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Aliases for SETD2 Gene

Aliases for SETD2 Gene

  • SET Domain Containing 2 2 3
  • SET2 3 4 6
  • HYPB 3 4 6
  • Huntingtin-Interacting Protein B 3 4
  • Lysine N-Methyltransferase 3A 3 4
  • Huntingtin Yeast Partner B 3 4
  • EC 2.1.1.43 4 63
  • KIAA1732 4 6
  • P231HBP 3 4
  • HBP231 3 6
  • HIF-1 3 4
  • HIP-1 3 4
  • KMT3A 3 4
  • Histone-Lysine N-Methyltransferase SETD2 3
  • Huntingtin Interacting Protein 1 3
  • Huntingtin-Interacting Protein 1 4
  • SET Domain-Containing Protein 2 4
  • HSPC069 3
  • HSET2 4
  • HIF1 4

External Ids for SETD2 Gene

Summaries for SETD2 Gene

Entrez Gene Summary for SETD2 Gene

  • Huntington's disease (HD), a neurodegenerative disorder characterized by loss of striatal neurons, is caused by an expansion of a polyglutamine tract in the HD protein huntingtin. This gene encodes a protein belonging to a class of huntingtin interacting proteins characterized by WW motifs. This protein is a histone methyltransferase that is specific for lysine-36 of histone H3, and methylation of this residue is associated with active chromatin. This protein also contains a novel transcriptional activation domain and has been found associated with hyperphosphorylated RNA polymerase II. [provided by RefSeq, Aug 2008]

GeneCards Summary for SETD2 Gene

SETD2 (SET Domain Containing 2) is a Protein Coding gene. Diseases associated with SETD2 include retinal ischemia and sotos syndrome 1. Among its related pathways are Lysine degradation. GO annotations related to this gene include histone-lysine N-methyltransferase activity. An important paralog of this gene is EHMT1.

UniProtKB/Swiss-Prot for SETD2 Gene

  • Histone methyltransferase that specifically trimethylates Lys-36 of histone H3 (H3K36me3) using dimethylated Lys-36 (H3K36me2) as substrate. Represents the main enzyme generating H3K36me3, a specific tag for epigenetic transcriptional activation. Plays a role in chromatin structure modulation during elongation by coordinating recruitment of the FACT complex and by interacting with hyperphosphorylated POLR2A. Acts as a key regulator of DNA mismatch repair in G1 and early S phase by generating H3K36me3, a mark required to recruit MSH6 subunit of the MutS alpha complex: early recruitment of the MutS alpha complex to chromatin to be replicated allows a quick identification of mismatch DNA to initiate the mismatch repair reaction. H3K36me3 also plays an essential role in the maintenance of a heterochromatic state, by recruiting DNA methyltransferase DNMT3A. H3K36me3 is also enhanced in intron-containing genes, suggesting that SETD2 recruitment is enhanced by splicing and that splicing is coupled to recruitment of elongating RNA polymerase. Required during angiogenesis. Recruited to the promoters of adenovirus 12 E1A gene in case of infection, possibly leading to regulate its expression.

Gene Wiki entry for SETD2 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SETD2 Gene

Genomics for SETD2 Gene

Regulatory Elements for SETD2 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for SETD2 Gene

Start:
47,016,408 bp from pter
End:
47,163,977 bp from pter
Size:
147,570 bases
Orientation:
Minus strand

Genomic View for SETD2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SETD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETD2 Gene

Proteins for SETD2 Gene

  • Protein details for SETD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BYW2-SETD2_HUMAN
    Recommended name:
    Histone-lysine N-methyltransferase SETD2
    Protein Accession:
    Q9BYW2
    Secondary Accessions:
    • O75397
    • O75405
    • Q17RW8
    • Q5BKS9
    • Q5QGN2
    • Q69YI5
    • Q6IN64
    • Q6ZN53
    • Q6ZS25
    • Q8N3R0
    • Q8TCN0
    • Q9C0D1
    • Q9H696
    • Q9NZW9

