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Protein

Photoreceptor-specific nuclear receptor

Gene

NR2E3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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.2 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi44 – 120Nuclear receptorPROSITE-ProRule annotationAdd BLAST77
Zinc fingeri47 – 67NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri83 – 108NR C4-typePROSITE-ProRule annotationAdd BLAST26

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Receptor, Repressor
Biological processSensory transduction, Transcription, Transcription regulation, Vision
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-383280 Nuclear Receptor transcription pathway
SignaLinkiQ9Y5X4
SIGNORiQ9Y5X4

Names & Taxonomyi

Protein namesi
Recommended name:
Photoreceptor-specific nuclear receptor
Alternative name(s):
Nuclear receptor subfamily 2 group E member 3
Retina-specific nuclear receptor
Gene namesi
Name:NR2E3
Synonyms:PNR, RNR
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 15

Organism-specific databases

EuPathDBiHostDB:ENSG00000278570.4
HGNCiHGNC:7974 NR2E3
MIMi604485 gene
neXtProtiNX_Q9Y5X4

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Enhanced S cone syndrome (ESCS)8 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAutosomal 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.
See also OMIM:268100
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_00926567 – 69Missing in ESCS. 3 Publications3
Natural variantiVAR_00926676R → Q in ESCS. 1 PublicationCorresponds to variant dbSNP:rs104894493EnsemblClinVar.1
Natural variantiVAR_00926776R → W in ESCS. 1 PublicationCorresponds to variant dbSNP:rs104894492EnsemblClinVar.1
Natural variantiVAR_02083988G → V in ESCS. 1 Publication1
Natural variantiVAR_01002597R → H in ESCS. 3 Publications1
Natural variantiVAR_010026104R → W in ESCS. 2 PublicationsCorresponds to variant dbSNP:rs990307718Ensembl.1
Natural variantiVAR_010027121E → K in ESCS. 1 PublicationCorresponds to variant dbSNP:rs146403122EnsemblClinVar.1
Natural variantiVAR_010031234W → S in ESCS. 2 Publications1
Natural variantiVAR_020840256A → E in ESCS. 2 PublicationsCorresponds to variant dbSNP:rs377257254EnsemblClinVar.1
Natural variantiVAR_020841263L → P in ESCS; impairs protein folding. 2 Publications1
Natural variantiVAR_010033309R → G in ESCS; impairs protein folding and stability. 3 Publications1
Natural variantiVAR_010034311R → Q in ESCS; impairs protein folding and stability and hinders the ability to form stable dimers. 7 PublicationsCorresponds to variant dbSNP:rs28937873EnsemblClinVar.1
Natural variantiVAR_020842336L → P in ESCS; impairs protein folding and stability. 2 PublicationsCorresponds to variant dbSNP:rs752883545EnsemblClinVar.1
Natural variantiVAR_020843353L → V in ESCS; impairs protein folding and stability. 2 Publications1
Natural variantiVAR_010035385R → P in ESCS. 1 PublicationCorresponds to variant dbSNP:rs766769900Ensembl.1
Natural variantiVAR_010036407M → K in ESCS; impairs protein folding and stability. 3 Publications1
Retinitis pigmentosa 37 (RP37)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:611131
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_03702656G → R in RP37. 2 PublicationsCorresponds to variant dbSNP:rs121912631EnsemblClinVar.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi372L → R: Reduces transcription repressor activity. 1 Publication1
Mutagenesisi375L → R: Reduces transcription repressor activity. 1 Publication1

Keywords - Diseasei

Disease mutation, Retinitis pigmentosa

Organism-specific databases

DisGeNETi10002
GeneReviewsiNR2E3
MalaCardsiNR2E3
MIMi268100 phenotype
611131 phenotype
OpenTargetsiENSG00000278570
Orphaneti53540 Goldmann-Favre syndrome
791 Retinitis pigmentosa
PharmGKBiPA31757

Chemistry databases

ChEMBLiCHEMBL4374

Polymorphism and mutation databases

BioMutaiNR2E3
DMDMi8928275

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000535991 – 410Photoreceptor-specific nuclear receptorAdd BLAST410

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki185Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity
Cross-linki330Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity
Cross-linki337Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity

Post-translational modificationi

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).By similarity

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

PeptideAtlasiQ9Y5X4
PRIDEiQ9Y5X4
ProteomicsDBi86529
86530 [Q9Y5X4-2]

