Human Gene LTA (uc011gye.2) Description and Page Index
Description: Homo sapiens lymphotoxin alpha (TNF superfamily, member 1) (LTA), transcript variant 1, mRNA. RefSeq Summary (NM_001159740): 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]. Transcript (Including UTRs) Position: chr6_mann_hap4:2,882,760-2,884,984 Size: 2,225 Total Exon Count: 4 Strand: + Coding Region Position: chr6_mann_hap4:2,883,404-2,884,354 Size: 951 Coding Exon Count: 3
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Comments and Description Text from UniProtKB
ID:TNFB_HUMAN DESCRIPTION: RecName: Full=Lymphotoxin-alpha; Short=LT-alpha; AltName: Full=TNF-beta; AltName: Full=Tumor necrosis factor ligand superfamily member 1; Flags: Precursor; FUNCTION: Cytokine that in its homotrimeric form binds to TNFRSF1A/TNFR1, TNFRSF1B/TNFBR and TNFRSF14/HVEM. In its heterotrimeric form with LTB binds to TNFRSF3/LTBR. Lymphotoxin is produced by lymphocytes and cytotoxic for a wide range of tumor cells in vitro and in vivo. SUBUNIT: Homotrimer, and heterotrimer of either two LTB and one LTA subunits or (less prevalent) two LTA and one LTB subunits. SUBCELLULAR LOCATION: Secreted. Membrane. Note=The homotrimer is secreted. The heterotrimer is membrane-associated. POLYMORPHISM: A polymorphism in LTA accounts, in part, for susceptibility to leprosy linked to chromosome 6p21.3 (LPRS4) [MIM:610988]. DISEASE: Psoriatic arthritis (PSORAS) [MIM:607507]: An inflammatory, seronegative arthritis associated with psoriasis. It is a heterogeneous disorder ranging from a mild, non-destructive disease to a severe, progressive, erosive arthropathy. Five types of psoriatic arthritis have been defined: asymmetrical oligoarthritis characterized by primary involvement of the small joints of the fingers or toes; asymmetrical arthritis which involves the joints of the extremities; symmetrical polyarthritis characterized by a rheumatoid like pattern that can involve hands, wrists, ankles, and feet; arthritis mutilans, which is a rare but deforming and destructive condition; arthritis of the sacroiliac joints and spine (psoriatic spondylitis). Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. SIMILARITY: Belongs to the tumor necrosis factor family. WEB RESOURCE: Name=Wikipedia; Note=Lymphotoxin entry; URL="http://en.wikipedia.org/wiki/Lymphotoxin"; WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/LTAID41209ch6p21.html"; WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/lta/"; WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/lta/"; WEB RESOURCE: Name=SHMPD; Note=The Singapore human mutation and polymorphism database; URL="http://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=LTA";
Genetic Association Studies of Complex Diseases and Disorders
Alzheimer's Disease Alvarez, V. et al. 2002, Association between the TNFalpha-308 A/G polymorphism and the onset-age of Alzheimer disease., American journal of medical genetics. 2002 Jul;114(5):574-7.
Our data suggest an effect of the TNFalpha-308 polymorphism on the age at onset of late AD. This represents additional evidence of the importance of genetic variation at the proinflammatory components in the origin and progression of this common NEUROLOGICALenerative disease.
Asthma Albuquerque R 1998, , Clinical and experimental allergy. 1998 May;28(5):578-84.
These results suggest an important role for the TNFalpha gene or a linked locus in an inherited asthma diathesis.
atherosclerosis, coronary Li, Y. et al. 2004, [Association between tumor necrosis factor-beta polymorphisms and coronary heart disease in a Chinese population.], Zhonghua yi xue yi chuan xue za zhi. 2004 Dec;21(6):583-6.
The single nucleotide polymorphism (SNP) at position 804 in the exon 3 of TNF-beta gene is associated with CHD and the allele A may be a risk factor for CHD in Chinese. The polymorphism of G252A may not play an important role in the pathogenesis of CHD.
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
ModBase Predicted Comparative 3D Structure on P01374
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.
Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.