    Protein attributes for SETD2 Gene

    Size:
    2564 amino acids
    Molecular mass:
    287597 Da
    Quaternary structure:
    • Specifically interacts with hyperphosphorylated C-terminal domain (CTD) of RNA polymerase II large subunit (POLR2A): binds to CTD heptad repeats doubly phosphorylated on Ser-2 and Ser-5 of each heptad. Interacts with HTT and IWS1. Interacts with p53/TP53; leading to regulate p53/TP53 target genes. Component of a complex with HNRNPL.
    SequenceCaution:
    • Sequence=AAF29041.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305}; Sequence=AAH72440.1; Type=Erroneous termination; Positions=463; Note=Translated as Glu.; Evidence={ECO:0000305}; Sequence=AAI17163.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAI17165.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAT77612.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAT77613.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB15367.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB15367.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAC87131.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAC28349.1; Type=Erroneous termination; Positions=385; Note=Translated as Arg.; Evidence={ECO:0000305}; Sequence=CAD38601.2; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SETD2 Gene

    Alternative splice isoforms for SETD2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SETD2 Gene

Proteomics data for SETD2 Gene at MOPED

Selected DME Specific Peptides for SETD2 Gene

Post-translational modifications for SETD2 Gene

Other Protein References for SETD2 Gene

Domains for SETD2 Gene

Gene Families for SETD2 Gene

HGNC:
  • KMT :Chromatin-modifying enzymes / K-methyltransferases

Protein Domains for SETD2 Gene

Suggested Antigen Peptide Sequences for SETD2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9BYW2

UniProtKB/Swiss-Prot:

SETD2_HUMAN :
  • Q9BYW2
Domain:
  • The low charge region mediates the transcriptional activation activity.
  • Contains 1 AWS domain.
  • Contains 1 post-SET domain.
  • Contains 1 SET domain.
  • Contains 1 WW domain.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. SET2 subfamily.
genes like me logo Genes that share domains with SETD2: view

Function for SETD2 Gene

Molecular function for SETD2 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties: Kinetic parameters: KM=1.21 uM for S-adenosyl-L-methionine {ECO:0000269 PubMed:23043551}; KM=0.42 uM for histone H3 {ECO:0000269 PubMed:23043551}; Note=Kcat is 0.14 min(-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 EnzymeRegulation: Specifically inhibited by sinefungin derivatives. N-propyl sinefungin (Pr-SNF) interacts preferentially with SETD2.
UniProtKB/Swiss-Prot Function: Histone methyltransferase that specifically trimethylates Lys-36 of histone H3 (H3K36me3) using dimethylated Lys-36 (H3K36me2) as substrate. Represents the main enzyme generating H3K36me3, a specific tag for epigenetic transcriptional activation. Plays a role in chromatin structure modulation during elongation by coordinating recruitment of the FACT complex and by interacting with hyperphosphorylated POLR2A. Acts as a key regulator of DNA mismatch repair in G1 and early S phase by generating H3K36me3, a mark required to recruit MSH6 subunit of the MutS alpha complex: early recruitment of the MutS alpha complex to chromatin to be replicated allows a quick identification of mismatch DNA to initiate the mismatch repair reaction. H3K36me3 also plays an essential role in the maintenance of a heterochromatic state, by recruiting DNA methyltransferase DNMT3A. H3K36me3 is also enhanced in intron-containing genes, suggesting that SETD2 recruitment is enhanced by splicing and that splicing is coupled to recruitment of elongating RNA polymerase. Required during angiogenesis. Recruited to the promoters of adenovirus 12 E1A gene in case of infection, possibly leading to regulate its expression.

