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Smyd3 SET and MYND domain containing 3 [ Mus musculus (house mouse) ]

Gene ID: 69726, updated on 21-Apr-2024

Summary

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Official Symbol
Smyd3provided by MGI
Official Full Name
SET and MYND domain containing 3provided by MGI
Primary source
MGI:MGI:1916976
See related
Ensembl:ENSMUSG00000055067 AllianceGenome:MGI:1916976
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Zmynd1; 2410008A19Rik
Summary
Enables RNA polymerase II complex binding activity; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and histone-lysine N-methyltransferase activity. Acts upstream of or within several processes, including cellular response to dexamethasone stimulus; nucleosome assembly; and regulation of protein phosphorylation. Located in nucleus. Is expressed in brain; embryo; metanephros; ovary; and thymus. Orthologous to human SMYD3 (SET and MYND domain containing 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E18 (RPKM 2.4), cerebellum adult (RPKM 2.2) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
1 H4; 1 83.48 cM
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (178779525..179345618, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (178951960..179518053, complement)

Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene kinesin family member 26B Neighboring gene predicted gene, 24405 Neighboring gene STARR-seq mESC enhancer starr_03157 Neighboring gene STARR-seq mESC enhancer starr_03158 Neighboring gene coiled-coil domain-containing protein 121-like Neighboring gene STARR-seq mESC enhancer starr_03160 Neighboring gene STARR-seq mESC enhancer starr_03161 Neighboring gene STARR-seq mESC enhancer starr_03163 Neighboring gene STARR-seq mESC enhancer starr_03164 Neighboring gene STARR-seq mESC enhancer starr_03166 Neighboring gene STARR-seq mESC enhancer starr_03168 Neighboring gene STARR-seq mESC enhancer starr_03170 Neighboring gene predicted gene, 31349 Neighboring gene STARR-seq mESC enhancer starr_03171 Neighboring gene STARR-seq mESC enhancer starr_03172 Neighboring gene STARR-positive B cell enhancer ABC_E10067 Neighboring gene STARR-positive B cell enhancer ABC_E3339 Neighboring gene STARR-positive B cell enhancer mm9_chr1:181437064-181437364 Neighboring gene STARR-positive B cell enhancer mm9_chr1:181447992-181448293 Neighboring gene STARR-positive B cell enhancer ABC_E2590 Neighboring gene ribosomal protein L29 pseudogene Neighboring gene transcription factor B2, mitochondrial

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Inhibition of histone methyltransferase Smyd3 rescues NMDAR and cognitive deficits in a tauopathy mouse model. Williams JB, et al. Nat Commun, 2023 Jan 6. PMID 36609445, Free PMC Article
  2. H3K4 Methyltransferase Smyd3 Mediates Vascular Smooth Muscle Cell Proliferation, Migration, and Neointima Formation. Yang D, et al. Arterioscler Thromb Vasc Biol, 2021 Jun. PMID 33827259
  3. Cell geometry and the cytoskeleton impact the nucleo-cytoplasmic localisation of the SMYD3 methyltransferase. Pereira D, et al. Sci Rep, 2020 Nov 26. PMID 33244033, Free PMC Article
  4. Smyd3 Is a Transcriptional Potentiator of Multiple Cancer-Promoting Genes and Required for Liver and Colon Cancer Development. Sarris ME, et al. Cancer Cell, 2016 Mar 14. PMID 26908355
  5. Histone methyltransferase Smyd3 regulates early embryonic lineage commitment in mice. Suzuki S, et al. Reproduction, 2015 Jul. PMID 25918436

