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Aliases for SETDB1 Gene

Aliases for SETDB1 Gene

  • SET Domain Bifurcated 1 2 3 4
  • SET Domain, Bifurcated 1 2 3 5
  • ERG-Associated Protein With SET Domain 3 4
  • Histone H3-K9 Methyltransferase 4 3 4
  • Lysine N-Methyltransferase 1E 3 4
  • Tudor Domain Containing 21 2 3
  • H3-K9-HMTase 4 3 4
  • EC 2.1.1.43 4 63
  • KMT1E 3 4
  • ESET 3 4
  • Histone-Lysine N-Methyltransferase, H3lysine-9 Specific 4 3
  • ERG-Associated Protein With A SET Domain, ESET 3
  • H3-K9-HMTase4 3
  • KIAA0067 4
  • TDRD21 3
  • KG1T 3

External Ids for SETDB1 Gene

Previous GeneCards Identifiers for SETDB1 Gene

  • GC01P148740
  • GC01P146646
  • GC01P147673
  • GC01P148115
  • GC01P147711
  • GC01P149165
  • GC01P150898
  • GC01P122275

Summaries for SETDB1 Gene

Entrez Gene Summary for SETDB1 Gene

  • This gene encodes a histone methyltransferase which regulates histone methylation, gene silencing, and transcriptional repression. This gene has been identified as a target for treatment in Huntington Disease, given that gene silencing and transcription dysfunction likely play a role in the disease pathogenesis. Alternatively spliced transcript variants of this gene have been described.[provided by RefSeq, Jun 2011]

GeneCards Summary for SETDB1 Gene

SETDB1 (SET Domain Bifurcated 1) is a Protein Coding gene. Diseases associated with SETDB1 include dracunculiasis and huntington disease. Among its related pathways are Lysine degradation and Chromatin organization. GO annotations related to this gene include histone-lysine N-methyltransferase activity. An important paralog of this gene is EHMT1.

UniProtKB/Swiss-Prot for SETDB1 Gene

  • Histone methyltransferase that specifically trimethylates Lys-9 of histone H3. H3 Lys-9 trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. H3 Lys-9 trimethylation is coordinated with DNA methylation. Probably forms a complex with MBD1 and ATF7IP that represses transcription and couples DNA methylation and histone Lys-9 trimethylation. Its activity is dependent on MBD1 and is heritably maintained through DNA replication by being recruited by CAF-1. SETDB1 is targeted to histone H3 by TRIM28/TIF1B, a factor recruited by KRAB zinc-finger proteins. Probably forms a corepressor complex required for activated KRAS-mediated promoter hypermethylation and transcriptional silencing of tumor suppressor genes (TSGs) or other tumor-related genes in colorectal cancer (CRC) cells (PubMed:24623306). Also required to maintain a transcriptionnally repressive state of genes in undifferentiated embryonic stem cells (ESCs) (PubMed:24623306). Associates at promoter regions of tumor suppressor genes (TSGs) leading to their gene silencing (PubMed:24623306).

Gene Wiki entry for SETDB1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SETDB1 Gene

Genomics for SETDB1 Gene

Regulatory Elements for SETDB1 Gene

Transcription factor binding sites by QIAGEN in the SETDB1 gene promoter:

Genomic Location for SETDB1 Gene

Chromosome:
1
Start:
150,926,263 bp from pter
End:
150,964,901 bp from pter
Size:
38,639 bases
Orientation:
Plus strand

Genomic View for SETDB1 Gene

Genes around SETDB1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SETDB1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SETDB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETDB1 Gene

Proteins for SETDB1 Gene

  • Protein details for SETDB1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15047-SETB1_HUMAN
    Recommended name:
    Histone-lysine N-methyltransferase SETDB1
    Protein Accession:
    Q15047
    Secondary Accessions:
    • A6NEW2
    • Q5SZD8
    • Q5SZD9
    • Q5SZE0
    • Q5SZE7
    • Q96GM9

