Human Gene SIN3A (uc002bai.3) Description and Page Index
  Description: Homo sapiens SIN3 transcription regulator homolog A (yeast) (SIN3A), transcript variant 2, mRNA.
RefSeq Summary (NM_015477): The protein encoded by this gene is a transcriptional regulatory protein. It contains paired amphipathic helix (PAH) domains, which are important for protein-protein interactions and may mediate repression by the Mad-Max complex. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr15:75,661,720-75,743,926 Size: 82,207 Total Exon Count: 21 Strand: -
Coding Region
   Position: hg19 chr15:75,664,320-75,722,716 Size: 58,397 Coding Exon Count: 20 

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 (chr15:75,661,720-75,743,926)mRNA (may differ from genome)Protein (1273 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Paired amphipathic helix protein Sin3a; AltName: Full=Histone deacetylase complex subunit Sin3a; AltName: Full=Transcriptional corepressor Sin3a;
FUNCTION: Acts as a transcriptional repressor. Corepressor for REST. Interacts with MXI1 to repress MYC responsive genes and antagonize MYC oncogenic activities. Also interacts with MXD1-MAX heterodimers to repress transcription by tethering SIN3A to DNA (By similarity). Acts cooperatively with OGT to repress transcription in parallel with histone deacetylation.
SUBUNIT: Interacts with BAZ2A, MXD3, MXD4, MBD2, NCOR1, NR4A2, REST, RLIM, SAP30, SETDB1 and SMYD2. Interacts with PHF12 in a complex composed of HDAC1, PHF12 and SAP30 (By similarity). Interacts with ARID4B, BRMS1L, DACH1, HCFC1, HDAC1, HDAC2, MXI1, SAP30L, SAP130, SFPQ, SUDS3 and TOPORS. Interacts with TET1; the interaction recruits SIN3A to gene promoters. Interacts with OGT (via TPRs 1-6); the interaction mediates transcriptional repression in parallel with histone deacetylase.
INTERACTION: P51610:HCFC1; NbExp=6; IntAct=EBI-347218, EBI-396176; Q92769:HDAC2; NbExp=3; IntAct=EBI-347218, EBI-301821; Q9UQ80:PA2G4; NbExp=4; IntAct=EBI-347218, EBI-924893; P23246:SFPQ; NbExp=2; IntAct=EBI-347218, EBI-355453; P04637:TP53; NbExp=2; IntAct=EBI-347218, EBI-366083;
SUBCELLULAR LOCATION: Nucleus. Nucleus, nucleolus. Note=Recruited to the nucleolus by SAP30L.
PTM: SUMO1 sumoylated by TOPORS. Probably desumoylated by SENP2.
SIMILARITY: Contains 3 PAH (paired amphipathic helix) domains.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SIN3A
CDC HuGE Published Literature: SIN3A
Positive Disease Associations: Death, Sudden, Cardiac , height
Related Studies:
  1. Death, Sudden, Cardiac
    Bradley E Aouizerat et al. BMC cardiovascular disorders 2012, GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease., BMC cardiovascular disorders. [PubMed 21658281]
    We demonstrate 11 gene associations for sudden cardiac arrest due to ventricular tachycardia/ventricular fibrillation in patients with coronary artery disease. Validation studies in independent cohorts and functional studies are required to confirm these associations.
  2. height
    Okada ,et al. Hum Mol Genet 2010, A genome-wide association study in 19,633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci , Human molecular genetics 2010 . [PubMed 20189936]

-  MalaCards Disease Associations
  MalaCards Gene Search: SIN3A
Diseases sorted by gene-association score: witteveen-kolk syndrome* (1025), chromosome 15q24 deletion syndrome (7), rett syndrome (6)
* = Manually curated disease association

-  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: 8.62 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 230.73 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 -121.40259-0.469 Picture PostScript Text
3' UTR -764.612600-0.294 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
IPR013194 - HDAC_interact
IPR003822 - PAH

Pfam Domains:
PF02671 - Paired amphipathic helix repeat
PF08295 - Sin3 family co-repressor
PF16879 - C-terminal domain of Sin3a protein

