SIN3A Gene (Protein Coding)

SIN3 Transcription Regulator Family Member A

GC15M075369
GIFtS:
47
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] See more...

Aliases for SIN3A Gene

Aliases for SIN3A Gene

  • SIN3 Transcription Regulator Family Member A 2 3 5
  • Histone Deacetylase Complex Subunit Sin3a 3 4
  • Paired Amphipathic Helix Protein Sin3a 3 4
  • Transcriptional Corepressor Sin3a 3 4
  • SIN3 Homolog A, Transcription Regulator (Yeast) 2
  • SIN3 Transcription Regulator Homolog A (Yeast) 2
  • SIN3 Homolog A, Transcription Regulator 3
  • Transcriptional Co-Repressor Sin3A 3
  • Transcriptional Regulator, SIN3A 3
  • WITKOS 3

External Ids for SIN3A Gene

Previous GeneCards Identifiers for SIN3A Gene

  • GC15M071541
  • GC15M068754
  • GC15M073239
  • GC15M073379
  • GC15M073450
  • GC15M075661
  • GC15M052420

Summaries for SIN3A Gene

Entrez Gene Summary for SIN3A Gene

  • 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]

GeneCards Summary for SIN3A Gene

SIN3A (SIN3 Transcription Regulator Family Member A) is a Protein Coding gene. Diseases associated with SIN3A include Witteveen-Kolk Syndrome and Mental Retardation, Autosomal Dominant 13. Among its related pathways are Nur77 Signaling in T-Cell and Macrophage Differentiation and Growth Inhibition by METS. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and transcription factor binding. An important paralog of this gene is SIN3B.

UniProtKB/Swiss-Prot Summary for SIN3A Gene

  • 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. Acts cooperatively with OGT to repress transcription in parallel with histone deacetylation. Involved in the control of the circadian rhythms. Required for the transcriptional repression of circadian target genes, such as PER1, mediated by the large PER complex through histone deacetylation. Cooperates with FOXK1 to regulate cell cycle progression probably by repressing cell cycle inhibitor genes expression (By similarity). Required for cortical neuron differentiation and callosal axon elongation (By similarity).

Gene Wiki entry for SIN3A Gene

Additional gene information for SIN3A Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SIN3A Gene

Genomics for SIN3A Gene

GeneHancer (GH) Regulatory Elements for SIN3A Gene

Promoters and enhancers for SIN3A Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SIN3A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SIN3A gene promoter:
  • HFH-1
  • Ik-2
  • NRF-2
  • Sox9

Genomic Locations for SIN3A Gene

Genomic Locations for SIN3A Gene
chr15:75,369,379-75,455,842
(GRCh38/hg38)
Size:
86,464 bases
Orientation:
Minus strand
chr15:75,661,720-75,748,183
(GRCh37/hg19)
Size:
86,464 bases
Orientation:
Minus strand

Genomic View for SIN3A Gene

Genes around SIN3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SIN3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SIN3A Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SIN3A Gene

Proteins for SIN3A Gene

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  • Protein details for SIN3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96ST3-SIN3A_HUMAN
    Recommended name:
    Paired amphipathic helix protein Sin3a
    Protein Accession:
    Q96ST3
    Secondary Accessions:
    • B2RNS5
    • Q8N8N4
    • Q8NC83
    • Q8WV18
    • Q96L98
    • Q9UFQ1

