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NR4A3 (nuclear receptor subfamily 4, group A, member 3)

Written2003-07Goran Stenman
Lundberg Laboratory for Cancer Research, Department of Pathology, Goteborg University, Sahlgrenska University Hospital, SE-413 45 Goteborg, Sweden

(Note : for Links provided by Atlas : click)

Identity

Alias_namesnuclear receptor subfamily 4
Alias_symbol (synonym)CSMF
CHN
NOR1
MINOR
Other aliasTEC
NR4A3
HGNC (Hugo) NR4A3
LocusID (NCBI) 8013
Atlas_Id 75
Location 9q22.33  [Link to chromosome band 9q22]
Location_base_pair Starts at 102584137 and ends at 102629173 bp from pter ( according to hg19-Feb_2009)  [Mapping NR4A3.png]
Fusion genes
(updated 2016)
EWSR1 (22q12.2) / NR4A3 (9q22.33)FUS (16p11.2) / NR4A3 (9q22.33)NR4A3 (9q22.33) / ABL2 (1q25.2)
NR4A3 (9q22.33) / EWSR1 (22q12.2)NR4A3 (9q22.33) / TAF15 (17q12)NR4A3 (9q22.33) / TCF12 (15q21.3)
NR4A3 (9q22.33) / TFG (3q12.2)STX17 (9q31.1) / NR4A3 (9q22.33)TAF15 (17q12) / NR4A3 (9q22.33)
TCF12 (15q21.3) / NR4A3 (9q22.33)TFG (3q12.2) / NR4A3 (9q22.33)

DNA/RNA

Description spans about 46 kb; 9 exons
Transcription four transcript variants (6382 bp, 5635 bp, 4983bp and 2588 bp)

Protein

Description three isoforms (637 aa, 626 aa and 443 aa); N-terminal activation domain; central bipartite zinc finger DNA-binding domain; C-terminal ligand binding domain.
Expression most tissues, highest expression levels in the central nervous system.
Localisation nuclear
Function orphan nuclear receptor; implicated in the control of cell proliferation as an immediate-early protein and in differentiation and apoptosis; binds as a monomer to the DNA-response element NBRE; activate transcription constitutively when bound to NBRE; the homeotic protein Six3 is a coactivator of TEC.
Homology belongs to the steroid/thyroid receptor gene super family; highly homologous to the nuclear receptors NGFI-B and NURR1.

Implicated in

Note
  
Entity Extraskeletal myxoid chondrosarcoma with t(9;22)(q22;q12).
Disease rare type of sarcoma (2.3% of all soft tissue sarcomas) characteristically involving the deep, soft tissues of the extremities; morphological resemblance to embryonic cartilage.
Hybrid/Mutated Gene EWSR1-TEC
Abnormal Protein N-terminal transactivation domain of EWSR1 fused to the entire TEC protein.
  
  
Entity Extraskeletal myxoid chondrosarcoma with t(9;17)(q22;q11).
Disease rare type of sarcoma (2.3% of all soft tissue sarcomas) characteristically involving the deep, soft tissues of the extremities; morphological resemblance to embryonic cartilage.
Hybrid/Mutated Gene TAF2N-TEC
Abnormal Protein N-terminal transactivation domain of TAF2N fused to the entire TEC protein.
  
  
Entity Extraskeletal myxoid chondrosarcoma with t(9;15)(q22;q21).
Disease rare type of sarcoma (2.3% of all soft tissue sarcomas) characteristically involving the deep, soft tissues of the extremities; morphological resemblance to embryonic cartilage.
Hybrid/Mutated Gene TCF12-TEC
Abnormal Protein N-terminal domain of TCF12 fused to the entire TEC protein; the N-terminal of TCF12 shows no sequence homology to the N-terminals of EWSR1 or TAF2N.
  

