Human Gene NR2E1 (uc003psg.3) Description and Page Index
  Description: Homo sapiens nuclear receptor subfamily 2, group E, member 1 (NR2E1), mRNA.
RefSeq Summary (NM_003269): The protein encoded by this gene is an orphan receptor involved in retinal development. The encoded protein also regulates adult neural stem cell proliferation and may be involved in control of aggressive behavior. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2015].
Transcript (Including UTRs)
   Position: hg19 chr6:108,487,215-108,510,013 Size: 22,799 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr6:108,487,970-108,508,667 Size: 20,698 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:108,487,215-108,510,013)mRNA (may differ from genome)Protein (385 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: NR2E1_HUMAN
DESCRIPTION: RecName: Full=Nuclear receptor subfamily 2 group E member 1; AltName: Full=Nuclear receptor TLX; AltName: Full=Protein tailless homolog; Short=Tll; Short=hTll;
FUNCTION: Orphan receptor that binds DNA as a monomer to hormone response elements (HRE) containing an extended core motif half- site sequence 5'-AAGGTCA-3' in which the 5' flanking nucleotides participate in determining receptor specificity (By similarity). May be required to pattern anterior brain differentiation. Involved in the regulation of retinal development and essential for vision. During retinogenesis, regulates PTEN-Cyclin D expression via binding to the promoter region of PTEN and suppressing its activity (By similarity). May be involved in retinoic acic receptor (RAR) regulation in retinal cells.
SUBUNIT: Monomer (By similarity). Interacts with ATN1; the interaction represses the transcription (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Brain specific. Present in all brain sections tested, highest levels in the caudate nucleus and hippocampus, weakest levels in the thalamus.
SIMILARITY: Belongs to the nuclear hormone receptor family. NR2 subfamily.
SIMILARITY: Contains 1 nuclear receptor DNA-binding domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NR2E1
CDC HuGE Published Literature: NR2E1

-  MalaCards Disease Associations
  MalaCards Gene Search: NR2E1
Diseases sorted by gene-association score: aniridia (6)

