Gene Report

Basic information

Related studies

Functional annotation

Related other genetic factors

Overlap with SZ and MDD

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Basic Info

Approved Symbol	NCOR2
Symbol Alias	SMRT, SMRTE, TRAC-1, CTG26, TNRC14
Approved Name	nuclear receptor corepressor 2
Previous Name	nuclear receptor co-repressor 2
Location	12q24
Position	chr12:124324415-124567589, -1
External Links	HGNC: 7673 Entrez Gene: 9612 Ensembl: ENSG00000196498 UCSC: uc010tbb.2
No. of Studies	1 (Positive: 0; Negative: 1; trend: 0)
Overlap with SZ?	NO
Overlap with MDD?	NO

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Shink, E.,2005(b)	SNP: rs2227277, rs2229840, rs2230944, rs3040832 Other variant: NCOR2_GC34E20A	Our results do not provide support for the existence of a common nsSNP (minor allele frequency >0.05) in the SMRT/N-CoR2 gene that would have a major effect on the BP phenotype in the SLSJ population.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 23)

GO terms by PBA (count: 4)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0016020	membrane	cellular component	IDA[19946888]	137
GO:0005634	nucleus	cellular component	IC[18052923]; IDA[10097068]	283
GO:0003677	DNA binding	molecular function	IEA	83
GO:0003714	transcription corepressor activity	molecular function	IDA[18052923]; IMP[12628926]	21

GO terms by database search (count: 19)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0007219	Notch signaling pathway	biological process	TAS	14
GO:0005654	nucleoplasm	cellular component	IDA; TAS	163
GO:0003682	chromatin binding	molecular function	IEA	23
GO:0016363	nuclear matrix	cellular component	IDA[21328542]	7
GO:0006325	chromatin organization	biological process	TAS	14
GO:0005112	Notch binding	molecular function	IPI[10713164]	1
GO:0010467	gene expression	biological process	TAS	41
GO:0006367	transcription initiation from RNA polymerase II promoter	biological process	TAS	20
GO:0005515	protein binding	molecular function	IPI[10395741]	563
GO:0042826	histone deacetylase binding	molecular function	IPI[11804585]	13
GO:0007179	transforming growth factor beta receptor signaling pathway	biological process	TAS	5
GO:0047485	protein N-terminus binding	molecular function	IPI[16893456]	12
GO:0072365	regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter	biological process	IMP[19955185]	1
GO:0016604	nuclear body	cellular component	IDA[16030140]	3
GO:0044281	small molecule metabolic process	biological process	TAS	117
GO:0006351	transcription, DNA-templated	biological process	TAS	103
GO:0017053	transcriptional repressor complex	cellular component	IDA[11804585]	5
GO:0044255	cellular lipid metabolic process	biological process	TAS	13
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	biological process	IDA[10097068]; IMP[12628926]; TAS	62

Gene related KEGG pathways (count: 1)

KEGG pathways by PBA (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04330	Notch signaling pathway	7

KEGG pathways by database search (count: 0)

Gene related BioCarta pathways (count: 4)

BioCarta pathways by PBA (count: 0)

BioCarta pathways by database search (count: 4)

ID	Name	No. of Genes in BDgene
pparaPathway	Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa(alpha)	12
egfr_smrtePathway	Map Kinase Inactivation of SMRT Corepressor	3
etsPathway	METS affect on Macrophage Differentiation	1
rarrxrPathway	Nuclear receptors coordinate the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription in carcinoma cells	2

