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Aliases for SMYD3 Gene

Aliases for SMYD3 Gene

  • SET And MYND Domain Containing 3 2 3 5
  • Zinc Finger MYND Domain-Containing Protein 1 3 4
  • SET And MYND Domain-Containing Protein 3 3 4
  • Zinc Finger, MYND Domain Containing 1 2 3
  • EC 4 63
  • ZNFN3A1 3 4
  • ZMYND1 3 4
  • Zinc Finger Protein, Subfamily 3A (MYND Domain Containing), 1 3
  • BA74P14.1 (Novel Protein) 3
  • BA74P14.1 3
  • EC 2.1.1 63
  • KMT3E 3

External Ids for SMYD3 Gene

Previous HGNC Symbols for SMYD3 Gene

  • ZNFN3A1
  • ZMYND1

Previous GeneCards Identifiers for SMYD3 Gene

  • GC01M242118
  • GC01M242859
  • GC01M242239
  • GC01M243979
  • GC01M245912
  • GC01M216300

Summaries for SMYD3 Gene

Entrez Gene Summary for SMYD3 Gene

  • This gene encodes a histone methyltransferase which functions in RNA polymerase II complexes by an interaction with a specific RNA helicase. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

GeneCards Summary for SMYD3 Gene

SMYD3 (SET And MYND Domain Containing 3) is a Protein Coding gene. Diseases associated with SMYD3 include Hepatocellular Carcinoma. Among its related pathways are Chromatin organization and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. GO annotations related to this gene include RNA polymerase II core promoter sequence-specific DNA binding and RNA polymerase II core binding. An important paralog of this gene is SMYD1.

UniProtKB/Swiss-Prot for SMYD3 Gene

  • Histone methyltransferase. Specifically methylates Lys-4 and Lys-5 of histone H3, inducing di- and tri-methylation, but not monomethylation. Plays an important role in transcriptional activation as a member of an RNA polymerase complex. Binds DNA containing 5-CCCTCC-3 or 5-GAGGGG-3 sequences.

Gene Wiki entry for SMYD3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMYD3 Gene

Genomics for SMYD3 Gene

Regulatory Elements for SMYD3 Gene

Enhancers for SMYD3 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around SMYD3 on UCSC Golden Path with GeneCards custom track

Promoters for SMYD3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SMYD3 on UCSC Golden Path with GeneCards custom track

Genomic Location for SMYD3 Gene

245,749,340 bp from pter
246,507,342 bp from pter
758,003 bases
Minus strand

Genomic View for SMYD3 Gene

Genes around SMYD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMYD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMYD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMYD3 Gene

Proteins for SMYD3 Gene

  • Protein details for SMYD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Histone-lysine N-methyltransferase SMYD3
    Protein Accession:
    Secondary Accessions:
    • A8K0P0
    • B1AN38
    • Q86TL8
    • Q8N5Z6
    • Q96AI5

    Protein attributes for SMYD3 Gene

    428 amino acids
    Molecular mass:
    49097 Da
    Quaternary structure:
    • Interacts with HSPCA. Interacts with HELZ. Interacts with POLR2A; the interaction may be indirect and may be mediated by HELZ.
    • Sequence=CAI14744.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAI16628.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SMYD3 Gene

    Alternative splice isoforms for SMYD3 Gene


neXtProt entry for SMYD3 Gene

Proteomics data for SMYD3 Gene at MOPED

Selected DME Specific Peptides for SMYD3 Gene

Post-translational modifications for SMYD3 Gene

  • Ubiquitination at Lys 378 and Lys 391
  • Modification sites at PhosphoSitePlus

Other Protein References for SMYD3 Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for SMYD3 (SMYD3)

Domains & Families for SMYD3 Gene

Protein Domains for SMYD3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 SET domain.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family.
  • Contains 1 MYND-type zinc finger.
  • Contains 1 SET domain.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family.
  • Contains 1 MYND-type zinc finger.
genes like me logo Genes that share domains with SMYD3: view

Function for SMYD3 Gene

Molecular function for SMYD3 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 EnzymeRegulation:
Histone methyltransferase activity strongly stimulated by HSPCA.
UniProtKB/Swiss-Prot Function:
Histone methyltransferase. Specifically methylates Lys-4 and Lys-5 of histone H3, inducing di- and tri-methylation, but not monomethylation. Plays an important role in transcriptional activation as a member of an RNA polymerase complex. Binds DNA containing 5-CCCTCC-3 or 5-GAGGGG-3 sequences.