    Protein attributes for SETDB1 Gene

    Size:
    1291 amino acids
    Molecular mass:
    143157 Da
    Quaternary structure:
    • Part of a complex containing at least CDYL, REST, WIZ, SETB1, EHMT1 and EHMT2 (PubMed:19061646). During DNA replication, it is recruited by SETDB1 to form a S phase-specific complex that facilitates methylation of H3 Lys-9 during replication-coupled chromatin assembly and is at least composed of the CAF-1 subunit CHAF1A, MBD1 and SETDB1 (PubMed:15327775). Probably part of a corepressor complex containing ZNF304, TRIM28, SETDB1 and DNMT1 (PubMed:24623306). Interacts with TRIM28/TIF1B (PubMed:11959841). Interacts with ATF7IP and ATF7IP2; the interaction with ATF7IP is required to stimulate histone methyltransferase activity and facilitate the conversion of dimethylated to trimethylated H3 Lys-9 (PubMed:14536086, PubMed:15691849). Interacts with MBD1; interaction is abolished when MBD1 is sumoylated (PubMed:15327775, PubMed:17066076). Interacts with CBX1 and CBX5 (PubMed:15899859). Interacts with DNMT3A and DNMT3B (PubMed:16682412). Interacts with SUMO2. Interacts with CHD7, NLK1 and PPARG (PubMed:17952062). Interacts with MPHOSPH8 (PubMed:20871592). Interacts with ERG (By similarity). Interacts with HDAC1, HDAC2, SIN3A and SIN3B (By similarity).
    Miscellaneous:
    • Highly up-regulated in Huntington disease patients, suggesting that participates in the altered chromatin modulation and transcription dysfunction observed in Huntington disease. Its down-regulation has salubrious effects on patients, suggesting that it may be a promising treatment in Huntington disease patients.
    SequenceCaution:
    • Sequence=BAA06689.2; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAI13325.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAI13326.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SETDB1 Gene

    Alternative splice isoforms for SETDB1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SETDB1 Gene

Proteomics data for SETDB1 Gene at MOPED

Post-translational modifications for SETDB1 Gene

  • Ubiquitination at Lys 59, Lys 182, and Lys 597
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for SETDB1 (SETDB1)

Domains & Families for SETDB1 Gene

Graphical View of Domain Structure for InterPro Entry

Q15047

UniProtKB/Swiss-Prot:

SETB1_HUMAN :
  • The pre-SET, SET and post-SET domains are all required for methyltransferase activity. The 347-amino-acid insertion in the SET domain has no effect on the catalytic activity.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. Suvar3-9 subfamily.
Domain:
  • The pre-SET, SET and post-SET domains are all required for methyltransferase activity. The 347-amino-acid insertion in the SET domain has no effect on the catalytic activity.
  • Isoform 2 lacks all domains required for histone methyltransferase activity.
  • In the pre-SET domain, Cys residues bind 3 zinc ions that are arranged in a triangular cluster; some of these Cys residues contribute to the binding of two zinc ions within the cluster.
  • Contains 1 MBD (methyl-CpG-binding) domain.
  • Contains 1 post-SET domain.
  • Contains 1 pre-SET domain.
  • Contains 1 SET domain.
  • Contains 2 Tudor domains.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. Suvar3-9 subfamily.
genes like me logo Genes that share domains with SETDB1: view

Function for SETDB1 Gene

Molecular function for SETDB1 Gene

GENATLAS Biochemistry:
protein with an unusual bifurcated SET domain protein 1
UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
UniProtKB/Swiss-Prot Function:
Histone methyltransferase that specifically trimethylates Lys-9 of histone H3. H3 Lys-9 trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. H3 Lys-9 trimethylation is coordinated with DNA methylation. Probably forms a complex with MBD1 and ATF7IP that represses transcription and couples DNA methylation and histone Lys-9 trimethylation. Its activity is dependent on MBD1 and is heritably maintained through DNA replication by being recruited by CAF-1. SETDB1 is targeted to histone H3 by TRIM28/TIF1B, a factor recruited by KRAB zinc-finger proteins. Probably forms a corepressor complex required for activated KRAS-mediated promoter hypermethylation and transcriptional silencing of tumor suppressor genes (TSGs) or other tumor-related genes in colorectal cancer (CRC) cells (PubMed:24623306). Also required to maintain a transcriptionnally repressive state of genes in undifferentiated embryonic stem cells (ESCs) (PubMed:24623306). Associates at promoter regions of tumor suppressor genes (TSGs) leading to their gene silencing (PubMed:24623306).

