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    Lta lymphotoxin alpha [ Rattus norvegicus (Norway rat) ]

    Gene ID: 25008, updated on 27-Nov-2024

    Summary

    Symbol
    Ltaprovided by RGD
    Full Name
    lymphotoxin alphaprovided by RGD
    Primary source
    RGD:3020
    See related
    EnsemblRapid:ENSRNOG00000000838 AllianceGenome:RGD:3020
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Tnfb
    Summary
    Predicted to enable cytokine activity. Involved in several processes, including negative regulation of fibroblast proliferation; positive regulation of glial cell proliferation; and response to lipopolysaccharide. Located in extracellular space. Biomarker of cystitis. Human ortholog(s) of this gene implicated in several diseases, including artery disease (multiple); autoimmune disease (multiple); glucose metabolism disease (multiple); leishmaniasis (multiple); and lung disease (multiple). Orthologous to human LTA (lymphotoxin alpha). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Spleen (RPKM 15.3), Thymus (RPKM 13.0) and 1 other tissue See more
    Orthologs
    NEW
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    Genomic context

    See Lta in Genome Data Viewer
    Location:
    20p12
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (3622291..3625852)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (3618853..3621324)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (4851889..4854677)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene DExD-box helicase 39B Neighboring gene small nucleolar RNA SNORD83 Neighboring gene ATPase H+ transporting V1 subunit G2 Neighboring gene NFKB inhibitor like 1 Neighboring gene tumor necrosis factor Neighboring gene lymphotoxin beta

    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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables cytokine activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables tumor necrosis factor receptor binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in cell surface receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within defense response to Gram-positive bacterium ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within humoral immune response ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within lymph node development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of fibroblast proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of canonical NF-kappaB signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within positive regulation of chronic inflammatory response to antigenic stimulus ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of extrinsic apoptotic signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of glial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of humoral immune response mediated by circulating immunoglobulin ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of type II interferon production ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in response to hypoxia IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to lipopolysaccharide IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to nutrient IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to xenobiotic stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    lymphotoxin-alpha
    Names
    LT-alpha
    TNF-beta
    lymphotoxin A
    lymphotoxin alpha (TNF superfamily, member 1)
    lymphotoxin-alpha-like
    tumor necrosis factor beta
    tumor necrosis factor ligand superfamily member 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_080769.2NP_542947.1  lymphotoxin-alpha precursor

      See identical proteins and their annotated locations for NP_542947.1

      Status: VALIDATED

      Source sequence(s)
      BX883046
      UniProtKB/Swiss-Prot
      Q06332
      Related
      ENSRNOP00000001111.1, ENSRNOT00000001111.4
      Conserved Domains (1) summary
      pfam00229
      Location:74202
      TNF; TNF(tumor Necrosis Factor) family

    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_086038.1 Reference GRCr8

      Range
      3622291..3625852
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039098430.2XP_038954358.1  lymphotoxin-alpha isoform X1

      UniProtKB/Swiss-Prot
      Q06332
      Conserved Domains (1) summary
      pfam00229
      Location:74202
      TNF; TNF(tumor Necrosis Factor) family