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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
  • 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
  • N-Lysine Methyltransferase SMYD2 3
  • EC 2.1.1.43 4
  • 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 Chromatin organization and p53 pathway (Pathway Interaction Database). GO annotations related to this gene include p53 binding and protein-lysine N-methyltransferase activity. An important paralog of this gene is SMYD1.

UniProtKB/Swiss-Prot 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 , fRNAdb sequence ontologies and piRNA Summary for SMYD2 Gene

Genomics for SMYD2 Gene

Regulatory Elements for SMYD2 Gene

Enhancers for SMYD2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H214318 1.1 ENCODE dbSUPER 18.8 +37.8 37782 2 ELF3 SOX13 CTCF ESRRA MXI1 FOXA2 SAP130 ARID4B CEBPG BATF SMYD2 PTPN14 PIR44288
GH01H214328 1.1 ENCODE dbSUPER 17.8 +47.9 47901 0 GTF2F1 HDGF CTCF PKNOX1 RB1 ZSCAN4 ARID4B MAX ZNF2 RAD21 SMYD2 PIR44288 GC01M214349
GH01H214326 1 ENCODE dbSUPER 18.7 +46.4 46369 1 SMARCE1 PKNOX1 TAL1 ZEB2 TCF12 NFIC GATA3 CTBP1 HDAC2 KLF16 SMYD2 PTPN14 PIR44288 GC01M214349
GH01H214317 1 FANTOM5 ENCODE dbSUPER 18.1 +36.3 36309 0 SOX5 SOX13 POLR2A SMYD2 PIR44288
GH01H214279 1.3 ENCODE dbSUPER 11.6 +0.4 442 3 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF207 ZNF143 SP3 SMYD2 PIR44288
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SMYD2 on UCSC Golden Path with GeneCards custom track

Promoters for SMYD2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000019865 298 2001 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF207 ZNF143 SP3 MXD4

Genomic Location for SMYD2 Gene

Chromosome:
1
Start:
214,281,102 bp from pter
End:
214,337,134 bp from pter
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:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for SMYD2 (SMYD2)
  • Santa Cruz Biotechnology (SCBT) Antibodies for SMYD2

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

Suggested Antigen Peptide Sequences for SMYD2 Gene

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 CatalyticActivity:
S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
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 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 core binding IEA,ISS --
GO:0002039 p53 binding IPI 17108971
GO:0005515 protein binding IPI 17353931
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:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SMYD2
  • Applied Biological Materials Clones for SMYD2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
nucleus 5
cytosol 5
mitochondrion 3
cytoskeleton 2
extracellular 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 GeneTex pathway for SMYD2 Gene
1 Cell Signaling Technology 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 from RNA polymerase II promoter IMP 17108971
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007507 heart development IEA --
GO:0008285 negative regulation of cell proliferation ISS,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
  • 2-S-Adenosyl-L-methionine
  • 5'-Deoxyadenosine-5'-L-methionine disulfate ditosylate
  • 5'-Deoxyadenosine-5'-L-methionine disulphate ditosylate
  • Active methionine
29908-03-0

(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

Unigene Clusters for SMYD2 Gene

SET and MYND domain containing 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SMYD2
  • Applied Biological Materials Clones for SMYD2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
ECgene alternative splicing isoforms for
SMYD2

Expression for SMYD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for SMYD2 Gene



Protein tissue co-expression partners for SMYD2 Gene

NURSA nuclear receptor signaling pathways regulating expression of SMYD2 Gene:

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(2.6)
genes like me logo Genes that share expression patterns with SMYD2: view

Primer Products

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 33 34
  • 96.69 (n)
cow
(Bos Taurus)
Mammalia SMYD2 33 34
  • 92.99 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SMYD2 34
  • 92 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMYD2 34
  • 90 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SMYD2 33 34
  • 89.8 (n)
rat
(Rattus norvegicus)
Mammalia Smyd2 33
  • 87.45 (n)
mouse
(Mus musculus)
Mammalia Smyd2 33 16 34
  • 87.3 (n)
chicken
(Gallus gallus)
Aves SMYD2 33 34
  • 80.83 (n)
lizard
(Anolis carolinensis)
Reptilia SMYD2 34
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100495522 33
  • 76.89 (n)
Str.15286 33
African clawed frog
(Xenopus laevis)
Amphibia smyd2-prov 33
zebrafish
(Danio rerio)
Actinopterygii smyd2a 33 34
  • 72.62 (n)
wufc02f02 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.13835 33
fruit fly
(Drosophila melanogaster)
Insecta Bzd 34
  • 21 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea set-14 34
  • 21 (a)
ManyToMany
set-10 34
  • 18 (a)
ManyToMany
set-18 34
  • 17 (a)
ManyToMany
set-30 34
  • 16 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SET6 36
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)

Paralogs for SMYD2 Gene

Paralogs for SMYD2 Gene

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

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

Variants for SMYD2 Gene

Sequence variations from dbSNP and Humsavar for SMYD2 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1000010084 -- 214,296,387(+) TTCCT(C/T)TGTGG intron-variant
rs1000029442 -- 214,300,694(+) GAAGG(A/T)TGCTT intron-variant
rs1000034019 -- 214,289,040(+) GCTAT(A/G)GGAGG intron-variant
rs1000290844 -- 214,333,496(+) CACCT(C/T)TTACA intron-variant
rs1000332451 -- 214,320,303(+) CATAA(C/T)GTAAA intron-variant

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)

Relevant External Links for SMYD2 Gene

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

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

Disorders for SMYD2 Gene

Relevant External Links for SMYD2

Genetic Association Database (GAD)
SMYD2
Human Genome Epidemiology (HuGE) Navigator
SMYD2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SMYD2

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. 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 60
  2. Structural basis of substrate methylation and inhibition of SMYD2. (PMID: 21782458) Ferguson AD … Keen N (Structure (London, England : 1993) 2011) 3 4 60
  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 60
  4. Methylation of the retinoblastoma tumor suppressor by SMYD2. (PMID: 20870719) Saddic LA … Sage J (The Journal of biological chemistry 2010) 3 4 60
  5. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PMID: 19240061) Trynka G … Wijmenga C (Gut 2009) 3 45 60

Products for SMYD2 Gene

  • Addgene plasmids for SMYD2

Sources for SMYD2 Gene

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