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SIN3B SIN3 transcription regulator family member B [ Homo sapiens (human) ]

Gene ID: 23309, updated on 11-Apr-2024

Summary

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Official Symbol
SIN3Bprovided by HGNC
Official Full Name
SIN3 transcription regulator family member Bprovided by HGNC
Primary source
HGNC:HGNC:19354
See related
Ensembl:ENSG00000127511 MIM:607777; AllianceGenome:HGNC:19354
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Predicted to enable transcription corepressor activity. Predicted to be involved in histone deacetylation; negative regulation of transcription by RNA polymerase II; and striated muscle tissue development. Predicted to be located in nucleus. Predicted to be part of Sin3 complex. Predicted to be active in chromatin. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 19.2), endometrium (RPKM 17.1) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
19p13.11
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (16829398..16880349)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (16964243..17015192)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (16940209..16991160)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:16772303-16773111 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:16790368-16790868 Neighboring gene transmembrane protein 38A Neighboring gene NACHT and WD repeat domain containing 1 Neighboring gene uncharacterized LOC124904648 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:16928291-16928487 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr19:16936141-16936818 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:16939935-16940436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14248 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:16947461-16947962 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:16957617-16958116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:16957115-16957616 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14249 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:16996894-16997394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17000485-17001084 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14252 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10316 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10317 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10318 Neighboring gene RNA, 7SL, cytoplasmic 835, pseudogene Neighboring gene C3 and PZP like alpha-2-macroglobulin domain containing 8 Neighboring gene F2R like thrombin or trypsin receptor 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex. Wan MSM, et al. Nat Commun, 2023 May 3. PMID 37137925, Free PMC Article
  2. Haploinsufficiency of the Sin3/HDAC corepressor complex member SIN3B causes a syndromic intellectual disability/autism spectrum disorder. Latypova X, et al. Am J Hum Genet, 2021 May 6. PMID 33811806, Free PMC Article
  3. The HDAC-Associated Sin3B Protein Represses DREAM Complex Targets and Cooperates with APC/C to Promote Quiescence. Bainor AJ, et al. Cell Rep, 2018 Dec 4. PMID 30517867, Free PMC Article
  4. pH might play a role in regulating the function of paired amphipathic helices domains of human Sin3B by altering structure and thermodynamic stability. Hasan T, et al. Biochemistry (Mosc), 2015 Apr. PMID 25869359
  5. Establishment of Novel Protein Interaction Assays between Sin3 and REST Using Surface Plasmon Resonance and Time-Resolved Fluorescence Energy Transfer. Harada M, et al. Int J Mol Sci, 2021 Feb 26. PMID 33652591, Free PMC Article

See all (110) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex.
    Title: Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex.
  2. Haploinsufficiency of the Sin3/HDAC corepressor complex member SIN3B causes a syndromic intellectual disability/autism spectrum disorder.
    Title: Haploinsufficiency of the Sin3/HDAC corepressor complex member SIN3B causes a syndromic intellectual disability/autism spectrum disorder.
  3. Differential Complex Formation via Paralogs in the Human Sin3 Protein Interaction Network.
    Title: Differential Complex Formation via Paralogs in the Human Sin3 Protein Interaction Network.
  4. Establishment of Novel Protein Interaction Assays between Sin3 and REST Using Surface Plasmon Resonance and Time-Resolved Fluorescence Energy Transfer.
    Title: Establishment of Novel Protein Interaction Assays between Sin3 and REST Using Surface Plasmon Resonance and Time-Resolved Fluorescence Energy Transfer.
  5. These studies identify Sin3B as a transcriptional corepressor associated with the DREAM complex in quiescence.
    Title: The HDAC-Associated Sin3B Protein Represses DREAM Complex Targets and Cooperates with APC/C to Promote Quiescence.
  6. High mRNA expression of SIN3A/low mRNA expression of SIN3B correlates with longer relapse free survival specifically in patients with triple negative breast cancer.
    Title: SIN3A and SIN3B differentially regulate breast cancer metastasis.
  7. Low SIN3B expression is associated with Prostate Cancer Progression.
    Title: Chromatin-Associated Protein SIN3B Prevents Prostate Cancer Progression by Inducing Senescence.
  8. these results suggest that stress-induced Sin3B activation is p53-dependent and is essential for p53-mediated repression of its selective target genes.
    Title: Stress-mediated Sin3B activation leads to negative regulation of subset of p53 target genes.
  9. The study suggests that the difference in the conformation of native state structure or structural flexibility of the paired amphi pathic helices (PAH) domains of Sin3B might be responsible for interacting with specific binding partners.
    Title: pH might play a role in regulating the function of paired amphipathic helices domains of human Sin3B by altering structure and thermodynamic stability.
  10. A conserved Myc region (amino acids 186-203) is required for the interaction with Sin3 proteins. Histone deacetylase 1 is recruited to Myc-Sin3b complexes, and its deacetylase activity is required for the effects of Sin3b on Myc.
    Title: Sin3b interacts with Myc and decreases Myc levels.
Submit: New GeneRIF Correction See all GeneRIFs (21)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0700

