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    LTA lymphotoxin alpha (TNF superfamily, member 1) [ Homo sapiens ]

    Gene ID: 4049, updated on 19-May-2012
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    Summary

    Official Symbol
    LTAprovided by HGNC
    Official Full Name
    lymphotoxin alpha (TNF superfamily, member 1)provided by HGNC
    Primary source
    HGNC:6709
    Locus tag
    DAMA-25N12.13-004
    See related
    Ensembl:ENSG00000226979; HPRD:01084; 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
    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 and psoriatic arthritis.[provided by RefSeq, Apr 2009]
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    Genomic context

    Location :
    6p21.3
    Sequence :
    Chromosome: 6; NC_000006.11 (31539876..31542098)
    See LTA in Epigenomics, MapViewer

    Chromosome 6 - NC_000006.11Genomic Context describing neighboring genes Neighboring gene ATP6V1G2-DDX39B readthrough (non-protein coding) Neighboring gene ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2 Neighboring gene nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1 Neighboring gene uncharacterized LOC100287329 Neighboring gene tumor necrosis factor Neighboring gene lymphotoxin beta (TNF superfamily, member 3)

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    Genomic regions, transcripts, and products

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details
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    Bibliography

    Related articles in PubMed

    1. Tumor necrosis factor -308 and lymphotoxin +252 polymorphisms in Mexican children with Kawasaki disease and coronary aneurysms. Cruz-Olivo F, et al. Arch Med Res, 2011 Oct. PMID 22100609.
    2. Tumour necrosis factor gene polymorphisms and migraine: a systematic review and meta-analysis. Schürks M, et al. Cephalalgia, 2011 Oct. PMID 22001640.
    3. Haplotype-based association of four lymphotoxin-alpha gene polymorphisms with the risk of coronary artery disease in Han Chinese. Liu Y, et al. Tohoku J Exp Med, 2011. PMID 21628868.
    4. [Identification of a novel lymphotoxin-alpha (LTA) gene associated with ankylosing spondylitis in Ningxia population]. Chen J, et al. Yi Chuan, 2011 Apr. PMID 21482522.
    5. Lymphotoxin-α 252 A>G polymorphism: a link between disease susceptibility and dyslipidemia in rheumatoid arthritis? Santos MJ, et al. J Rheumatol, 2011 Jul. PMID 21459939.

    See all (468) citations in PubMed

    See citations in PubMed for homologs of this gene provided by HomoloGene

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. Comparative analysis by group did not show a significant difference in the frequency of the alleles and genotypes between KD with CA vs. KD without CA vs. controls, for both TNF -308 and LTA +252
      Title: Tumor necrosis factor -308 and lymphotoxin +252 polymorphisms in Mexican children with Kawasaki disease and coronary aneurysms.
    2. No overall association was seen between TNFbeta gene variants and migraine.
      Title: Tumour necrosis factor gene polymorphisms and migraine: a systematic review and meta-analysis.
    3. The lymphotoxin-alpha 252 A>G polymorphism highlights a possible common genetic predisposition to rheumatoid arthritis and dyslipidemia.
      Title: Lymphotoxin-α 252 A>G polymorphism: a link between disease susceptibility and dyslipidemia in rheumatoid arthritis?
    4. A haplotype-based association of four lymphotoxin-alpha gene polymorphisms is found with the risk of coronary artery disease in Han Chinese.
      Title: Haplotype-based association of four lymphotoxin-alpha gene polymorphisms with the risk of coronary artery disease in Han Chinese.
    5. The NFB +252A>G polymorphism was not (p = 0.6) associated with risk of asthma in the children in Egyptian population.
      Title: The impact of common tumor necrosis factor haplotypes on the development of asthma in children: an Egyptian model.
    6. The LTA +252 A/G polymorphism is associated with both susceptibility to and mortality from sepsis.
      Title: Association between lymphotoxin-α intron +252 polymorphism and sepsis: a meta-analysis.
    7. TNF-beta SNPs did not appear to be a contributing factor influencing the morbidity of the patients with acute respiratory distress syndrome after operation for esophageal carcinoma.
      Title: [Relationship between tumor necrosis factor beta gene polymorphism and acute respiratory distress syndrome after operation for esophageal carcinoma].
    8. TNF-beta +252GG genotype was found more frequent in Turkish breast cancer patients than controls.
      Title: Tumor necrosis factor alpha and beta and interferon gamma gene polymorphisms in Turkish breast cancer patients.
    9. These results provide the first report of an association between TNFA, TNFB and TNFRII polymorphic features and outcome of allo-HSCT in a Chinese population, and suggest an interaction between TNFA-857 and TNFB+252 genotypes and risk of aGVHD.
      Title: Relationship between TNFA, TNFB and TNFRII gene polymorphisms and outcome after unrelated hematopoietic cell transplantation in a Chinese population.
    10. TNF-alpha and -beta polymorphisms are strongly associated with breast cancer in the Dravidian but not in the Indo-European group
      Title: Role of ethnic variations in TNF-α and TNF-β polymorphisms and risk of breast cancer in India.
    Submit: New GeneRIF Correction See all (131)
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    Phenotypes

    Review eQTL and phenotype association data in this region using PheGenI

    Identification of candidate loci at 6p21 and 21q22 in a genome-wide association study of cardiac manifestations of neonatal lupus.

