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

    Gene ID: 224440, updated on 27-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
    • 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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