Human Gene SIN3B (ENST00000379803.5) from GENCODE V44
  Description: Homo sapiens SIN3 transcription regulator family member B (SIN3B), transcript variant 1, mRNA. (from RefSeq NM_015260)
Gencode Transcript: ENST00000379803.5
Gencode Gene: ENSG00000127511.10
Transcript (Including UTRs)
   Position: hg38 chr19:16,829,407-16,880,353 Size: 50,947 Total Exon Count: 20 Strand: +
Coding Region
   Position: hg38 chr19:16,829,421-16,878,727 Size: 49,307 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:16,829,407-16,880,353)mRNA (may differ from genome)Protein (1162 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SIN3B_HUMAN
DESCRIPTION: RecName: Full=Paired amphipathic helix protein Sin3b; AltName: Full=Histone deacetylase complex subunit Sin3b; AltName: Full=Transcriptional corepressor Sin3b;
FUNCTION: Acts as a transcriptional repressor. Interacts with MXI1 to repress MYC responsive genes and antagonize MYC oncogenic activities. Interacts with MAD-MAX heterodimers by binding to MAD. The heterodimer then represses transcription by tethering SIN3B to DNA. Also forms a complex with FOXK1 which represses transcription (By similarity).
SUBUNIT: Interacts with FOXK1/MNF, MXI, MAD, NCOR1 and SAP30. Interaction with SDS3 enhances the interaction with HDAC1 to form a complex. Interacts with MAD3, MAD4, MAEL, REST and SETDB1 (By similarity). Interacts with RNF220 (By similarity). Interacts with HCFC1.
SUBCELLULAR LOCATION: Nucleus (By similarity).
PTM: Ubiquitinated by RNF220 that leads to proteasomal degradation (By similarity).
SIMILARITY: Contains 3 PAH (paired amphipathic helix) domains.
SEQUENCE CAUTION: Sequence=BAA31675.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SIN3B
Diseases sorted by gene-association score: cranial nerve malignant neoplasm (8), olfactory nerve neoplasm (6)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 32.62 RPKM in Testis
Total median expression: 815.36 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
3' UTR -655.701626-0.403 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

ModBase Predicted Comparative 3D Structure on O75182
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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
Genome BrowserNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGI     
Protein Sequence     
Alignment     

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001106 RNA polymerase II transcription corepressor activity
GO:0003682 chromatin binding
GO:0003714 transcription corepressor activity
GO:0005515 protein binding
GO:0004407 histone deacetylase activity

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0016575 histone deacetylation
GO:0019216 regulation of lipid metabolic process
GO:0045892 negative regulation of transcription, DNA-templated

Cellular Component:
GO:0000805 X chromosome
GO:0000806 Y chromosome
GO:0001741 XY body
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0016580 Sin3 complex
GO:0030849 autosome