Breakpoints

 

Bibliography

Identification of a novel fusion gene involving hTAFII68 and CHN from a t(9;17)(q22;q11.2) translocation in an extraskeletal myxoid chondrosarcoma.
Attwooll C, Tariq M, Harris M, Coyne JD, Telford N, Varley JM
Oncogene. 1999 ; 18 (52) : 7599-7601.
PMID 10602520
 
Fusion of the EWS gene to CHN, a member of the steroid/thyroid receptor gene superfamily, in a human myxoid chondrosarcoma.
Clark J, Benjamin H, Gill S, Sidhar S, Goodwin G, Crew J, Gusterson BA, Shipley J, Cooper CS
Oncogene. 1996 ; 12 (2) : 229-235.
PMID 8570200
 
The isolation and characterization of MINOR, a novel mitogen-inducible nuclear orphan receptor.
Hedvat CV, Irving SG
Molecular endocrinology (Baltimore, Md.). 1995 ; 9 (12) : 1692-1700.
PMID 8614405
 
The EWS/TEC fusion protein encoded by the t(9;22) chromosomal translocation in human chondrosarcomas is a highly potent transcriptional activator.
Labelle Y, Bussières J, Courjal F, Goldring MB
Oncogene. 1999 ; 18 (21) : 3303-3308.
PMID 10359536
 
Oncogenic conversion of a novel orphan nuclear receptor by chromosome translocation.
Labelle Y, Zucman J, Stenman G, Kindblom LG, Knight J, Turc-Carel C, Dockhorn-Dworniczak B, Mandahl N, Desmaze C, Peter M
Human molecular genetics. 1995 ; 4 (12) : 2219-2226.
PMID 8634690
 
The homeotic protein Six3 is a coactivator of the nuclear receptor NOR-1 and a corepressor of the fusion protein EWS/NOR-1 in human extraskeletal myxoid chondrosarcomas.
Laflamme C, Filion C, Bridge JA, Ladanyi M, Goldring MB, Labelle Y
Cancer research. 2003 ; 63 (2) : 449-454.
PMID 12543801
 
The AF2 domain of the orphan nuclear receptor TEC is essential for the transcriptional activity of the oncogenic fusion protein EWS/TEC.
Maltais A, Filion C, Labelle Y
Cancer letters. 2002 ; 183 (1) : 87-94.
PMID 12049818
 
Molecular cloning of a novel thyroid/steroid receptor superfamily gene from cultured rat neuronal cells.
Ohkura N, Hijikuro M, Yamamoto A, Miki K
Biochemical and biophysical research communications. 1994 ; 205 (3) : 1959-1965.
PMID 7811288
 
The EWS/NOR1 fusion gene product gains a novel activity affecting pre-mRNA splicing.
Ohkura N, Yaguchi H, Tsukada T, Yamaguchi K
The Journal of biological chemistry. 2002 ; 277 (1) : 535-543.
PMID 11673470
 
Fusion of the NH2-terminal domain of the basic helix-loop-helix protein TCF12 to TEC in extraskeletal myxoid chondrosarcoma with translocation t(9;15)(q22;q21).
Sjögren H, Wedell B, Meis-Kindblom JM, Kindblom LG, Stenman G
Cancer research. 2000 ; 60 (24) : 6832-6835.
PMID 11156374
 

Citation

This paper should be referenced as such :
Stenman, G
NR4A3 (nuclear receptor subfamily 4, group A, member 3)
Atlas Genet Cytogenet Oncol Haematol. 2003;7(3):176-177.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/TECID75.html


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 4 ]
  Soft Tissues: Angiomatoid fibrous histiocytoma
Bone: Chondrosarcoma
Soft Tissues: Extraskeletal myxoid chondrosarcoma
Soft tissue tumors: an overview


