Human Gene SMYD2 (ENST00000366957.10_4) from GENCODE V47lift37
  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 IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
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 SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
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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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  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
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -40.1096-0.418 Picture PostScript Text
3' UTR -65.80347-0.190 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
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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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details   Gene Details
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 RGDEnsembl  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
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.