Human Gene SMYD2 (ENST00000366957.10_4) from GENCODE V47lift37

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Description: SET and MYND domain containing 2 (from RefSeq NM_020197.3)
Gencode Transcript: ENST00000366957.10_4
Gencode Gene: ENSG00000143499.14_10
Transcript (Including UTRs)
Position: hg19 chr1:214,454,502-214,510,474 Size: 55,973 Total Exon Count: 12 Strand: +
Coding Region
Position: hg19 chr1:214,454,598-214,510,127 Size: 55,530 Coding Exon Count: 12

Page Index	Sequence and Links	UniProtKB Comments	Primers	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr1:214,454,502-214,510,474)			mRNA (may differ from genome)		Protein (433 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	MGI	OMIM	PubMed	Reactome	UniProtKB
BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: SMYD2_HUMAN DESCRIPTION: RecName: Full=N-lysine methyltransferase SMYD2; EC=2.1.1.-; AltName: Full=HSKM-B; AltName: Full=Histone methyltransferase SMYD2; EC=2.1.1.43; AltName: Full=Lysine N-methyltransferase 3C; AltName: Full=SET and MYND domain-containing protein 2; FUNCTION: Protein-lysine N-methyltransferase that methylates both histones and non-histone proteins. Specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). Has also methyltransferase activity toward non-histone proteins such as p53/TP53 and RB1. Monomethylates 'Lys-370' of p53/TP53, leading to decreased DNA-binding activity and subsequent transcriptional regulation activity of p53/TP53. Monomethylates 'Lys-860' of RB1/RB. CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone]. SUBUNIT: 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. SUBCELLULAR LOCATION: Cytoplasm, cytosol (By similarity). Nucleus (By similarity). INDUCTION: Expression is repressed by CEBPA. SIMILARITY: Contains 1 MYND-type zinc finger. SIMILARITY: Contains 1 SET domain.

Primer design for this transcript

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Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D000082 Acetaminophen D013749 Tetrachlorodibenzodioxin D014635 Valproic Acid C029141 2,2,5,7,8-pentamethyl-1-hydroxychroman C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone D015127 9,10-Dimethyl-1,2-benzanthracene C547126 AZM551248 D001564 Benzo(a)pyrene D019327 Copper Sulfate D003375 Coumestrol D005839 Gentamicins D016912 Levonorgestrel D010634 Phenobarbital D014212 Tretinoin D014810 Vitamin E D024483 Vitamin K 3 D015032 Zinc C018021 cobaltous chloride C028007 nickel monoxide C010792 testosterone undecanoate C012589 trichostatin A C025643 vinclozolin

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 53.21 RPKM in Heart - Left Ventricle Total median expression: 385.30 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-40.10	96	-0.418	Picture	PostScript	Text
3' UTR	-65.80	347	-0.190	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR001214 - SET_dom
IPR011990 - TPR-like_helical
IPR002893 - Znf_MYND

Pfam Domains:
PF00856 - SET domain
PF01753 - MYND finger
PF13181 - Tetratricopeptide repeat

SCOP Domains:
81901 - HCP-like
48452 - TPR-like
82199 - SET domain
144232 - HIT/MYND zinc finger-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help

3RIB - X-ray MuPIT

3S7B - X-ray MuPIT

3S7D - X-ray MuPIT

3S7F - X-ray MuPIT

3S7J - X-ray MuPIT

3TG4 - X-ray MuPIT

3TG5 - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q9NRG4


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	Genome Browser
Gene Details	Gene Details				Gene Details
Gene Sorter	Gene Sorter				Gene Sorter
	RGD	Ensembl			SGD
					Protein Sequence
					Alignment

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0000993 RNA polymerase II core binding GO:0002039 p53 binding GO:0005515 protein binding GO:0008168 methyltransferase activity GO:0016278 lysine N-methyltransferase activity GO:0016279 protein-lysine N-methyltransferase activity GO:0016740 transferase activity GO:0018024 histone-lysine N-methyltransferase activity GO:0046872 metal ion binding GO:0046975 histone methyltransferase activity (H3-K36 specific) Biological Process: GO:0000122 negative regulation of transcription from RNA polymerase II promoter GO:0006325 chromatin organization GO:0006351 transcription, DNA-templated GO:0006355 regulation of transcription, DNA-templated GO:0007507 heart development GO:0008285 negative regulation of cell proliferation GO:0010452 histone H3-K36 methylation GO:0016571 histone methylation GO:0018026 peptidyl-lysine monomethylation GO:0018027 peptidyl-lysine dimethylation GO:0032259 methylation GO:0034968 histone lysine methylation GO:0043516 regulation of DNA damage response, signal transduction by p53 class mediator GO:1901796 regulation of signal transduction by p53 class mediator Cellular Component: GO:0005634 nucleus GO:0005654 nucleoplasm GO:0005737 cytoplasm GO:0005829 cytosol

