This gene encodes a methyltransferase that adds a methyl group to the histone H2AZ, which is involved in nuclear receptor-dependent transcription. The protein also interacts with several endogenous proteins which are involved in nuclear hormone receptor signaling. A related pseudogene is located on chromosome 2. Alternative splicing results in multiple transcript variants. [pro... See more...

Aliases for SETD6 Gene

Aliases for SETD6 Gene

  • SET Domain Containing 6, Protein Lysine Methyltransferase 2 3 5
  • N-Lysine Methyltransferase SETD6 3 4
  • SET Domain-Containing Protein 6 3 4
  • SET Domain Containing 6 2 3
  • EC 2.1.1.- 4

External Ids for SETD6 Gene

Previous GeneCards Identifiers for SETD6 Gene

  • GC16P057107
  • GC16P058549
  • GC16P044417

Summaries for SETD6 Gene

Entrez Gene Summary for SETD6 Gene

  • This gene encodes a methyltransferase that adds a methyl group to the histone H2AZ, which is involved in nuclear receptor-dependent transcription. The protein also interacts with several endogenous proteins which are involved in nuclear hormone receptor signaling. A related pseudogene is located on chromosome 2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

GeneCards Summary for SETD6 Gene

SETD6 (SET Domain Containing 6, Protein Lysine Methyltransferase) is a Protein Coding gene. Diseases associated with SETD6 include B-Cell Childhood Acute Lymphoblastic Leukemia and Familial Colorectal Cancer Type X. Among its related pathways are PKMTs methylate histone lysines and Chromatin organization. Gene Ontology (GO) annotations related to this gene include NF-kappaB binding and protein-lysine N-methyltransferase activity. An important paralog of this gene is SETD3.

UniProtKB/Swiss-Prot Summary for SETD6 Gene

  • Protein-lysine N-methyltransferase. Monomethylates 'Lys-310' of the RELA subunit of NF-kappa-B complex, leading to down-regulate NF-kappa-B transcription factor activity (PubMed:21131967). Monomethylates 'Lys-8' of H2AZ (H2AZK8me1) (PubMed:23324626). Required for the maintenance of embryonic stem cell self-renewal (By similarity).

Additional gene information for SETD6 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SETD6 Gene

Genomics for SETD6 Gene

GeneHancer (GH) Regulatory Elements for SETD6 Gene

Promoters and enhancers for SETD6 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SETD6 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SETD6

Top Transcription factor binding sites by QIAGEN in the SETD6 gene promoter:
  • AP-4
  • C/EBPalpha
  • GATA-3
  • NF-AT1
  • NF-AT3
  • NF-AT4
  • PPAR-gamma1
  • PPAR-gamma2
  • Roaz
  • YY1

Genomic Locations for SETD6 Gene

Genomic Locations for SETD6 Gene
chr16:58,515,479-58,521,181
(GRCh38/hg38)
Size:
5,703 bases
Orientation:
Plus strand
chr16:58,549,383-58,554,431
(GRCh37/hg19)
Size:
5,049 bases
Orientation:
Plus strand

Genomic View for SETD6 Gene

Genes around SETD6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SETD6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SETD6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETD6 Gene

Proteins for SETD6 Gene

  • Protein details for SETD6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TBK2-SETD6_HUMAN
    Recommended name:
    N-lysine methyltransferase SETD6
    Protein Accession:
    Q8TBK2
    Secondary Accessions:
    • A8K380
    • B5ME38
    • Q9H787

    Protein attributes for SETD6 Gene

    Size:
    473 amino acids
    Molecular mass:
    53189 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for SETD6 Gene

    Alternative splice isoforms for SETD6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SETD6 Gene

Post-translational modifications for SETD6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SETD6 Gene

Domains & Families for SETD6 Gene

Gene Families for SETD6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SETD6 Gene

Suggested Antigen Peptide Sequences for SETD6 Gene

GenScript: Design optimal peptide antigens:
  • SET domain-containing protein 6 (SETD6_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8TBK2

UniProtKB/Swiss-Prot:

SETD6_HUMAN :
  • Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. SETD6 subfamily.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. SETD6 subfamily.
genes like me logo Genes that share domains with SETD6: view

Function for SETD6 Gene

Molecular function for SETD6 Gene

UniProtKB/Swiss-Prot Function:
Protein-lysine N-methyltransferase. Monomethylates 'Lys-310' of the RELA subunit of NF-kappa-B complex, leading to down-regulate NF-kappa-B transcription factor activity (PubMed:21131967). Monomethylates 'Lys-8' of H2AZ (H2AZK8me1) (PubMed:23324626). Required for the maintenance of embryonic stem cell self-renewal (By similarity).