External links

Nomenclature
HGNC (Hugo)NR4A3   7982
Cards
AtlasTECID75
Entrez_Gene (NCBI)NR4A3  8013  nuclear receptor subfamily 4 group A member 3
AliasesCHN; CSMF; MINOR; NOR1; 
TEC
GeneCards (Weizmann)NR4A3
Ensembl hg19 (Hinxton)ENSG00000119508 [Gene_View]  chr9:102584137-102629173 [Contig_View]  NR4A3 [Vega]
Ensembl hg38 (Hinxton)ENSG00000119508 [Gene_View]  chr9:102584137-102629173 [Contig_View]  NR4A3 [Vega]
ICGC DataPortalENSG00000119508
TCGA cBioPortalNR4A3
AceView (NCBI)NR4A3
Genatlas (Paris)NR4A3
WikiGenes8013
SOURCE (Princeton)NR4A3
Genetics Home Reference (NIH)NR4A3
Genomic and cartography
GoldenPath hg19 (UCSC)NR4A3  -     chr9:102584137-102629173 +  9q22   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)NR4A3  -     9q22   [Description]    (hg38-Dec_2013)
EnsemblNR4A3 - 9q22 [CytoView hg19]  NR4A3 - 9q22 [CytoView hg38]
Mapping of homologs : NCBINR4A3 [Mapview hg19]  NR4A3 [Mapview hg38]
OMIM600542   612237   
Gene and transcription
Genbank (Entrez)AK226108 BX649089 D78579 D85241 D85242
RefSeq transcript (Entrez)NM_006981 NM_173198 NM_173199 NM_173200
RefSeq genomic (Entrez)NC_000009 NC_018920 NG_028910 NT_008470 NW_004929366
Consensus coding sequences : CCDS (NCBI)NR4A3
Cluster EST : UnigeneHs.279522 [ NCBI ]
CGAP (NCI)Hs.279522
Alternative Splicing GalleryENSG00000119508
Gene ExpressionNR4A3 [ NCBI-GEO ]   NR4A3 [ EBI - ARRAY_EXPRESS ]   NR4A3 [ SEEK ]   NR4A3 [ MEM ]
Gene Expression Viewer (FireBrowse)NR4A3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8013
GTEX Portal (Tissue expression)NR4A3
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ92570   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ92570  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ92570
Splice isoforms : SwissVarQ92570
PhosPhoSitePlusQ92570
Domaine pattern : Prosite (Expaxy)NUCLEAR_REC_DBD_1 (PS00031)    NUCLEAR_REC_DBD_2 (PS51030)   
Domains : Interpro (EBI)NOR1_rcpt    Nuc_orph_rcpt    Nucl_hrmn_rcpt_lig-bd    Nuclear_hrmn_rcpt    Znf_hrmn_rcpt    Znf_NHR/GATA   
Domain families : Pfam (Sanger)Hormone_recep (PF00104)    zf-C4 (PF00105)   
Domain families : Pfam (NCBI)pfam00104    pfam00105   
Domain families : Smart (EMBL)HOLI (SM00430)  ZnF_C4 (SM00399)  
Conserved Domain (NCBI)NR4A3
DMDM Disease mutations8013
Blocks (Seattle)NR4A3
SuperfamilyQ92570
Human Protein AtlasENSG00000119508
Peptide AtlasQ92570
HPRD02766
IPIIPI00328269   IPI00293038   IPI00334557   IPI00748100   
Protein Interaction databases
DIP (DOE-UCLA)Q92570
IntAct (EBI)Q92570
FunCoupENSG00000119508
BioGRIDNR4A3
STRING (EMBL)NR4A3
ZODIACNR4A3
Ontologies - Pathways
QuickGOQ92570
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  RNA polymerase II core promoter proximal region sequence-specific DNA binding  core promoter sequence-specific DNA binding  transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding  transcription coactivator binding  mesoderm formation  DNA binding  steroid hormone receptor activity  thyroid hormone receptor activity  protein binding  nucleus  nucleoplasm  transcription factor complex  transcription initiation from RNA polymerase II promoter  gastrulation  axon guidance  biological_process  zinc ion binding  pyruvate oxidation  positive regulation of cardiac muscle hypertrophy  positive regulation of glucose transport  protein kinase binding  hippocampus development  intracellular receptor signaling pathway  intracellular receptor signaling pathway  