Enzyme Numbers (IUBMB) for SMYD3 Gene

Gene Ontology (GO) - Molecular Function for SMYD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001162 RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with SMYD3: view
genes like me logo Genes that share phenotypes with SMYD3: view

Animal Model Products

miRNA for SMYD3 Gene

miRTarBase miRNAs that target SMYD3

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SMYD3 Gene

Localization for SMYD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMYD3 Gene

Cytoplasm. Nucleus. Note=Mainly cytoplasmic when cells are arrested at G0/G1. Accumulates in the nucleus at S phase and G2/M.

Subcellular locations from

Jensen Localization Image for SMYD3 Gene COMPARTMENTS Subcellular localization image for SMYD3 gene
Compartment Confidence
nucleus 5
cytosol 2
golgi apparatus 2
mitochondrion 2
extracellular 1

Gene Ontology (GO) - Cellular Components for SMYD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with SMYD3: view

Pathways & Interactions for SMYD3 Gene

genes like me logo Genes that share pathways with SMYD3: view

Pathways by source for SMYD3 Gene

1 GeneTex pathway for SMYD3 Gene
1 Cell Signaling Technology pathway for SMYD3 Gene

Interacting Proteins for SMYD3 Gene

Gene Ontology (GO) - Biological Process for SMYD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IEA --
GO:0006469 negative regulation of protein kinase activity IEA --
GO:0034968 histone lysine methylation IEA --
GO:0071549 cellular response to dexamethasone stimulus IEA --
genes like me logo Genes that share ontologies with SMYD3: view

No data available for SIGNOR curated interactions for SMYD3 Gene

Drugs & Compounds for SMYD3 Gene

(2) Drugs for SMYD3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
S-Adenosylmethionine Approved Nutra 0
s-adenosylhomocysteine Experimental Pharma 0
genes like me logo Genes that share compounds with SMYD3: view

Transcripts for SMYD3 Gene

Unigene Clusters for SMYD3 Gene

SET and MYND domain containing 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SMYD3 Gene

No ASD Table

Relevant External Links for SMYD3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SMYD3 Gene

mRNA expression in normal human tissues for SMYD3 Gene

Protein differential expression in normal tissues from HIPED for SMYD3 Gene

This gene is overexpressed in Urine (19.7), Peripheral blood mononuclear cells (14.7), and Fetal Brain (7.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MOPED, and MaxQB for SMYD3 Gene

SOURCE GeneReport for Unigene cluster for SMYD3 Gene Hs.567571

mRNA Expression by UniProt/SwissProt for SMYD3 Gene

Tissue specificity: Expressed in skeletal muscles and testis. Overexpressed in a majority of colorectal and hepatocellular carcinomas.
genes like me logo Genes that share expression patterns with SMYD3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Protein tissue co-expression partners for SMYD3 Gene

Orthologs for SMYD3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SMYD3 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia SMYD3 35
  • 91.54 (n)
  • 92.82 (a)
SMYD3 36
  • 92 (a)
(Canis familiaris)
Mammalia SMYD3 35
  • 90.65 (n)
  • 93.69 (a)
-- 36
  • 92 (a)
-- 36
  • 92 (a)
(Mus musculus)
Mammalia Smyd3 35
  • 87.31 (n)
  • 93.93 (a)
Smyd3 16
Smyd3 36
  • 94 (a)
(Pan troglodytes)
Mammalia SMYD3 35
  • 99.3 (n)
  • 99.53 (a)
SMYD3 36
  • 97 (a)
(Rattus norvegicus)
Mammalia Smyd3 35
  • 88.01 (n)
  • 94.86 (a)
(Monodelphis domestica)
Mammalia SMYD3 36
  • 69 (a)
(Ornithorhynchus anatinus)
Mammalia SMYD3 36
  • 50 (a)
(Gallus gallus)
Aves SMYD3 35
  • 69.25 (n)
  • 58.22 (a)
SMYD3 36
  • 58 (a)
(Anolis carolinensis)
Reptilia SMYD3 36
  • 57 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia smyd3 35
  • 63.63 (n)
  • 54.92 (a)
(Danio rerio)
Actinopterygii smyd3 35
  • 55.26 (n)
  • 46.95 (a)
smyd3 36
  • 46 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008954 35
  • 47.89 (n)
  • 34.21 (a)
fruit fly
(Drosophila melanogaster)
Insecta Bzd 35
  • 44.81 (n)
  • 31.65 (a)
Bzd 36
  • 26 (a)
(Caenorhabditis elegans)
Secernentea set-30 35
  • 45.23 (n)
  • 34.8 (a)
set-10 36
  • 20 (a)
set-14 36
  • 23 (a)
set-18 36
  • 21 (a)
set-30 36
  • 17 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons SDG37 35
  • 43.08 (n)
  • 30.29 (a)
(Oryza sativa)
Liliopsida Os03g0704200 35
  • 46.05 (n)
  • 38.14 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes set6 35
  • 42.6 (n)
  • 31.42 (a)
Species with no ortholog for SMYD3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SMYD3 Gene