Enzyme Numbers (IUBMB) for SETDB1 Gene

Gene Ontology (GO) - Molecular Function for SETDB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:1990841 promoter-specific chromatin binding IDA 24623306
genes like me logo Genes that share ontologies with SETDB1: view
genes like me logo Genes that share phenotypes with SETDB1: view

Animal Models for SETDB1 Gene

MGI Knock Outs for SETDB1:

Animal Model Products

CRISPR Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SETDB1 Gene

Localization for SETDB1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SETDB1 Gene

Nucleus. Chromosome. Note=Associated with non-pericentromeric regions of chromatin. Excluded from nucleoli and islands of condensed chromatin.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SETDB1 Gene COMPARTMENTS Subcellular localization image for SETDB1 gene
Compartment Confidence
nucleus 5
plasma membrane 5
cytosol 3

Gene Ontology (GO) - Cellular Components for SETDB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA --
genes like me logo Genes that share ontologies with SETDB1: view

Pathways & Interactions for SETDB1 Gene

genes like me logo Genes that share pathways with SETDB1: view

Pathways by source for SETDB1 Gene

1 GeneTex pathway for SETDB1 Gene
1 BioSystems pathway for SETDB1 Gene

Gene Ontology (GO) - Biological Process for SETDB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization TAS --
GO:0006351 transcription, DNA-templated IEA --
GO:0007265 Ras protein signal transduction IMP 24623306
genes like me logo Genes that share ontologies with SETDB1: view

No data available for SIGNOR curated interactions for SETDB1 Gene

Drugs & Compounds for SETDB1 Gene

(3) Drugs for SETDB1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Lysine Approved Nutra Full agonist, Agonist 0
S-Adenosylmethionine Approved Nutra 0
s-adenosylhomocysteine Experimental Pharma 0
genes like me logo Genes that share compounds with SETDB1: view

Transcripts for SETDB1 Gene

Unigene Clusters for SETDB1 Gene

SET domain, bifurcated 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SETDB1 Gene

No ASD Table

Relevant External Links for SETDB1 Gene

GeneLoc Exon Structure for
SETDB1
ECgene alternative splicing isoforms for
SETDB1

Expression for SETDB1 Gene

mRNA expression in normal human tissues for SETDB1 Gene

Protein differential expression in normal tissues from HIPED for SETDB1 Gene

This gene is overexpressed in Testis (15.3), Peripheral blood mononuclear cells (11.2), Lung (8.1), Breast (8.1), and Plasma (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for SETDB1 Gene



SOURCE GeneReport for Unigene cluster for SETDB1 Gene Hs.643565

mRNA Expression by UniProt/SwissProt for SETDB1 Gene

Q15047-SETB1_HUMAN
Tissue specificity: Widely expressed. High expression in testis.
genes like me logo Genes that share expression patterns with SETDB1: view

Protein tissue co-expression partners for SETDB1 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for SETDB1 Gene