adult behavior  organ regeneration  positive regulation of mast cell cytokine production  histone acetyltransferase binding  glucocorticoid receptor binding  common myeloid progenitor cell proliferation  positive regulation of mast cell activation by Fc-epsilon receptor signaling pathway  response to hydrogen peroxide  mast cell granule  protein homodimerization activity  mast cell degranulation  steroid hormone mediated signaling pathway  negative regulation of neuron apoptotic process  cellular response to leptin stimulus  cellular respiration  fat cell differentiation  positive regulation of cell cycle  positive regulation of transcription from RNA polymerase II promoter  positive regulation of fatty acid oxidation  regulation of smooth muscle cell proliferation  positive regulation of smooth muscle cell proliferation  semicircular canal morphogenesis  positive regulation of epithelial cell proliferation  neuromuscular process controlling balance  vestibular reflex  regulation of type B pancreatic cell proliferation  cellular response to corticotropin-releasing hormone stimulus  cellular response to catecholamine stimulus  energy homeostasis  positive regulation of monocyte aggregation  negative regulation of hydrogen peroxide-induced neuron death  positive regulation of leukocyte apoptotic process  positive regulation of feeding behavior  regulation of energy homeostasis  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  RNA polymerase II core promoter proximal region sequence-specific DNA binding  core promoter sequence-specific DNA binding  transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding  transcription coactivator binding  mesoderm formation  DNA binding  steroid hormone receptor activity  thyroid hormone receptor activity  protein binding  nucleus  nucleoplasm  transcription factor complex  transcription initiation from RNA polymerase II promoter  gastrulation  axon guidance  biological_process  zinc ion binding  pyruvate oxidation  positive regulation of cardiac muscle hypertrophy  positive regulation of glucose transport  protein kinase binding  hippocampus development  intracellular receptor signaling pathway  intracellular receptor signaling pathway  adult behavior  organ regeneration  positive regulation of mast cell cytokine production  histone acetyltransferase binding  glucocorticoid receptor binding  common myeloid progenitor cell proliferation  positive regulation of mast cell activation by Fc-epsilon receptor signaling pathway  response to hydrogen peroxide  mast cell granule  protein homodimerization activity  mast cell degranulation  steroid hormone mediated signaling pathway  negative regulation of neuron apoptotic process  cellular response to leptin stimulus  cellular respiration  fat cell differentiation  positive regulation of cell cycle  positive regulation of transcription from RNA polymerase II promoter  positive regulation of fatty acid oxidation  regulation of smooth muscle cell proliferation  positive regulation of smooth muscle cell proliferation  semicircular canal morphogenesis  positive regulation of epithelial cell proliferation  neuromuscular process controlling balance  vestibular reflex  regulation of type B pancreatic cell proliferation  cellular response to corticotropin-releasing hormone stimulus  cellular response to catecholamine stimulus  energy homeostasis  positive regulation of monocyte aggregation  negative regulation of hydrogen peroxide-induced neuron death  positive regulation of leukocyte apoptotic process  positive regulation of feeding behavior  regulation of energy homeostasis  
