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Setd4 SET domain containing 4 [ Mus musculus (house mouse) ]

Gene ID: 224440, updated on 14-Nov-2024

Summary

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Official Symbol
Setd4provided by MGI
Official Full Name
SET domain containing 4provided by MGI
Primary source
MGI:MGI:2136890
See related
Ensembl:ENSMUSG00000022948 AllianceGenome:MGI:2136890
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
ORF21; C21orf18
Summary
Enables histone H3K4 methyltransferase activity. Involved in several processes, including positive regulation of cytokine production; positive regulation of inflammatory response; and regulation of cell proliferation in bone marrow. Predicted to be located in cytosol and nucleus. Is expressed in several structures, including alimentary system; genitourinary system; heart; nervous system; and sensory organ. Orthologous to human SETD4 (SET domain containing 4). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in CNS E18 (RPKM 1.7), CNS E14 (RPKM 1.5) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Setd4 in Genome Data Viewer
Location:
16 C4; 16 54.52 cM
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (93380345..93401693, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (93583457..93604791, complement)

Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 1700029J03 gene Neighboring gene STARR-seq mESC enhancer starr_41529 Neighboring gene STARR-seq mESC enhancer starr_41530 Neighboring gene STARR-seq mESC enhancer starr_41531 Neighboring gene predicted gene, 30695 Neighboring gene STARR-seq mESC enhancer starr_41532 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:93572605-93572851 Neighboring gene STARR-seq mESC enhancer starr_41534 Neighboring gene STARR-positive B cell enhancer mm9_chr16:93607761-93608062 Neighboring gene carbonyl reductase 1 Neighboring gene carbonyl reductase 1B

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 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. Activated dormant stem cells recover spermatogenesis in chemoradiotherapy-induced infertility. Yang SH, et al. Cell Rep, 2024 Aug 27. PMID 39096488
  2. The novel methyltransferase SETD4 regulates TLR agonist-induced expression of cytokines through methylation of lysine 4 at histone 3 in macrophages. Zhong Y, et al. Mol Immunol, 2019 Oct. PMID 31376731
  3. SETD4 in the Proliferation, Migration, Angiogenesis, Myogenic Differentiation and Genomic Methylation of Bone Marrow Mesenchymal Stem Cells. Liao X, et al. Stem Cell Rev Rep, 2021 Aug. PMID 33506343
  4. SETD4-mediated KU70 methylation suppresses apoptosis. Wang Y, et al. Cell Rep, 2022 May 10. PMID 35545041, Free PMC Article
  5. SETD4-expressing cells contribute to pancreatic development and response to cerulein induced pancreatitis injury. Tian JZ, et al. Sci Rep, 2021 Jun 15. PMID 34131249, Free PMC Article

See all (34) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SETD4-mediated KU70 methylation suppresses apoptosis.
    Title: SETD4-mediated KU70 methylation suppresses apoptosis.
  2. SETD4 in the Proliferation, Migration, Angiogenesis, Myogenic Differentiation and Genomic Methylation of Bone Marrow Mesenchymal Stem Cells.
    Title: SETD4 in the Proliferation, Migration, Angiogenesis, Myogenic Differentiation and Genomic Methylation of Bone Marrow Mesenchymal Stem Cells.
  3. Setd4 controlled quiescent c-Kit(+) cells contribute to cardiac neovascularization of capillaries beyond activation.
    Title: Setd4 controlled quiescent c-Kit(+) cells contribute to cardiac neovascularization of capillaries beyond activation.
  4. SETD4-expressing cells contribute to pancreatic development and response to cerulein induced pancreatitis injury.
    Title: SETD4-expressing cells contribute to pancreatic development and response to cerulein induced pancreatitis injury.
  5. Loss of Setd4 delays radiation-induced thymic lymphoma in mice.
    Title: Loss of Setd4 delays radiation-induced thymic lymphoma in mice.
Submit: New GeneRIF Correction

Variation

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Alleles

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

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables histone H3K36 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
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 histone H3K4 monomethyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H4K20 methyltransferase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H4K20 methyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables histone H4K20 monomethyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H4K20me methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables transcription coactivator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chromatin remodeling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in inflammatory response IEA
Inferred from Electronic Annotation
more info
  
involved_in methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of inflammatory response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of interleukin-6 production IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of tumor necrosis factor production IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of cell proliferation in bone marrow IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
located_in cytosol ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
SET domain-containing protein 4
NP_001404050.1
NP_001404051.1
NP_001404052.1
NP_001404053.1
NP_001404054.1
NP_001404055.1
NP_001404056.1
NP_001404057.1
NP_001404058.1
NP_001404059.1
NP_001404060.1
NP_663457.2
XP_011244423.1
XP_017172462.1
XP_017172466.1
XP_030104955.1
XP_030104957.1
XP_030104958.1
XP_036015803.1