Enzyme Numbers (IUBMB) for SETD2 Gene

Gene Ontology (GO) - Molecular Function for SETD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17500595
GO:0018024 histone-lysine N-methyltransferase activity IMP 23622243
genes like me logo Genes that share ontologies with SETD2: view
genes like me logo Genes that share phenotypes with SETD2: view

Animal Models for SETD2 Gene

MGI Knock Outs for SETD2:

Animal Model Products

CRISPR Products

miRNA for SETD2 Gene

miRTarBase miRNAs that target SETD2

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SETD2

In Situ Assay Products

Flow Cytometry Products

No data available for Transcription Factor Targeting and HOMER Transcription for SETD2 Gene

Localization for SETD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SETD2 Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SETD2 Gene COMPARTMENTS Subcellular localization image for SETD2 gene
Compartment Confidence
nucleus 4
cytosol 1
extracellular 1
mitochondrion 1
peroxisome 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for SETD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus --
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with SETD2: view

Pathways for SETD2 Gene

SuperPathways for SETD2 Gene

Superpath Contained pathways
1 Lysine degradation
genes like me logo Genes that share pathways with SETD2: view

Pathways by source for SETD2 Gene

1 KEGG pathway for SETD2 Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • Epigenetic Chromatin Modification Enzymes in human,mouse,rat

Gene Ontology (GO) - Biological Process for SETD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001525 angiogenesis IEA --
GO:0001570 vasculogenesis --
GO:0001763 morphogenesis of a branching structure IEA --
GO:0001843 neural tube closure IEA --
GO:0006298 mismatch repair IMP 23622243
genes like me logo Genes that share ontologies with SETD2: view

Compounds for SETD2 Gene

(3) HMDB Compounds for SETD2 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

(95) Novoseek inferred chemical compound relationships for SETD2 Gene

Compound -log(P) Hits PubMed IDs
vegf 87.7 231
cobalt chloride 81.8 13
oxygen 79.5 144
cocl2 72.2 10
deferoxamine 70.2 22
genes like me logo Genes that share compounds with SETD2: view

Transcripts for SETD2 Gene

Unigene Clusters for SETD2 Gene

SET domain containing 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SETD2

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for SETD2
  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SETD2 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b · 11c · 11d ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^
SP1: - - - - -
SP2: - - - - - -
SP3: - - - - - -
SP4: - - - -
SP5: - - -
SP6: - - - -
SP7: - - -
SP8:
SP9:

ExUns: 19a · 19b ^ 20 ^ 21a · 21b ^ 22 ^ 23 ^ 24 ^ 25
SP1:
SP2:
SP3:
SP4: - -
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for SETD2 Gene

GeneLoc Exon Structure for
SETD2
ECgene alternative splicing isoforms for
SETD2

Expression for SETD2 Gene

mRNA expression in normal human tissues for SETD2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for SETD2 Gene

SOURCE GeneReport for Unigene cluster for SETD2 Gene Hs.517941

mRNA Expression by UniProt/SwissProt for SETD2 Gene

Q9BYW2-SETD2_HUMAN
Tissue specificity: Ubiquitously expressed.
genes like me logo Genes that share expressions with SETD2: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for SETD2 Gene

Orthologs for SETD2 Gene

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

Orthologs for SETD2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SETD2 35
  • 99.59 (n)
  • 99.57 (a)
SETD2 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SETD2 35
  • 90.64 (n)
  • 90.45 (a)
SETD2 36
  • 90 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SETD2 35
  • 92.44 (n)
  • 92.33 (a)
SETD2 36
  • 92 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Setd2 35
  • 87.27 (n)
  • 86.29 (a)
Setd2 16
Setd2 36
  • 86 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SETD2 36
  • 74 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Setd2 35
  • 86.93 (n)
  • 87.53 (a)
chicken
(Gallus gallus)
Aves SETD2 35
  • 67.84 (n)
  • 67.8 (a)
SETD2 36
  • 66 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SETD2 36
  • 60 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.26109 35
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100492810 35
  • 64.62 (n)
  • 62.46 (a)
Str.16666 35
zebrafish
(Danio rerio)
Actinopterygii setd2 35
  • 58.44 (n)
  • 54.43 (a)
setd2 36
  • 38 (a)
OneToOne
wufb97h09 35
fruit fly
(Drosophila melanogaster)
Insecta Set2 36
  • 20 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea met-1 36
  • 24 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SET2 36
  • 26 (a)
OneToMany
SET2 38
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 53 (a)
OneToOne
Species with no ortholog for SETD2:
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • 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 SETD2 Gene

