SMYD3 (SET and MYND domain containing 3)

Gene

• Entrez ID: 64754
• Gene name: SET and MYND domain containing 3
• Gene symbol: SMYD3
• Synonyms: KMT3E, ZMYND1, ZNFN3A1, bA74P14.1
• Chromosome: 1
• Chromosome location: 1q44
• Summary: 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 2

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT004725	hsa-miR-124-3p	Luciferase reporter assay, qRT-PCR, Western blot	19843643
MIRT004725	hsa-miR-124-3p	Luciferase reporter assay, qRT-PCR, Western blot	19843643
MIRT004725	hsa-miR-124-3p	Luciferase reporter assay	22819820
MIRT004725	hsa-miR-124-3p	Luciferase reporter assay	22819820
MIRT439578	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT439578	hsa-miR-218-5p	HITS-CLIP	23212916

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA
GO:0000993	Function	RNA polymerase II complex binding	IEA
GO:0001162	Function	RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	25738358, 32296183
GO:0005634	Component	Nucleus	IBA	21873635
GO:0005634	Component	Nucleus	IDA	25738358
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005829	Component	Cytosol	IDA
GO:0006334	Process	Nucleosome assembly	IEA
GO:0006469	Process	Negative regulation of protein kinase activity	IEA
GO:0014904	Process	Myotube cell development	IEA
GO:0018024	Function	Histone-lysine N-methyltransferase activity	IBA	21873635
GO:0018024	Function	Histone-lysine N-methyltransferase activity	IMP	25738358
GO:0018024	Function	Histone-lysine N-methyltransferase activity	ISS
GO:0033138	Process	Positive regulation of peptidyl-serine phosphorylation	IEA
GO:0034968	Process	Histone lysine methylation	IBA	21873635
GO:0045184	Process	Establishment of protein localization	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0071549	Process	Cellular response to dexamethasone stimulus	IEA

Other IDs

• MIM: 608783
• HGNC: 15513
• e!Ensembl: ENSG00000185420

Protein

• UniProt ID: Q9H7B4
• Protein name: Histone-lysine N-methyltransferase SMYD3 (EC 2.1.1.354) (SET and MYND domain-containing protein 3) (Zinc finger MYND domain-containing protein 1)
• Protein function: Histone methyltransferase. Specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation (PubMed:15235609, PubMed:22419068). Also methylates 'Lys-5' of histone H4 (PubMed:22419068). Plays an important r
• PDB: 3MEK, 3OXF, 3OXG, 3OXL, 3PDN, 3QWP, 3RU0, 5CCL, 5CCM, 5EX0, 5EX3, 5HI7, 5HQ8, 5V37, 5XXD, 5XXG, 5XXJ, 5YJO, 6IJL, 6O9O, 6P6G, 6P6K, 6P7Z, 6PAF, 6YUH, 6ZRB, 7BJ1, 7O2A, 7O2B, 7O2C, 7QLB, 7QNR, 7QNU, 8OWO
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00856	SET	15 → 240	SET domain	Family
  PF01753	zf-MYND	47 → 87	MYND finger	Domain

• Sequence:

  MEPLKVEKFATAKRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLM
  RCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSES
  EKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVIC
  NSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYL
  DMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHW
  KWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRI
  FFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEE
  CDANIRAS

• Sequence length: 428

Pathways

KEGG:

Lysine degradation
Metabolic pathways

Reactome:

PKMTs methylate histone lysines

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Glioma	Glioma	rs121909219, rs121909224, rs587776667, rs587776671, rs121909239, rs121909241, rs28933368, rs121913500, rs55863639, rs786201995, rs786202517, rs786201044, rs398123317, rs1057518425, rs121913499, rs1060500122, rs781647403, rs1060500126, rs1554897889, rs1114167629, rs1114167656, rs587782603, rs1554893824, rs1554900615, rs1564568660, rs786204900, rs762518389, rs1339631701	19578366
Leukemia	Leukemia, Myelocytic, Acute	rs121909646, rs121913488, rs587776834, rs752746786, rs869312821, rs767454740, rs1554564297, rs11978267, rs4132601	27903959

Unknown
Disease name	Disease term	dbSNP ID	References
Central nervous system neoplasms	Central Nervous System Neoplasms		19578366
Impaired cognition	Impaired cognition		31201950
Lupus erythematosus	Lupus Erythematosus, Systemic		29848360