    Leprosy, susceptibility to, 4

    Myocardial infarction, susceptibility to

    Psoriatic arthritis, susceptibility to

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    HIV-1 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 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 Protein Interaction Database

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    Interactions

    Products Interactant Other Gene Complex Source Pubs Description
    NP_000586.2 NP_006489.1 LGALS2    BIND  PubMed LTA interacts with galectin-2. 
    P01374 P05162 LGALS2    HPRD  PubMed  
    P01374 P01374 LTA    HPRD  PubMed  
    P01374 Q06643 LTB    HPRD  PubMed  
    P01374 P36941 LTBR    HPRD  PubMed  
    P01374 Q92956 TNFRSF14    HPRD  PubMed  
    P01374 P19438 TNFRSF1A    HPRD  PubMed  
    P01374 P20333 TNFRSF1B    HPRD  PubMed  
    P01374 P68366 TUBA4A    HPRD  PubMed  
    P01374 P07911 UMOD    HPRD  PubMed  
    BioGRID:110227 BioGRID:122015 CLSPN    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:110227 BioGRID:110228 LTB    BioGRID  PubMed Affinity Capture-Western; Reconstituted Complex 
    BioGRID:110227 BioGRID:112986 TNFRSF1A    BioGRID  PubMed Co-crystal Structure 
    BioGRID:110227 BioGRID:113216 UMOD    BioGRID  PubMed Reconstituted Complex 
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    General gene information

    Markers

    Genotypes

    Homology

    Pathways from BioSystems

    • 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-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
    • 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...

    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 
    defense response to Gram-positive bacterium IEA
    Inferred from Electronic Annotation
    more info
    		  
    humoral immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    induction of apoptosis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    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 chronic inflammatory response to antigenic stimulus 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 
    Component Evidence Code Pubs
    extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    extracellular space IEA
    Inferred from Electronic Annotation
    more info
    		  
    membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
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    General protein information

    Preferred Names
    lymphotoxin-alpha
    Names
    lymphotoxin-alpha
    LT-alpha
    TNF-beta
    tumor necrosis factor beta
    tumor necrosis factor ligand superfamily member 1
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    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.

    Genomic

    1. NG_012010.1 RefSeqGene

      Range
      5001..7223
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      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)
      D12614, M55913
      Consensus CDS
      CCDS4701.1
      UniProtKB/Swiss-Prot
      P01374
      UniProtKB/TrEMBL
      Q5STV3
      Related
      ENSP00000413450, OTTHUMP00000029184, ENST00000418386, OTTHUMT00000076237
      Conserved Domains (1) summary
      cd00184
      Location:63 – 203
      Blast Score: 316
      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_001159740.1 → NP_001153212.1  lymphotoxin-alpha precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      BC034729, BP338937
      Consensus CDS
      CCDS4701.1
      UniProtKB/Swiss-Prot
      P01374
      UniProtKB/TrEMBL
      Q5STV3
      Related
      ENSP00000403495, OTTHUMP00000165897, ENST00000454783, OTTHUMT00000259097
      Conserved Domains (1) summary
      cd00184
      Location:63 – 203
      Blast Score: 316
      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: Build 37.3

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

    Reference GRCh37.p5 Primary Assembly

    Genomic

    1. NC_000006.11 Reference GRCh37.p5 Primary Assembly

      Range
      31539876..31542098
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh37.p5 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.2 Reference GRCh37.p5 ALT_REF_LOCI_2

      Range
      3049492..3051714
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh37.p5 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.1 Reference GRCh37.p5 ALT_REF_LOCI_3

      Range
      2825415..2827639
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh37.p5 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.1 Reference GRCh37.p5 ALT_REF_LOCI_4

      Range
      2882760..2884982
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh37.p5 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.1 Reference GRCh37.p5 ALT_REF_LOCI_5

      Range
      2919580..2921804
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh37.p5 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.1 Reference GRCh37.p5 ALT_REF_LOCI_6

      Range
      2833512..2835736
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh37.p5 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.1 Reference GRCh37.p5 ALT_REF_LOCI_7

      Range
      2870677..2872899
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000138.1 Alternate HuRef

