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

Gene ID: 498295, updated on 14-Nov-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 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, Nov 2024]
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
  
involved_in methylation IEA
Inferred from Electronic Annotation
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
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
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

    Related
    ENSRNOP00000095032.1, ENSRNOT00000102694.2
Nucleotide Protein Strain
Heading Accession and Version

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