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    LTA lymphotoxin alpha [ Homo sapiens (human) ]

    Gene ID: 4049, updated on 25-Jun-2017
    Official Symbol
    LTAprovided by HGNC
    Official Full Name
    lymphotoxin alphaprovided by HGNC
    Primary source
    HGNC:HGNC:6709
    See related
    Ensembl:ENSG00000226979 MIM:153440; Vega:OTTHUMG00000031135
    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
    LT; TNFB; TNFSF1; TNLG1E
    Summary
    The encoded protein, a member of the tumor necrosis factor family, is a cytokine produced by lymphocytes. The protein is highly inducible, secreted, and forms heterotrimers with lymphotoxin-beta which anchor lymphotoxin-alpha to the cell surface. This protein also mediates a large variety of inflammatory, immunostimulatory, and antiviral responses, is involved in the formation of secondary lymphoid organs during development and plays a role in apoptosis. Genetic variations in this gene are associated with susceptibility to leprosy type 4, myocardial infarction, non-Hodgkin's lymphoma, and psoriatic arthritis. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012]
    Orthologs
    Location:
    6p21.33
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 6 NC_000006.12 (31560550..31574324)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31539876..31542101)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATP6V1G2-DDX39B readthrough (NMD candidate) Neighboring gene ATPase H+ transporting V1 subunit G2 Neighboring gene uncharacterized LOC100287329 Neighboring gene NFKB inhibitor like 1 Neighboring gene tumor necrosis factor Neighboring gene lymphotoxin beta

    • 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?

    Associated conditions

    Description Tests
    Leprosy 4
    MedGen: C1970254 OMIM: 610988 GeneReviews: Not available
    Compare labs
    Myocardial infarction 1
    MedGen: C1838021 OMIM: 608446 GeneReviews: Not available
    Compare labs
    Psoriatic arthritis, susceptibility to
    MedGen: C1835223 OMIM: 607507 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    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
    Envelope surface glycoprotein gp120 env In endometrial epithelium-derived cells, gp120 from CCR5-tropic HIV-1 increases the release of monocytes/chemokines-attracting chemokines (IL-8 and GRO) and proinflammatory cytokines (TNF-beta and IL-1alpha) PubMed
    Tat tat HIV-1 Tat101 upregulates the expression of lymphotoxin alpha (LTA; TNFB) in Jurkat cells PubMed
    tat HIV-1 Tat downregulates TNF-beta expression in central nervous system-derived glial cells, suggesting a novel mechanism whereby HIV-1 is able to establish latent infection of glial cells PubMed
    tat HIV-1 Tat upregulates TNF-beta expression through binding to a TAR-like RNA structure in the TNF-beta promoter PubMed

    Go to the HIV-1, Human Interaction Database

    • Apoptosis, organism-specific biosystem (from WikiPathways)
      Apoptosis, organism-specific biosystemApoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and ...
    • 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 ...
    • HTLV-I infection, organism-specific biosystem (from KEGG)
      HTLV-I infection, organism-specific biosystemHuman T-lymphotropic virus type 1 (HTLV-1) is a pathogenic retrovirus that is associated with adult T-cell leukemia/lymphoma (ATL). It is also strongly implicated in non-neoplastic chronic inflammato...
    • HTLV-I infection, conserved biosystem (from KEGG)
      HTLV-I infection, conserved biosystemHuman T-lymphotropic virus type 1 (HTLV-1) is a pathogenic retrovirus that is associated with adult T-cell leukemia/lymphoma (ATL). It is also strongly implicated in non-neoplastic chronic inflammato...
    • Herpes simplex infection, organism-specific biosystem (from KEGG)
      Herpes simplex infection, organism-specific biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
    • Herpes simplex infection, conserved biosystem (from KEGG)
      Herpes simplex infection, conserved biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
    • IL2 signaling events mediated by STAT5, organism-specific biosystem (from Pathway Interaction Database)
      IL2 signaling events mediated by STAT5, organism-specific biosystem
      IL2 signaling events mediated by STAT5
    • IL4-mediated signaling events, organism-specific biosystem (from Pathway Interaction Database)
      IL4-mediated signaling events, organism-specific biosystem
      IL4-mediated signaling events
    • 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...
    • 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...
    • TNF signaling pathway, organism-specific biosystem (from KEGG)
      TNF signaling pathway, organism-specific biosystemTumor necrosis factor (TNF), as a critical cytokine, can induce a wide range of intracellular signal pathways including apoptosis and cell survival as well as inflammation and immunity. Activated TNF...
    • TNF signaling pathway, conserved biosystem (from KEGG)
      TNF signaling pathway, conserved biosystemTumor necrosis factor (TNF), as a critical cytokine, can induce a wide range of intracellular signal pathways including apoptosis and cell survival as well as inflammation and immunity. Activated TNF...
    • 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...
    • TNFs bind their physiological receptors, organism-specific biosystem (from REACTOME)
      TNFs bind their physiological receptors, organism-specific biosystemMembers of the tumour necrosis factor superfamily (TNFSF) and TNF receptor superfamily (TNFRSF) have crucial roles in both innate and adaptive immunity. These members are implicated in various acquir...
    • Type I diabetes mellitus, organism-specific biosystem (from KEGG)
      Type I diabetes mellitus, organism-specific biosystemType I diabetes mellitus is a disease that results from autoimmune destruction of the insulin-producing beta-cells. Certain beta-cell proteins act as autoantigens after being processed by antigen-pre...
    • Type I diabetes mellitus, conserved biosystem (from KEGG)
      Type I diabetes mellitus, conserved biosystemType I diabetes mellitus is a disease that results from autoimmune destruction of the insulin-producing beta-cells. Certain beta-cell proteins act as autoantigens after being processed by antigen-pre...
    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
    apoptotic process TAS
    Traceable Author Statement
    more info
    PubMed 
    cell-cell signaling TAS
    Traceable Author Statement
    more info
    PubMed 
    defense response to Gram-positive bacterium IEA
    Inferred from Electronic Annotation
    more info
     
