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

    Gene ID: 69726, updated on 9-Dec-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 H3K36 dimethyltransferase 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 several structures, including cerebral cortex; early conceptus; gonad; hemolymphoid system gland; and liver. Orthologous to human SMYD3 (SET and MYND domain containing 3). [provided by Alliance of Genome Resources, Dec 2024]
    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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    See Smyd3 in Genome Data Viewer
    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. Histone methyltransferase Smyd3 regulates early embryonic lineage commitment in mice. Suzuki S, et al. Reproduction, 2015 Jul. PMID 25918436
    3. 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
    4. 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
    5. 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

    See all (41) 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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H4 methyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 establishment of protein localization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in 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 cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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