    Protein attributes for SIN3A Gene

    Size:
    1273 amino acids
    Molecular mass:
    145175 Da
    Quaternary structure:
    • Interacts with ARID4B, BRMS1L, HCFC1, HDAC1, HDAC2, MXI1, SAP30L, SAP130, SFPQ and TOPORS (PubMed:11259580, PubMed:11897684, PubMed:12670868, PubMed:12724404, PubMed:15451426, PubMed:16820529, PubMed:17803295). Interacts with OGT (via TPRs 1-6); the interaction mediates transcriptional repression in parallel with histone deacetylase (PubMed:12150998). Interacts with BAZ2A, MXD1, MXD3, MXD4, MBD2, DACH1, NCOR1, NR4A2, REST, RLIM, SAP30, SETDB1, SMYD2, and SUDS3 (PubMed:14525983). Interacts with PHF12 in a complex composed of HDAC1, PHF12 and SAP30 (By similarity). Interacts with TET1; the interaction recruits SIN3A to gene promoters (PubMed:21490601). The large PER complex involved in the histone deacetylation is composed of at least HDAC1, PER2, SFPQ and SIN3A (By similarity). Interacts with KLF11 (By similarity). Interacts with PPHLN1 (PubMed:17963697). Found in a complex with YY1, GON4L and HDAC1 (By similarity). Interacts (via PAH2) with FOXK1 (By similarity). Interacts with FOXK2 (By similarity). Found in a complex composed of at least SINHCAF, SIN3A, HDAC1, SAP30, RBBP4, OGT and TET1. Interacts with SINHCAF (By similarity). Interacts with SPHK2 (PubMed:19729656).

    Three dimensional structures from OCA and Proteopedia for SIN3A Gene

neXtProt entry for SIN3A Gene

Protein Expression for SIN3A Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SIN3A Gene

  • SUMO1 sumoylated by TOPORS. Probably desumoylated by SENP2.
  • Ubiquitination at Lys343, Lys727, and Lys747
  • Modification sites at PhosphoSitePlus

Other Protein References for SIN3A Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for SIN3A
  • Boster Bio Antibodies for SIN3A

No data available for DME Specific Peptides for SIN3A Gene

Domains & Families for SIN3A Gene

Gene Families for SIN3A Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for SIN3A Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SIN3A Gene

GenScript: Design optimal peptide antigens:
  • Transcriptional corepressor Sin3a (SIN3A_HUMAN)
genes like me logo Genes that share domains with SIN3A: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SIN3A Gene

Function for SIN3A Gene

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  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
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Molecular function for SIN3A Gene

UniProtKB/Swiss-Prot 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. Acts cooperatively with OGT to repress transcription in parallel with histone deacetylation. Involved in the control of the circadian rhythms. Required for the transcriptional repression of circadian target genes, such as PER1, mediated by the large PER complex through histone deacetylation. Cooperates with FOXK1 to regulate cell cycle progression probably by repressing cell cycle inhibitor genes expression (By similarity). Required for cortical neuron differentiation and callosal axon elongation (By similarity).

Phenotypes From GWAS Catalog for SIN3A Gene

Gene Ontology (GO) - Molecular Function for SIN3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000976 transcription regulatory region sequence-specific DNA binding ISS --
GO:0001102 RNA polymerase II activating transcription factor binding IPI 22783022
GO:0001103 RNA polymerase II repressing transcription factor binding IEA --
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA --
genes like me logo Genes that share ontologies with SIN3A: view
genes like me logo Genes that share phenotypes with SIN3A: view

Human Phenotype Ontology for SIN3A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SIN3A Gene

MGI Knock Outs for SIN3A:

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SIN3A Gene

Localization for SIN3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SIN3A Gene

Nucleus. Nucleus, nucleolus. Note=Recruited to the nucleolus by SAP30L.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SIN3A gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 0
cytoskeleton 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SIN3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000776 kinetochore IEA --
GO:0000785 chromatin IBA 21873635
GO:0005634 nucleus IEA,ISS --
GO:0005654 nucleoplasm TAS,IDA --
GO:0005667 transcription factor complex IEA --
genes like me logo Genes that share ontologies with SIN3A: view

Pathways & Interactions for SIN3A Gene

genes like me logo Genes that share pathways with SIN3A: view

Pathways by source for SIN3A Gene

8 Qiagen pathways for SIN3A Gene
  • DNA Methylation and Transcriptional Repression
  • Estrogen Pathway
  • Glucocorticoid Receptor Signaling
  • Huntington's Disease Pathway
  • Macrophage Differentiation and Growth Inhibition by METS
1 Cell Signaling Technology pathway for SIN3A Gene
1 GeneTex pathway for SIN3A Gene

