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    Setd4 SET domain containing 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 245975, updated on 9-Dec-2024

    Summary

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    Symbol
    Setd4provided by RGD
    Full Name
    SET domain containing 4provided by RGD
    Primary source
    RGD:619899
    See related
    EnsemblRapid:ENSRNOG00000001699 AllianceGenome:RGD:619899
    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
    Also known as
    Rda279
    Summary
    Predicted to enable protein-lysine N-methyltransferase activity and transcription coactivator activity. Predicted to be involved in several processes, including positive regulation of inflammatory response; positive regulation of macromolecule biosynthetic process; and regulation of cell proliferation in bone marrow. Predicted to be located in cytosol and nucleus. Orthologous to human SETD4 (SET domain containing 4). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 53.0), Spleen (RPKM 35.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Setd4 in Genome Data Viewer
    Location:
    11q11
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (46315340..46344024, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (32829509..32859162, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (33781869..33803121, complement)

    Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134480977 Neighboring gene microRNA 802 Neighboring gene RGD1562683 Neighboring gene U4 spliceosomal RNA Neighboring gene TruB pseudouridine synthase family member 2, pseudogene 1 Neighboring gene carbonyl reductase 1

    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
    • 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. SET Domain-Containing Protein 4 Epigenetically Controls Breast Cancer Stem Cell Quiescence. Ye S, et al. Cancer Res, 2019 Sep 15. PMID 31308046
    2. SET domain-containing Protein 4 (SETD4) is a Newly Identified Cytosolic and Nuclear Lysine Methyltransferase involved in Breast Cancer Cell Proliferation. Faria JA, et al. J Cancer Sci Ther, 2013 Jan 21. PMID 24738023, Free PMC Article
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H4K20 methyltransferase activity ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of interleukin-6 production ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of cell proliferation in bone marrow ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol 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
    SET domain-containing protein 4
    Names
    hypothetical protein RDA279
    NP_001107219.1
    XP_038943899.1
    XP_038943907.1
    XP_063126348.1
    XP_063126350.1
    XP_063126351.1
    XP_063126352.1

    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_001113747.1 → NP_001107219.1  SET domain-containing protein 4

      See identical proteins and their annotated locations for NP_001107219.1

      Status: PROVISIONAL

      Source sequence(s)
      BC158669
      UniProtKB/TrEMBL
      A6JLL4, B0BN36
      Related
      ENSRNOP00000002308.5, ENSRNOT00000002308.7
      Conserved Domains (1) summary
      pfam09273
      Location:316 → 424
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    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_086029.1 Reference GRCr8

      Range
      46315340..46344024 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039087979.1 → XP_038943907.1  SET domain-containing protein 4 isoform X2

      UniProtKB/TrEMBL
      A6JLL5
      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_039087971.1 → XP_038943899.1  SET domain-containing protein 4 isoform X1

      UniProtKB/TrEMBL
      A6JLL5
      Conserved Domains (2) summary
      cd19177
      Location:23 → 241
      SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins
      pfam09273
      Location:268 → 379
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    3. XM_063270278.1 → XP_063126348.1  SET domain-containing protein 4 isoform X1

      UniProtKB/TrEMBL
      A6JLL5

    4. XM_063270280.1 → XP_063126350.1  SET domain-containing protein 4 isoform X2

      UniProtKB/TrEMBL
      A6JLL5

    5. XM_063270281.1 → XP_063126351.1  SET domain-containing protein 4 isoform X3

    6. XM_063270282.1 → XP_063126352.1  SET domain-containing protein 4 isoform X4

    RNA

    1. XR_005490970.2 RNA Sequence

    2. XR_594989.4 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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