SCOP Domains:
47762 - PAH2 domain

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

- Model

ModBase Predicted Comparative 3D Structure on Q96ST3
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:0000976 transcription regulatory region sequence-specific DNA binding
GO:0001102 RNA polymerase II activating transcription factor binding
GO:0001103 RNA polymerase II repressing transcription factor binding
GO:0001106 RNA polymerase II transcription corepressor activity
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003714 transcription corepressor activity
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0033558 protein deacetylase activity
GO:0044877 macromolecular complex binding
GO:0004407 histone deacetylase activity

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001701 in utero embryonic development
GO:0002218 activation of innate immune response
GO:0002230 positive regulation of defense response to virus by host
GO:0002244 hematopoietic progenitor cell differentiation
GO:0006260 DNA replication
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006476 protein deacetylation
GO:0007568 aging
GO:0010243 response to organonitrogen compound
GO:0010817 regulation of hormone levels
GO:0010971 positive regulation of G2/M transition of mitotic cell cycle
GO:0016575 histone deacetylation
GO:0019216 regulation of lipid metabolic process
GO:0031937 positive regulation of chromatin silencing
GO:0034613 cellular protein localization
GO:0042754 negative regulation of circadian rhythm
GO:0043066 negative regulation of apoptotic process
GO:0043619 regulation of transcription from RNA polymerase II promoter in response to oxidative stress
GO:0045652 regulation of megakaryocyte differentiation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048511 rhythmic process
GO:0051595 response to methylglyoxal
GO:0071333 cellular response to glucose stimulus
GO:1900181 negative regulation of protein localization to nucleus
GO:1901675 negative regulation of histone H3-K27 acetylation
GO:1903351 cellular response to dopamine
GO:2000678 negative regulation of transcription regulatory region DNA binding

Cellular Component:
GO:0000776 kinetochore
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription factor complex
GO:0005730 nucleolus
GO:0016580 Sin3 complex
GO:0017053 transcriptional repressor complex
GO:0032991 macromolecular complex

-  Descriptions from all associated GenBank mRNAs
  AK074800 - Homo sapiens cDNA FLJ90319 fis, clone NT2RP2001538, highly similar to Paired amphipathic helix protein Sin3a.
BC052275 - Homo sapiens SIN3 homolog A, transcription regulator (yeast), mRNA (cDNA clone IMAGE:4565171).
BC030563 - Homo sapiens SIN3 homolog A, transcription regulator (yeast), mRNA (cDNA clone IMAGE:4471026), with apparent retained intron.
BC041047 - Homo sapiens SIN3 homolog A, transcription regulator (yeast), mRNA (cDNA clone IMAGE:4905696), with apparent retained intron.
BC018973 - Homo sapiens SIN3 homolog A, transcription regulator (yeast), mRNA (cDNA clone IMAGE:3604034), partial cds.
AL832463 - Homo sapiens mRNA; cDNA DKFZp313F111 (from clone DKFZp313F111).
AL117513 - Homo sapiens mRNA; cDNA DKFZp434K2235 (from clone DKFZp434K2235); partial cds.
JD182938 - Sequence 163962 from Patent EP1572962.
JD168747 - Sequence 149771 from Patent EP1572962.
JD465103 - Sequence 446127 from Patent EP1572962.
AF418569 - Homo sapiens MSIN3A mRNA, complete cds.
AK074903 - Homo sapiens cDNA FLJ90422 fis, clone NT2RP3000378, weakly similar to PAIRED AMPHIPATHIC HELIX PROTEIN.
BX649162 - Homo sapiens mRNA; cDNA DKFZp686N1529 (from clone DKFZp686N1529).
JD081274 - Sequence 62298 from Patent EP1572962.
JD468315 - Sequence 449339 from Patent EP1572962.
JD433238 - Sequence 414262 from Patent EP1572962.
JD525992 - Sequence 507016 from Patent EP1572962.
JD559719 - Sequence 540743 from Patent EP1572962.
JD070928 - Sequence 51952 from Patent EP1572962.
JD217870 - Sequence 198894 from Patent EP1572962.
JD039386 - Sequence 20410 from Patent EP1572962.
JD283965 - Sequence 264989 from Patent EP1572962.
JD549115 - Sequence 530139 from Patent EP1572962.
BC137098 - Homo sapiens SIN3 homolog A, transcription regulator (yeast), mRNA (cDNA clone MGC:168718 IMAGE:9021095), complete cds.
BC137099 - Homo sapiens SIN3 homolog A, transcription regulator (yeast), mRNA (cDNA clone MGC:168719 IMAGE:9021096), complete cds.
AB527438 - Synthetic construct DNA, clone: pF1KE1029, Homo sapiens SIN3A gene for SIN3 homolog A, transcription regulator, without stop codon, in Flexi system.
AK027559 - Homo sapiens cDNA FLJ14653 fis, clone NT2RP2002252, highly similar to Mus musculus (clone pVZmSin3A9) mSin3A9 mRNA.
AK096477 - Homo sapiens cDNA FLJ39158 fis, clone OCBBF2002086, highly similar to Transcriptional regulator, SIN3A.
AY044430 - Homo sapiens transcriptional co-repressor Sin3A mRNA, partial cds.
JD027318 - Sequence 8342 from Patent EP1572962.
JD031436 - Sequence 12460 from Patent EP1572962.
BC066364 - Homo sapiens SIN3 homolog A, transcription regulator (yeast), mRNA (cDNA clone IMAGE:6171525), with apparent retained intron.
KJ902394 - Synthetic construct Homo sapiens clone ccsbBroadEn_11788 SIN3A gene, encodes complete protein.
KT336104 - Homo sapiens SIN3A/RUNX1 fusion transcript mRNA sequence.
LF208509 - JP 2014500723-A/16012: Polycomb-Associated Non-Coding RNAs.
JD408988 - Sequence 390012 from Patent EP1572962.
JD100627 - Sequence 81651 from Patent EP1572962.
MA444086 - JP 2018138019-A/16012: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa05016 - Huntington's disease