PTM databases

iPTMnetiQ9Y5X4
PhosphoSitePlusiQ9Y5X4

Expressioni

Tissue specificityi

Eye specific; found solely in the outer nuclear layer of the adult neurosensory retina, where the nuclei of cone and rod photoreceptors reside.1 Publication

Gene expression databases

BgeeiENSG00000278570 Expressed in 96 organ(s), highest expression level in buccal mucosa cell
CleanExiHS_NR2E3
ExpressionAtlasiQ9Y5X4 baseline and differential
GenevisibleiQ9Y5X4 HS

Interactioni

Subunit structurei

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 directly 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.By similarity2 Publications

Protein-protein interaction databases

BioGridi115320, 19 interactors
IntActiQ9Y5X4, 1 interactor

Chemistry databases

BindingDBiQ9Y5X4

Structurei

Secondary structure

1410
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ9Y5X4
SMRiQ9Y5X4
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini169 – 410NR LBDPROSITE-ProRule annotationAdd BLAST242

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi371 – 375Poly-Leu5

Sequence similaritiesi

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri47 – 67NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri83 – 108NR C4-typePROSITE-ProRule annotationAdd BLAST26

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00760000118948
HOGENOMiHOG000260820
HOVERGENiHBG005606
InParanoidiQ9Y5X4
KOiK08546
OMAiTRPTALM
OrthoDBiEOG091G0AV3
PhylomeDBiQ9Y5X4

Family and domain databases

Gene3Di3.30.50.10, 1 hit
InterProiView protein in InterPro
IPR035500 NHR_like_dom_sf
IPR000536 Nucl_hrmn_rcpt_lig-bd
IPR001723 Nuclear_hrmn_rcpt
IPR000003 Retinoid-X_rcpt/HNF4
IPR001628 Znf_hrmn_rcpt
IPR013088 Znf_NHR/GATA
PfamiView protein in Pfam
PF00104 Hormone_recep, 1 hit
PF00105 zf-C4, 1 hit
PRINTSiPR00545 RETINOIDXR
PR00398 STRDHORMONER
PR00047 STROIDFINGER
SMARTiView protein in SMART
SM00430 HOLI, 1 hit
SM00399 ZnF_C4, 1 hit
SUPFAMiSSF48508 SSF48508, 1 hit
PROSITEiView protein in PROSITE
PS51843 NR_LBD, 1 hit
PS00031 NUCLEAR_REC_DBD_1, 1 hit
PS51030 NUCLEAR_REC_DBD_2, 1 hit

Sequences (2+)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 2 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All

Isoform Long (identifier: Q9Y5X4-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
METRPTALMS STVAAAAPAA GAASRKESPG RWGLGEDPTG VSPSLQCRVC
60 70 80 90 100
GDSSSGKHYG IYACNGCSGF FKRSVRRRLI YRCQVGAGMC PVDKAHRNQC
110 120 130 140 150
QACRLKKCLQ AGMNQDAVQN ERQPRSTAQV HLDSMESNTE SRPESLVAPP
160 170 180 190 200
APAGRSPRGP TPMSAARALG HHFMASLITA ETCAKLEPED ADENIDVTSN
210 220 230 240 250
DPEFPSSPYS SSSPCGLDSI HETSARLLFM AVKWAKNLPV FSSLPFRDQV
260 270 280 290 300
ILLEEAWSEL FLLGAIQWSL PLDSCPLLAP PEASAAGGAQ GRLTLASMET
310 320 330 340 350
RVLQETISRF RALAVDPTEF ACMKALVLFK PETRGLKDPE HVEALQDQSQ
360 370 380 390 400
VMLSQHSKAH HPSQPVRFGK LLLLLPSLRF ITAERIELLF FRKTIGNTPM
410
EKLLCDMFKN
Length:410
Mass (Da):44,692
Last modified:November 1, 1999 - v1
Checksum:iD49525830ED0A000
GO
Isoform Short (identifier: Q9Y5X4-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     368-410: Missing.

