Human Gene NCOR1 (uc002gpo.3) Description and Page Index
  Description: Homo sapiens nuclear receptor corepressor 1 (NCOR1), transcript variant 1, mRNA.
RefSeq Summary (NM_006311): This gene encodes a protein that mediates ligand-independent transcription repression of thyroid-hormone and retinoic-acid receptors by promoting chromatin condensation and preventing access of the transcription machinery. It is part of a complex which also includes histone deacetylases and transcriptional regulators similar to the yeast protein Sin3p. This gene is located between the Charcot-Marie-Tooth and Smith-Magenis syndrome critical regions on chromosome 17. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 17 and 20.[provided by RefSeq, Jun 2010].
Transcript (Including UTRs)
   Position: hg19 chr17:15,933,408-16,118,874 Size: 185,467 Total Exon Count: 46 Strand: -
Coding Region
   Position: hg19 chr17:15,935,610-16,097,883 Size: 162,274 Coding Exon Count: 45 

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 (chr17:15,933,408-16,118,874)mRNA (may differ from genome)Protein (2440 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: NCOR1_HUMAN
DESCRIPTION: RecName: Full=Nuclear receptor corepressor 1; Short=N-CoR; Short=N-CoR1;
FUNCTION: Mediates transcriptional repression by certain nuclear receptors. Part of a complex which promotes histone deacetylation and the formation of repressive chromatin structures which may impede the access of basal transcription factors.
SUBUNIT: Interacts with C1D, SIAH2, HDAC7, SAP30, SIN3A and SIN3B (By similarity). Forms a large corepressor complex that contains. SIN3A/B and histone deacetylases HDAC1 and HDAC2. This complex associates with the thyroid (TR) and the retinoid acid receptors (RAR) in the absence of ligand. Interacts directly with RARA; the interaction is faciliated with RARA trimethylation. Interacts with DACH1. Component of the N-Cor repressor complex, at least composed of NCOR1, NCOR2, HDAC3, TBL1X, TBL1XR1, CORO2A and GPS2. Interacts with TRIM28 and KDM3A. Interacts with ZBTB33; the interaction serves to recruit the N-CoR complex to promoter regions containing methylated CpG dinucleotides. Interacts with HDAC9 (via its catalytic domain). Interacts with CBFA2T3 and HEXIM1. Interacts (via the RRFD1 domain) with BAZ1A (via its N-terminal); the interaction corepresses a number of NCOR1-regulated genes.
INTERACTION: Q9UI36:DACH1; NbExp=2; IntAct=EBI-347233, EBI-347111; O15379:HDAC3; NbExp=2; IntAct=EBI-347233, EBI-607682; P10276:RARA; NbExp=3; IntAct=EBI-347233, EBI-413374; Q13263:TRIM28; NbExp=4; IntAct=EBI-347233, EBI-78139;
SUBCELLULAR LOCATION: Nucleus (By similarity).
DOMAIN: The N-terminal region contains three independent domains that are capable of mediating transcriptional repression (RD1, RD2 and RD3).
DOMAIN: The C-terminal region contains two separate nuclear receptor-interacting domains (ID1 and ID2), each of which contains a conserved sequence referred to as the CORNR box. This motif is necessary and sufficient for binding to unligated nuclear hormone receptors, while sequences flanking the CORNR box determine the precise nuclear hormone receptor specificity (By similarity).
PTM: Ubiquitinated; mediated by SIAH2 and leading to its subsequent proteasomal degradation (By similarity).
SIMILARITY: Belongs to the N-CoR nuclear receptor corepressors family.
SIMILARITY: Contains 2 SANT domains.
SEQUENCE CAUTION: Sequence=BAA82999.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NCOR1
CDC HuGE Published Literature: NCOR1

-  MalaCards Disease Associations
  MalaCards Gene Search: NCOR1
Diseases sorted by gene-association score: leukemia, acute promyelocytic, somatic (7), rett syndrome (6), huntington disease (3), leukemia, acute myeloid (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 14.55 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 459.41 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -120.21269-0.447 Picture PostScript Text
3' UTR -559.152202-0.254 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
IPR009057 - Homeodomain-like
IPR001005 - SANT/Myb
IPR017884 - SANT_dom

Pfam Domains:
PF00249 - Myb-like DNA-binding domain
PF15784 - G-protein pathway suppressor 2-interacting domain

SCOP Domains:
46689 - Homeodomain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2EQR
- NMR MuPIT

