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LTA lymphotoxin alpha [ Homo sapiens (human) ]

Gene ID: 4049, updated on 14-Apr-2014
Official Symbol
LTAprovided by HGNC
Official Full Name
lymphotoxin alphaprovided 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, myocardial infarction, non-Hodgkin's lymphoma, and psoriatic arthritis. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012]
Location :
6p21.3
Sequence :
Chromosome: 6; NC_000006.12 (31572099..31574324)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATP6V1G2-DDX39B readthrough (NMD candidate) 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 tumor necrosis factor Neighboring gene lymphotoxin beta (TNF superfamily, member 3)

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

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

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, p14 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

  • 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
  • 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...
  • 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...
  • 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 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 space IEA
Inferred from Electronic Annotation
more info
 
membrane IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
lymphotoxin-alpha
Names
lymphotoxin-alpha
LT-alpha
TNF-beta
TNF superfamily, member 1
tumor necrosis factor beta
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 proteins identical to 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, OTTHUMP00000029184, ENST00000418386, OTTHUMT00000076237
    Conserved Domains (1) summary
    cd00184
    Location:63203
    Blast Score: 359
    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 proteins identical to 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, OTTHUMP00000165897, ENST00000454783, OTTHUMT00000259097
    Conserved Domains (1) summary
    cd00184
    Location:63203
    Blast Score: 359
    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 106

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

Reference GRCh38 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38 ALT_REF_LOCI_2

    Range
    3049386..3051611
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38 ALT_REF_LOCI_3

    Range
    2819830..2822057
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38 ALT_REF_LOCI_4

    Range
    2877140..2879365
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38 ALT_REF_LOCI_5

    Range
    2913995..2916222
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38 ALT_REF_LOCI_6

    Range
    2827916..2830143
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38 ALT_REF_LOCI_7

    Range
    2871379..2873604
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38 Primary Assembly

    Range
    31572099..31574324
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000138.1 Alternate HuRef

    Range
    31326608..31328835
    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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