Gene Tree for SMYD3 (if available)
Gene Tree for SMYD3 (if available)

Paralogs for SMYD3 Gene

Paralogs for SMYD3 Gene

genes like me logo Genes that share paralogs with SMYD3: view

Variants for SMYD3 Gene

Sequence variations from dbSNP and Humsavar for SMYD3 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs8025 -- 245,749,538(-) AATAC(A/G)GCGTG nc-transcript-variant, utr-variant-3-prime
rs875299 -- 246,403,344(+) AAAAA(A/T)TTAAT intron-variant
rs960227 -- 246,394,264(+) GTAAG(C/T)ATTCA intron-variant
rs997871 -- 246,330,027(+) AATGA(C/T)GCTTC intron-variant
rs915193 -- 246,403,951(+) TCTCA(C/G/T)GGAAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SMYD3 Gene

Variant ID Type Subtype PubMed ID
nsv7191 OTHER Inversion 18451855
nsv873404 CNV Gain 21882294
esv2727062 CNV Deletion 23290073
nsv508069 CNV Loss 20534489
nsv160896 CNV Loss 16902084
nsv468805 CNV Loss 19166990
nsv873405 CNV Loss 21882294
esv2472512 CNV Insertion 19546169
nsv526429 CNV Loss 19592680
nsv468816 CNV Loss 19166990
esv270680 CNV Insertion 20981092
esv274327 CNV Insertion 20981092
esv1341719 CNV Insertion 17803354
nsv873406 CNV Gain 21882294
dgv201e1 CNV Complex 17122850
nsv441746 CNV CNV 18776908
esv2675765 CNV Deletion 23128226
esv2569869 CNV Deletion 19546169
esv2727073 CNV Deletion 23290073
esv2741327 CNV Deletion 23290073
esv2193501 CNV Deletion 18987734
esv2664184 CNV Deletion 23128226
esv2727084 CNV Deletion 23290073
nsv160904 CNV Loss 16902084
nsv873407 CNV Gain 21882294
nsv506990 CNV Insertion 20534489
nsv873408 CNV Loss 21882294
dgv559n71 CNV Loss 21882294
esv2727095 CNV Deletion 23290073
esv4687 CNV Deletion 18987735
esv2727106 CNV Deletion 23290073
esv2658377 CNV Deletion 23128226
nsv5243 CNV Loss 18451855
esv1006575 CNV Loss 20482838
nsv820737 CNV Deletion 20802225
esv23200 CNV Gain+Loss 19812545
esv2727117 CNV Deletion 23290073
esv1406170 CNV Deletion 17803354
nsv514921 CNV Complex 21397061
esv1098694 CNV Deletion 17803354
esv1372253 CNV Deletion 17803354
esv2562033 CNV Deletion 19546169
esv29332 CNV Loss 19812545
esv2727128 CNV Deletion 23290073
esv1739621 CNV Insertion 17803354
esv2155069 CNV Deletion 18987734
esv1407105 CNV Deletion 17803354
esv1003540 CNV Deletion 20482838
esv6772 CNV Loss 19470904
esv2727140 CNV Deletion 23290073
esv2332007 CNV Deletion 18987734
esv2727151 CNV Deletion 23290073
esv2499203 CNV Deletion 19546169
esv2727162 CNV Deletion 23290073
esv2727173 CNV Deletion 23290073
esv2663295 CNV Deletion 23128226
esv1003030 CNV Deletion 20482838
esv1389764 CNV Deletion 17803354
esv2727184 CNV Deletion 23290073
nsv526469 CNV Gain 19592680
esv2473608 CNV Insertion 19546169
esv1341852 CNV Insertion 17803354
esv2671763 CNV Deletion 23128226
esv2727195 CNV Deletion 23290073
nsv873410 CNV Loss 21882294
esv2605359 CNV Insertion 19546169
esv2727206 CNV Deletion 23290073
esv24517 CNV Gain+Loss 19812545
esv2434687 CNV Insertion 19546169
esv2727217 CNV Deletion 23290073
esv1782018 CNV Insertion 17803354
esv1371383 CNV Insertion 17803354
nsv873412 CNV Loss 21882294
esv33357 CNV Loss 17666407
nsv159602 CNV Loss 16902084
esv2675120 CNV Deletion 23128226
nsv515510 CNV Loss 19592680
esv2607117 CNV Insertion 19546169
esv2727228 CNV Deletion 23290073
esv1623049 CNV Insertion 17803354
esv2727239 CNV Deletion 23290073
nsv873413 CNV Gain 21882294
esv2664400 CNV Deletion 23128226
dgv109e199 CNV Deletion 23128226
dgv114n67 CNV Loss 20364138
nsv827731 CNV Loss 20364138
nsv9014 CNV Loss 18304495
esv25241 CNV Gain+Loss 19812545
esv2727252 CNV Deletion 23290073
esv2727263 CNV Deletion 23290073
esv1565797 CNV Deletion 17803354
esv1763627 CNV Deletion 17803354
esv1037683 CNV Insertion 17803354
esv2727274 CNV Deletion 23290073
esv269977 CNV Insertion 20981092
esv273036 CNV Insertion 20981092
dgv202e1 CNV Complex 17122850
nsv428346 CNV Gain 18775914
nsv9025 CNV Gain 18304495
esv1008315 CNV Loss 20482838
esv22703 CNV Gain+Loss 19812545
nsv820560 CNV Deletion 20802225
esv2727285 CNV Deletion 23290073
esv1396451 CNV Deletion 17803354
esv1098199 CNV Deletion 17803354
nsv873414 CNV Loss 21882294
nsv511750 CNV Loss 21212237
esv2727296 CNV Deletion 23290073
esv2727307 CNV Deletion 23290073
esv1309596 CNV Deletion 17803354
esv2727318 CNV Deletion 23290073
esv1404916 CNV Deletion 17803354
dgv560n71 CNV Loss 21882294
nsv873416 CNV Loss 21882294
esv2516817 CNV Insertion 19546169
esv1589863 CNV Insertion 17803354
esv1003896 CNV Insertion 20482838
nsv873418 CNV Loss 21882294
esv29109 CNV Loss 19812545
esv1643982 CNV Deletion 17803354
esv2727329 CNV Deletion 23290073
esv2590335 CNV Deletion 19546169
esv2727340 CNV Deletion 23290073
esv2074719 CNV Deletion 18987734
esv2727351 CNV Deletion 23290073
esv1644154 CNV Deletion 17803354
esv990691 CNV Deletion 20482838
esv268272 CNV Insertion 20981092
esv273894 CNV Insertion 20981092
nsv524498 CNV Loss 19592680
dgv110e199 CNV Deletion 23128226
esv2521573 CNV Insertion 19546169
esv274048 CNV Insertion 20981092
esv270446 CNV Insertion 20981092
esv1640065 CNV Insertion 17803354
esv2727363 CNV Deletion 23290073
esv2727374 CNV Deletion 23290073
esv1477661 CNV Deletion 17803354
esv1000792 CNV Deletion 20482838
nsv873419 CNV Loss 21882294
esv2100000 CNV Deletion 18987734
esv2390771 CNV Deletion 18987734
esv27324 CNV Loss 19812545
esv1544511 CNV Deletion 17803354
esv2727385 CNV Deletion 23290073
esv2727396 CNV Deletion 23290073
esv2727407 CNV Deletion 23290073
esv989400 CNV Deletion 20482838
esv1205920 CNV Deletion 17803354
esv2672276 CNV Deletion 23128226
nsv522303 CNV Loss 19592680
nsv525447 CNV Gain 19592680

