Human Gene NCOR2 (uc010tbb.2) Description and Page Index
  Description: Homo sapiens nuclear receptor corepressor 2 (NCOR2), transcript variant 1, mRNA.
RefSeq Summary (NM_006312): This gene encodes a nuclear receptor co-repressor that mediates transcriptional silencing of certain target genes. The encoded protein is a member of a family of thyroid hormone- and retinoic acid receptor-associated co-repressors. This protein acts as part of a multisubunit complex which includes histone deacetylases to modify chromatin structure that prevents basal transcriptional activity of target genes. Aberrant expression of this gene is associated with certain cancers. Alternate splicing results in multiple transcript variants encoding different isoforms.[provided by RefSeq, Apr 2011].
Transcript (Including UTRs)
   Position: hg19 chr12:124,808,957-125,052,010 Size: 243,054 Total Exon Count: 49 Strand: -
Coding Region
   Position: hg19 chr12:124,809,948-124,979,797 Size: 169,850 Coding Exon Count: 47 

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 (chr12:124,808,957-125,052,010)mRNA (may differ from genome)Protein (2514 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: C9JFD3_HUMAN
DESCRIPTION: SubName: Full=Nuclear receptor corepressor 2;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NCOR2
CDC HuGE Published Literature: NCOR2
Positive Disease Associations: Body Height , Cholesterol, HDL , Cognitive performance , Diabetic Nephropathies , HIV Infections|[X]Human immunodeficiency virus disease , Iron , Neoplasms , Socioeconomic Factors
Related Studies:
  1. Body Height
    , , . [PubMed 0]
  2. Body Height
    , , . [PubMed 0]
  3. Body Height
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           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: NCOR2
Diseases sorted by gene-association score: leukemia, acute promyelocytic, somatic (6), lymphoma, non-hodgkin (3), leukemia, acute myeloid (0)

-  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: 46.57 RPKM in Pituitary
Total median expression: 1097.15 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 -154.50321-0.481 Picture PostScript Text
3' UTR -419.80991-0.424 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

ModBase Predicted Comparative 3D Structure on C9JFD3
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001012 RNA polymerase II regulatory region DNA binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0016922 ligand-dependent nuclear receptor binding
GO:0035259 glucocorticoid receptor binding
GO:0042974 retinoic acid receptor binding
GO:0044877 macromolecular complex binding
GO:0046965 retinoid X receptor binding

Biological Process:
GO:0007595 lactation
GO:0010243 response to organonitrogen compound
GO:0032355 response to estradiol
GO:0044849 estrous cycle

Cellular Component:
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  AF113003 - Homo sapiens silencing mediator of retinoic acid and thyroid hormone receptor alpha mRNA, complete cds.
AF125672 - Homo sapiens silencing mediator of retinoic acid and thyroid hormone receptor extended isoform (SMRTE) mRNA, complete cds.
AY965853 - Homo sapiens SMRTE-tau mRNA, complete cds, alternatively spliced.
AB463148 - Synthetic construct DNA, clone: pF1KB0999, Homo sapiens NCOR2 gene for nuclear receptor co-repressor 2, without stop codon, in Flexi system.
AB209089 - Homo sapiens mRNA for nuclear receptor co-repressor 2 variant protein.
BC051312 - Homo sapiens nuclear receptor co-repressor 2, mRNA (cDNA clone IMAGE:5922788), **** WARNING: chimeric clone ****.
BC033087 - Homo sapiens nuclear receptor co-repressor 2, mRNA (cDNA clone IMAGE:5016291), **** WARNING: chimeric clone ****.
L32841 - Homo sapiens (clone tec53) mRNA.
X79269 - H.sapiens Tera-2 clone 13 embryonal carcinoma mRNA poly-A signal.
BC004326 - Homo sapiens, clone IMAGE:3629785, mRNA, partial cds.
U37146 - Human silencing mediator of retinoid and thyroid hormone action (SMRT) mRNA, complete cds.
JD253997 - Sequence 235021 from Patent EP1572962.
JD283743 - Sequence 264767 from Patent EP1572962.
JD490756 - Sequence 471780 from Patent EP1572962.
JD234281 - Sequence 215305 from Patent EP1572962.
JD190702 - Sequence 171726 from Patent EP1572962.
JD406307 - Sequence 387331 from Patent EP1572962.
JD415919 - Sequence 396943 from Patent EP1572962.
JD264223 - Sequence 245247 from Patent EP1572962.
JD275097 - Sequence 256121 from Patent EP1572962.
JD211771 - Sequence 192795 from Patent EP1572962.
JD057663 - Sequence 38687 from Patent EP1572962.
JD547347 - Sequence 528371 from Patent EP1572962.
S83390 - T3 receptor-associating cofactor-1 [human, fetal liver, mRNA, 2930 nt].
JD193992 - Sequence 175016 from Patent EP1572962.
JD406425 - Sequence 387449 from Patent EP1572962.
BC109239 - Homo sapiens cDNA clone IMAGE:40015228, **** WARNING: chimeric clone ****.
AK127788 - Homo sapiens cDNA FLJ45889 fis, clone OCBBF3022166.
BC020427 - Homo sapiens nuclear receptor co-repressor 2, mRNA (cDNA clone IMAGE:4179307).
U80750 - Homo sapiens CTG26 mRNA, partial cds.
MH507335 - Homo sapiens nuclear receptor corepressor 2 splice variant (NCOR2) mRNA, partial cds, alternatively spliced.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04330 - Notch signaling pathway

BioCarta from NCI Cancer Genome Anatomy Project
h_egfr_smrtePathway - Map Kinase Inactivation of SMRT Corepressor
h_carm-erPathway - CARM1 and Regulation of the Estrogen Receptor
h_etsPathway - METS affect on Macrophage Differentiation
h_pparaPathway - Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa(alpha)
h_rarrxrPathway - Nuclear receptors coordinate the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription in carcinoma cells

-  Other Names for This Gene
  Alternate Gene Symbols: C9JFD3, C9JFD3_HUMAN, NM_006312, NP_006303, uc021rga.1
UCSC ID: uc010tbb.2
RefSeq Accession: NM_006312
Protein: C9JFD3 CCDS: CCDS41857.2, CCDS41858.2, CCDS55892.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006312.5
exon count: 49CDS single in 3' UTR: no RNA size: 8857
ORF size: 7545CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 15086.50frame shift in genome: no % Coverage: 100.00
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.