      Range
      31326608..31328832
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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    Related Sequences

    Nucleotide Protein
    Heading Accession and Version
    genomic AB088112.1 BAC54943.1
    genomic AB103618.1 BAF31278.1
    genomic AB202113.1 BAE78638.1
    genomic AF129756.1 AAD18092.1
    genomic AL662801.7 (44768..46990) None
    genomic AL662847.6 (58534..60756) None
    genomic AL929587.5 CAI18648.1
    genomic AY070490.1 AAL49956.1
    genomic AY216498.1 AAO21135.1
    genomic AY274903.1 AAP51421.1
    genomic AY274904.1 AAP51422.1
    genomic AY274905.1 AAP51423.1
    genomic AY274906.1 AAP51424.1
    genomic AY274907.1 AAP51425.1
    genomic AY274908.1 AAP51426.1
    genomic AY274909.1 AAP51427.1
    genomic AY274910.1 AAP51428.1
    genomic AY274911.1 AAP51429.1
    genomic AY274912.1 AAP51430.1
    genomic AY274913.1 AAP51431.1
    genomic AY274914.1 AAP51432.1
    genomic AY274915.1 AAP51433.1
    genomic AY274916.1 AAP51434.1
    genomic AY274917.1 AAP51435.1
    genomic AY274918.1 AAP51436.1
    genomic AY274919.1 AAP51437.1
    genomic AY274920.1 AAP51438.1
    genomic AY274921.1 AAP51439.1
    genomic AY274922.1 AAP51440.1
    genomic AY274923.1 AAP51441.1
    genomic AY274924.1 AAP51442.1
    genomic AY274925.1 AAP51443.1
    genomic AY274926.1 AAP51444.1
    genomic BA000025.2 BAB63397.1
    genomic BX248519.7 CAI41938.2
    genomic BX927320.5 CAQ09992.1
    genomic CH471081.1 EAX03422.1
      EAX03423.1
    genomic CR753892.5 (29165..31172) None
    genomic CR942185.8 (27701..29708) None
    genomic CS081477.1 CAI95949.1
    genomic M16441.1 AAA61199.1
    genomic M55913.1 AAB59455.1
    genomic X02911.1 CAA26670.1
    genomic Y14768.1 CAA75071.1
    genomic Z15026.1 CAA78746.1
    mRNA BC034729.1 AAH34729.1
    mRNA BP338937.1 None
    mRNA CR542253.1 CAG47049.1
    mRNA CR542273.1 CAG47069.1
    mRNA D00102.1 BAA00064.1
    mRNA D12614.1 BAA02139.1
    mRNA DQ123821.1 AAZ32914.1
    mRNA DQ123822.1 AAZ32915.1
    mRNA DQ123823.1 AAZ32916.1
    mRNA DQ123824.1 AAZ32917.1
    mRNA DQ123825.2 AAZ32918.2
    mRNA DQ123826.1 AAZ32919.1
    mRNA DQ123827.1 AAZ32920.1
    mRNA X01393.1 CAA25649.1
    mRNA A06316.1 CAA00536.1
    other-genetic DQ891119.2 ABM82045.1
    other-genetic DQ894298.2 ABM85224.1
    Protein Accession Links
    GenPept Link UniProtKB Link
    P01374.2 GenPept UniProtKB/Swiss-Prot:P01374
    Q45NE3 GenPept UniProtKB/TrEMBL:Q45NE3
    Q45NE4 GenPept UniProtKB/TrEMBL:Q45NE4
    Q45NE5 GenPept UniProtKB/TrEMBL:Q45NE5
    Q45NE6 GenPept UniProtKB/TrEMBL:Q45NE6
    Q45NE7 GenPept UniProtKB/TrEMBL:Q45NE7
    Q45NE8 GenPept UniProtKB/TrEMBL:Q45NE8
    Q45NE9 GenPept UniProtKB/TrEMBL:Q45NE9
    Q5HYS4 GenPept UniProtKB/TrEMBL:Q5HYS4
    Q5ST95 GenPept UniProtKB/TrEMBL:Q5ST95
    Q5STV3 GenPept UniProtKB/TrEMBL:Q5STV3
    Q6FG55 GenPept UniProtKB/TrEMBL:Q6FG55
    Q6WQT9 GenPept UniProtKB/TrEMBL:Q6WQT9
    Q6WQU7 GenPept UniProtKB/TrEMBL:Q6WQU7
    Q6WQV4 GenPept UniProtKB/TrEMBL:Q6WQV4
    Q6WQV6 GenPept UniProtKB/TrEMBL:Q6WQV6
    Q6WQV7 GenPept UniProtKB/TrEMBL:Q6WQV7
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    Additional Links

    Additional Links

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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