-  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.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.19 RPKM in Brain - Caudate (basal ganglia)
Total median expression: 76.64 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -320.50755-0.425 Picture PostScript Text
3' UTR -331.671346-0.246 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
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 Q9Y466
FrontTopSide
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 orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003707 steroid hormone receptor activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0019899 enzyme binding
GO:0042826 histone deacetylase 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:0001662 behavioral fear response
GO:0002118 aggressive behavior
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006367 transcription initiation from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0007399 nervous system development
GO:0007420 brain development
GO:0007601 visual perception
GO:0008284 positive regulation of cell proliferation
GO:0008347 glial cell migration
GO:0021542 dentate gyrus development
GO:0021764 amygdala development
GO:0021772 olfactory bulb development
GO:0021819 layer formation in cerebral cortex
GO:0021872 forebrain generation of neurons
GO:0021895 cerebral cortex neuron differentiation
GO:0021960 anterior commissure morphogenesis
GO:0021987 cerebral cortex development
GO:0030198 extracellular matrix organization
GO:0035019 somatic stem cell population maintenance
GO:0035176 social behavior
GO:0043010 camera-type eye development
GO:0043066 negative regulation of apoptotic process
GO:0043401 steroid hormone mediated signaling pathway
GO:0045165 cell fate commitment
GO:0045665 negative regulation of neuron differentiation
GO:0045766 positive regulation of angiogenesis
GO:0045787 positive regulation of cell cycle
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048712 negative regulation of astrocyte differentiation
GO:0048814 regulation of dendrite morphogenesis
GO:0051128 regulation of cellular component organization
GO:0060041 retina development in camera-type eye
GO:0060164 regulation of timing of neuron differentiation
GO:0060291 long-term synaptic potentiation
GO:0090049 regulation of cell migration involved in sprouting angiogenesis
GO:2000178 negative regulation of neural precursor cell proliferation
GO:2000179 positive regulation of neural precursor cell proliferation
GO:2000648 positive regulation of stem cell proliferation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  AF220532 - Homo sapiens orphan nuclear receptor (NR2E1) mRNA, complete cds.
JD128465 - Sequence 109489 from Patent EP1572962.
JD192176 - Sequence 173200 from Patent EP1572962.
JD064720 - Sequence 45744 from Patent EP1572962.
JD244043 - Sequence 225067 from Patent EP1572962.
JD351433 - Sequence 332457 from Patent EP1572962.
JD495302 - Sequence 476326 from Patent EP1572962.
JD550066 - Sequence 531090 from Patent EP1572962.
JD261383 - Sequence 242407 from Patent EP1572962.
JD361286 - Sequence 342310 from Patent EP1572962.
AF411525 - Homo sapiens nuclear receptor subfamily 2 group E member 1 mRNA, complete cds.
JD538391 - Sequence 519415 from Patent EP1572962.
BC028031 - Homo sapiens nuclear receptor subfamily 2, group E, member 1, mRNA (cDNA clone MGC:39998 IMAGE:5242079), complete cds.
JD093816 - Sequence 74840 from Patent EP1572962.
Y13276 - Homo sapiens mRNA for tailless gene homologue.
JD547239 - Sequence 528263 from Patent EP1572962.
JD226595 - Sequence 207619 from Patent EP1572962.
JD339858 - Sequence 320882 from Patent EP1572962.
JD200375 - Sequence 181399 from Patent EP1572962.
KJ892286 - Synthetic construct Homo sapiens clone ccsbBroadEn_01680 NR2E1 gene, encodes complete protein.
AB527300 - Synthetic construct DNA, clone: pF1KB4185, Homo sapiens NR2E1 gene for nuclear receptor subfamily 2, group E, member 1, without stop codon, in Flexi system.
AB307709 - Homo sapiens NR2E1 mRNA for tailes-related receptor, complete cds.
HQ692846 - Homo sapiens nuclear receptor TLX (NR2E1) mRNA, complete cds.
AK131541 - Homo sapiens cDNA FLJ16774 fis, clone BRCAN2019772, highly similar to Orphan nuclear receptor NR2E1.
JD429890 - Sequence 410914 from Patent EP1572962.
JD309875 - Sequence 290899 from Patent EP1572962.
JD128884 - Sequence 109908 from Patent EP1572962.
JD273826 - Sequence 254850 from Patent EP1572962.
JD286072 - Sequence 267096 from Patent EP1572962.
JD501809 - Sequence 482833 from Patent EP1572962.
JD266835 - Sequence 247859 from Patent EP1572962.
JD186022 - Sequence 167046 from Patent EP1572962.
JD172141 - Sequence 153165 from Patent EP1572962.

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

Protein Q9Y466 (Reactome details) participates in the following event(s):

R-HSA-6807077 NR2E1 associated with transcription repressors binds PTEN promoter
R-HSA-376419 Formation of NR-MED1 Coactivator Complex
R-HSA-8943724 Regulation of PTEN gene transcription
R-HSA-383280 Nuclear Receptor transcription pathway
R-HSA-6807070 PTEN Regulation
R-HSA-212436 Generic Transcription Pathway
R-HSA-1257604 PIP3 activates AKT signaling
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-9006925 Intracellular signaling by second messengers
R-HSA-74160 Gene expression (Transcription)
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: NM_003269, NP_003260, NR2E1_HUMAN, Q9Y466, TLX
UCSC ID: uc003psg.3
RefSeq Accession: NM_003269
Protein: Q9Y466 (aka NR2E1_HUMAN or NR21_HUMAN)
CCDS: CCDS5063.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003269.3
exon count: 9CDS single in 3' UTR: no RNA size: 3271
ORF size: 1158CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2316.00frame shift in genome: no % Coverage: 99.63
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.