    humoral immune response IEA
    Inferred from Electronic Annotation
    more info
     
    lymph node development IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of fibroblast proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of growth of symbiont in host IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of chronic inflammatory response to antigenic stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of glial cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of humoral immune response mediated by circulating immunoglobulin IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of interferon-gamma production IEA
    Inferred from Electronic Annotation
    more info
     
    response to drug IEA
    Inferred from Electronic Annotation
    more info
     
    response to hypoxia IEA
    Inferred from Electronic Annotation
    more info
     
    response to lipopolysaccharide IEA
    Inferred from Electronic Annotation
    more info
     
    response to nutrient IEA
    Inferred from Electronic Annotation
    more info
     
    signal transduction TAS
    Traceable Author Statement
    more info
    PubMed 
    tumor necrosis factor-mediated signaling pathway TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    extracellular space IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    Preferred Names
    lymphotoxin-alpha
    Names
    LT-alpha
    TNF superfamily, member 1
    TNF-beta
    tumor necrosis factor beta
    tumor necrosis factor ligand 1E
    tumor necrosis factor ligand superfamily member 1

    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.

    Genomic

    1. NG_012010.1 RefSeqGene

      Range
      5001..7226
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000595.3NP_000586.2  lymphotoxin-alpha precursor

      See identical proteins and their annotated locations for NP_000586.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      BG685356, BX108399, D12614
      Consensus CDS
      CCDS4701.1
      UniProtKB/Swiss-Prot
      P01374
      UniProtKB/TrEMBL
      Q5STV3
      Related
      ENSP00000413450.2, OTTHUMP00000029184, ENST00000418386.2, OTTHUMT00000076237
      Conserved Domains (1) summary
      cd00184
      Location:63203
      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 ...
    2. NM_001159740.2NP_001153212.1  lymphotoxin-alpha precursor

      See identical proteins and their annotated locations for NP_001153212.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      BP338937, BX108399, D12614
      Consensus CDS
      CCDS4701.1
      UniProtKB/Swiss-Prot
      P01374
      UniProtKB/TrEMBL
      Q5STV3
      Related
      ENSP00000403495.1, OTTHUMP00000165897, ENST00000454783.5, OTTHUMT00000259097
      Conserved Domains (1) summary
      cd00184
      Location:63203
      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: 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
      31560550..31574324
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011514618.1XP_011512920.1  lymphotoxin-alpha isoform X1

      See identical proteins and their annotated locations for XP_011512920.1

      UniProtKB/Swiss-Prot
      P01374
      UniProtKB/TrEMBL
      Q5STV3
      Conserved Domains (1) summary
      cd00184
      Location:63203
      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 ...
    2. XM_011514615.2XP_011512917.1  lymphotoxin-alpha isoform X1

      See identical proteins and their annotated locations for XP_011512917.1

      UniProtKB/Swiss-Prot
      P01374
      UniProtKB/TrEMBL
      Q5STV3
      Conserved Domains (1) summary
      cd00184
      Location:63203
      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 ...
    3. XM_011514616.2XP_011512918.1  lymphotoxin-alpha isoform X1

      See identical proteins and their annotated locations for XP_011512918.1

      UniProtKB/Swiss-Prot
      P01374
      UniProtKB/TrEMBL
      Q5STV3
      Conserved Domains (1) summary
      cd00184
      Location:63203
      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 ...
    4. XM_011514617.2XP_011512919.1  lymphotoxin-alpha isoform X1

      See identical proteins and their annotated locations for XP_011512919.1

      UniProtKB/Swiss-Prot
      P01374
      UniProtKB/TrEMBL
      Q5STV3
      Conserved Domains (1) summary
      cd00184
      Location:63203
      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 ...

    Reference GRCh38.p7 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p7 ALT_REF_LOCI_2

      Range
      3049386..3051611
      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
      2819830..2822057
      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
      2877140..2879365
      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
      2913995..2916222
      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
      2827916..2830143
      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
      2871379..2873604
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018917.2 Alternate CHM1_1.1

      Range
      31542008..31544233
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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