Orthologs for SETDB1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SETDB1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SETDB1 35
  • 99.74 (n)
  • 99.77 (a)
SETDB1 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SETDB1 36
  • 96 (a)
OneToOne
SETDB1 35
  • 91.98 (n)
  • 96.66 (a)
dog
(Canis familiaris)
Mammalia SETDB1 35
  • 92.29 (n)
  • 96.28 (a)
SETDB1 36
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Setdb1 36
  • 91 (a)
OneToOne
Setdb1 16
Setdb1 35
  • 88.98 (n)
  • 91.93 (a)
oppossum
(Monodelphis domestica)
Mammalia SETDB1 36
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SETDB1 36
  • 85 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Setdb1 35
  • 88.17 (n)
  • 91.54 (a)
chicken
(Gallus gallus)
Aves -- 36
  • 77 (a)
OneToMany
-- 36
  • 76 (a)
OneToMany
LOC101751150 35
  • 70.92 (n)
  • 78.05 (a)
lizard
(Anolis carolinensis)
Reptilia SETDB1 36
  • 62 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.16848 35
tropical clawed frog
(Silurana tropicalis)
Amphibia setdb1 35
  • 70.84 (n)
  • 77 (a)
Str.4156 35
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5926 35
zebrafish
(Danio rerio)
Actinopterygii setdb1a 36
  • 33 (a)
OneToMany
setdb1b 36
  • 61 (a)
OneToMany
setdb1b 35
  • 62.55 (n)
  • 63.52 (a)
wufa04a12 35
fruit fly
(Drosophila melanogaster)
Insecta CG30422 37
  • 35 (a)
CG30426 37
  • 44 (a)
egg 36
  • 30 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea met-2 36
  • 20 (a)
ManyToMany
set-11 36
  • 26 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SET2 36
  • 10 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.12807 35
Species with no ortholog for SETDB1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SETDB1 Gene

ENSEMBL:
Gene Tree for SETDB1 (if available)
TreeFam:
Gene Tree for SETDB1 (if available)

Paralogs for SETDB1 Gene

genes like me logo Genes that share paralogs with SETDB1: view

Variants for SETDB1 Gene

Sequence variations from dbSNP and Humsavar for SETDB1 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs771196 -- 150,938,521(+) gagac(A/G)gagtc intron-variant
rs771422 -- 150,927,355(-) tgagg(G/T)cagga intron-variant
rs1045628 -- 150,964,427(+) CCTGA(C/T)TGTTG utr-variant-3-prime
rs1763447 -- 150,936,747(-) gatag(C/G)actac intron-variant
rs2124952 -- 150,951,298(-) TACAC(A/T)TGTAC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SETDB1 Gene

Variant ID Type Subtype PubMed ID
esv2661989 CNV Deletion 23128226
nsv522317 CNV Loss 19592680
nsv522840 CNV Gain 19592680

Variation tolerance for SETDB1 Gene

Residual Variation Intolerance Score: 7.75% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.98; 60.02% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SETDB1 Gene

HapMap Linkage Disequilibrium report
SETDB1
Human Gene Mutation Database (HGMD)
SETDB1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SETDB1 Gene

Disorders for SETDB1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SETDB1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
dracunculiasis
  • dracontiasis
huntington disease
  • congenital anomalies of kidney and urinary tract 2
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for SETDB1

Genetic Association Database (GAD)
SETDB1
Human Genome Epidemiology (HuGE) Navigator
SETDB1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SETDB1
genes like me logo Genes that share disorders with SETDB1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SETDB1 Gene

Publications for SETDB1 Gene

  1. The histone methyltransferase SETDB1 and the DNA methyltransferase DNMT3A interact directly and localize to promoters silenced in cancer cells. (PMID: 16682412) Li H. … Pfeifer G.P. (J. Biol. Chem. 2006) 3 4 23 67
  2. ESET/SETDB1 gene expression and histone H3 (K9) trimethylation in Huntington's disease. (PMID: 17142323) Ryu H. … Ferrante R.J. (Proc. Natl. Acad. Sci. U.S.A. 2006) 3 23
  3. Transcriptional repression and heterochromatin formation by MBD1 and MCAF/AM family proteins. (PMID: 15691849) Ichimura T. … Nakao M. (J. Biol. Chem. 2005) 3 23
  4. Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation. (PMID: 12869583) Ayyanathan K. … Rauscher F.J. III (Genes Dev. 2003) 3 23
  5. SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. (PMID: 11959841) Schultz D.C. … Rauscher F.J. III (Genes Dev. 2002) 3 23

Products for SETDB1 Gene

Sources for SETDB1 Gene

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