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SAP30L SAP30 like [ Homo sapiens (human) ]

Gene ID: 79685, updated on 2-Nov-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, Nov 2024]
Expression
Ubiquitous expression in ovary (RPKM 11.8), endometrium (RPKM 9.2) and 25 other tissues See more
Orthologs
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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)

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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