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    LTB lymphotoxin beta [ Homo sapiens (human) ]

    Gene ID: 4050, updated on 25-May-2017
    Official Symbol
    LTBprovided by HGNC
    Official Full Name
    lymphotoxin betaprovided by HGNC
    Primary source
    HGNC:HGNC:6711
    See related
    Ensembl:ENSG00000227507 MIM:600978; Vega:OTTHUMG00000031136
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    p33; TNFC; TNFSF3; TNLG1C
    Summary
    Lymphotoxin beta is a type II membrane protein of the TNF family. It anchors lymphotoxin-alpha to the cell surface through heterotrimer formation. The predominant form on the lymphocyte surface is the lymphotoxin-alpha 1/beta 2 complex (e.g. 1 molecule alpha/2 molecules beta) and this complex is the primary ligand for the lymphotoxin-beta receptor. The minor complex is lymphotoxin-alpha 2/beta 1. LTB is an inducer of the inflammatory response system and involved in normal development of lymphoid tissue. Lymphotoxin-beta isoform b is unable to complex with lymphotoxin-alpha suggesting a function for lymphotoxin-beta which is independent of lympyhotoxin-alpha. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
    Orthologs
    Location:
    6p21.33
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 6 NC_000006.12 (31580558..31582425, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31548335..31550202, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100287329 Neighboring gene lymphotoxin alpha Neighboring gene tumor necrosis factor Neighboring gene leukocyte specific transcript 1 Neighboring gene natural cytotoxicity triggering receptor 3 Neighboring gene ubiquinol-cytochrome c reductase hinge protein pseudogene 1

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    NHGRI GWA Catalog
    Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02).
    NHGRI GWA Catalog
    Identification of candidate loci at 6p21 and 21q22 in a genome-wide association study of cardiac manifestations of neonatal lupus.
    NHGRI GWA Catalog

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat upregulates the expression of lymphotoxin beta (TNF superfamily, member 3, LTB) gene in mammary epithelial cells PubMed

    Go to the HIV-1, Human Interaction Database

    • Cytokine Signaling in Immune system, organism-specific biosystem (from REACTOME)
      Cytokine Signaling in Immune system, organism-specific biosystemCytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concen...
    • Cytokine-cytokine receptor interaction, organism-specific biosystem (from KEGG)
      Cytokine-cytokine receptor interaction, organism-specific biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
    • Cytokine-cytokine receptor interaction, conserved biosystem (from KEGG)
      Cytokine-cytokine receptor interaction, conserved biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
    • Immune System, organism-specific biosystem (from REACTOME)
      Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
    • NF-kappa B signaling pathway, organism-specific biosystem (from KEGG)
      NF-kappa B signaling pathway, organism-specific biosystemNuclear factor-kappa B (NF-kappa B) is the generic name of a family of transcription factors that function as dimers and regulate genes involved in immunity, inflammation and cell survival. There are...
    • NF-kappa B signaling pathway, conserved biosystem (from KEGG)
      NF-kappa B signaling pathway, conserved biosystemNuclear factor-kappa B (NF-kappa B) is the generic name of a family of transcription factors that function as dimers and regulate genes involved in immunity, inflammation and cell survival. There are...
    • Rheumatoid arthritis, organism-specific biosystem (from KEGG)
      Rheumatoid arthritis, organism-specific biosystemRheumatoid arthritis (RA) is a chronic autoimmune joint disease where persistent inflammation affects bone remodeling leading to progressive bone destruction. In RA, abnormal activation of the immune...
    • Rheumatoid arthritis, conserved biosystem (from KEGG)
      Rheumatoid arthritis, conserved biosystemRheumatoid arthritis (RA) is a chronic autoimmune joint disease where persistent inflammation affects bone remodeling leading to progressive bone destruction. In RA, abnormal activation of the immune...
    • Spinal Cord Injury, organism-specific biosystem (from WikiPathways)
      Spinal Cord Injury, organism-specific biosystemThis pathway provides an overview of cell types, therapeutic targets, drugs, new proposed targets and pathways implicated in spinal cord injury. Spinal cord injury is a complex multistep process that...
    • TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway, organism-specific biosystem (from REACTOME)
      TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway, organism-specific biosystemActivation of NF-kB is fundamental to signal transduction by members of the TNFRSF. Expression of NF-kB target genes is essential for mounting innate immune responses to infectious microorganisms but...
    • TNFR2 non-canonical NF-kB pathway, organism-specific biosystem (from REACTOME)
      TNFR2 non-canonical NF-kB pathway, organism-specific biosystemTumor necrosis factor-alpha (TNFA) exerts a wide range of biological effects through TNF receptor 1 (TNFR1) and TNF receptor 2 (TNFR2). Under normal physiological conditions TNFR2 exhibits more restr...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    cytokine activity IEA
    Inferred from Electronic Annotation
    more info
     
