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    SAP30L SAP30 like [ Homo sapiens (human) ]

    Gene ID: 79685, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SAP30Lprovided by HGNC
    Official Full Name
    SAP30 likeprovided by HGNC
    Primary source
    HGNC:HGNC:25663
    See related
    Ensembl:ENSG00000164576 MIM:610398; AllianceGenome:HGNC:25663
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NS4ATP2
    Summary
    Enables several functions, including non-sequence-specific DNA binding activity, bending; phosphatidylinositol phosphate binding activity; and zinc ion binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in fibrillar center and nucleoplasm. Part of histone deacetylase complex. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 11.8), endometrium (RPKM 9.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SAP30L in Genome Data Viewer
    Location:
    5q33.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (154445997..154461053)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (154979944..154995012)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (153825557..153840613)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene polypeptide N-acetylgalactosaminyltransferase 10 Neighboring gene RNA, 7SL, cytoplasmic 655, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:153749600-153750258 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23476 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:153775267-153775987 Neighboring gene SAP30L antisense RNA 1 (head to head) Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16540 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:153789944-153790444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23477 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:153825354-153825854 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:153851993-153852964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:153852965-153853936 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:153855265-153855452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:153855607-153856461 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:153859235-153859744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:153863719-153864218 Neighboring gene VPS37A, ESCRT-I subunit pseudogene Neighboring gene myotubularin related protein 7 pseudogene Neighboring gene heart and neural crest derivatives expressed 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. TGF-beta induces the expression of SAP30L, a novel nuclear protein. Lindfors K, et al. BMC Genomics, 2003 Dec 18. PMID 14680513, Free PMC Article
    2. Long non-coding RNA SAP30L-AS1 promotes prostate cancer growth through repressing SAP30L. Qin X, et al. Gene, 2019 Mar 30. PMID 30599235
    3. Redox-dependent disulfide bond formation in SAP30L corepressor protein: Implications for structure and function. Laitaoja M, et al. Protein Sci, 2016 Mar. PMID 26609676, Free PMC Article
    4. Alternative mRNA splicing of SAP30L regulates its transcriptional repression activity. Korkeamäki H, et al. FEBS Lett, 2008 Jan 23. PMID 18070604
    5. Transcription mapping of the 5q- syndrome critical region: cloning of two novel genes and sequencing, expression, and mapping of a further six novel cDNAs. Boultwood J, et al. Genomics, 2000 May 15. PMID 10843801

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Results show that expression of SAP30L was negatively associated with that of SAP30L-AS1 in prostate cancer specimens. Its expression is directly repressed by SAP30L-AS1 in prostate neoplasm. Also, SAP30L overexpression attenuated the roles of SAP30L-AS1 in prostate cancer proliferation and apoptosis.
      Title: Long non-coding RNA SAP30L-AS1 promotes prostate cancer growth through repressing SAP30L.
    2. Upon oxidative stress SAP30L undergoes the formation of two specific disulfide bonds, a vicinal Cys29-Cys30 and Cys38-Cys74, with a concomitant release of the coordinated zinc ion. The oxidized protein was shown to remain folded in solution and to bind signaling phospholipids.
      Title: Redox-dependent disulfide bond formation in SAP30L corepressor protein: Implications for structure and function.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Dengue hemorrhagic fever is associated with polymorphisms in JAK1.
    4. findings demonstrate new functions for SAP30L and SAP30 by showing that they can associate directly with core histones as well as naked DNA
      Title: DNA-binding and -bending activities of SAP30L and SAP30 are mediated by a zinc-dependent module and monophosphoinositides.
    5. transcriptional repression mediated by SAP30L can be influenced by alternative mRNA splicing
      Title: Alternative mRNA splicing of SAP30L regulates its transcriptional repression activity.
    6. SAP30L, a nuclear protein, is upregulated by transforming growth factor-beta in intestinal epithelial cells
      Title: TGF-beta induces the expression of SAP30L, a novel nuclear protein.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study of the rate of cognitive decline in Alzheimer's disease.
    EBI GWAS Catalog
    Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ11526, FLJ23595, FLJ36497, DKFZp667L2214

