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Setd3 SET domain containing 3 [ Mus musculus (house mouse) ]

Gene ID: 52690, updated on 21-Apr-2024

Summary

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Official Symbol
Setd3provided by MGI
Official Full Name
SET domain containing 3provided by MGI
Primary source
MGI:MGI:1289184
See related
Ensembl:ENSMUSG00000056770 AllianceGenome:MGI:1289184
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
D12Ertd771e; 2610102I01Rik; 2610305M23Rik; 6030490B17Rik
Summary
Enables N-methyltransferase activity and RNA polymerase II-specific DNA-binding transcription factor binding activity. Involved in actin modification; peptidyl-histidine methylation; and regulation of uterine smooth muscle contraction. Acts upstream of or within positive regulation of muscle cell differentiation and positive regulation of transcription by RNA polymerase II. Located in chromatin. Orthologous to human SETD3 (SET domain containing 3, actin histidine methyltransferase). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in cerebellum adult (RPKM 15.5), bladder adult (RPKM 14.4) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
12 F1; 12 59.23 cM
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (108072690..108145616, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (108106431..108179345, complement)

Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 33341 Neighboring gene STARR-seq mESC enhancer starr_33229 Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:109157062-109157245 Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:109164383-109164658 Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:109166259-109166489 Neighboring gene STARR-seq mESC enhancer starr_33230 Neighboring gene B cell leukemia/lymphoma 11B Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:109202967-109203154 Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:109231387-109231540 Neighboring gene STARR-seq mESC enhancer starr_33235 Neighboring gene STARR-positive B cell enhancer ABC_E743 Neighboring gene cyclin K Neighboring gene coiled-coil domain containing 85C Neighboring gene STARR-positive B cell enhancer mm9_chr12:109513689-109513989 Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:109514813-109514922 Neighboring gene hedgehog interacting protein-like 1

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. Enterovirus pathogenesis requires the host methyltransferase SETD3. Diep J, et al. Nat Microbiol, 2019 Dec. PMID 31527793, Free PMC Article
  2. SETD3 is regulated by a couple of microRNAs and plays opposing roles in proliferation and metastasis of hepatocellular carcinoma. Xu L, et al. Clin Sci (Lond), 2019 Oct 30. PMID 31654063
  3. SETD3 is an actin histidine methyltransferase that prevents primary dystocia. Wilkinson AW, et al. Nature, 2019 Jan. PMID 30626964, Free PMC Article
  4. Differentially expressed genes in endothelial differentiation. Ishii H, et al. DNA Cell Biol, 2005 Jul. PMID 16008511
  5. Histone methyltransferase SETD3 regulates muscle differentiation. Eom GH, et al. J Biol Chem, 2011 Oct 7. PMID 21832073, Free PMC Article

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SETD3 regulates endoderm differentiation of mouse embryonic stem cells through canonical Wnt signaling pathway.
    Title: SETD3 regulates endoderm differentiation of mouse embryonic stem cells through canonical Wnt signaling pathway.
  2. Enterovirus pathogenesis requires the host methyltransferase SETD3. SETD3 is essential for in vivo replication and pathogenesis in multiple mouse models for EV infection, including CV-A10, EV-A71 and EV-D68.
    Title: Enterovirus pathogenesis requires the host methyltransferase SETD3.
  3. SETD3 is regulated by a couple of microRNAs and plays opposing roles in proliferation and metastasis of hepatocellular carcinoma.
    Title: SETD3 is regulated by a couple of microRNAs and plays opposing roles in proliferation and metastasis of hepatocellular carcinoma.
  4. results identify a mammalian histidine methyltransferase and uncover a pivotal role for SETD3 and actin His73 methylation in the regulation of smooth muscle contractility; data also support the broader hypothesis that protein histidine methylation acts as a common regulatory mechanism
    Title: SETD3 is an actin histidine methyltransferase that prevents primary dystocia.
  5. SETD3 is a H3K4/K36 methyltransferase and plays an important role in the transcriptional regulation of muscle cell differentiation
    Title: Histone methyltransferase SETD3 regulates muscle differentiation.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Gene trapped (1) 
  • Targeted (2) 
  • Endonuclease-mediated (3) 