SIGNOR curated interactions for SIN3A Gene

Inactivates:
Is activated by:

Gene Ontology (GO) - Biological Process for SIN3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IMP 22783022
GO:0001701 in utero embryonic development IEA --
GO:0002218 activation of innate immune response IMP 22783022
GO:0002230 positive regulation of defense response to virus by host IMP 22783022
GO:0002244 hematopoietic progenitor cell differentiation IEA --
genes like me logo Genes that share ontologies with SIN3A: view

Drugs & Compounds for SIN3A Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for SIN3A Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for SIN3A Gene

(3) REFSEQ mRNAs :
(19) Additional mRNA sequences :
(219) Selected AceView cDNA sequences:
(15) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SIN3A Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b · 10c · 10d · 10e ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^
SP1: - - - - - - -
SP2: - - - - -
SP3: - - - -
SP4: - -
SP5: -
SP6: - - - - - - - -
SP7: - - - - - -
SP8: - - - - - -
SP9: - -
SP10: - - - -
SP11:

ExUns: 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25a · 25b ^ 26a · 26b ^ 27
SP1: -
SP2: -
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for SIN3A Gene

GeneLoc Exon Structure for
SIN3A
ECgene alternative splicing isoforms for
SIN3A

Expression for SIN3A Gene

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  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SIN3A Gene

mRNA expression in normal human tissues for SIN3A Gene
mRNA expression by GTEx for SIN3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SIN3A Gene

This gene is overexpressed in Lymph node (15.3) and Peripheral blood mononuclear cells (13.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SIN3A Gene



Protein tissue co-expression partners for SIN3A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SIN3A Gene:

SIN3A

SOURCE GeneReport for Unigene cluster for SIN3A Gene:

Hs.513039

mRNA Expression by UniProt/SwissProt for SIN3A Gene:

Q96ST3-SIN3A_HUMAN
Tissue specificity: Expressed in the developing brain, with highest levels of expression detected in the ventricular zone of various cortical regions.

Evidence on tissue expression from TISSUES for SIN3A Gene

  • Nervous system(4.7)
  • Lung(4.3)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with SIN3A: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SIN3A Gene

Orthologs for SIN3A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SIN3A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia SIN3A 33 32
  • 99.74 (n)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia SIN3A 33
  • 95 (a)
 OneToOne
cow
(Bos Taurus)
 Mammalia SIN3A 33 32
  • 93.43 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia SIN3A 33 32
  • 93.11 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Sin3a 17 33 32
  • 90.91 (n)
rat
(Rattus norvegicus)
 Mammalia Sin3a 32
  • 90.25 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia SIN3A 33
  • 90 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves SIN3A 33 32
  • 81.95 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia SIN3A 33
  • 45 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia sin3a 32
  • 74.08 (n)
Str.14936 32
African clawed frog
(Xenopus laevis)
 Amphibia Sin3 32
zebrafish
(Danio rerio)
 Actinopterygii sin3aa 33
  • 77 (a)
 OneToMany
sin3ab 33
  • 75 (a)
 OneToMany
wufb95g11 32
fruit fly
(Drosophila melanogaster)
 Insecta Sin3A 33 32
  • 58.9 (n)
 OneToMany
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP007892 32
  • 58.26 (n)
worm
(Caenorhabditis elegans)
 Secernentea sin-3 33
  • 13 (a)
 OneToMany
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes SIN3 35 33
  • 18 (a)
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.3742 33
  • 39 (a)
 OneToMany
Cin.4585 32
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.4585 32
Species where no ortholog for SIN3A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SIN3A Gene

ENSEMBL:
Gene Tree for SIN3A (if available)
TreeFam:
Gene Tree for SIN3A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SIN3A: view image

Paralogs for SIN3A Gene

Paralogs for SIN3A Gene

(1) SIMAP similar genes for SIN3A Gene using alignment to 9 proteins:

  • SIN3A_HUMAN
  • H3BMA2_HUMAN
  • H3BNA0_HUMAN
  • H3BNZ3_HUMAN
  • H3BP90_HUMAN
  • H3BQ76_HUMAN
  • H3BQ88_HUMAN
  • H3BQL7_HUMAN
  • H3BT34_HUMAN

