Human Gene SAP30L (ENST00000297109.11_4) from GENCODE V47lift37
  Description: SAP30 like, transcript variant 4 (from RefSeq NR_024084.2)
Gencode Transcript: ENST00000297109.11_4
Gencode Gene: ENSG00000164576.12_7
Transcript (Including UTRs)
   Position: hg19 chr5:153,825,557-153,840,613 Size: 15,057 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr5:153,826,165-153,835,588 Size: 9,424 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 (chr5:153,825,557-153,840,613)mRNA (may differ from genome)Protein (183 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SP30L_HUMAN
DESCRIPTION: RecName: Full=Histone deacetylase complex subunit SAP30L; AltName: Full=HCV non-structural protein 4A-transactivated protein 2; AltName: Full=Sin3 corepressor complex subunit SAP30L; AltName: Full=Sin3-associated protein p30-like;
FUNCTION: Involved in the functional recruitment of the class 1 Sin3-histone deacetylase complex (HDAC) to the nucleolus.
SUBUNIT: Interacts with components of the histone deacetylase complex SIN3A, HDAC1 and HDAC2. Interacts with FEZ1.
SUBCELLULAR LOCATION: Nucleus, nucleolus.
TISSUE SPECIFICITY: Expressed in all tissues tested with highest levels in testis.
INDUCTION: Up-regulated by TGFB1.
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           more ... click here to view the complete list

+  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: 14.31 RPKM in Cervix - Endocervix
Total median expression: 413.14 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 -381.00608-0.627 Picture PostScript Text
3' UTR -1504.805025-0.299 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

ModBase Predicted Comparative 3D Structure on Q9HAJ7
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 Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003712 transcription cofactor activity
GO:0004407 histone deacetylase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0008289 lipid binding
GO:0010314 phosphatidylinositol-5-phosphate binding
GO:0031491 nucleosome binding
GO:0032266 phosphatidylinositol-3-phosphate binding
GO:0042393 histone binding
GO:0044378 non-sequence-specific DNA binding, bending
GO:0046872 metal ion binding
GO:0070273 phosphatidylinositol-4-phosphate 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

Cellular Component:
GO:0000118 histone deacetylase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus


-  Descriptions from all associated GenBank mRNAs
  AK021588 - Homo sapiens cDNA FLJ11526 fis, clone HEMBA1002555, weakly similar to Homo sapiens mSin3A associated polypeptide p30 mRNA.
BC009829 - Homo sapiens SAP30-like, mRNA (cDNA clone MGC:15059 IMAGE:3937610), complete cds.
AY341060 - Homo sapiens Sin3A associated protein p30-like mRNA, complete cds.
JD394612 - Sequence 375636 from Patent EP1572962.
JD208300 - Sequence 189324 from Patent EP1572962.
JD460747 - Sequence 441771 from Patent EP1572962.
JD395957 - Sequence 376981 from Patent EP1572962.
JD477057 - Sequence 458081 from Patent EP1572962.
JD071568 - Sequence 52592 from Patent EP1572962.
JD137773 - Sequence 118797 from Patent EP1572962.
JD176033 - Sequence 157057 from Patent EP1572962.
JF432631 - Synthetic construct Homo sapiens clone IMAGE:100073868 SAP30-like (SAP30L) gene, encodes complete protein.
AY846876 - Homo sapiens NS4ATP2 (NS4ATP2) mRNA, complete cds.
AK093816 - Homo sapiens cDNA FLJ36497 fis, clone THYMU2018997, weakly similar to Mus musculus Sin3-associated protein (sap30) mRNA.
AF157115 - Homo sapiens clone 214338, mRNA sequence.
AF085957 - Homo sapiens full length insert cDNA clone YR87G10.
JD141754 - Sequence 122778 from Patent EP1572962.
JD498368 - Sequence 479392 from Patent EP1572962.
JD436647 - Sequence 417671 from Patent EP1572962.
AF157116 - Homo sapiens clone 274512, mRNA sequence.
AL833381 - Homo sapiens mRNA; cDNA DKFZp667L2214 (from clone DKFZp667L2214).
AK027248 - Homo sapiens cDNA: FLJ23595 fis, clone LNG15262.
AL833219 - Homo sapiens mRNA; cDNA DKFZp667G087 (from clone DKFZp667G087).

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

Protein Q9HAJ7 (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-3214815 HDACs deacetylate 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: E9PAU7, E9PAY2, ENST00000297109.1, ENST00000297109.10, ENST00000297109.2, ENST00000297109.3, ENST00000297109.4, ENST00000297109.5, ENST00000297109.6, ENST00000297109.7, ENST00000297109.8, ENST00000297109.9, NR_024084, NS4ATP2, Q9HAJ7, SP30L_HUMAN, uc317lyf.1, uc317lyf.2
UCSC ID: ENST00000297109.11_4
RefSeq Accession: NM_024632.6
Protein: Q9HAJ7 (aka SP30L_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.