SET domain-containing proteins, such as SMYD2, catalyze lysine methylation (Brown et al., 2006 [PubMed 16805913]).[supplied by OMIM, Nov 2008] See more...

Aliases for SMYD2 Gene

Aliases for SMYD2 Gene

  • SET And MYND Domain Containing 2 2 3 5
  • SET And MYND Domain-Containing Protein 2 3 4
  • N-Lysine Methyltransferase SMYD2 3 4
  • Histone Methyltransferase SMYD2 3 4
  • Lysine N-Methyltransferase 3C 3 4
  • HSKM-B 3 4
  • KMT3C 3 4
  • Zinc Finger, MYND Domain Containing 14 3
  • EC 2.1.1.- 4
  • ZMYND14 3

External Ids for SMYD2 Gene

Previous GeneCards Identifiers for SMYD2 Gene

  • GC01P211070
  • GC01P211511
  • GC01P210842
  • GC01P212521
  • GC01P214454
  • GC01P185129

Summaries for SMYD2 Gene

Entrez Gene Summary for SMYD2 Gene

  • SET domain-containing proteins, such as SMYD2, catalyze lysine methylation (Brown et al., 2006 [PubMed 16805913]).[supplied by OMIM, Nov 2008]

GeneCards Summary for SMYD2 Gene

SMYD2 (SET And MYND Domain Containing 2) is a Protein Coding gene. Among its related pathways are Regulation of TP53 Activity and Gene Expression. Gene Ontology (GO) annotations related to this gene include p53 binding and protein-lysine N-methyltransferase activity. An important paralog of this gene is SMYD3.

UniProtKB/Swiss-Prot Summary for SMYD2 Gene

  • Protein-lysine N-methyltransferase that methylates both histones and non-histone proteins, including p53/TP53 and RB1. Specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). Shows even higher methyltransferase activity on p53/TP53. Monomethylates 'Lys-370' of p53/TP53, leading to decreased DNA-binding activity and subsequent transcriptional regulation activity of p53/TP53. Monomethylates RB1 at 'Lys-860'.

Tocris Summary for SMYD2 Gene

  • Lysine methyltransferases are enyzmes that catalyze the transfer of methyl groups from S-adenosylmethionine (SAM) to the lysine residues on histones, particularly histones H3 and H4. The dysregulation of this methylation is critical in the development of cancer.

Additional gene information for SMYD2 Gene

No data available for CIViC Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SMYD2 Gene

Genomics for SMYD2 Gene

GeneHancer (GH) Regulatory Elements for SMYD2 Gene

Promoters and enhancers for SMYD2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J214279 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 511.5 +0.6 584 3.8 HNRNPK EP300 ZSCAN5C TCF12 POLR2G PHF8 ZFX POLR2A ZBTB10 CLOCK SMYD2 lnc-PTPN14-2 piR-50289
GH01J214318 Enhancer 1.1 Ensembl ENCODE dbSUPER 18.8 +38.1 38127 2.7 CTCF NCOR1 KDM6A ATF2 FOXA2 SAP130 RBM22 BATF ZGPAT IKZF1 SMYD2 PTPN14 piR-50289 lnc-PTPN14-2
GH01J214328 Enhancer 1.1 Ensembl ENCODE dbSUPER 18.2 +48.9 48947 2.9 EP300 CTCF REST RAD21 CTBP1 MYC TRIM22 SMC3 RELA FOS SMYD2 piR-50289 RF00017-474
GH01J214602 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 9.8 +323.1 323132 3.9 FOXK2 ZNF217 ZSCAN5C SIN3A NRF1 TCF12 MYC POLR2G USF1 SP1 CENPF SMYD2 ABHD17AP3 piR-52290-001
GH01J214326 Enhancer 1 Ensembl ENCODE dbSUPER 18.7 +46.2 46198 1.9 CTBP1 NFIC ESR1 GATA3 TAL1 FOS NR2F1 POU2F2 STAT5A PKNOX1 SMYD2 PTPN14 piR-50289 RF00017-474
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SMYD2 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SMYD2

Top Transcription factor binding sites by QIAGEN in the SMYD2 gene promoter:
  • GR
  • GR-alpha
  • GR-beta
  • NRSF form 1
  • Pax-2
  • Pax-2a
  • Pax-2b
  • SRY
  • TBP
  • TFIID

Genomic Locations for SMYD2 Gene

Genomic Locations for SMYD2 Gene
chr1:214,281,102-214,337,134
(GRCh38/hg38)
Size:
56,033 bases
Orientation:
Plus strand
chr1:214,454,445-214,510,477
(GRCh37/hg19)
Size:
56,033 bases
Orientation:
Plus strand

Genomic View for SMYD2 Gene

Genes around SMYD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMYD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMYD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMYD2 Gene

Proteins for SMYD2 Gene

  • Protein details for SMYD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NRG4-SMYD2_HUMAN
    Recommended name:
    N-lysine methyltransferase SMYD2
    Protein Accession:
    Q9NRG4
    Secondary Accessions:
    • B2R9P9
    • I6L9H7
    • Q4V765
    • Q5VSH9
    • Q96AI4

    Protein attributes for SMYD2 Gene

    Size:
    433 amino acids
    Molecular mass:
    49688 Da
    Quaternary structure:
    • Interacts with RNA polymerase II and HELZ. Interacts with SIN3A and HDAC1 (By similarity). Interacts (via MYND-type zinc finger) with EPB41L3. Interacts (via SET domain) with p53/TP53. Interacts with RB1 and HSP90AA1.