Pseudogenes.org Pseudogenes for SIN3A Gene

genes like me logo Genes that share paralogs with SIN3A: view

Variants for SIN3A Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for SIN3A Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs1135401768 pathogenic, Witteveen-kolk syndrome 75,384,340(-) TGTGTGT/TGTGT coding_sequence_variant, frameshift
rs1555443682 likely-pathogenic, Inborn genetic diseases 75,392,614(-) GGG/G coding_sequence_variant, frameshift
rs1555444885 pathogenic, Inborn genetic diseases 75,400,810(-) G/A coding_sequence_variant, stop_gained
rs1567368243 pathogenic, Witteveen-kolk syndrome 75,411,652(-) T/TT coding_sequence_variant, frameshift
rs879255618 pathogenic, Witteveen-kolk syndrome 75,411,697(-) GGGGG/GGGGGG coding_sequence_variant, frameshift

Structural Variations from Database of Genomic Variants (DGV) for SIN3A Gene

Variant ID Type Subtype PubMed ID
dgv1243n106 CNV deletion 24896259
dgv2621n100 CNV gain 25217958
esv2749894 CNV deletion 23290073
esv2749895 CNV deletion 23290073
esv3636926 CNV gain 21293372
nsv1116463 OTHER inversion 24896259
nsv1615 CNV insertion 18451855
nsv474716 CNV novel sequence insertion 20440878
nsv525265 CNV gain 19592680
nsv827389 CNV gain 20364138
nsv976952 CNV duplication 23825009
nsv977737 CNV duplication 23825009

Variation tolerance for SIN3A Gene

Residual Variation Intolerance Score: 1.44% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.02; 37.25% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SIN3A Gene

Human Gene Mutation Database (HGMD)
SIN3A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SIN3A

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SIN3A Gene

Disorders for SIN3A Gene

MalaCards: The human disease database

(4) MalaCards diseases for SIN3A Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
witteveen-kolk syndrome
  • witkos
mental retardation, autosomal dominant 13
  • mrd13
rett syndrome
  • rts
chromosome 15q24 deletion syndrome
  • 15q24 microdeletion syndrome
- elite association - COSMIC cancer census association via MalaCards
Search SIN3A in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SIN3A_HUMAN
  • Witteveen-Kolk syndrome (WITKOS) [MIM:613406]: An autosomal dominant syndrome characterized by global developmental delay, mild to severe intellectual disability, and facial dysmorphism. Additional features include short stature, microcephaly, joint hypermotility, and small hands and feet with digital abnormalities. Brain imaging shows dilated ventricles, thin corpus callosum and, in some cases, dysgyria or polymicrogyria. {ECO:0000269 PubMed:27399968, ECO:0000269 PubMed:30267900}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SIN3A

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SIN3A: view

No data available for Genatlas for SIN3A Gene

Publications for SIN3A Gene

  1. PSF is a novel corepressor that mediates its effect through Sin3A and the DNA binding domain of nuclear hormone receptors. (PMID: 11259580) Mathur M … Samuels HH (Molecular and cellular biology 2001) 3 4 23 56
  2. Haploinsufficiency of MeCP2-interacting transcriptional co-repressor SIN3A causes mild intellectual disability by affecting the development of cortical integrity. (PMID: 27399968) Witteveen JS … Kolk SM (Nature genetics 2016) 3 4 56
  3. GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease. (PMID: 21658281) Aouizerat BE … Tseng ZH (BMC cardiovascular disorders 2011) 3 43 56
  4. A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci. (PMID: 20189936) Okada Y … Kamatani N (Human molecular genetics 2010) 3 43 56
  5. Regulation of histone acetylation in the nucleus by sphingosine-1-phosphate. (PMID: 19729656) Hait NC … Spiegel S (Science (New York, N.Y.) 2009) 3 4 56

ExternalLinks

View latest publications for SIN3A gene in Mastermind

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