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription corepressor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in negative regulation of cell migration NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of Sin3-type complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in X chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in XY body IEA
Inferred from Electronic Annotation
more info
  
located_in Y chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in autosome IEA
Inferred from Electronic Annotation
more info
  
part_of chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
paired amphipathic helix protein Sin3b
Names
SIN3 homolog B, transcriptional regulator
SIN3 transcription regulator homolog B
histone deacetylase complex subunit Sin3b
transcriptional corepressor Sin3b

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001297595.2 → NP_001284524.1  paired amphipathic helix protein Sin3b isoform 2

    See identical proteins and their annotated locations for NP_001284524.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. It encodes isoform 2, which lacks an internal segment and is shorter, compared to isoform 1.
    Source sequence(s)
    AB014600, AY706204, HY055983
    Consensus CDS
    CCDS74308.1
    UniProtKB/Swiss-Prot
    O75182
    Related
    ENSP00000248054.4, ENST00000248054.10
    Conserved Domains (3) summary
    pfam02671
    Location:60 → 104
    PAH; Paired amphipathic helix repeat
    pfam08295
    Location:395 → 489
    Sin3_corepress; Sin3 family co-repressor
    pfam16879
    Location:743 → 1043
    Sin3a_C; C-terminal domain of Sin3a protein

  2. NM_001297597.2 → NP_001284526.1  paired amphipathic helix protein Sin3b isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. It encodes isoform 3, which is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AB014600, AK295618, AY706204, DC332740
    Consensus CDS
    CCDS77254.1
    UniProtKB/TrEMBL
    B7Z392, M0QYC5
    Related
    ENSP00000469740.1, ENST00000595541.1
    Conserved Domains (2) summary
    pfam08295
    Location:12 → 79
    Sin3_corepress; Sin3 family co-repressor
    pfam16879
    Location:333 → 633
    Sin3a_C; C-terminal domain of Sin3a protein

  3. NM_015260.4 → NP_056075.1  paired amphipathic helix protein Sin3b isoform 1

    See identical proteins and their annotated locations for NP_056075.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AY706204, HY055983
    Consensus CDS
    CCDS32946.1
    UniProtKB/Swiss-Prot
    O75182, Q2NL91, Q68GC2, Q6P4B8, Q8TB34, Q9BSC8
    Related
    ENSP00000369131.1, ENST00000379803.5
    Conserved Domains (3) summary
    pfam02671
    Location:60 → 104
    PAH; Paired amphipathic helix repeat
    pfam08295
    Location:395 → 521
    Sin3_corepress; Sin3 family co-repressor
    pfam16879
    Location:775 → 1075
    Sin3a_C; C-terminal domain of Sin3a protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    16829398..16880349
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006722704.2 → XP_006722767.1  paired amphipathic helix protein Sin3b isoform X1

    UniProtKB/TrEMBL
    B7Z392
    Conserved Domains (1) summary
    pfam16879
    Location:258 → 558
    Sin3a_C; C-terminal domain of Sin3a protein

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    16964243..17015192
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054320368.1 → XP_054176343.1  paired amphipathic helix protein Sin3b isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75182.2 GenPept UniProtKB/Swiss-Prot:O75182

Gene LinkOut

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