Variation tolerance for SMYD3 Gene

Residual Variation Intolerance Score: 25.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.82; 34.24% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SMYD3 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMYD3 Gene

Disorders for SMYD3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SMYD3 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
hepatocellular carcinoma
  • hepatocellular carcinoma, somatic
- elite association - COSMIC cancer census association via MalaCards
Search SMYD3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SMYD3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with SMYD3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SMYD3 Gene

Publications for SMYD3 Gene

  1. SMYD3 encodes a histone methyltransferase involved in the proliferation of cancer cells. (PMID: 15235609) Hamamoto R. … Nakamura Y. (Nat. Cell Biol. 2004) 3 4 23 67
  2. Overexpression of SMYD3 was associated with increased STAT3 activation in gastric cancer. (PMID: 25471787) Liu Y. … Liang H. (Med. Oncol. 2015) 3
  3. SMYD3 overexpression was a risk factor in the biological behavior and prognosis of gastric carcinoma. (PMID: 25472580) Liu Y. … Liang H. (Tumour Biol. 2015) 3
  4. Overexpression of SMYD3 and matrix metalloproteinase-9 are associated with poor prognosis of patients with gastric cancer. (PMID: 25627005) Liu Y. … Liang H. (Tumour Biol. 2015) 3
  5. A SMYD3 Small-Molecule Inhibitor Impairing Cancer Cell Growth. (PMID: 25728514) Peserico A. … Simone C. (J. Cell. Physiol. 2015) 3

Products for SMYD3 Gene

Sources for SMYD3 Gene