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    SET SET nuclear proto-oncogene [ Homo sapiens (human) ]

    Gene ID: 6418, updated on 17-Jun-2024

    Summary

    Official Symbol
    SETprovided by HGNC
    Official Full Name
    SET nuclear proto-oncogeneprovided by HGNC
    Primary source
    HGNC:HGNC:10760
    See related
    Ensembl:ENSG00000119335 MIM:600960; AllianceGenome:HGNC:10760
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    2PP2A; IGAAD; MRD58; TAF-I; I2PP2A; IPP2A2; PHAPII; TAF-IBETA
    Summary
    The protein encoded by this gene inhibits acetylation of nucleosomes, especially histone H4, by histone acetylases (HAT). This inhibition is most likely accomplished by masking histone lysines from being acetylated, and the consequence is to silence HAT-dependent transcription. The encoded protein is part of a complex localized to the endoplasmic reticulum but is found in the nucleus and inhibits apoptosis following attack by cytotoxic T lymphocytes. This protein can also enhance DNA replication of the adenovirus genome. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
    Expression
    Ubiquitous expression in lymph node (RPKM 55.8), appendix (RPKM 46.5) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See SET in Genome Data Viewer
    Location:
    9q34.11
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (128683424..128696396)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (140888163..140901135)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (131445703..131458675)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene dynein 2 intermediate chain 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131418538-131419182 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131419183-131419826 Neighboring gene vesicle transport through interaction with t-SNAREs 1B pseudogene 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131430084-131430584 Neighboring gene high mobility group AT-hook 1 pseudogene 4 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131445235-131445871 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131445872-131446509 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29088 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29089 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131449798-131450674 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20347 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20348 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131465059-131465598 Neighboring gene protein kinase N3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131475223-131475724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131475725-131476224 Neighboring gene RNA, 7SL, cytoplasmic 560, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20350 Neighboring gene zinc finger DHHC-type palmitoyltransferase 12

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    Related articles in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Intellectual disability, autosomal dominant 58
    MedGen: C4748195 OMIM: 618106 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Genetic variants associated with disordered eating.
    EBI GWAS Catalog
    Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, SET nuclear oncogene, is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with SET is decreased by RRE PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein phosphatase inhibitor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein phosphatase regulator activity TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lipid droplet IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus HDA PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    protein SET
    Names
    HLA-DR-associated protein II
    SET nuclear oncogene
    SET translocation (myeloid leukemia-associated)
    Template-Activating Factor-I, chromatin remodelling factor
    chromatin remodelling factor
    inhibitor of granzyme A-activated DNase
    inhibitor-2 of protein phosphatase-2A
    phosphatase 2A inhibitor I2PP2A
    protein phosphatase type 2A inhibitor

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_030356.1 RefSeqGene

      Range
      10568..17742
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001122821.2NP_001116293.1  protein SET isoform 1

      See identical proteins and their annotated locations for NP_001116293.1

      Status: REVIEWED

      Source sequence(s)
      BP343325, BQ774097, CB129868, CN408133, D45198
      Consensus CDS
      CCDS48037.1
      UniProtKB/Swiss-Prot
      A5A5H4, A6NGV1, B4DUE2, Q01105, Q15541, Q5VXV1, Q5VXV2, Q6FHZ5
      UniProtKB/TrEMBL
      B2RCX0, Q5VXV3
      Related
      ENSP00000361777.4, ENST00000372692.8
      Conserved Domains (1) summary
      pfam00956
      Location:50234
      NAP; Nucleosome assembly protein (NAP)
    2. NM_001248000.2NP_001234929.1  protein SET isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL356481, AL359678, BC032749, BU543146, CA419540
      Consensus CDS
      CCDS59149.1
      UniProtKB/TrEMBL
      B2RCX0
      Related
      ENSP00000387321.3, ENST00000409104.7
      Conserved Domains (1) summary
      pfam00956
      Location:23212
      NAP; Nucleosome assembly protein (NAP)
    3. NM_001248001.2NP_001234930.1  protein SET isoform 4

      See identical proteins and their annotated locations for NP_001234930.1

      Status: REVIEWED

      Source sequence(s)
      AL356481, AL359678
      Consensus CDS
      CCDS59150.1
      UniProtKB/TrEMBL
      A0A8J8YYJ1, B2RCX0
      Related
      ENSP00000361771.6, ENST00000372686.6
      Conserved Domains (1) summary
      pfam00956
      Location:21210
      NAP; Nucleosome assembly protein (NAP)
    4. NM_001374326.1NP_001361255.1  protein SET isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL356481, AL359678
      Consensus CDS
      CCDS48037.1
      UniProtKB/Swiss-Prot
      A5A5H4, A6NGV1, B4DUE2, Q01105, Q15541, Q5VXV1, Q5VXV2, Q6FHZ5
      UniProtKB/TrEMBL
      B2RCX0, Q5VXV3
      Related
      ENSP00000509032.1, ENST00000686840.1
      Conserved Domains (1) summary
      pfam00956
      Location:50234
      NAP; Nucleosome assembly protein (NAP)
    5. NM_003011.4NP_003002.2  protein SET isoform 2

      See identical proteins and their annotated locations for NP_003002.2

      Status: REVIEWED

      Source sequence(s)
      AK223556, AL356481, BP343325, BQ774097, CA392072, CN408133
      Consensus CDS
      CCDS6907.1
      UniProtKB/TrEMBL
      B2RCX0
      Related
      ENSP00000318012.9, ENST00000322030.13
      Conserved Domains (1) summary
      pfam00956
      Location:32221
      NAP; Nucleosome assembly protein (NAP)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      128683424..128696396
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      140888163..140901135
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363514.1XP_054219489.1  protein SET isoform X1

      UniProtKB/Swiss-Prot
      A5A5H4, A6NGV1, B4DUE2, Q01105, Q15541, Q5VXV1, Q5VXV2, Q6FHZ5
      UniProtKB/TrEMBL
      B2RCX0, Q5VXV3