Show »
Length:367
Mass (Da):39,638
Checksum:iF67A09D430754B3D
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
Q8IVZ9Q8IVZ9_HUMAN
NR2E3 protein
NR2E3
322Annotation score:

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06276844S → L Associated with autosomal recessive retinitis pigmentosa. 1 PublicationCorresponds to variant dbSNP:rs202098481EnsemblClinVar.1
Natural variantiVAR_03702656G → R in RP37. 2 PublicationsCorresponds to variant dbSNP:rs121912631EnsemblClinVar.1
Natural variantiVAR_00926567 – 69Missing in ESCS. 3 Publications3
Natural variantiVAR_00926676R → Q in ESCS. 1 PublicationCorresponds to variant dbSNP:rs104894493EnsemblClinVar.1
Natural variantiVAR_00926776R → W in ESCS. 1 PublicationCorresponds to variant dbSNP:rs104894492EnsemblClinVar.1
Natural variantiVAR_02083988G → V in ESCS. 1 Publication1
Natural variantiVAR_01002597R → H in ESCS. 3 Publications1
Natural variantiVAR_062769104R → Q Associated with ESCS. 1 PublicationCorresponds to variant dbSNP:rs766096417EnsemblClinVar.1
Natural variantiVAR_010026104R → W in ESCS. 2 PublicationsCorresponds to variant dbSNP:rs990307718Ensembl.1
Natural variantiVAR_010027121E → K in ESCS. 1 PublicationCorresponds to variant dbSNP:rs146403122EnsemblClinVar.1
Natural variantiVAR_010028140E → G2 PublicationsCorresponds to variant dbSNP:rs1805020EnsemblClinVar.1
Natural variantiVAR_010029163M → T2 PublicationsCorresponds to variant dbSNP:rs1805021EnsemblClinVar.1
Natural variantiVAR_010030232V → I1 PublicationCorresponds to variant dbSNP:rs1805023EnsemblClinVar.1
Natural variantiVAR_010031234W → S in ESCS. 2 Publications1
Natural variantiVAR_020840256A → E in ESCS. 2 PublicationsCorresponds to variant dbSNP:rs377257254EnsemblClinVar.1
Natural variantiVAR_020841263L → P in ESCS; impairs protein folding. 2 Publications1
Natural variantiVAR_062770287G → S Associated with autosomal recessive retinitis pigmentosa. 1 PublicationCorresponds to variant dbSNP:rs764901119Ensembl.1
Natural variantiVAR_010032302V → I1 PublicationCorresponds to variant dbSNP:rs1805025EnsemblClinVar.1
Natural variantiVAR_010033309R → G in ESCS; impairs protein folding and stability. 3 Publications1
Natural variantiVAR_010034311R → Q in ESCS; impairs protein folding and stability and hinders the ability to form stable dimers. 7 PublicationsCorresponds to variant dbSNP:rs28937873EnsemblClinVar.1
Natural variantiVAR_062771324K → R Associated with autosomal recessive retinitis pigmentosa. 1 Publication1
Natural variantiVAR_062772334R → G Associated with ESCS; impairs protein folding and stability. 2 Publications1
Natural variantiVAR_020842336L → P in ESCS; impairs protein folding and stability. 2 PublicationsCorresponds to variant dbSNP:rs752883545EnsemblClinVar.1
Natural variantiVAR_020843353L → V in ESCS; impairs protein folding and stability. 2 Publications1
Natural variantiVAR_010035385R → P in ESCS. 1 PublicationCorresponds to variant dbSNP:rs766769900Ensembl.1
Natural variantiVAR_010036407M → K in ESCS; impairs protein folding and stability. 3 Publications1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_003679368 – 410Missing in isoform Short. 1 PublicationAdd BLAST43

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF121129 mRNA Translation: AAD28301.1
AF148128 mRNA Translation: AAF22227.1
AJ276674 Genomic DNA Translation: CAB82769.1
AB307710 mRNA Translation: BAH02301.1
CH471082 Genomic DNA Translation: EAW77876.1
CCDSiCCDS73750.1 [Q9Y5X4-1]
CCDS73751.1 [Q9Y5X4-2]
RefSeqiNP_055064.1, NM_014249.3 [Q9Y5X4-1]
NP_057430.1, NM_016346.3 [Q9Y5X4-2]
UniGeneiHs.187354
Hs.636007

Genome annotation databases

EnsembliENST00000617575; ENSP00000482504; ENSG00000278570 [Q9Y5X4-1]
ENST00000621098; ENSP00000479962; ENSG00000278570 [Q9Y5X4-2]
GeneIDi10002
KEGGihsa:10002
UCSCiuc032cik.2 human [Q9Y5X4-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Web resourcesi