    Three dimensional structures from OCA and Proteopedia for SMYD2 Gene

    Alternative splice isoforms for SMYD2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMYD2 Gene

Post-translational modifications for SMYD2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SMYD2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SMYD2 Gene

Domains & Families for SMYD2 Gene

Gene Families for SMYD2 Gene

Protein Domains for SMYD2 Gene

Blocks:
  • Zn-finger, MYND type
  • Nuclear protein SET
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SMYD2 Gene

GenScript: Design optimal peptide antigens:
  • SET and MYND domain containing 2 (B0R0U3_HUMAN)
  • SMYD2 protein (Q05C86_HUMAN)
  • SET and MYND domain-containing protein 2 (SMYD2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NRG4

UniProtKB/Swiss-Prot:

SMYD2_HUMAN :
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
genes like me logo Genes that share domains with SMYD2: view

Function for SMYD2 Gene

Molecular function for SMYD2 Gene

UniProtKB/Swiss-Prot Function:
Protein-lysine N-methyltransferase that methylates both histones and non-histone proteins, including p53/TP53 and RB1. Specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). Shows even higher methyltransferase activity on p53/TP53. Monomethylates 'Lys-370' of p53/TP53, leading to decreased DNA-binding activity and subsequent transcriptional regulation activity of p53/TP53. Monomethylates RB1 at 'Lys-860'.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-lysyl-[histone] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl-[histone] + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:10024, Rhea:RHEA-COMP:9845, Rhea:RHEA-COMP:9846, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61929; Evidence={ECO:0000269 PubMed:18065756, ECO:0000269 PubMed:21782458, ECO:0000269 PubMed:21880715};.
UniProtKB/Swiss-Prot Induction:
Expression is repressed by CEBPA.

Enzyme Numbers (IUBMB) for SMYD2 Gene

Phenotypes From GWAS Catalog for SMYD2 Gene

Gene Ontology (GO) - Molecular Function for SMYD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000993 RNA polymerase II complex binding IEA,ISS --
GO:0002039 p53 binding IPI 17108971
GO:0005515 protein binding IPI,IEA 17805299
GO:0008168 methyltransferase activity IEA --
GO:0016278 lysine N-methyltransferase activity TAS --
genes like me logo Genes that share ontologies with SMYD2: view
genes like me logo Genes that share phenotypes with SMYD2: view

Animal Models for SMYD2 Gene

MGI Knock Outs for SMYD2:
  • Smyd2 Smyd2<tm1a(KOMP)Wtsi>

Animal Model Products

CRISPR Products

Clone Products

  • Addgene plasmids for SMYD2

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SMYD2 Gene

Localization for SMYD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMYD2 Gene

Cytoplasm, cytosol. Nucleus.

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 SMYD2 gene
Compartment Confidence
cytosol 5
nucleus 4
cytoskeleton 3
mitochondrion 3
plasma membrane 1
extracellular 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Intermediate filaments (2)
  • Mitochondria (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SMYD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm ISS --
GO:0005829 cytosol ISS --
genes like me logo Genes that share ontologies with SMYD2: view

Pathways & Interactions for SMYD2 Gene

genes like me logo Genes that share pathways with SMYD2: view

Pathways by source for SMYD2 Gene

1 Cell Signaling Technology pathway for SMYD2 Gene
1 GeneTex pathway for SMYD2 Gene

Gene Ontology (GO) - Biological Process for SMYD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IMP 17108971
GO:0006325 chromatin organization IEA --
GO:0007507 heart development IEA --
GO:0008285 negative regulation of cell proliferation IEA,ISS --
GO:0010452 histone H3-K36 methylation IEA --
genes like me logo Genes that share ontologies with SMYD2: view

No data available for SIGNOR curated interactions for SMYD2 Gene

Drugs & Compounds for SMYD2 Gene

(3) Drugs for SMYD2 Gene - From: ApexBio, DGIdb, and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
s-adenosylhomocysteine Experimental Pharma 0
AZ505 Pharma SMYD2 inhibitor,potent and selective 0
AZ505 ditrifluoroacetate Pharma SMYD2 inhibitor 0

(1) Additional Compounds for SMYD2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-Carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
485-80-3

(2) ApexBio Compounds for SMYD2 Gene

Compound Action Cas Number
AZ505 SMYD2 inhibitor,potent and selective 1035227-43-0
AZ505 ditrifluoroacetate SMYD2 inhibitor 1035227-44-1
genes like me logo Genes that share compounds with SMYD2: view

