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Aliases for SETDB1 Gene

Aliases for SETDB1 Gene

  • SET Domain, Bifurcated 1 2 3
  • 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 64
  • KMT1E 3 4
  • ESET 3 4
  • Histone-Lysine N-Methyltransferase, H3lysine-9 Specific 4 3
  • ERG-Associated Protein With A SET Domain, ESET 3
  • Histone-Lysine N-Methyltransferase SETDB1 3
  • SET Domain Bifurcated 1 4
  • H3-K9-HMTase4 3
  • KIAA0067 4
  • TDRD21 3
  • KG1T 3

External Ids for SETDB1 Gene

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 huntington disease. Among its related pathways are Chromatin Regulation / Acetylation and Noncanonical Wnt signaling pathway. 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.

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

Genomic Location for SETDB1 Gene

Start:
150,926,263 bp from pter
End:
150,964,913 bp from pter
Size:
38,651 bases
Orientation:
Plus strand

Genomic View for SETDB1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SETDB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETDB1 Gene

Regulatory Elements for SETDB1 Gene

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

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:
    • Interacts with MBD1; interaction is abolished when MBD1 is sumoylated. 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. 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. Interacts with ERG, TRIM28/TIF1B, CBX1, CBX5, CHD7, DNMT3A, HDAC1, HDAC2, NLK, PPARG, SIN3A, SIN3B, DNMT3B and SUMO2. Interacts with MPHOSPH8. Part of a complex containing at least CDYL, REST, WIZ, SETB1, EHMT1 and EHMT2.
    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

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys59, Lys182, and Lys597

Domains for SETDB1 Gene

Gene Families for SETDB1 Gene

HGNC:
  • TDRD :Tudor domain containing
  • KMT :Chromatin-modifying enzymes / K-methyltransferases

UniProtKB/Swiss-Prot:

SETB1_HUMAN
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:
    • Q15047
  • Isoform 2 lacks all domains required for histone methyltransferase activity:
    • Q15047
  • 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.:
    • Q15047
  • Contains 1 MBD (methyl-CpG-binding) domain.:
    • Q15047
  • Contains 1 post-SET domain.:
    • Q15047
  • Contains 1 pre-SET domain.:
    • Q15047
  • Contains 1 SET domain.:
    • Q15047
  • Contains 2 Tudor domains.:
    • Q15047
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. Suvar3-9 subfamily.:
    • Q15047
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.

Enzyme Numbers (IUBMB) for SETDB1 Gene

Gene Ontology (GO) - Molecular Function for SETDB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 16682412
GO:0008270 zinc ion binding IEA --
GO:0018024 histone-lysine N-methyltransferase activity IEA --
genes like me logo Genes that share ontologies with SETDB1: view
genes like me logo Genes that share phenotypes with SETDB1: view

miRNA for SETDB1 Gene

No data available for Animal Models , Transcription Factor Targeting 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
golgi apparatus 4
plasma membrane 4
cytosol 3

Gene Ontology (GO) - Cellular Components for SETDB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin IEA --
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome --
GO:0005737 cytoplasm IDA --
genes like me logo Genes that share ontologies with SETDB1: view

Pathways for SETDB1 Gene

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

Pathways by source for SETDB1 Gene

1 Cell Signaling Technology pathway for SETDB1 Gene
1 BioSystems pathway for SETDB1 Gene
1 KEGG pathway for SETDB1 Gene

Gene Ontology (GO) - Biological Process for SETDB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0001833 inner cell mass cell proliferation IEA --
GO:0006325 chromatin organization TAS --
GO:0006351 transcription, DNA-templated IEA --
GO:0034968 histone lysine methylation --
genes like me logo Genes that share ontologies with SETDB1: view

Compounds for SETDB1 Gene

(3) HMDB Compounds for SETDB1 Gene

Compound Synonyms Cas Number PubMed IDs
L-Lysine
  • (+)-S-Lysine
56-87-1
S-Adenosylhomocysteine
  • (S)-5'-(S)-(3-Amino-3-carboxypropyl)-5'-thioadenosine
979-92-0
S-Adenosylmethionine
  • (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine
29908-03-0
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:

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

Integrated Proteomics: protein expression 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 expressions with SETDB1: view

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 36
  • 99.74 (n)
  • 99.77 (a)
SETDB1 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SETDB1 36
  • 91.98 (n)
  • 96.66 (a)
SETDB1 37
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SETDB1 36
  • 92.29 (n)
  • 96.28 (a)
SETDB1 37
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Setdb1 36
  • 88.98 (n)
  • 91.93 (a)
Setdb1 16
Setdb1 37
  • 91 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SETDB1 37
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SETDB1 37
  • 85 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Setdb1 36
  • 88.17 (n)
  • 91.54 (a)
chicken
(Gallus gallus)
Aves -- 37
  • 77 (a)
OneToMany
-- 37
  • 76 (a)
OneToMany
LOC101751150 36
  • 70.92 (n)
  • 78.05 (a)
lizard
(Anolis carolinensis)
Reptilia SETDB1 37
  • 62 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.16848 36
tropical clawed frog
(Silurana tropicalis)
Amphibia setdb1 36
  • 70.84 (n)
  • 77 (a)
Str.4156 36
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5926 36
zebrafish
(Danio rerio)
Actinopterygii setdb1a 37
  • 33 (a)
OneToMany
setdb1b 36
  • 62.55 (n)
  • 63.52 (a)
setdb1b 37
  • 61 (a)
OneToMany
wufa04a12 36
fruit fly
(Drosophila melanogaster)
Insecta egg 37
  • 30 (a)
OneToOne
CG30426 38
  • 44 (a)
CG30422 38
  • 35 (a)
worm
(Caenorhabditis elegans)
Secernentea met-2 37
  • 20 (a)
ManyToMany
set-11 37
  • 26 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SET2 37
  • 10 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.12807 36
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 MAF
rs525676 -- 150,962,841(-) AATAA(A/C/G/T)GCAGG intron-variant
rs569751 -- 150,927,385(-) acttt(G/T)agagg intron-variant
rs569752 -- 150,927,384(-) ctttt(A/G)gaggc intron-variant
rs771196 -- 150,938,521(+) gagac(A/G)gagtc intron-variant
rs771422 -- 150,927,355(-) tgagg(G/T)cagga 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

Relevant External Links for SETDB1 Gene

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

Disorders for SETDB1 Gene

(1) MalaCards Diseases for SETDB1 Gene

Search for SETDB1 Gene in MalaCards »

Relevant External Links for SETDB1

Genetic Association Database (GAD)
SETDB1
Human Genome Epidemiology (HuGE) Navigator
SETDB1
genes like me logo Genes that share disorders with SETDB1: view

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

Publications for SETDB1 Gene

  1. 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 4 23
  2. 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 4 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 4 23
  4. 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
  5. 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 4 23

Products for SETDB1 Gene

Sources for SETDB1 Gene

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