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

Gene ID: 245975, updated on 27-Nov-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, Nov 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

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

  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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