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_001417121.1 → NP_001404050.1  SET domain-containing protein 4 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC160993
    UniProtKB/Swiss-Prot
    G3X9W6, P58467

  2. NM_001417122.1 → NP_001404051.1  SET domain-containing protein 4 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC160993
    UniProtKB/Swiss-Prot
    G3X9W6, P58467

  3. NM_001417123.1 → NP_001404052.1  SET domain-containing protein 4 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC160993
    UniProtKB/Swiss-Prot
    G3X9W6, P58467

  4. NM_001417124.1 → NP_001404053.1  SET domain-containing protein 4 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC160993
    UniProtKB/Swiss-Prot
    G3X9W6, P58467

  5. NM_001417125.1 → NP_001404054.1  SET domain-containing protein 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC160993

  6. NM_001417126.1 → NP_001404055.1  SET domain-containing protein 4 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC160993

  7. NM_001417127.1 → NP_001404056.1  SET domain-containing protein 4 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC160993
    Related
    ENSMUSP00000156698.2, ENSMUST00000232870.2

  8. NM_001417128.1 → NP_001404057.1  SET domain-containing protein 4 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC160993

  9. NM_001417129.1 → NP_001404058.1  SET domain-containing protein 4 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC160993

  10. NM_001417130.1 → NP_001404059.1  SET domain-containing protein 4 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC160993

  11. NM_001417131.1 → NP_001404060.1  SET domain-containing protein 4 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC160993

  12. NM_145482.4 → NP_663457.2  SET domain-containing protein 4 isoform 1

    See identical proteins and their annotated locations for NP_663457.2

    Status: VALIDATED

    Source sequence(s)
    AC160993
    Consensus CDS
    CCDS28340.1
    UniProtKB/Swiss-Prot
    G3X9W6, P58467
    UniProtKB/TrEMBL
    A0A3B2WB63
    Related
    ENSMUSP00000156723.2, ENSMUST00000233931.2
    Conserved Domains (2) summary
    pfam09273
    Location:313 → 424
    Rubis-subs-bind; Rubisco LSMT substrate-binding
    cd19177
    Location:49 → 286
    SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins

RNA

  1. NR_184423.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC160993

  2. NR_184424.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC160993

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_000082.7 Reference GRCm39 C57BL/6J

    Range
    93380345..93401693 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030249098.2 → XP_030104958.1  SET domain-containing protein 4 isoform X4

    UniProtKB/TrEMBL
    A0A3B2WB63
    Conserved Domains (2) summary
    cd19177
    Location:1 → 225
    SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins
    pfam09273
    Location:252 → 363
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  2. XM_017316973.3 → XP_017172462.1  SET domain-containing protein 4 isoform X2

    UniProtKB/TrEMBL
    A0A3B2WB63
    Conserved Domains (2) summary
    cd19177
    Location:49 → 286
    SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins
    pfam09273
    Location:313 → 395
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  3. XM_030249095.2 → XP_030104955.1  SET domain-containing protein 4 isoform X3

    UniProtKB/TrEMBL
    A0A3B2WB63
    Conserved Domains (2) summary
    pfam09273
    Location:262 → 373
    Rubis-subs-bind; Rubisco LSMT substrate-binding
    cd19177
    Location:3 → 235
    SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins

  4. XM_030249097.2 → XP_030104957.1  SET domain-containing protein 4 isoform X4

    UniProtKB/TrEMBL
    A0A3B2WB63
    Conserved Domains (2) summary
    cd19177
    Location:1 → 225
    SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins
    pfam09273
    Location:252 → 363
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  5. XM_011246121.4 → XP_011244423.1  SET domain-containing protein 4 isoform X3

    See identical proteins and their annotated locations for XP_011244423.1

    UniProtKB/TrEMBL
    A0A3B2WB63
    Conserved Domains (2) summary
    pfam09273
    Location:262 → 373
    Rubis-subs-bind; Rubisco LSMT substrate-binding
    cd19177
    Location:3 → 235
    SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins

  6. XM_036159910.1 → XP_036015803.1  SET domain-containing protein 4 isoform X5

    Conserved Domains (1) summary
    cd19177
    Location:49 → 286
    SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins

  7. XM_017316977.3 → XP_017172466.1  SET domain-containing protein 4 isoform X6

    UniProtKB/TrEMBL
    A0A3B2WCJ7
    Related
    ENSMUSP00000156553.2, ENSMUST00000154355.3
    Conserved Domains (1) summary
    cd19177
    Location:49 → 241
    SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins

RNA

  1. XR_004939189.1 RNA Sequence

  2. XR_001781817.3 RNA Sequence

  3. XR_003951789.2 RNA Sequence

  4. XR_003951787.2 RNA Sequence

  5. XR_001781818.3 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P58467.2 GenPept UniProtKB/Swiss-Prot:P58467

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