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-specific DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables actin binding IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K36 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone H3K36 methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3K4 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone H3K4 methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein-L-histidine N-tele-methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein-L-histidine N-tele-methyltransferase activity ISO
Inferred from Sequence Orthology
more info
  
enables transcription coactivator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables transferase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in actin modification IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in actin modification ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in peptidyl-histidine methylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in peptidyl-histidine methylation ISO
Inferred from Sequence Orthology
more info
  
involved_in peptidyl-lysine monomethylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in peptidyl-lysine trimethylation IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within positive regulation of muscle cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in regulation of uterine smooth muscle contraction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
actin-histidine N-methyltransferase
Names
SET domain-containing protein 3
endothelial differentiation inhibitory protein D10
histone-lysine N-methyltransferase setd3
protein-L-histidine N-tele-methyltransferase
NP_001351195.1
NP_001351196.1
NP_001351197.1
NP_001351198.1
NP_001351199.1
NP_082538.2
XP_006516141.4
XP_006516144.4
XP_017170622.1
XP_030102671.1

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_001364266.1 → NP_001351195.1  actin-histidine N-methyltransferase isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC152059, AL583892
    Conserved Domains (2) summary
    pfam00856
    Location:112 → 146
    SET; SET domain
    pfam09273
    Location:357 → 482
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  2. NM_001364267.1 → NP_001351196.1  actin-histidine N-methyltransferase isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC152059, AL583892
    Conserved Domains (2) summary
    pfam00856
    Location:72 → 106
    SET; SET domain
    pfam09273
    Location:317 → 442
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  3. NM_001364268.1 → NP_001351197.1  actin-histidine N-methyltransferase isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC152059, AL583892
    Conserved Domains (2) summary
    pfam00856
    Location:105 → 256
    SET; SET domain
    pfam09273
    Location:292 → 417
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  4. NM_001364269.1 → NP_001351198.1  actin-histidine N-methyltransferase isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC152059, AL583892
    Conserved Domains (2) summary
    pfam09273
    Location:222 → 347
    Rubis-subs-bind; Rubisco LSMT substrate-binding
    cd19176
    Location:1 → 201
    SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins

  5. NM_001364270.1 → NP_001351199.1  actin-histidine N-methyltransferase isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC152059, AL583892
    Conserved Domains (2) summary
    pfam09273
    Location:164 → 289
    Rubis-subs-bind; Rubisco LSMT substrate-binding
    cd19176
    Location:1 → 143
    SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins

  6. NM_028262.3 → NP_082538.2  actin-histidine N-methyltransferase isoform 2

    See identical proteins and their annotated locations for NP_082538.2

    Status: VALIDATED

    Source sequence(s)
    AK031371, BC016123, BY087049
    Consensus CDS
    CCDS26159.1
    UniProtKB/Swiss-Prot
    Q6PEN3, Q8CD86, Q8CDX8, Q91WC0, Q9CZZ1
    Related
    ENSMUSP00000066413.8, ENSMUST00000071095.14
    Conserved Domains (2) summary
    pfam00856
    Location:105 → 180
    SET; SET domain
    pfam09273
    Location:353 → 475
    Rubis-subs-bind; Rubisco LSMT substrate-binding

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_000078.7 Reference GRCm39 C57BL/6J

    Range
    108072690..108145616 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017315133.1 → XP_017170622.1  actin-histidine N-methyltransferase isoform X2

    Conserved Domains (2) summary
    pfam09273
    Location:299 → 424
    Rubis-subs-bind; Rubisco LSMT substrate-binding
    cd19176
    Location:87 → 278
    SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins

  2. XM_006516081.4 → XP_006516144.4  actin-histidine N-methyltransferase isoform X3

    Conserved Domains (2) summary
    pfam09273
    Location:164 → 289
    Rubis-subs-bind; Rubisco LSMT substrate-binding
    cd19176
    Location:1 → 143
    SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins

  3. XM_030246811.2 → XP_030102671.1  actin-histidine N-methyltransferase isoform X1

    Conserved Domains (2) summary
    pfam09273
    Location:222 → 347
    Rubis-subs-bind; Rubisco LSMT substrate-binding
    cd19176
    Location:1 → 201
    SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins

  4. XM_006516078.5 → XP_006516141.4  actin-histidine N-methyltransferase isoform X1

    Conserved Domains (2) summary
    pfam09273
    Location:222 → 347
    Rubis-subs-bind; Rubisco LSMT substrate-binding
    cd19176
    Location:1 → 201
    SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins

RNA

  1. XR_003950066.2 RNA Sequence

  2. XR_003950065.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q91WC0.1 GenPept UniProtKB/Swiss-Prot:Q91WC0

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