Pathways : KEGGTranscriptional misregulation in cancer   
NDEx NetworkNR4A3
Atlas of Cancer Signalling NetworkNR4A3
Wikipedia pathwaysNR4A3
Orthology - Evolution
OrthoDB8013
GeneTree (enSembl)ENSG00000119508
Phylogenetic Trees/Animal Genes : TreeFamNR4A3
HOVERGENQ92570
HOGENOMQ92570
Homologs : HomoloGeneNR4A3
Homology/Alignments : Family Browser (UCSC)NR4A3
Gene fusions - Rearrangements
Fusion : MitelmanEWSR1/NR4A3 [22q12.2/9q22.33]  [t(9;22)(q31;q12)]  
Fusion : MitelmanFUS/NR4A3 [16p11.2/9q22.33]  [t(9;16)(q31;p11)]  
Fusion : MitelmanTCF12/NR4A3 [15q21.3/9q22.33]  [t(9;15)(q31;q21)]  
Fusion : MitelmanTFG/NR4A3 [3q12.2/9q22.33]  [t(3;9)(q12;q31)]  
Fusion : COSMICEWSR1 [22q12.2]  -  NR4A3 [9q22.33]  [fusion_352]  [fusion_353]  [fusion_355]  [fusion_356]  [fusion_358]  [fusion_359]  [fusion_361]  
[fusion_364]  [fusion_365]  [fusion_366]  [fusion_367]  [fusion_369]  [fusion_370]  [fusion_371]  [fusion_374]  [fusion_375]  [fusion_376]  
[fusion_378]  [fusion_380]  [fusion_381]  [fusion_397]  [fusion_398]  [fusion_399]  [fusion_400]  [fusion_496]  
Fusion : COSMICNR4A3 [9q22.33]  -  EWSR1 [22q12.2]  [fusion_386]  [fusion_401]  [fusion_402]  
Fusion : COSMICNR4A3 [9q22.33]  -  TAF15 [17q12]  [fusion_960]  [fusion_961]  
Fusion : COSMICTAF15 [17q12]  -  NR4A3 [9q22.33]  [fusion_589]  [fusion_657]  [fusion_658]  [fusion_957]  [fusion_958]  [fusion_959]  
Fusion : COSMICTCF12 [15q21.3]  -  NR4A3 [9q22.33]  [fusion_754]  [fusion_755]  
Fusion : COSMICTFG [3q12.2]  -  NR4A3 [9q22.33]  [fusion_1187]  [fusion_610]  
Fusion : TICdbEWSR1 [22q12.2]  -  NR4A3 [9q22.33]
Fusion : TICdbTAF15 [17q12]  -  NR4A3 [9q22.33]
Fusion : TICdbTFG [3q12.2]  -  NR4A3 [9q22.33]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerNR4A3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)NR4A3
dbVarNR4A3
ClinVarNR4A3
1000_GenomesNR4A3 
Exome Variant ServerNR4A3
ExAC (Exome Aggregation Consortium)NR4A3 (select the gene name)
Genetic variants : HAPMAP8013
Genomic Variants (DGV)NR4A3 [DGVbeta]
DECIPHER (Syndromes)9:102584137-102629173  ENSG00000119508
CONAN: Copy Number AnalysisNR4A3 
Mutations
ICGC Data PortalNR4A3 
TCGA Data PortalNR4A3 
Broad Tumor PortalNR4A3
OASIS PortalNR4A3 [ Somatic mutations - Copy number]
Cancer Gene: CensusNR4A3 
Mutations and Diseases : HGMDNR4A3
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch NR4A3
DgiDB (Drug Gene Interaction Database)NR4A3
DoCM (Curated mutations)NR4A3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)NR4A3 (select a term)
intoGenNR4A3
NCG5 (London)NR4A3
Cancer3DNR4A3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600542    612237   
Orphanet18668   
MedgenNR4A3
Genetic Testing Registry NR4A3
NextProtQ92570 [Medical]
TSGene8013
GENETestsNR4A3
Huge Navigator NR4A3 [HugePedia]
snp3D : Map Gene to Disease8013
BioCentury BCIQNR4A3
ClinGenNR4A3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD8013
Chemical/Pharm GKB GenePA31763
Clinical trialNR4A3
Miscellaneous
canSAR (ICR)NR4A3 (select the gene name)
Probes
Litterature
PubMed66 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineNR4A3
EVEXNR4A3
GoPubMedNR4A3
iHOPNR4A3
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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