Gene related interactors from protein-protein interactions data in HPRD (count: 59)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
NCOR2	NR4A1	NO	in vitro;in vivo	11559707
NCOR2	HDAC4	NO	in vitro	11804585
NCOR2	TBL1X	NO	in vitro;in vivo	10809664
NCOR2	SNW1	NO	in vitro;in vivo;yeast 2-hybrid	11509665 , 10713164
NCOR2	NFKBIA	NO	in vivo	12589049
NCOR2	NR1D1	YES	in vitro;yeast 2-hybrid	16219912 , 15604093
NCOR2	HDAC5	NO	in vitro;in vivo;yeast 2-hybrid	10869435
NCOR2	RARA	NO	in vitro;in vivo;yeast 2-hybrid	7566127 , 15604093
NCOR2	CIR1	NO	in vivo	11509665
NCOR2	POU2F1	NO	in vitro;in vivo	11134019
NCOR2	CBFA2T2	NO	in vitro;in vivo	12242670
NCOR2	RXRA	NO	in vitro;in vivo;yeast 2-hybrid	12665583 , 15604093
NCOR2	RARG	NO	in vitro;in vivo;yeast 2-hybrid	12665583 , 15604093
NCOR2	RXRG	NO	yeast 2-hybrid	15604093
NCOR2	ESR1	YES	in vivo	9702189
NCOR2	MYBL2	NO	in vitro;in vivo	11997503
NCOR2	STAT5A	NO	in vitro;in vivo;yeast 2-hybrid	11726519
NCOR2	NR1H2	NO	in vitro;yeast 2-hybrid	16219912 , 15604093
NCOR2	HDAC1	NO	in vivo	11739383
NCOR2	SPEN	NO	in vitro;in vivo;yeast 2-hybrid	11331609
NCOR2	ZBTB16	NO	in vitro;in vivo;yeast 2-hybrid	9256429 , 14982881
NCOR2	HDAC10	NO	in vivo	11739383
NCOR2	PPARA	NO	in vitro	11845213
NCOR2	SRF	NO	in vitro	10777532
NCOR2	ARNT	NO	in vivo	10395741
NCOR2	BCL6	NO	in vitro;in vivo	9765306 , 16147992
NCOR2	THRB	NO	in vitro	9751500
NCOR2	PPARD	YES	in vitro	11867749
NCOR2	AHR	YES	in vivo	10395741
NCOR2	RARB	NO	in vitro;in vivo;yeast 2-hybrid	12665583 , 15604093
NCOR2	HDAC7	NO	in vitro;in vivo;yeast 2-hybrid	10640276
NCOR2	FOS	NO	in vitro;yeast 2-hybrid	10777532
NCOR2	NCOA6	YES	yeast 2-hybrid	11158331
NCOR2	PML	NO	in vivo	11585900
NCOR2	SP1	NO	in vitro;in vivo	15878880
NCOR2	HDAC3	NO	in vitro	11804585 , 10944117 , 11509652
NCOR2	NR2F2	NO	in vitro	16219912
NCOR2	RBPJ	NO	in vivo;yeast 2-hybrid	11509665
NCOR2	NR3C1	YES	in vitro	12011091
NCOR2	DDX20	NO	in vitro	12007404
NCOR2	SAP30	NO	in vitro	9702189
NCOR2	NR2F1	NO	in vitro	16219912
NCOR2	AR	NO	in vitro;in vivo;yeast 2-hybrid	11923464 , 15062576
NCOR2	RUNX1T1	NO	in vitro;in vivo	11113190
NCOR2	YWHAE	YES	in vitro	15494311
NCOR2	RUNX1	YES	yeast 2-hybrid	16042694
NCOR2	SKIL	NO	yeast 2-hybrid	15231748
NCOR2	NFKB1	NO	in vitro	10777532
NCOR2	ESR2	NO	in vitro	12904255
NCOR2	C1D	NO	in vitro	9405624
NCOR2	CHUK	NO	in vitro	15494311
NCOR2	RELA	NO	in vitro;in vivo	10777532 , 12589049
NCOR2	NR1H4	NO	in vitro	16219912
NCOR2	NR1I2	YES	in vitro;in vivo;yeast 2-hybrid	16219912 , 12072427
NCOR2	NCOA3	NO	in vitro	9267036
NCOR2	PPARG	NO	in vitro;yeast 2-hybrid	16219912 , 15604093
NCOR2	STAT5B	NO	in vitro;yeast 2-hybrid	11726519
NCOR2	THRA	YES	in vivo;yeast 2-hybrid	7566127
NCOR2	MYOD1	NO	in vitro	10406466

Related other genetic factors

Gene related SNPs (count: 6)

Literature-origin SNPs (count: 4)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs2227277	chr12:124336870 - 124336870(1)	downstream_gene_variant; missense_variant; upstream_gene_variant	1(0/1/0)
rs3040832	chr12:124402550 - 124402550(1)	synonymous_variant	1(0/1/0)
rs2230944	chr12:124336867 - 124336867(1)	downstream_gene_variant; missense_variant; upstream_gene_variant	1(0/1/0)
rs2229840	chr12:124341916 - 124341916(1)	downstream_gene_variant; missense_variant; upstream_gene_variant	1(0/1/0)

LD-proxies (count: 2)

rs_ID	Literature-origin SNPs with LD	Location	Functional Annotation
rs8546		chr12:124324481 - 124324481(1)	3_prime_UTR_variant; downstream_gene_variant
rs12580372		chr12:124452057 - 124452057(1)	intron_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 1)

Variant Name	Variant Type	Location in Gene	No. of Studies (Positive/Negative/Trend)
NCOR2_GC34E20A	duplication		1 (0/1/0)

Gene related regions (count: 6)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
12q24.3	chr12:120300000-133275309	1 (1/0/0)
Chr 12	chr12:0-133275309	3 (0/3/0)
12q24	chr12:108600000-133275309	4 (1/1/2)
12q23-q24	chr12:95800000-133275309	3 (2/0/1)
12q24.31	chr12:120300000-125400000	1 (1/0/0)
12q	chr12:38200000-133851895	1 (1/0/0)

Overlap with schizophrenia (SZ) and major depressive disorder (MDD)

Gene relationship with SZ

Gene relationship with MDD

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Region: chr12:124324415..124567589 View in gBrowse