Mutations of the NR2E3 gene

Retina International's Scientific Newsletter

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF121129 mRNA Translation: AAD28301.1
AF148128 mRNA Translation: AAF22227.1
AJ276674 Genomic DNA Translation: CAB82769.1
AB307710 mRNA Translation: BAH02301.1
CH471082 Genomic DNA Translation: EAW77876.1
CCDSiCCDS73750.1 [Q9Y5X4-1]
CCDS73751.1 [Q9Y5X4-2]
RefSeqiNP_055064.1, NM_014249.3 [Q9Y5X4-1]
NP_057430.1, NM_016346.3 [Q9Y5X4-2]
UniGeneiHs.187354
Hs.636007

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LOGX-ray2.70A/B217-410[»]
ProteinModelPortaliQ9Y5X4
SMRiQ9Y5X4
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115320, 19 interactors
IntActiQ9Y5X4, 1 interactor

Chemistry databases

BindingDBiQ9Y5X4
ChEMBLiCHEMBL4374

PTM databases

iPTMnetiQ9Y5X4
PhosphoSitePlusiQ9Y5X4

Polymorphism and mutation databases

BioMutaiNR2E3
DMDMi8928275

Proteomic databases

PeptideAtlasiQ9Y5X4
PRIDEiQ9Y5X4
ProteomicsDBi86529
86530 [Q9Y5X4-2]

Protocols and materials databases

DNASUi10002
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000617575; ENSP00000482504; ENSG00000278570 [Q9Y5X4-1]
ENST00000621098; ENSP00000479962; ENSG00000278570 [Q9Y5X4-2]
GeneIDi10002
KEGGihsa:10002
UCSCiuc032cik.2 human [Q9Y5X4-1]

Organism-specific databases

CTDi10002
DisGeNETi10002
EuPathDBiHostDB:ENSG00000278570.4
GeneCardsiNR2E3
GeneReviewsiNR2E3
HGNCiHGNC:7974 NR2E3
MalaCardsiNR2E3
MIMi268100 phenotype
604485 gene
611131 phenotype
neXtProtiNX_Q9Y5X4
OpenTargetsiENSG00000278570
Orphaneti53540 Goldmann-Favre syndrome
791 Retinitis pigmentosa
PharmGKBiPA31757
GenAtlasiSearch...

Phylogenomic databases

GeneTreeiENSGT00760000118948
HOGENOMiHOG000260820
HOVERGENiHBG005606
InParanoidiQ9Y5X4
KOiK08546
OMAiTRPTALM
OrthoDBiEOG091G0AV3
PhylomeDBiQ9Y5X4

Enzyme and pathway databases

ReactomeiR-HSA-383280 Nuclear Receptor transcription pathway
SignaLinkiQ9Y5X4
SIGNORiQ9Y5X4

Miscellaneous databases

GeneWikiiPhotoreceptor_cell-specific_nuclear_receptor
GenomeRNAii10002
PROiPR:Q9Y5X4
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000278570 Expressed in 96 organ(s), highest expression level in buccal mucosa cell
CleanExiHS_NR2E3
ExpressionAtlasiQ9Y5X4 baseline and differential
GenevisibleiQ9Y5X4 HS

Family and domain databases

Gene3Di3.30.50.10, 1 hit
InterProiView protein in InterPro
IPR035500 NHR_like_dom_sf
IPR000536 Nucl_hrmn_rcpt_lig-bd
IPR001723 Nuclear_hrmn_rcpt
IPR000003 Retinoid-X_rcpt/HNF4
IPR001628 Znf_hrmn_rcpt
IPR013088 Znf_NHR/GATA
PfamiView protein in Pfam
PF00104 Hormone_recep, 1 hit
PF00105 zf-C4, 1 hit
PRINTSiPR00545 RETINOIDXR
PR00398 STRDHORMONER
PR00047 STROIDFINGER
SMARTiView protein in SMART
SM00430 HOLI, 1 hit
SM00399 ZnF_C4, 1 hit
SUPFAMiSSF48508 SSF48508, 1 hit
PROSITEiView protein in PROSITE
PS51843 NR_LBD, 1 hit
PS00031 NUCLEAR_REC_DBD_1, 1 hit
PS51030 NUCLEAR_REC_DBD_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiNR2E3_HUMAN
AccessioniPrimary (citable) accession number: Q9Y5X4
Secondary accession number(s): B6ZGU0, Q9UHM4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: November 1, 1999
Last modified: November 7, 2018
This is version 180 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. Human chromosome 15
    Human chromosome 15: entries, gene names and cross-references to MIM
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