See all (37) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SMYD3: a new regulator of adipocyte precursor proliferation at the early steps of differentiation.
    Title: SMYD3: a new regulator of adipocyte precursor proliferation at the early steps of differentiation.
  2. Inhibition of histone methyltransferase Smyd3 rescues NMDAR and cognitive deficits in a tauopathy mouse model.
    Title: Inhibition of histone methyltransferase Smyd3 rescues NMDAR and cognitive deficits in a tauopathy mouse model.
  3. The Lysine Methylase SMYD3 Modulates Mesendodermal Commitment during Development.
    Title: The Lysine Methylase SMYD3 Modulates Mesendodermal Commitment during Development.
  4. H3K4 Methyltransferase Smyd3 Mediates Vascular Smooth Muscle Cell Proliferation, Migration, and Neointima Formation.
    Title: H3K4 Methyltransferase Smyd3 Mediates Vascular Smooth Muscle Cell Proliferation, Migration, and Neointima Formation.
  5. Cell geometry and the cytoskeleton impact the nucleo-cytoplasmic localisation of the SMYD3 methyltransferase.
    Title: Cell geometry and the cytoskeleton impact the nucleo-cytoplasmic localisation of the SMYD3 methyltransferase.
  6. The SMYD3 methyltransferase promotes myogenesis by activating the myogenin regulatory network.
    Title: The SMYD3 methyltransferase promotes myogenesis by activating the myogenin regulatory network.
  7. The transcription-potentiating function of Smyd3 is restricted to a particular set of genes.
    Title: Smyd3 Is a Transcriptional Potentiator of Multiple Cancer-Promoting Genes and Required for Liver and Colon Cancer Development.
  8. Epigenetic control of Foxp3 by SMYD3 H3K4 histone methyltransferase controls iTreg development and regulates pathogenic T-cell responses during pulmonary viral infection.
    Title: Epigenetic control of Foxp3 by SMYD3 H3K4 histone methyltransferase controls iTreg development and regulates pathogenic T-cell responses during pulmonary viral infection.
  9. These findings indicate that SMYD3 plays an important role in early embryonic lineage commitment and peri-implantation development through the activation of lineage-specific genes.
    Title: Histone methyltransferase Smyd3 regulates early embryonic lineage commitment in mice.
  10. represent the proof of principle that SMYD3 is a druggable target
    Title: A SMYD3 Small-Molecule Inhibitor Impairing Cancer Cell Growth.
Submit: New GeneRIF Correction See all GeneRIFs (13)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II complex binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3K36 dimethyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3K4 trimethyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H4 methyltransferase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transferase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within cellular response to dexamethasone stimulus IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within establishment of protein localization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within methylation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within myotube cell development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within negative regulation of protein kinase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within nucleosome assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within positive regulation of peptidyl-serine phosphorylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
histone-lysine N-methyltransferase SMYD3
Names
SET and MYND domain-containing protein 3
zinc finger MYND domain-containing protein 1
zinc finger, MYND domain containing 1
NP_081464.1
XP_006497045.1
XP_011237166.1
XP_017167700.1
XP_017167702.1
XP_030098701.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_027188.4 → NP_081464.1  histone-lysine N-methyltransferase SMYD3

    See identical proteins and their annotated locations for NP_081464.1

    Status: VALIDATED

    Source sequence(s)
    AC117756, AC120870, AC130279, AC138225
    Consensus CDS
    CCDS15560.1
    UniProtKB/Swiss-Prot
    Q6P7V6, Q8BG90, Q9CWR2
    UniProtKB/TrEMBL
    Q3TR55
    Related
    ENSMUSP00000117410.2, ENSMUST00000128302.8
    Conserved Domains (2) summary
    pfam00856
    Location:201 → 239
    SET; SET domain
    pfam01753
    Location:49 → 87
    zf-MYND; MYND finger

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000067.7 Reference GRCm39 C57BL/6J

    Range
    178779525..179345618 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006496982.5 → XP_006497045.1  histone-lysine N-methyltransferase SMYD3 isoform X2

    See identical proteins and their annotated locations for XP_006497045.1

    UniProtKB/Swiss-Prot
    Q9CWR2
    Conserved Domains (1) summary
    cl40432
    Location:1 → 79
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

  2. XM_017312211.3 → XP_017167700.1  histone-lysine N-methyltransferase SMYD3 isoform X2

    UniProtKB/Swiss-Prot
    Q9CWR2
    Conserved Domains (1) summary
    cl40432
    Location:1 → 79
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

  3. XM_017312213.1 → XP_017167702.1  histone-lysine N-methyltransferase SMYD3 isoform X2

    UniProtKB/Swiss-Prot
    Q9CWR2
    Related
    ENSMUST00000068437.13
    Conserved Domains (1) summary
    cl40432
    Location:1 → 79
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

  4. XM_030242841.1 → XP_030098701.1  histone-lysine N-methyltransferase SMYD3 isoform X2

    Related
    ENSMUST00000131684.8
    Conserved Domains (1) summary
    cl40432
    Location:1 → 79
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

  5. XM_011238864.2 → XP_011237166.1  histone-lysine N-methyltransferase SMYD3 isoform X1

    UniProtKB/TrEMBL
    Q3TR55
    Conserved Domains (2) summary
    pfam01753
    Location:49 → 87
    zf-MYND; MYND finger
    cd19203
    Location:5 → 268
    SET_SMYD3; SET domain (including post-SET domain) found in SET and MYND domain-containing protein 3 (SMYD3) and similar proteins
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9CWR2.1 GenPept UniProtKB/Swiss-Prot:Q9CWR2

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