3H52
- X-ray MuPIT

3KMZ
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
3N00 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O75376
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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001102 RNA polymerase II activating transcription factor binding
GO:0003677 DNA binding
GO:0003714 transcription corepressor activity
GO:0005515 protein binding
GO:0016922 ligand-dependent nuclear receptor binding
GO:0035257 nuclear hormone receptor binding
GO:0042826 histone deacetylase binding
GO:0044212 transcription regulatory region DNA binding
GO:0046966 thyroid hormone receptor binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007623 circadian rhythm
GO:0019216 regulation of lipid metabolic process
GO:0046329 negative regulation of JNK cascade
GO:0051225 spindle assembly
GO:0072362 regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter
GO:0072368 regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter
GO:1903799 negative regulation of production of miRNAs involved in gene silencing by miRNA
GO:2000191 regulation of fatty acid transport

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0005876 spindle microtubule
GO:0016020 membrane
GO:0017053 transcriptional repressor complex
GO:0000118 histone deacetylase complex
GO:0016580 Sin3 complex


-  Descriptions from all associated GenBank mRNAs
  BC167431 - Homo sapiens nuclear receptor co-repressor 1, mRNA (cDNA clone MGC:166905 IMAGE:8860107), complete cds.
AF087856 - Homo sapiens nuclear receptor co-repressor mRNA, complete cds.
AB028970 - Homo sapiens KIAA1047 mRNA for KIAA1047 protein.
AB019524 - Homo sapiens mRNA for nuclear receptor co-repressor, partial cds.
AF044209 - Homo sapiens nuclear receptor co-repressor N-CoR mRNA, complete cds.
BC172437 - Synthetic construct Homo sapiens clone IMAGE:100069131, MGC:199142 nuclear receptor co-repressor 1 (NCOR1) mRNA, encodes complete protein.
AB385422 - Synthetic construct DNA, clone: pF1KA1047, Homo sapiens NCOR1 gene for nuclear receptor corepressor 1, complete cds, without stop codon, in Flexi system.
AB028450 - Homo sapiens mRNA for nuclear receptor co-repressor isoform 1, partial cds.
AK024136 - Homo sapiens cDNA FLJ14074 fis, clone HEMBB1001869.
LF211498 - JP 2014500723-A/19001: Polycomb-Associated Non-Coding RNAs.
AF303584 - Homo sapiens NCOR isoform d mRNA, complete cds.
AF303585 - Homo sapiens NCOR isoform c mRNA, complete cds.
AL137641 - Homo sapiens mRNA; cDNA DKFZp434M075 (from clone DKFZp434M075).
JD165058 - Sequence 146082 from Patent EP1572962.
AK310405 - Homo sapiens cDNA, FLJ17447.
LF380481 - JP 2014500723-A/187984: Polycomb-Associated Non-Coding RNAs.
AK295893 - Homo sapiens cDNA FLJ52302 complete cds, highly similar to Nuclear receptor corepressor 1.
LF380480 - JP 2014500723-A/187983: Polycomb-Associated Non-Coding RNAs.
JD205105 - Sequence 186129 from Patent EP1572962.
JD533522 - Sequence 514546 from Patent EP1572962.
LF380479 - JP 2014500723-A/187982: Polycomb-Associated Non-Coding RNAs.
AB028451 - Homo sapiens mRNA for nuclear receptor co-repressor isoform 2, partial cds.
AK302746 - Homo sapiens cDNA FLJ50924 partial cds, highly similar to Nuclear receptor corepressor 1.
MA447075 - JP 2018138019-A/19001: Polycomb-Associated Non-Coding RNAs.
MA616058 - JP 2018138019-A/187984: Polycomb-Associated Non-Coding RNAs.
MA616057 - JP 2018138019-A/187983: Polycomb-Associated Non-Coding RNAs.
MA616056 - JP 2018138019-A/187982: Polycomb-Associated Non-Coding RNAs.
AF303586 - Homo sapiens NCOR isoform b mRNA, complete cds.
BC050594 - Homo sapiens nuclear receptor co-repressor 1, mRNA (cDNA clone IMAGE:6024800), partial cds.
AK307614 - Homo sapiens cDNA, FLJ97562.
BC035748 - Homo sapiens nuclear receptor co-repressor 1, mRNA (cDNA clone IMAGE:5749816), with apparent retained intron.
BC026028 - Homo sapiens nuclear receptor co-repressor 1, mRNA (cDNA clone IMAGE:3836580), partial cds.
BC058511 - Homo sapiens nuclear receptor co-repressor 1, mRNA (cDNA clone IMAGE:5190073), partial cds.
BC142648 - Homo sapiens nuclear receptor co-repressor 1, mRNA (cDNA clone IMAGE:40147982), partial cds.
BC068996 - Homo sapiens nuclear receptor co-repressor 1, mRNA (cDNA clone IMAGE:5474358), partial cds.
BC056862 - Homo sapiens nuclear receptor co-repressor 1, mRNA (cDNA clone IMAGE:3904576), partial cds.
BC107772 - Homo sapiens nuclear receptor co-repressor 1, mRNA (cDNA clone IMAGE:6451988), complete cds.
JD276390 - Sequence 257414 from Patent EP1572962.
JD309658 - Sequence 290682 from Patent EP1572962.
JD542125 - Sequence 523149 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_vdrPathway - Control of Gene Expression by Vitamin D Receptor
h_pparaPathway - Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa(alpha)