Descriptions from all associated GenBank mRNAs


	BC068511 - Homo sapiens SET and MYND domain containing 2, mRNA (cDNA clone IMAGE:30342191). BC049367 - Homo sapiens SET and MYND domain containing 2, mRNA (cDNA clone MGC:57151 IMAGE:4826617), complete cds. BC094747 - Homo sapiens SET and MYND domain containing 2, mRNA (cDNA clone IMAGE:30331437), with apparent retained intron. BC057793 - Homo sapiens cDNA clone IMAGE:5311405, containing frame-shift errors. BC098133 - Homo sapiens SET and MYND domain containing 2, mRNA (cDNA clone MGC:119303 IMAGE:40005281), complete cds. BC098276 - Homo sapiens SET and MYND domain containing 2, mRNA (cDNA clone MGC:119304 IMAGE:40005283), complete cds. BC098305 - Homo sapiens SET and MYND domain containing 2, mRNA (cDNA clone MGC:119305 IMAGE:40005284), complete cds. BC098335 - Homo sapiens SET and MYND domain containing 2, mRNA (cDNA clone MGC:119302 IMAGE:40005280), complete cds. AF226053 - Homo sapiens HSKM-B (HSKM-B) mRNA, complete cds. BC028104 - Homo sapiens SET and MYND domain containing 2, mRNA (cDNA clone IMAGE:5246939), partial cds. KJ904828 - Synthetic construct Homo sapiens clone ccsbBroadEn_14222 SMYD2 gene, encodes complete protein. AK313868 - Homo sapiens cDNA, FLJ94501, Homo sapiens SET and MYND domain containing 2 (SMYD2), mRNA. AB590916 - Synthetic construct DNA, clone: pFN21AE1903, Homo sapiens SMYD2 gene for SET and MYND domain containing 2, without stop codon, in Flexi system. BC039890 - Homo sapiens SET and MYND domain containing 2, mRNA (cDNA clone IMAGE:5198510), partial cds. AK098683 - Homo sapiens cDNA FLJ25817 fis, clone TST07537, highly similar to Homo sapiens HSKM-B (HSKM-B) mRNA. BC017080 - Homo sapiens SET and MYND domain containing 2, mRNA (cDNA clone IMAGE:3848215), partial cds. AK091590 - Homo sapiens cDNA FLJ34271 fis, clone FEBRA2003115, moderately similar to Homo sapiens HSKM-B (HSKM-B) mRNA. AX747078 - Sequence 603 from Patent EP1308459. AK090571 - Homo sapiens cDNA FLJ33252 fis, clone ASTRO2005273. JD168502 - Sequence 149526 from Patent EP1572962. JD316376 - Sequence 297400 from Patent EP1572962. JD091967 - Sequence 72991 from Patent EP1572962. JD048413 - Sequence 29437 from Patent EP1572962. AF070592 - Homo sapiens clone 24503 mRNA sequence. JD327620 - Sequence 308644 from Patent EP1572962. JD280189 - Sequence 261213 from Patent EP1572962.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein Q9NRG4 (Reactome details) participates in the following event(s): R-HSA-3222237 SMYD2 methylates TP53 R-HSA-4827383 WHSC1 (KMT3G), NSD1 (KMT3B), SMYD2 (KMT3C) methylate lysine-37 of histone H3 (H3K36) R-HSA-5638157 WHSC1 (KMT3G), NSD1 (KMT3B), SMYD2 (KMT3C), ASH1L methylate methyl-lysine-37 of histone H3 (H3K36) R-HSA-6804760 Regulation of TP53 Activity through Methylation R-HSA-3214841 PKMTs methylate histone lysines R-HSA-5633007 Regulation of TP53 Activity R-HSA-3247509 Chromatin modifying enzymes R-HSA-3700989 Transcriptional Regulation by TP53 R-HSA-4839726 Chromatin organization R-HSA-212436 Generic Transcription Pathway R-HSA-73857 RNA Polymerase II Transcription R-HSA-74160 Gene expression (Transcription)

Other Names for This Gene


	Alternate Gene Symbols: B2R9P9, ENST00000366957.1, ENST00000366957.2, ENST00000366957.3, ENST00000366957.4, ENST00000366957.5, ENST00000366957.6, ENST00000366957.7, ENST00000366957.8, ENST00000366957.9, I6L9H7, KMT3C, NM_020197, Q4V765, Q5VSH9, Q96AI4, Q9NRG4, SMYD2_HUMAN, uc318fmr.1, uc318fmr.2 UCSC ID: ENST00000366957.10_4 RefSeq Accession: NM_020197.3 Protein: Q9NRG4 (aka SMYD2_HUMAN or SMY2_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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