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Aliases for SIN3A Gene

Aliases for SIN3A Gene

  • SIN3 Transcription Regulator Family Member A 2 3 5
  • Histone Deacetylase Complex Subunit 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
  • Paired Amphipathic Helix Protein Sin3a 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 Rett Syndrome. Among its related pathways are C-MYB transcription factor network and SMAD Signaling Network. 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 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 he 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).

Gene Wiki entry for SIN3A Gene

Additional gene information for SIN3A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SIN3A Gene

Genomics for SIN3A Gene

GeneHancer (GH) Regulatory Elements for SIN3A Gene

Promoters and enhancers for SIN3A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH15J075449 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 721.3 +2.5 2486 8.1 CLOCK MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SIN3A ENSG00000276744 MAN2C1 ENSG00000260274 SNUPN EDC3 CLK3 DNM1P34 LOC101929333 FBXO22
GH15J075447 Promoter 0.5 EPDnew 650.4 +8.4 8440 0.1 SIN3A ENSG00000276744 ENSG00000261714
GH15J074539 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE 76.1 +913.9 913882 4.1 HDGF PKNOX1 SMAD1 ARID4B SIN3A FEZF1 ZNF2 ZBTB7B IRF4 YY1 ARID3B SIN3A MAN2C1 ENSG00000260274 EDC3 PML UBL7-AS1 CLK3 LOC101929333 ISLR
GH15J075624 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE 74.8 -170.4 -170388 3.8 MLX DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC SSRP1 ZNF610 SNUPN ENSG00000260235 SIN3A MAN2C1 ENSG00000260274 EDC3 FBXO22 COMMD4 DNM1P35 TYRO3P
GH15J075366 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 78.8 +87.1 87087 3.8 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 MAN2C1 ENSG00000260274 SIN3A DNM1P35 EDC3 LOC441728 FBXO22 SNUPN CLK3 COMMD4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SIN3A on UCSC Golden Path with GeneCards custom track

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

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 StructureGene Density

RefSeq DNA sequence for SIN3A Gene

Proteins for SIN3A Gene

  • 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. Interacts with OGT (via TPRs 1-6); the interaction mediates transcriptional repression in parallel with histone deacetylase (By similarity). Interacts with BAZ2A, MXD3, MXD4, MBD2, DACH1, NCOR1, NR4A2, REST, RLIM, SAP30, SETDB1, SMYD2, and SUDS3. Interacts with PHF12 in a complex composed of HDAC1, PHF12 and SAP30. Interacts with TET1; the interaction recruits SIN3A to gene promoters. The large PER complex involved in the histone deacetylation is composed of at least HDAC1, PER2, SFPQ and SIN3A. 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). Found in a complex composed of at least SINHCAF, SIN3A, HDAC1, SAP30, RBBP4, OGT and TET1. Interacts with SINHCAF (By similarity).

    Three dimensional structures from OCA and Proteopedia for SIN3A Gene

neXtProt entry for SIN3A Gene

Post-translational modifications for SIN3A Gene

  • SUMO1 sumoylated by TOPORS. Probably desumoylated by SENP2.
  • Ubiquitination at isoforms=747, isoforms=727, and isoforms=343
  • Modification sites at PhosphoSitePlus

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

Suggested Antigen Peptide Sequences for SIN3A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot for SIN3A Gene

Function for SIN3A Gene

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 he 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).

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

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SIN3A

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 1
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SIN3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000118 histone deacetylase complex IBA --
GO:0000776 kinetochore IEA --
GO:0000785 chromatin IEA,IBA --
GO:0005634 nucleus ISS,IEA --
GO:0005654 nucleoplasm IDA,TAS --
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

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

No data available for SIGNOR curated interactions for SIN3A Gene

Drugs & Compounds for SIN3A Gene

No Compound Related Data Available

Transcripts for SIN3A Gene

Unigene Clusters for SIN3A Gene

SIN3 transcription regulator homolog A (yeast):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SIN3A

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

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

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 , mRNA Expression by UniProt/SwissProt 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 34 33
  • 99.74 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SIN3A 34
  • 95 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SIN3A 34 33
  • 93.43 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SIN3A 34 33
  • 93.11 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Sin3a 16 34 33
  • 90.91 (n)
rat
(Rattus norvegicus)
Mammalia Sin3a 33
  • 90.25 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SIN3A 34
  • 90 (a)
OneToOne
chicken
(Gallus gallus)
Aves SIN3A 34 33
  • 81.95 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SIN3A 34
  • 45 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sin3a 33
  • 74.08 (n)
Str.14936 33
African clawed frog
(Xenopus laevis)
Amphibia Sin3 33
zebrafish
(Danio rerio)
Actinopterygii sin3aa 34
  • 77 (a)
OneToMany
sin3ab 34
  • 75 (a)
OneToMany
wufb95g11 33
fruit fly
(Drosophila melanogaster)
Insecta Sin3A 34 33
  • 58.9 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007892 33
  • 58.26 (n)
worm
(Caenorhabditis elegans)
Secernentea sin-3 34
  • 13 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SIN3 36 34
  • 18 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3742 34
  • 39 (a)
OneToMany
Cin.4585 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4585 33
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
genes like me logo Genes that share paralogs with SIN3A: view

Variants for SIN3A Gene

Sequence variations from dbSNP and Humsavar for SIN3A Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs879255618 pathogenic, Witteveen-kolk syndrome 75,411,697(-) GGGGG/GGGGGG coding_sequence_variant, frameshift
rs879255619 pathogenic, Witteveen-kolk syndrome 75,410,282(-) TCTTTCT/TCT coding_sequence_variant, splice_acceptor_variant
rs879255620 pathogenic, Witteveen-kolk syndrome 75,400,135(-) AAA/AA coding_sequence_variant, frameshift
rs879255621 pathogenic, Witteveen-kolk syndrome 75,380,702(-) G/A coding_sequence_variant, stop_gained
rs886037847 pathogenic, Witteveen-kolk syndrome 75,389,717(-) TCTCTCTC/TCTCTC coding_sequence_variant, frameshift

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

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

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

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

Disorder Aliases PubMed IDs
witteveen-kolk syndrome
  • witkos
rett syndrome
  • rtt
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

Additional Disease Information for SIN3A

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

No data available for UniProtKB/Swiss-Prot and 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 22 58
  2. 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 44 58
  3. 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 44 58
  4. Genetic identification of a network of factors that functionally interact with the nucleosome remodeling ATPase ISWI. (PMID: 18535655) Burgio G … Corona DF (PLoS genetics 2008) 3 22 58
  5. TOPORS functions as a SUMO-1 E3 ligase for chromatin-modifying proteins. (PMID: 17803295) Pungaliya P … Rubin EH (Journal of proteome research 2007) 3 4 58

Products for SIN3A Gene

Sources for SIN3A Gene

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