Reactome (by CSHL, EBI, and GO)

Protein O75376 (Reactome details) participates in the following event(s):

R-HSA-381290 PPARG:RXRA heterodimer binds to PPARG corepressors
R-HSA-1368069 NR1D1 (REV-ERBA) binds heme, the ARNTL gene, and recruits corepressors.
R-HSA-5663245 NR1D1 (REV-ERBA) binds heme, the NPAS2 gene, and recruits corepressors
R-HSA-5663252 NR1D1 (REV-ERBA) binds heme, the ELOVL3 gene, and recruits corepressors
R-HSA-5663258 NR1D1 (REV-ERBA) binds heme, the PPARGC1A gene, and recruits corepressors
R-HSA-5663265 NR1D1 (REV-ERBA) binds heme, the NR1D1 gene, and recruits corepressors
R-HSA-5663271 NR1D1 (REV-ERBA) binds heme, the CLOCK gene, and recruits corepressors
R-HSA-381309 PPARG:RXRA heterodimer binds to fatty acid-like ligands
R-HSA-173481 SKI/SKIL binds SMAD complex, suppressing TGF-beta signaling
R-HSA-2186747 Ubiquitination of SKI/SKIL by RNF111/SMURF2
R-NUL-2186755 Ubiquitination of SKI/SKIL by Rnf111
R-HSA-400183 PPARA:RXRA heterodimer recruits corepressors
R-HSA-400143 Fatty acid ligands activate PPARA
R-HSA-1253325 ERBB4s80 binds TAB2:NCOR1 complex
R-HSA-8954182 ERBB4s80:TAB2:NCOR1 complex binds S100B gene promoter
R-HSA-8954185 ERBB4s80:TAB2:NCOR1 complex binds GFAP gene promoter
R-HSA-1253319 ERBB4s80:TAB2:NCOR1 complex translocates to the nucleus
R-NUL-2186736 Rnf111 binds SKI/SKIL in complex with SMAD2/3:SMAD4 upon TGF-beta stimulation
R-HSA-2186741 SMAD2/3 activation induces binding of RNF111/SMURF2 to SKI/SKIL
R-HSA-1912388 NICD1 displaces co-repressor complex from RBPJ (CSL)
R-HSA-2220982 NICD1 PEST domain mutants displace co-repressor complex from RBPJ (CSL)
R-NUL-2064264 NICD1 displaces NCOR co-repressor complex from CSL
R-HSA-3777129 HDAC3 containing complexes deacetylate histone
R-HSA-381340 Transcriptional regulation of white adipocyte differentiation
R-HSA-400253 Circadian Clock
R-HSA-1368071 NR1D1 (REV-ERBA) represses gene expression
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-2173795 Downregulation of SMAD2/3:SMAD4 transcriptional activity
R-HSA-400206 Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
R-HSA-1266738 Developmental Biology
R-HSA-5619507 Activation of HOX genes during differentiation
R-HSA-1251985 Nuclear signaling by ERBB4
R-HSA-2122947 NOTCH1 Intracellular Domain Regulates Transcription
R-HSA-2644606 Constitutive Signaling by NOTCH1 PEST Domain Mutants
R-HSA-2894862 Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants
R-HSA-2173793 Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer
R-HSA-556833 Metabolism of lipids
R-HSA-1236394 Signaling by ERBB4
R-HSA-1980143 Signaling by NOTCH1
R-HSA-2644602 Signaling by NOTCH1 PEST Domain Mutants in Cancer
R-HSA-2894858 Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer
R-HSA-3214815 HDACs deacetylate histones
R-HSA-170834 Signaling by TGF-beta Receptor Complex
R-HSA-212436 Generic Transcription Pathway
R-HSA-1430728 Metabolism
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-157118 Signaling by NOTCH
R-HSA-2644603 Signaling by NOTCH1 in Cancer
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-9006936 Signaling by TGF-beta family members
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-162582 Signal Transduction
R-HSA-5663202 Diseases of signal transduction
R-HSA-4839726 Chromatin organization
R-HSA-74160 Gene expression (Transcription)
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: B3DLF8, KIAA1047, NCOR1_HUMAN, NM_006311, NP_006302, O75376, Q9UPV5, Q9UQ18
UCSC ID: uc002gpo.3
RefSeq Accession: NM_006311
Protein: O75376 (aka NCOR1_HUMAN or NCR1_HUMAN)
CCDS: CCDS11175.1, CCDS54095.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006311.3
exon count: 46CDS single in 3' UTR: no RNA size: 9809
ORF size: 7323CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 14453.00frame shift in genome: no % Coverage: 99.85
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.