Drug Products

Transcripts for SMYD2 Gene

mRNA/cDNA for SMYD2 Gene

1 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

  • Addgene plasmids for SMYD2

Alternative Splicing Database (ASD) splice patterns (SP) for SMYD2 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12a · 12b
SP1: - - -
SP2: - - - - -
SP3: - -
SP4:
SP5:
SP6:

Relevant External Links for SMYD2 Gene

GeneLoc Exon Structure for
SMYD2

Expression for SMYD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SMYD2 Gene

mRNA differential expression in normal tissues according to GTEx for SMYD2 Gene

This gene is overexpressed in Heart - Left Ventricle (x10.8).

Protein differential expression in normal tissues from HIPED for SMYD2 Gene

This gene is overexpressed in Heart (21.7), Testis (20.5), and Adipocyte (20.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SMYD2 Gene



Protein tissue co-expression partners for SMYD2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SMYD2

SOURCE GeneReport for Unigene cluster for SMYD2 Gene:

Hs.66170

Evidence on tissue expression from TISSUES for SMYD2 Gene

  • Intestine(4.2)
  • Nervous system(2.9)
  • Muscle(2.7)
  • Heart(2.5)
genes like me logo Genes that share expression patterns with SMYD2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SMYD2 Gene

Orthologs for SMYD2 Gene

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

Orthologs for SMYD2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMYD2 31 30
  • 96.69 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SMYD2 31 30
  • 92.99 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SMYD2 31
  • 92 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMYD2 31
  • 90 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SMYD2 31 30
  • 89.8 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smyd2 30
  • 87.45 (n)
mouse
(Mus musculus)
Mammalia Smyd2 17 31 30
  • 87.3 (n)
chicken
(Gallus gallus)
Aves SMYD2 31 30
  • 80.83 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMYD2 31
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100495522 30
  • 76.89 (n)
Str.15286 30
African clawed frog
(Xenopus laevis)
Amphibia smyd2-prov 30
zebrafish
(Danio rerio)
Actinopterygii smyd2a 31 30
  • 72.62 (n)
OneToOne
wufc02f02 30
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.13835 30
fruit fly
(Drosophila melanogaster)
Insecta Bzd 31
  • 21 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea set-14 31
  • 21 (a)
ManyToMany
set-10 31
  • 18 (a)
ManyToMany
set-18 31
  • 17 (a)
ManyToMany
set-30 31
  • 16 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SET6 33
Species where no ortholog for SMYD2 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)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 SMYD2 Gene

ENSEMBL:
Gene Tree for SMYD2 (if available)
TreeFam:
Gene Tree for SMYD2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SMYD2: view image

Paralogs for SMYD2 Gene

Paralogs for SMYD2 Gene

(3) SIMAP similar genes for SMYD2 Gene using alignment to 5 proteins:

  • SMYD2_HUMAN
  • B0R0U3_HUMAN
  • I6L9D1_HUMAN
  • I6L9H7_HUMAN
  • Q05C86_HUMAN
genes like me logo Genes that share paralogs with SMYD2: view

Variants for SMYD2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SMYD2 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs11120301 - p.Ile430Met
rs1134647 - p.Gly165Glu

Additional dbSNP identifiers (rs#s) for SMYD2 Gene

Structural Variations from Database of Genomic Variants (DGV) for SMYD2 Gene

Variant ID Type Subtype PubMed ID
esv2668267 CNV deletion 23128226
esv2722595 CNV deletion 23290073
esv3588786 CNV loss 21293372
nsv1141748 CNV insertion 24896259

Variation tolerance for SMYD2 Gene

Residual Variation Intolerance Score: 51% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.06; 50.52% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SMYD2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMYD2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMYD2 Gene

Disorders for SMYD2 Gene

Additional Disease Information for SMYD2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SMYD2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SMYD2 Gene

Publications for SMYD2 Gene

  1. Structural basis of substrate methylation and inhibition of SMYD2. (PMID: 21782458) Ferguson AD … Keen N (Structure (London, England : 1993) 2011) 3 4 54
  2. Structure of human SMYD2 protein reveals the basis of p53 tumor suppressor methylation. (PMID: 21880715) Wang L … Zhao K (The Journal of biological chemistry 2011) 3 4 54
  3. Structure of human lysine methyltransferase Smyd2 reveals insights into the substrate divergence in Smyd proteins. (PMID: 21724641) Xu S … Ding J (Journal of molecular cell biology 2011) 3 4 54
  4. Methylation of the retinoblastoma tumor suppressor by SMYD2. (PMID: 20870719) Saddic LA … Sage J (The Journal of biological chemistry 2010) 3 4 54
  5. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PMID: 19240061) Trynka G … Wijmenga C (Gut 2009) 3 41 54

Products for SMYD2 Gene

Sources for SMYD2 Gene