Human Gene SAP130 (ENST00000259235.7) from GENCODE V44
  Description: Homo sapiens Sin3A associated protein 130 (SAP130), transcript variant 2, mRNA. (from RefSeq NM_024545)
RefSeq Summary (NM_001145928): 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].
Gencode Transcript: ENST00000259235.7
Gencode Gene: ENSG00000136715.19
Transcript (Including UTRs)
   Position: hg38 chr2:127,941,218-128,027,293 Size: 86,076 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg38 chr2:127,942,006-128,027,163 Size: 85,158 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:127,941,218-128,027,293)mRNA (may differ from genome)Protein (1048 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid 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
 

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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


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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 40.40 RPKM in Testis
Total median expression: 400.92 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 -71.30130-0.548 Picture PostScript Text
3' UTR -240.20788-0.305 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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-  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 BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  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.
JD504074 - Sequence 485098 from Patent EP1572962.
JD094411 - Sequence 75435 from Patent EP1572962.
JD365790 - Sequence 346814 from Patent EP1572962.
JD521376 - Sequence 502400 from Patent EP1572962.
JD312488 - Sequence 293512 from Patent EP1572962.
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.
KJ903176 - Synthetic construct Homo sapiens clone ccsbBroadEn_12570 SAP130 gene, encodes complete protein.
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).
CU675986 - Synthetic construct Homo sapiens gateway clone IMAGE:100017454 5' read SAP130 mRNA.
AK055979 - Homo sapiens cDNA FLJ31417 fis, clone NT2NE2000327, weakly similar to GLUCOAMYLASE S1/S2 PRECURSOR (EC 3.2.1.3).
JD465767 - Sequence 446791 from Patent EP1572962.
JD542202 - Sequence 523226 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: B7ZLM3, C9K0X9, ENST00000259235.1, ENST00000259235.2, ENST00000259235.3, ENST00000259235.4, ENST00000259235.5, ENST00000259235.6, NM_024545, Q4ZFV4, Q53T46, Q8WVW4, Q9H0E3, Q9H9G8, SP130_HUMAN, uc002tpp.1, uc002tpp.2, uc002tpp.3
UCSC ID: ENST00000259235.7
RefSeq Accession: NM_001145928
Protein: Q9H0E3 (aka SP130_HUMAN)
CCDS: CCDS2153.1, CCDS54397.1, CCDS82510.1

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