Enzyme Numbers (IUBMB) for SETD6 Gene

Phenotypes From GWAS Catalog for SETD6 Gene

Gene Ontology (GO) - Molecular Function for SETD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21131967
GO:0008168 methyltransferase activity IEA --
GO:0016279 protein-lysine N-methyltransferase activity TAS --
GO:0016740 transferase activity IEA --
GO:0051059 NF-kappaB binding IPI,IBA 21131967
genes like me logo Genes that share ontologies with SETD6: view
genes like me logo Genes that share phenotypes with SETD6: view

Animal Models for SETD6 Gene

MGI Knock Outs for SETD6:
  • Setd6 Setd6<tm1.1(KOMP)Mbp>

Animal Model Products

CRISPR Products

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SETD6 Gene

Localization for SETD6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SETD6 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SETD6 gene
Compartment Confidence
nucleus 5
cytosol 5
cytoskeleton 1
extracellular 0
mitochondrion 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Cytosol (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SETD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IBA 21131967
GO:0005654 nucleoplasm TAS --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with SETD6: view

Pathways & Interactions for SETD6 Gene

genes like me logo Genes that share pathways with SETD6: view

Pathways by source for SETD6 Gene

1 BioSystems pathway for SETD6 Gene

Gene Ontology (GO) - Biological Process for SETD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0018026 peptidyl-lysine monomethylation IDA,IEA 21131967
GO:0019827 stem cell population maintenance ISS,IEA --
GO:0032088 negative regulation of NF-kappaB transcription factor activity IMP,IBA 21131967
GO:0032259 methylation IEA --
GO:0034968 histone lysine methylation IDA 23324626
genes like me logo Genes that share ontologies with SETD6: view

No data available for SIGNOR curated interactions for SETD6 Gene

Drugs & Compounds for SETD6 Gene

No Compound Related Data Available

Transcripts for SETD6 Gene

mRNA/cDNA for SETD6 Gene

2 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
13 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SETD6 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c ^ 9 ^ 10a · 10b · 10c · 10d · 10e
SP1: - - - -
SP2: - - -
SP3: -
SP4: -
SP5: - - - - - - - -
SP6:
SP7:
SP8:

Relevant External Links for SETD6 Gene

GeneLoc Exon Structure for
SETD6

Expression for SETD6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SETD6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SETD6 Gene

This gene is overexpressed in Pancreatic juice (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SETD6 Gene



Protein tissue co-expression partners for SETD6 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SETD6

SOURCE GeneReport for Unigene cluster for SETD6 Gene:

Hs.731691

Evidence on tissue expression from TISSUES for SETD6 Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with SETD6: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SETD6 Gene

Orthologs for SETD6 Gene

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

Orthologs for SETD6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SETD6 31 30
  • 99.18 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SETD6 31 30
  • 89.55 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SETD6 31 30
  • 89.51 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Setd6 17 31 30
  • 83.93 (n)
rat
(Rattus norvegicus)
Mammalia Setd6 30
  • 83.41 (n)
oppossum
(Monodelphis domestica)
Mammalia SETD6 31
  • 72 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SETD6 31
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves SETD6 31 31 30
  • 71.41 (n)
OneToMany
-- 31
  • 64 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 31
  • 63 (a)
OneToMany
-- 31
  • 59 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia setd6 30
  • 59.9 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.1397 30
zebrafish
(Danio rerio)
Actinopterygii setd6 31 30
  • 56.58 (n)
OneToOne
wufb58f11 30
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7724 30
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RKM4 33 31
  • 21 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU09827 30
  • 44.21 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 31 (a)
OneToOne
Species where no ortholog for SETD6 was found in the sources mined by GeneCards:
  • 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)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for SETD6 Gene

ENSEMBL:
Gene Tree for SETD6 (if available)
TreeFam:
Gene Tree for SETD6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SETD6: view image

Paralogs for SETD6 Gene

Paralogs for SETD6 Gene

Pseudogenes.org Pseudogenes for SETD6 Gene

genes like me logo Genes that share paralogs with SETD6: view

Variants for SETD6 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SETD6 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
rs771760548 Uncertain Significance: not provided 58,516,222(+) C/T NONSENSE,NON_CODING_TRANSCRIPT_VARIANT
rs11865588 - p.Asp340Asn
rs17852020 - p.Arg185Ser
rs17852021 - p.Arg206Gly
rs34965375 - p.Thr426Ala

Additional dbSNP identifiers (rs#s) for SETD6 Gene

Variation tolerance for SETD6 Gene

Residual Variation Intolerance Score: 32.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.67; 31.89% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SETD6 Gene

Human Gene Mutation Database (HGMD)
SETD6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SETD6

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for SETD6 Gene

Disorders for SETD6 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SETD6 Gene - From: DISEASES and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SETD6 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SETD6

genes like me logo Genes that share disorders with SETD6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SETD6 Gene

Publications for SETD6 Gene

  1. Lysine methylation of the NF-κB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-κB signaling. (PMID: 21131967) Levy D … Gozani O (Nature immunology 2011) 2 3 4 54
  2. SETD6 monomethylates H2AZ on lysine 7 and is required for the maintenance of embryonic stem cell self-renewal. (PMID: 23324626) Binda O … Richard S (Epigenetics 2013) 3 4 54
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  5. The methyltransferase SETD6 regulates Mitotic progression through PLK1 methylation. (PMID: 30622182) Feldman M … Levy D (Proceedings of the National Academy of Sciences of the United States of America 2019) 3 54

Products for SETD6 Gene

Sources for SETD6 Gene