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

Gene ID: 6418, updated on 5-Jul-2020

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
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

Genomic context

See SET in Genome Data Viewer
Location:
9q34.11
Exon count:
13
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (128683424..128696396)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (131445934..131458675)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene dynein 2 intermediate chain 2 Neighboring gene vesicle transport through interaction with t-SNAREs 1B pseudogene 4 Neighboring gene uncharacterized LOC105376287 Neighboring gene high mobility group AT-hook 1 pseudogene 4 Neighboring gene protein kinase N3 Neighboring gene RNA, 7SL, cytoplasmic 560, pseudogene 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
MENTAL RETARDATION, AUTOSOMAL DOMINANT 58
MedGen: C4748195 OMIM: 618106 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone binding TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein phosphatase inhibitor activity TAS
Traceable Author Statement
more info
PubMed 
protein phosphatase regulator activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
DNA replication TAS
Traceable Author Statement
more info
PubMed 
negative regulation of histone acetylation TAS
Traceable Author Statement
more info
PubMed 
negative regulation of neuron apoptotic process IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of phosphoprotein phosphatase activity IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
nucleosome assembly IEA
Inferred from Electronic Annotation
more info
 
nucleosome disassembly TAS
Traceable Author Statement
more info
PubMed 
regulation of mRNA stability TAS
Traceable Author Statement
more info
 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
lipid droplet IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus HDA PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus TAS
Traceable Author Statement
more info
PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
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)

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
    5139..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
    Q01105
    UniProtKB/TrEMBL
    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/Swiss-Prot
    Q01105
    Related
    ENSP00000387321.3, ENST00000409104.7
    Conserved Domains (1) summary
    pfam00956
    Location:28212
    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/Swiss-Prot
    Q01105
    UniProtKB/TrEMBL
    A0A0C4DFV9
    Related
    ENSP00000361771.5, ENST00000372686.5
    Conserved Domains (1) summary
    pfam00956
    Location:26210
    NAP; Nucleosome assembly protein (NAP)
  4. NM_001374326.1NP_001361255.1  protein SET isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL356481, AL359678
  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/Swiss-Prot
    Q01105
    UniProtKB/TrEMBL
    A0A024R895
    Related
    ENSP00000318012.8, ENST00000322030.12
    Conserved Domains (1) summary
    pfam00956
    Location:37221
    NAP; Nucleosome assembly protein (NAP)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_017015015.1XP_016870504.1  protein SET isoform X1

  2. XM_017015013.1XP_016870502.1  protein SET isoform X1

  3. XM_017015014.1XP_016870503.1  protein SET isoform X1

  4. XM_017015016.2XP_016870505.1  protein SET isoform X2

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