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables non-sequence-specific DNA binding, bending IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables nucleosome binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-3-phosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-4-phosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-5-phosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of cell migration NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of stem cell population maintenance NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of transforming growth factor beta receptor signaling pathway NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of stem cell population maintenance NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of Sin3-type complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
    		  
    part_of histone deacetylase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of histone deacetylase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    histone deacetylase complex subunit SAP30L
    Names
    HCV non-structural protein 4A-transactivated protein 2
    Sin3A associated protein p30-like
    sin3 corepressor complex subunit SAP30L
    sin3-associated protein p30-like

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001131062.2 → NP_001124534.1  histone deacetylase complex subunit SAP30L isoform 2

      See identical proteins and their annotated locations for NP_001124534.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1. The resulting protein (isoform 2) is shorter than isoform 1.
      Source sequence(s)
      AC008625, AC026688, AI436556, AK021588, AW874393
      Consensus CDS
      CCDS47321.1
      UniProtKB/Swiss-Prot
      Q9HAJ7
      Related
      ENSP00000390927.2, ENST00000440364.6
      Conserved Domains (2) summary
      pfam13866
      Location:26 → 68
      zf-SAP30; SAP30 zinc-finger
      pfam13867
      Location:73 → 125
      SAP30_Sin3_bdg; Sin3 binding region of histone deacetylase complex subunit SAP30

    2. NM_001131063.2 → NP_001124535.1  histone deacetylase complex subunit SAP30L isoform 3

      See identical proteins and their annotated locations for NP_001124535.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon and uses an alternate in-frame splice site, compared to variant 1. The resulting protein (isoform 3) is shorter than isoform 1.
      Source sequence(s)
      AC008625, AC026688, AI199517, AK021588, AW874393
      Consensus CDS
      CCDS47322.1
      UniProtKB/Swiss-Prot
      Q9HAJ7
      Related
      ENSP00000416393.2, ENST00000426761.2
      Conserved Domains (2) summary
      pfam13866
      Location:26 → 67
      zf-SAP30; SAP30 zinc-finger
      pfam13867
      Location:68 → 120
      SAP30_Sin3_bdg; Sin3 binding region of histone deacetylase complex subunit SAP30

    3. NM_024632.6 → NP_078908.1  histone deacetylase complex subunit SAP30L isoform 1

      See identical proteins and their annotated locations for NP_078908.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC008625, AC026688, AK021588, AW874393, BC009829
      Consensus CDS
      CCDS4326.1
      UniProtKB/Swiss-Prot
      E9PAU7, E9PAY2, Q9HAJ7
      Related
      ENSP00000297109.5, ENST00000297109.11
      Conserved Domains (2) summary
      pfam13866
      Location:24 → 95
      zf-SAP30; SAP30 zinc-finger
      pfam13867
      Location:114 → 166
      SAP30_Sin3_bdg; Sin3 binding region of histone deacetylase complex subunit SAP30

    RNA

    1. NR_024084.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) includes an alternate exon in the coding region, compared to variant 1, which results in a frameshift and early stop codon. The transcript is sufficiently abundant to represent as a RefSeq record; however, the predicted protein is not represented because the product is significantly truncated and the transcript is a candidate for nonsense-mediated decay (NMD).
      Source sequence(s)
      AC008625, AC026688, AI144341, AK021588, AW874393, BC009829

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      154445997..154461053
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417709.1 → XP_047273665.1  histone deacetylase complex subunit SAP30L isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      154979944..154995012
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353458.1 → XP_054209433.1  histone deacetylase complex subunit SAP30L isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HAJ7.1 GenPept UniProtKB/Swiss-Prot:Q9HAJ7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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