-  Descriptions from all associated GenBank mRNAs
  AB014600 - Homo sapiens KIAA0700 mRNA for KIAA0700 protein.
BC063531 - Homo sapiens SIN3 homolog B, transcription regulator (yeast), mRNA (cDNA clone IMAGE:4417458), complete cds.
AY706204 - Homo sapiens SIN3B long isoform (SIN3B) mRNA, complete cds, alternatively spliced.
BC110821 - Homo sapiens SIN3 homolog B, transcription regulator (yeast), mRNA (cDNA clone IMAGE:5498101), complete cds.
AB463259 - Synthetic construct DNA, clone: pF1KA0700, Homo sapiens SIN3B gene for SIN3 homolog B, transcription regulator, without stop codon, in Flexi system.
BC172412 - Synthetic construct Homo sapiens clone IMAGE:100069106, MGC:199117 SIN3 homolog B, transcription regulator (yeast) (SIN3B) mRNA, encodes complete protein.
BC025026 - Homo sapiens SIN3 homolog B, transcription regulator (yeast), mRNA (cDNA clone IMAGE:3923074), partial cds.
JD216933 - Sequence 197957 from Patent EP1572962.
JD464555 - Sequence 445579 from Patent EP1572962.
JD062211 - Sequence 43235 from Patent EP1572962.
JD099384 - Sequence 80408 from Patent EP1572962.
JD332142 - Sequence 313166 from Patent EP1572962.
JD205219 - Sequence 186243 from Patent EP1572962.
AK001633 - Homo sapiens cDNA FLJ10771 fis, clone NT2RP4000210, highly similar to Homo sapiens mRNA for KIAA0700 protein.
AK295618 - Homo sapiens cDNA FLJ59305 complete cds, highly similar to Paired amphipathic helix protein Sin3b.
BC005113 - Homo sapiens SIN3 homolog B, transcription regulator (yeast), mRNA (cDNA clone IMAGE:4040380), partial cds.
AK311023 - Homo sapiens cDNA, FLJ18065.
JD099233 - Sequence 80257 from Patent EP1572962.
JD395576 - Sequence 376600 from Patent EP1572962.
JD529825 - Sequence 510849 from Patent EP1572962.
JD281902 - Sequence 262926 from Patent EP1572962.
JD411667 - Sequence 392691 from Patent EP1572962.
JD322524 - Sequence 303548 from Patent EP1572962.
JD485779 - Sequence 466803 from Patent EP1572962.
JD085024 - Sequence 66048 from Patent EP1572962.
JD037139 - Sequence 18163 from Patent EP1572962.
JD063739 - Sequence 44763 from Patent EP1572962.
JD123031 - Sequence 104055 from Patent EP1572962.
JD380345 - Sequence 361369 from Patent EP1572962.
JD123641 - Sequence 104665 from Patent EP1572962.
JD227957 - Sequence 208981 from Patent EP1572962.
JD130785 - Sequence 111809 from Patent EP1572962.
JD188915 - Sequence 169939 from Patent EP1572962.
JD362113 - Sequence 343137 from Patent EP1572962.
JD368572 - Sequence 349596 from Patent EP1572962.
JD056000 - Sequence 37024 from Patent EP1572962.
JD298181 - Sequence 279205 from Patent EP1572962.
JD235625 - Sequence 216649 from Patent EP1572962.
JD282491 - Sequence 263515 from Patent EP1572962.
JD267936 - Sequence 248960 from Patent EP1572962.
JD195680 - Sequence 176704 from Patent EP1572962.
JD558080 - Sequence 539104 from Patent EP1572962.
JD520255 - Sequence 501279 from Patent EP1572962.
JD512447 - Sequence 493471 from Patent EP1572962.
JD187236 - Sequence 168260 from Patent EP1572962.
JD443197 - Sequence 424221 from Patent EP1572962.
JD335896 - Sequence 316920 from Patent EP1572962.
JD291528 - Sequence 272552 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_etsPathway - METS affect on Macrophage Differentiation

Reactome (by CSHL, EBI, and GO)

Protein O75182 (Reactome details) participates in the following event(s):

R-HSA-400183 PPARA:RXRA heterodimer recruits corepressors
R-HSA-400143 Fatty acid ligands activate PPARA
R-HSA-400206 Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism
R-HSA-8935732 RUNX1 binds SIN3A,(SIN3B) co-repressor
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-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-HSA-427413 NoRC negatively regulates rRNA expression
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-5250941 Negative epigenetic regulation of rRNA expression
R-HSA-212436 Generic Transcription Pathway
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: ENST00000379803.1, ENST00000379803.2, ENST00000379803.3, ENST00000379803.4, KIAA0700, NM_015260, O75182, Q2NL91, Q68GC2, Q6P4B8, Q8TB34, Q9BSC8, SIN3B_HUMAN, uc002ney.1, uc002ney.2, uc002ney.3
UCSC ID: ENST00000379803.5
RefSeq Accession: NM_015260
Protein: O75182 (aka SIN3B_HUMAN or SN3B_HUMAN)
CCDS: CCDS32946.1, CCDS74308.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.