Human Gene SAP130 (uc002tpp.1)
  Description: Sin3A-associated protein, 130kDa
RefSeq Summary (NM_024545): SAP130 is a subunit of the histone deacetylase (see HDAC1; MIM 601241)-dependent SIN3A (MIM 607776) corepressor complex (Fleischer et al., 2003 [PubMed 12724404]).[supplied by OMIM, Mar 2008].
Transcript (Including UTRs)
   Position: hg18 chr2:128,415,266-128,501,337 Size: 86,072 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg18 chr2:128,416,050-128,501,207 Size: 85,158 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated at UCSC: 2009-03-03

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:128,415,266-128,501,337)mRNA (may differ from genome)Protein (1048 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDMGIOMIM
PubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SP130_HUMAN
DESCRIPTION: RecName: Full=Histone deacetylase complex subunit SAP130; AltName: Full=130 kDa Sin3-associated polypeptide; AltName: Full=Sin3-associated polypeptide p130;
FUNCTION: Acts as a transcriptional repressor. May function in the assembly and/or enzymatic activity of the mSin3A corepressor complex or in mediating interactions between the complex and other regulatory complexes.
SUBUNIT: Component of a mSin3A corepressor complex that contains SIN3A, SAP130, SUDS3/SAP45, ARID4B/SAP180, HDAC1 and HDAC2. Interacts (released by dead or dying cells) with CLEC4E (By similarity).
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Expressed in various cancer cell ines.
DOMAIN: The N-terminus may interact with a transcriptional coactivator.
DOMAIN: The C-terminus may interact with HDAC-dependent and HDAC- independent corepressors.
PTM: Acetylated (Probable).
PTM: Sumoylated with SUMO1.
SIMILARITY: Belongs to the SAP130 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

-  Microarray Expression Data
 
Expression ratio colors:

GNF Expression Atlas 2 Data from U133A and GNF1H Chips

      
      
      
     
    
     
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Affymetrix All Exon Microarrays

           
Ratios

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -73.30130-0.564 Picture PostScript Text
3' UTR -245.45784-0.313 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
IPR024137 - His_deAcase_cplx_SAP130

ModBase Predicted Comparative 3D Structure on Q9H0E3
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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 orthologGenome BrowserNo orthologNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
MGI Ensembl  SGD
Protein Sequence Protein Sequence  Protein Sequence
Alignment Alignment  Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  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

Cellular Component:
GO:0005634 nucleus
GO:0016607 nuclear speck
GO:0070822 Sin3-type complex


-  Descriptions from all associated GenBank mRNAs
  AL136833 - Homo sapiens mRNA; cDNA DKFZp434A112 (from clone DKFZp434A112).
AK022823 - Homo sapiens cDNA FLJ12761 fis, clone NT2RP2001378, weakly similar to MUCIN 2 PRECURSOR.
BC017453 - Homo sapiens Sin3A-associated protein, 130kDa, mRNA (cDNA clone IMAGE:3906788), partial cds.
AK092234 - Homo sapiens cDNA FLJ34915 fis, clone NT2RP7001283, highly similar to Homo sapiens mSin3A-associated protein 130 (SAP130), mRNA.
AX747421 - Sequence 946 from Patent EP1308459.
BC117255 - Homo sapiens Sin3A-associated protein, 130kDa, mRNA (cDNA clone MGC:150864 IMAGE:40125806), complete cds.
BC143898 - Homo sapiens Sin3A-associated protein, 130kDa, mRNA (cDNA clone MGC:177433 IMAGE:9052416), complete cds.
AY220791 - Homo sapiens SIN3A-associated protein 130 mRNA, complete cds.
AK315185 - Homo sapiens cDNA, FLJ96166.
AB385164 - Synthetic construct DNA, clone: pF1KB6005, Homo sapiens SAP130 gene for histone deacetylase complex subunit SAP130, complete cds, without stop codon, in Flexi system.
AM392550 - Synthetic construct Homo sapiens clone IMAGE:100002307 for hypothetical protein (SAP130 gene).
AM393228 - Synthetic construct Homo sapiens clone IMAGE:100001821 for hypothetical protein (SAP130 gene).
AK055979 - Homo sapiens cDNA FLJ31417 fis, clone NT2NE2000327, weakly similar to GLUCOAMYLASE S1/S2 PRECURSOR (EC 3.2.1.3).
KJ903176 - Synthetic construct Homo sapiens clone ccsbBroadEn_12570 SAP130 gene, encodes complete protein.
JD365790 - Sequence 346814 from Patent EP1572962.
JD504074 - Sequence 485098 from Patent EP1572962.
JD521376 - Sequence 502400 from Patent EP1572962.
JD094411 - Sequence 75435 from Patent EP1572962.
JD312488 - Sequence 293512 from Patent EP1572962.
CU675986 - Synthetic construct Homo sapiens gateway clone IMAGE:100017454 5' read SAP130 mRNA.
JD542202 - Sequence 523226 from Patent EP1572962.
JD465767 - Sequence 446791 from Patent EP1572962.
JD211216 - Sequence 192240 from Patent EP1572962.

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

Protein Q9H0E3 (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-3301237 KAT2 complexes acetylate histone H3
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-3214847 HATs acetylate histones
R-HSA-74160 Gene expression (Transcription)
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-4839726 Chromatin organization

-  Other Names for This Gene
  Alternate Gene Symbols: NM_024545, NP_078821, Q4ZFV4, Q53T46, Q8WVW4, Q9H0E3, Q9H9G8, SP130_HUMAN
UCSC ID: uc002tpp.1
RefSeq Accession: NM_024545
Protein: Q9H0E3 (aka SP130_HUMAN)
CCDS: CCDS2153.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_024545.2
exon count: 20CDS single in 3' UTR: no RNA size: 4082
ORF size: 3147CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6278.50frame shift in genome: no % Coverage: 99.49
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.