BioCarta from NCI Cancer Genome Anatomy Project
h_etsPathway - METS affect on Macrophage Differentiation

Reactome (by CSHL, EBI, and GO)

Protein Q96ST3 (Reactome details) participates in the following event(s):

R-HSA-992696 p53, SIN3A and MYB form a complex
R-NUL-992753 p53 and Sin3a bind c-Myb
R-HSA-8935732 RUNX1 binds SIN3A,(SIN3B) co-repressor
R-HSA-400183 PPARA:RXRA heterodimer recruits corepressors
R-HSA-400143 Fatty acid ligands activate PPARA
R-HSA-427409 Nucleolar Remodelling Complex (NoRC) binds intergenic region of rDNA
R-HSA-8935730 RUNX1:CBFB, SIN3A(SIN3B), PRMT6 and HDAC1 bind the ITGA2B promoter
R-HSA-8936599 RUNX1:CBFB, SIN3A(SIN3B), PRMT6 and HDAC1 bind the GP1BA promoter
R-HSA-8936989 RUNX1:CBFB, SIN3A(SIN3B), PRMT6 and HDAC1 bind the THBS1 gene promoter
R-HSA-8937118 RUNX1:CBFB, SIN3A(SIN3B), PRMT6 and HDAC1 bind the MIR27A gene promoter
R-HSA-8936584 PRMT6 arginine methylates H3K4me2-Nucleosome at the ITGA2B gene promoter
R-HSA-8936608 PRMT6 arginine methylates H3K4me2-Nucleosome at the GP1BA gene promoter
R-HSA-8937022 PRMT6 arginine methylates H3K4me2-Nucleosome at the THBS1 gene promoter
R-HSA-8937113 PRMT6 arginine methylates H3K4me2-Nucleosome at the MIR27A gene promoter
R-HSA-5227490 NoRC:HDAC:DNMT methylates cytosine of the rRNA genes
R-HSA-983231 Factors involved in megakaryocyte development and platelet production
R-HSA-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-HSA-400206 Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
R-HSA-109582 Hemostasis
R-HSA-427413 NoRC negatively regulates rRNA expression
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-556833 Metabolism of lipids
R-HSA-5250941 Negative epigenetic regulation of rRNA expression
R-HSA-212436 Generic Transcription Pathway
R-HSA-1430728 Metabolism
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B2RNS5, NM_015477, NP_056292, Q8N8N4, Q8NC83, Q8WV18, Q96L98, Q96ST3, Q9UFQ1, SIN3A_HUMAN
UCSC ID: uc002bai.3
RefSeq Accession: NM_015477
Protein: Q96ST3 (aka SIN3A_HUMAN or SN3A_HUMAN)
CCDS: CCDS10279.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_015477.2
exon count: 21CDS single in 3' UTR: no RNA size: 6697
ORF size: 3822CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 7833.00frame shift in genome: no % Coverage: 99.76
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.