (ENST00000617575.5_4) from GENCODE V47lift37
  Description: nuclear receptor subfamily 2 group E member 3, transcript variant 2 (from RefSeq NM_014249.4)
Gencode Transcript: ENST00000617575.5_4
Gencode Gene: ENSG00000278570.5_7
Transcript (Including UTRs)
   Position: hg19 chr15:72,102,894-72,110,594 Size: 7,701 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr15:72,103,084-72,110,025 Size: 6,942 Coding Exon Count: 9 

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Gene AllelesMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:72,102,894-72,110,594)mRNA (may differ from genome)Protein (410 aa)
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UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NR2E3_HUMAN
DESCRIPTION: RecName: Full=Photoreceptor-specific nuclear receptor; AltName: Full=Nuclear receptor subfamily 2 group E member 3; AltName: Full=Retina-specific nuclear receptor;
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.
SUBUNIT: 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.
SUBCELLULAR LOCATION: Nucleus.
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.
PTM: 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).
DISEASE: Defects in NR2E3 are a cause of enhanced S cone syndrome (ESCS) [MIM:268100]. ESCS is an 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.
DISEASE: Defects in NR2E3 are the cause of retinitis pigmentosa type 37 (RP37) [MIM:611131]. RP leads to degeneration of retinal photoreceptor cells. 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. RP37 inheritance is autosomal dominant.
SIMILARITY: Belongs to the nuclear hormone receptor family. NR2 subfamily.
SIMILARITY: Contains 1 nuclear receptor DNA-binding domain.
WEB RESOURCE: Name=Mutations of the NR2E3 gene; Note=Retina International's Scientific Newsletter; URL="http://www.retina-international.org/files/sci-news/nr2e3mut.htm";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: NR2E3
Diseases sorted by gene-association score: enhanced s-cone syndrome* (1715), retinitis pigmentosa 37* (1229), goldmann-favre syndrome* (419), nr2e3-related retinitis pigmentosa* (100), retinitis pigmentosa* (51), retinal degeneration (9), achromatopsia (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -73.70190-0.388 Picture PostScript Text
3' UTR -132.50569-0.233 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008946 - Nucl_hormone_rcpt_ligand-bd
IPR000536 - Nucl_hrmn_rcpt_lig-bd_core
IPR000003 - Retinoid-X_rcpt/HNF4
IPR001723 - Str_hrmn_rcpt
IPR001628 - Znf_hrmn_rcpt
IPR013088 - Znf_NHR/GATA

Pfam Domains:
PF00104 - Ligand-binding domain of nuclear hormone receptor
PF00105 - Zinc finger, C4 type (two domains)

SCOP Domains:
48508 - Nuclear receptor ligand-binding domain
57716 - Glucocorticoid receptor-like (DNA-binding domain)

ModBase Predicted Comparative 3D Structure on Q9Y5X4
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGDEnsembl WormBase 
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003707 steroid hormone receptor activity
GO:0004879 RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding
GO:0008270 zinc ion binding
GO:0043565 sequence-specific DNA binding
GO:0046872 metal ion binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0006367 transcription initiation from RNA polymerase II promoter
GO:0007165 signal transduction
GO:0007601 visual perception
GO:0007602 phototransduction
GO:0008285 negative regulation of cell proliferation
GO:0030522 intracellular receptor signaling pathway
GO:0042462 eye photoreceptor cell development
GO:0043401 steroid hormone mediated signaling pathway
GO:0045872 positive regulation of rhodopsin gene expression
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0050896 response to stimulus
GO:0060041 retina development in camera-type eye

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription factor complex


-  Descriptions from all associated GenBank mRNAs
  BC041421 - Homo sapiens nuclear receptor subfamily 2, group E, member 3, mRNA (cDNA clone MGC:49976 IMAGE:3876974), complete cds.
JD328677 - Sequence 309701 from Patent EP1572962.
AF121129 - Homo sapiens photoreceptor-specific nuclear receptor (PNR) mRNA, complete cds.
AF148128 - Homo sapiens nuclear receptor mRNA, complete cds.
JD499946 - Sequence 480970 from Patent EP1572962.
JD441182 - Sequence 422206 from Patent EP1572962.
JD482888 - Sequence 463912 from Patent EP1572962.
JD473467 - Sequence 454491 from Patent EP1572962.
JD540001 - Sequence 521025 from Patent EP1572962.
JD107754 - Sequence 88778 from Patent EP1572962.
JD518899 - Sequence 499923 from Patent EP1572962.
JD041495 - Sequence 22519 from Patent EP1572962.
JD119586 - Sequence 100610 from Patent EP1572962.
HQ692847 - Homo sapiens photoreceptor cell-specific nuclear receptor variant 1 (NR2E3) mRNA, complete cds.
AB307710 - Homo sapiens NR2E3 mRNA for photoreceptor-specific nuclear receptor, complete cds.
CU691992 - Synthetic construct Homo sapiens gateway clone IMAGE:100021414 5' read NR2E3 mRNA.
KJ902049 - Synthetic construct Homo sapiens clone ccsbBroadEn_11443 NR2E3 gene, encodes complete protein.
JD168441 - Sequence 149465 from Patent EP1572962.
JD565101 - Sequence 546125 from Patent EP1572962.
JD293733 - Sequence 274757 from Patent EP1572962.
JD109906 - Sequence 90930 from Patent EP1572962.
JD557791 - Sequence 538815 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9Y5X4 (Reactome details) participates in the following event(s):

R-HSA-376419 Formation of NR-MED1 Coactivator Complex
R-HSA-383280 Nuclear Receptor transcription pathway
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)
R-HSA-376419 Formation of NR-MED1 Coactivator Complex
R-HSA-383280 Nuclear Receptor transcription pathway
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B6ZGU0, ENST00000617575.1, ENST00000617575.2, ENST00000617575.3, ENST00000617575.4, NM_014249, NR2E3_HUMAN, PNR, Q9UHM4, Q9Y5X4, RNR, uc327reg.1, uc327reg.2
UCSC ID: ENST00000617575.5_4
RefSeq Accession: NM_014249.4
Protein: Q9Y5X4 (aka NR2E3_HUMAN or NR23_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene NR2E3:
rp-overview (Nonsyndromic Retinitis Pigmentosa Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.