Human Gene SAP30 (ENST00000296504.4_4) from GENCODE V47lift37
  Description: Sin3A associated protein 30 (from RefSeq NM_003864.4)
Gencode Transcript: ENST00000296504.4_4
Gencode Gene: ENSG00000164105.4_7
Transcript (Including UTRs)
   Position: hg19 chr4:174,292,105-174,298,683 Size: 6,579 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr4:174,292,334-174,298,478 Size: 6,145 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:174,292,105-174,298,683)mRNA (may differ from genome)Protein (220 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SAP30_HUMAN
DESCRIPTION: RecName: Full=Histone deacetylase complex subunit SAP30; AltName: Full=30 kDa Sin3-associated polypeptide; AltName: Full=Sin3 corepressor complex subunit SAP30; AltName: Full=Sin3-associated polypeptide p30;
FUNCTION: Involved in the functional recruitment of the Sin3- histone deacetylase complex (HDAC) to a specific subset of N-CoR corepressor complexes. Capable of transcription repression by N- CoR. Active in deacetylating core histone octamers (when in a complex) but inactive in deacetylating nucleosomal histones.
SUBUNIT: Interacts with SIN3A, SIN3B, HDAC2 and NCOR1. Interacts with SAMS1 (By similarity). Component of the histone deacetylase complex that includes at least SIN3A, HDAC1 and HDAC2. Interacts with HDAC1 and HCFC1.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Expressed in all tissues tested with highest levels in pancreas, ovary, PBL, spleen and thymus; lowest levels in brain, placenta, lung and kidney.
SIMILARITY: Belongs to the SAP30 family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 26.14 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 480.41 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 -102.60229-0.448 Picture PostScript Text
3' UTR -35.30205-0.172 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
IPR024145 - His_deAcase_SAP30/SAP30L
IPR025718 - SAP30_Sin3-bd
IPR025717 - SAP30_zn-finger

Pfam Domains:
PF13866 - SAP30 zinc-finger
PF13867 - Sin3 binding region of histone deacetylase complex subunit SAP30

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2KDP - NMR MuPIT


ModBase Predicted Comparative 3D Structure on O75446
FrontTopSide
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003714 transcription corepressor activity
GO:0004407 histone deacetylase activity
GO:0005515 protein binding
GO:0046872 metal ion binding

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:0035914 skeletal muscle cell differentiation

Cellular Component:
GO:0000118 histone deacetylase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  AF055993 - Homo sapiens mSin3A associated polypeptide p30 mRNA, complete cds.
BC016757 - Homo sapiens Sin3A-associated protein, 30kDa, mRNA (cDNA clone MGC:13685 IMAGE:4074154), complete cds.
JD253437 - Sequence 234461 from Patent EP1572962.
JD210792 - Sequence 191816 from Patent EP1572962.
JD470172 - Sequence 451196 from Patent EP1572962.
JD064263 - Sequence 45287 from Patent EP1572962.
DQ892828 - Synthetic construct clone IMAGE:100005458; FLH190081.01X; RZPDo839E0475D Sin3A-associated protein, 30kDa (SAP30) gene, encodes complete protein.
JD499852 - Sequence 480876 from Patent EP1572962.
JD314725 - Sequence 295749 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O75446 (Reactome details) participates in the following event(s):

R-HSA-427409 Nucleolar Remodelling Complex (NoRC) binds intergenic region of rDNA
R-HSA-5227490 NoRC:HDAC:DNMT methylates cytosine of the rRNA genes
R-HSA-3769447 HDAC1/2 containing-complexes deacetylate histones
R-HSA-427413 NoRC negatively regulates rRNA expression
R-HSA-5250941 Negative epigenetic regulation of rRNA expression
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-74160 Gene expression (Transcription)
R-HSA-3214815 HDACs deacetylate histones
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-4839726 Chromatin organization

-  Other Names for This Gene
  Alternate Gene Symbols: D3DP38, ENST00000296504.1, ENST00000296504.2, ENST00000296504.3, NM_003864, O75446, SAP30 , SAP30_HUMAN, uc317lui.1, uc317lui.2
UCSC ID: ENST00000296504.4_4
RefSeq Accession: NM_003864.4
Protein: O75446 (aka SAP30_HUMAN)

-  Gene Model Information
  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.