ENSEMBL:
Gene Tree for SETD2 (if available)
TreeFam:
Gene Tree for SETD2 (if available)

Paralogs for SETD2 Gene

Selected SIMAP similar genes for SETD2 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with SETD2: view

Variants for SETD2 Gene

Sequence variations from dbSNP and Humsavar for SETD2 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type MAF
rs1109497 -- 47,018,454(-) GTAGA(A/C)TTTGT intron-variant
rs1141344 -- 47,147,698(+) gcggg(C/T)ggatc intron-variant
rs1874265 -- 47,160,498(+) AGAGA(C/T)GAGGT intron-variant
rs2017187 -- 47,096,816(+) AAGAG(C/T)TAAAG intron-variant
rs2290547 -- 47,019,693(+) ACTTA(A/C/G)GACAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SETD2 Gene

Variant ID Type Subtype PubMed ID
nsv428417 CNV Loss 18775914
nsv876755 CNV Loss 21882294
nsv876756 CNV Gain 21882294
nsv876757 CNV Loss 21882294
esv2725239 CNV Deletion 23290073
nsv3801 CNV Loss 18451855

Relevant External Links for SETD2 Gene

HapMap Linkage Disequilibrium report
SETD2
Human Gene Mutation Database (HGMD)
SETD2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SETD2 Gene

Disorders for SETD2 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (6) Diseases for SETD2 Gene including...

Search for SETD2 Gene in MalaCards »

UniProtKB/Swiss-Prot

SETD2_HUMAN
  • Renal cell carcinoma (RCC) [MIM:144700]: Renal cell carcinoma is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma. Clear cell renal cell carcinoma is the most common subtype. {ECO:0000269 PubMed:20054297, ECO:0000269 PubMed:23622243, ECO:0000269 PubMed:23792563}. Note=The disease may be caused by mutations affecting the gene represented in this entry. Defects of SETD2 are associated with loss of DNA methylation at non-promoter regions (PubMed:23792563). {ECO:0000269 PubMed:23792563}.

(96) Novoseek inferred disease relationships for SETD2 Gene

Disease -log(P) Hits PubMed IDs
solid tumor 70.3 23
tumors 69.5 207
cancer 66 135
renal clear cell carcinoma 55.1 4
neovascularization 53 11

Relevant External Links for SETD2

Genetic Association Database (GAD)
SETD2
Human Genome Epidemiology (HuGE) Navigator
SETD2
genes like me logo Genes that share disorders with SETD2: view

Publications for SETD2 Gene

  1. Identification of the full-length huntingtin-interacting protein p231HBP/HYPB as a DNA-binding factor. (PMID: 11461154) Rega S. … Puetzer B.M. (Mol. Cell. Neurosci. 2001) 2 3 4
  2. Identification and characterization of a novel human histone H3 lysine 36 specific methyltransferase. (PMID: 16118227) Sun X.-J. … Chen Z. (J. Biol. Chem. 2005) 2 3 4
  3. Solution structure of the Set2-Rpb1 interacting domain of human Set2 and its interaction with the hyperphosphorylated C-terminal domain of Rpb1. (PMID: 16314571) Li M. … Zhou P. (Proc. Natl. Acad. Sci. U.S.A. 2005) 3 4
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4
  5. Histone methyltransferase protein SETD2 interacts with p53 and selectively regulates its downstream genes. (PMID: 18585004) Xie P. … He F. (Cell. Signal. 2008) 3 4

Products for SETD2 Gene

  • Addgene plasmids for SETD2

Sources for SETD2 Gene

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