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    Smyd3 SET and MYND domain containing 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 498295, updated on 18-Sep-2024

    Summary

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    Official Symbol
    Smyd3provided by RGD
    Official Full Name
    SET and MYND domain containing 3provided by RGD
    Primary source
    RGD:1562635
    See related
    EnsemblRapid:ENSRNOG00000066304 AllianceGenome:RGD:1562635
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable RNA polymerase II complex binding activity; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and histone-lysine N-methyltransferase activity. Predicted to act upstream of or within several processes, including cellular response to dexamethasone stimulus; nucleosome assembly; and regulation of protein phosphorylation. Predicted to be located in cytosol and nucleoplasm. Orthologous to human SMYD3 (SET and MYND domain containing 3). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Brain (RPKM 59.6), Kidney (RPKM 40.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Smyd3 in Genome Data Viewer
    Location:
    13q26
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (93241274..93798221, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (90709263..91266209, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (97330120..97807813, complement)

    Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene kinesin family member 26B Neighboring gene uncharacterized LOC134481605 Neighboring gene uncharacterized LOC134481604 Neighboring gene uncharacterized LOC108352580 Neighboring gene uncharacterized LOC108352579 Neighboring gene ribosomal protein L23,pseudogene 6 Neighboring gene uncharacterized LOC108352581 Neighboring gene transcription factor B2, mitochondrial Neighboring gene consortin, connexin sorting protein

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Smyd3-PARP16 axis accelerates unfolded protein response and vascular aging. Yang D, et al. Aging (Albany NY), 2020 Nov 3. PMID 33144524, Free PMC Article
    2. C-terminal domain of SMYD3 serves as a unique HSP90-regulated motif in oncogenesis. Brown MA, et al. Oncotarget, 2015 Feb 28. PMID 25738358, Free PMC Article
    3. Identification and characterization of Smyd2: a split SET/MYND domain-containing histone H3 lysine 36-specific methyltransferase that interacts with the Sin3 histone deacetylase complex. Brown MA, et al. Mol Cancer, 2006 Jun 28. PMID 16805913, Free PMC Article
    4. The methyltransferase SMYD3 mediates the recruitment of transcriptional cofactors at the myostatin and c-Met genes and regulates skeletal muscle atrophy. Proserpio V, et al. Genes Dev, 2013 Jun 1. PMID 23752591, Free PMC Article
    5. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Black JC, et al. Mol Cell, 2012 Nov 30. PMID 23200123, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Smyd3-PARP16 axis accelerates unfolded protein response and vascular aging.
      Title: Smyd3-PARP16 axis accelerates unfolded protein response and vascular aging.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC114517

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K36 dimethyltransferase activity ISO
    Inferred from Sequence Orthology
    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
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within cellular response to dexamethasone stimulus ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within establishment of protein localization ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within myotube cell development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of protein kinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within nucleosome assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of peptidyl-serine phosphorylation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    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
    		  
    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
    NP_001020933.1
    XP_038946915.1
    XP_038946916.1
    XP_038946917.1
    XP_063128617.1

    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_001025762.1 → NP_001020933.1  histone-lysine N-methyltransferase SMYD3

      See identical proteins and their annotated locations for NP_001020933.1

      Status: PROVISIONAL

      Source sequence(s)
      BC097455
      UniProtKB/TrEMBL
      A6JGF2, Q4V8B9
      Related
      ENSRNOP00000084109.1, ENSRNOT00000105406.2
      Conserved Domains (2) summary
      pfam00856
      Location:201 → 239
      SET; SET domain
      pfam01753
      Location:49 → 87
      zf-MYND; MYND finger

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086031.1 Reference GRCr8

      Range
      93241274..93798221 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039090987.2 → XP_038946915.1  histone-lysine N-methyltransferase SMYD3 isoform X1

      UniProtKB/TrEMBL
      A6JGF2
      Conserved Domains (2) summary
      cd19203
      Location:47 → 217
      SET_SMYD3; SET domain (including post-SET domain) found in SET and MYND domain-containing protein 3 (SMYD3) and similar proteins
      pfam01753
      Location:2 → 36
      zf-MYND; MYND finger

    2. XM_039090988.2 → XP_038946916.1  histone-lysine N-methyltransferase SMYD3 isoform X2

      UniProtKB/TrEMBL
      A6JGF2
      Conserved Domains (2) summary
      cd19203
      Location:44 → 214
      SET_SMYD3; SET domain (including post-SET domain) found in SET and MYND domain-containing protein 3 (SMYD3) and similar proteins
      pfam01753
      Location:3 → 33
      zf-MYND; MYND finger

    3. XM_039090989.2 → XP_038946917.1  histone-lysine N-methyltransferase SMYD3 isoform X3

      UniProtKB/TrEMBL
      A6JGF3
      Conserved Domains (1) summary
      cl40432
      Location:1 → 120
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

    4. XM_063272547.1 → XP_063128617.1  histone-lysine N-methyltransferase SMYD3 isoform X4

      UniProtKB/TrEMBL
      A0A8I6ANX2
      Related
      ENSRNOP00000095032.1, ENSRNOT00000102694.2
    Nucleotide Protein Strain
    Heading Accession and Version

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