    receptor binding TAS
    Traceable Author Statement
    more info
    PubMed 
    tumor necrosis factor receptor binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    cell-cell signaling TAS
    Traceable Author Statement
    more info
    PubMed 
    gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    immune response IEA
    Inferred from Electronic Annotation
    more info
     
    lymph node development IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of interleukin-12 biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    signal transduction TAS
    Traceable Author Statement
    more info
    PubMed 
    skin development IEA
    Inferred from Electronic Annotation
    more info
     
    tumor necrosis factor-mediated signaling pathway TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    cellular_component ND
    No biological Data available
    more info
     
    extracellular space IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    Preferred Names
    lymphotoxin-beta
    Names
    LT-beta
    TNF superfamily member 3
    TNF-C
    lymphotoxin beta (TNF superfamily, member 3)
    tumor necrosis factor C
    tumor necrosis factor ligand 1C
    tumor necrosis factor ligand superfamily member 3

    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_002341.1NP_002332.1  lymphotoxin-beta isoform a

      See identical proteins and their annotated locations for NP_002332.1

      Status: REVIEWED

      Description
      Transcript Variant: This splice variant (1) represents the longer transcript, encodes the longer isoform (a), and can form the heterotrimeric complex with lymphotoxin-alpha.
      Source sequence(s)
      L11015
      Consensus CDS
      CCDS4703.1
      UniProtKB/Swiss-Prot
      Q06643
      UniProtKB/TrEMBL
      Q5STB2
      Related
      ENSP00000410481.2, OTTHUMP00000029185, ENST00000429299.2, OTTHUMT00000076239
      Conserved Domains (1) summary
      pfam00229
      Location:102243
      TNF; TNF(Tumour Necrosis Factor) family
    2. NM_009588.1NP_033666.1  lymphotoxin-beta isoform b

      See identical proteins and their annotated locations for NP_033666.1

      Status: REVIEWED

      Description
      Transcript Variant: This splice variant (2) lacks an exon in the coding region, compared to variant 1. The encoded protein (isoform b) has a premature stop codon and lacks the majority of the extracellular domain, compared to isoform a. This loss impairs its ability to complex with lympytoxin-alpha.
      Source sequence(s)
      U89922
      Consensus CDS
      CCDS4704.1
      UniProtKB/Swiss-Prot
      Q06643
      Related
      ENSP00000416113.2, OTTHUMP00000215145, ENST00000446745.2, OTTHUMT00000076240

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p7 Primary Assembly

      Range
      31580558..31582425 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p7 ALT_REF_LOCI_1

    Genomic

    1. NT_167244.2 Reference GRCh38.p7 ALT_REF_LOCI_1

      Range
      2913137..2915004 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p7 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p7 ALT_REF_LOCI_2

      Range
      3057845..3059712 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p7 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p7 ALT_REF_LOCI_3

      Range
      2828291..2830158 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p7 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p7 ALT_REF_LOCI_4

      Range
      2885599..2887466 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p7 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p7 ALT_REF_LOCI_5

      Range
      2922456..2924323 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p7 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p7 ALT_REF_LOCI_6

      Range
      2836379..2838246 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p7 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p7 ALT_REF_LOCI_7

      Range
      2879838..2881705 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018917.2 Alternate CHM1_1.1

      Range
      31550467..31552334 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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