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    Tnfsf4 TNF superfamily member 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 89814, updated on 18-Apr-2019

    Summary

    Official Symbol
    Tnfsf4provided by RGD
    Official Full Name
    TNF superfamily member 4provided by RGD
    Primary source
    RGD:619816
    See related
    Ensembl:ENSRNOG00000002968
    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
    Ox40l; Tnlg2b
    Summary
    ligand for the tumor necrosis factor receptor OX40 (CD134); exhibits costimulatory activity for T-cell proliferation [RGD, Feb 2006]
    Expression
    Biased expression in Uterus (RPKM 12.2), Thymus (RPKM 5.5) and 5 other tissues See more
    Orthologs

    Genomic context

    See Tnfsf4 in Genome Data Viewer
    Location:
    13q22
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (79269973..79293775)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 13 NC_005112.3 (84166838..84190566)

    Chromosome 13 - NC_005112.4Genomic Context describing neighboring genes Neighboring gene similar to Actin, cytoplasmic 2 (Gamma-actin) Neighboring gene glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial pseudogene Neighboring gene uncharacterized LOC103692000 Neighboring gene TNF superfamily member 18 Neighboring gene similar to Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)

    Genomic regions, transcripts, and products

    Expression

    • 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

    Related articles in PubMed

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    General gene information

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    cytokine activity IEA
    Inferred from Electronic Annotation
    more info
     
    tumor necrosis factor receptor binding IEA
    Inferred from Electronic Annotation
    more info
     
    tumor necrosis factor receptor binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    tumor necrosis factor receptor superfamily binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    tumor necrosis factor receptor superfamily binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    tumor necrosis factor receptor superfamily binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    tumor necrosis factor receptor superfamily binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    Process Evidence Code Pubs
    CD4-positive, alpha-beta T cell costimulation IEA
    Inferred from Electronic Annotation
    more info
     
    CD4-positive, alpha-beta T cell costimulation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    T cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    T-helper 2 cell activation IEA
    Inferred from Electronic Annotation
    more info
     
    T-helper 2 cell activation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    acute inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    acute inflammatory response ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cellular response to lipopolysaccharide ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cellular response to nitrogen dioxide IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to nitrogen dioxide ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cellular response to prostaglandin E stimulus ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    chemokine (C-C motif) ligand 11 production IEA
    Inferred from Electronic Annotation
    more info
     
    chemokine (C-C motif) ligand 11 production ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cholesterol metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    cholesterol metabolic process ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cytokine production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    defense response to nematode IEA
    Inferred from Electronic Annotation
    more info
     
    defense response to nematode ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    immune response IEA
    Inferred from Electronic Annotation
    more info
     
    inflammatory response IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    inflammatory response ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    memory T cell activation IEA
    Inferred from Electronic Annotation
    more info
     
    memory T cell activation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    negative regulation of DNA-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    negative regulation of T-helper 1 cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of T-helper 1 cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    negative regulation of cytokine secretion IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of cytokine secretion ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    negative regulation of interferon-gamma production IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of interferon-gamma production ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    negative regulation of interleukin-17 production ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    negative regulation of regulatory T cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of regulatory T cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    negative regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of B cell activation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of CD4-positive, alpha-beta T cell costimulation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of CD4-positive, alpha-beta T cell costimulation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of CD4-positive, alpha-beta T cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of T cell costimulation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of T cell cytokine production IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of T cell cytokine production ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of T-helper 2 cell activation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of T-helper 2 cell activation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of T-helper 2 cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of T-helper 2 cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of activated T cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of alpha-beta T cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of alpha-beta T cell proliferation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of immunoglobulin mediated immune response ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of immunoglobulin secretion IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of immunoglobulin secretion ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of inflammatory response ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of interferon-gamma production IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of interferon-gamma production ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of interleukin-10 production IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of interleukin-10 production ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of interleukin-12 production IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of interleukin-12 production ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of interleukin-13 production IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of interleukin-13 production ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of interleukin-2 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of interleukin-4 production IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of interleukin-4 production ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of interleukin-4-dependent isotype switching to IgE isotypes IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of interleukin-4-dependent isotype switching to IgE isotypes ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of interleukin-6 production IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of interleukin-6 production ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of memory T cell activation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of memory T cell activation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of memory T cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of memory T cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of type 2 immune response ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    regulation of adaptive immune response ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    regulation of inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of inflammatory response ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    regulation of signaling receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    response to nitrogen dioxide ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    response to virus IEA
    Inferred from Electronic Annotation
    more info
     
    response to virus ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    Component Evidence Code Pubs
    cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cell surface ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular space ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    tumor necrosis factor ligand superfamily member 4
    Names
    OX40 ligand
    tumor necrosis factor (ligand) superfamily, member 4
    tumor necrosis factor ligand 2b
    tumor necrosis factor superfamily member 4

    NCBI Reference Sequences (RefSeq)

    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_053552.1NP_446004.1  tumor necrosis factor ligand superfamily member 4

      See identical proteins and their annotated locations for NP_446004.1

      Status: PROVISIONAL

      Source sequence(s)
      AF037067
      UniProtKB/Swiss-Prot
      Q9Z2P3
      UniProtKB/TrEMBL
      A0A0U5JAD2
      Related
      ENSRNOP00000003969.3, ENSRNOT00000003969.5
      Conserved Domains (1) summary
      cl00147
      Location:75187
      TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005112.4 Reference Rnor_6.0 Primary Assembly

      Range
      79269973..79293775
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate Rn_Celera

    Genomic

    1. AC_000081.1 Alternate Rn_Celera

      Range
      73499753..73523609
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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