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 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDMicroarray
RNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated: 2013-06-14

+  Sequence and Links to Tools and Databases
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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
  Genetic Association Database: LTA
CDC HuGE Published Literature: LTA
Positive Disease Associations: Alzheimer's Disease , Asthma , atherosclerosis, coronary , atopy , Behcet Syndrome , Brain Ischemia|Hypertension|Osteoporosis|Stroke , Chagas Cardiomyopathy , chronic immune thrombocytopenic purpura. , chronic obstructive pulmonary disease/COPD; bronchiectatic disease , complications after major abdominal operations , diabetes, type 1 , diabetes, type 2 , endometriosis , erythrocyte catalase activity , gastric cancer , hepatitis B , intima-media thickness , limb deficiency anomalies , Lupus , myelopathy, HTLV-1 associated , myocardial infarct , myocardial infarction , oral submucous fibrosis , palmoplantar pustulosis , Postoperative infectious complications , rheumatoid arthritis , sepsis , sepsis; serum tumor necrosis factor-alpha levels , testicular cancer , Tuberculosis , urinary tract infections after renal transplantation , Uveitis , vasopressor infusion requirement
Related Studies:
  1. 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. [PubMed 12116197]
    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.
  2. Asthma
    Albuquerque R 1998, , Clinical and experimental allergy. 1998 May;28(5):578-84. [PubMed 9645594]
    These results suggest an important role for the TNFalpha gene or a linked locus in an inherited asthma diathesis.
  3. 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. [PubMed 15583987]
    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.
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  Microarray Expression Data
 
Expression ratio colors:

GNF Expression Atlas 2 Data from U133A and GNF1H Chips

      
      
      
     
    
     
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GNF Expression Atlas 1 Human Data on Affy U95 Chips

      
    
     
      
    
    
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -69.42213-0.326 Picture PostScript Text
3' UTR -208.67630-0.331 Picture PostScript Text

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.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR006053 - TNF
IPR002960 - TNF_beta
IPR021184 - TNF_CS
IPR006052 - TNF_dom
IPR008983 - Tumour_necrosis_fac-like_dom

Pfam Domains:
PF00229 - TNF(Tumour Necrosis Factor) family

SCOP Domains:
49842 - TNF-like

Protein Data Bank (PDB) 3-D Structure

1TNR
- X-ray Chimera LS-SNP

4MXV
- X-ray Chimera

4MXW
- X-ray Chimera
Chimera help

ModBase Predicted Comparative 3D Structure on P01374
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-  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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
Jackson LabRGD    
Protein Sequence     
Alignment     

-  Descriptions from all associated GenBank mRNAs
  DQ123821 - Homo sapiens lymphotoxin alpha transcript variant 2 (LTA) mRNA, partial cds, alternatively spliced.
D12614 - Homo sapiens LT mRNA for lymphotoxin (TNF-beta), complete cds.
DQ123822 - Homo sapiens lymphotoxin alpha transcript variant 3 (LTA) mRNA, complete cds, alternatively spliced.
X01393 - Human mRNA for lymphotoxin.
D00102 - Homo sapiens mRNA for lymphotoxin, complete cds.
DQ894298 - Synthetic construct Homo sapiens clone IMAGE:100008758; FLH169474.01L; RZPDo839C1095D lymphotoxin alpha (TNF superfamily, member 1) (LTA) gene, encodes complete protein.
DQ891119 - Synthetic construct clone IMAGE:100003749; FLH169478.01X; RZPDo839C1096D lymphotoxin alpha (TNF superfamily, member 1) (LTA) gene, encodes complete protein.
BC034729 - Homo sapiens lymphotoxin alpha (TNF superfamily, member 1), mRNA (cDNA clone MGC:17018 IMAGE:4341621), complete cds.
AB590443 - Synthetic construct DNA, clone: pFN21AE1386, Homo sapiens LTA gene for lymphotoxin alpha, without stop codon, in Flexi system.
CU689954 - Synthetic construct Homo sapiens gateway clone IMAGE:100020241 5' read LTA mRNA.
CR542273 - Homo sapiens full open reading frame cDNA clone RZPDo834H0626D for gene LTA, lymphotoxin alpha (TNF superfamily, member 1); complete cds, without stopcodon.
CR542253 - Homo sapiens full open reading frame cDNA clone RZPDo834D0626D for gene LTA, lymphotoxin alpha (TNF superfamily, member 1); complete cds, incl. stopcodon.
E01275 - cDNA encoding human lymphotoxin polypeptide.
E01241 - cDNA encoding a polypeptide having a lymphotoxin activity.
E01481 - cDNA encoding human lymphotoxin.
E01482 - cDNA encoding human lymphotoxin.
E01804 - cDNA encoding human polypeptide having lymphotoxin activity.
A06316 - H.sapiens mRNA for lymphotoxin.
E01474 - cDNA encoding human lymphotoxin.
E01539 - DNA encoding lymphotoxin.
E02166 - DNA encoding human lympho toxin.
E02581 - Human lymphotoxin gene.
DQ123823 - Homo sapiens lymphotoxin alpha transcript variant 4 (LTA) mRNA, partial cds, alternatively spliced.
DQ123827 - Homo sapiens lymphotoxin alpha transcript variant 8 (LTA) mRNA, partial cds, alternatively spliced.
DQ123824 - Homo sapiens lymphotoxin alpha transcript variant 5 (LTA) mRNA, partial cds, alternatively spliced.
DQ123826 - Homo sapiens lymphotoxin alpha transcript variant 7 (LTA) mRNA, partial cds, alternatively spliced.
DQ123825 - Homo sapiens lymphotoxin alpha transcript variant 6 (LTA) mRNA, partial cds, alternatively spliced.
E01538 - DNA encoding lymphotoxin.
E03042 - DNA encoding improved human lymphotoxin.
E09028 - cDNA encoding novel recombinant lymphotoxin as antitumor agent.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04060 - Cytokine-cytokine receptor interaction
hsa04612 - Antigen processing and presentation
hsa04940 - Type I diabetes mellitus

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001159740, NP_001153212, P01374, Q8N4C3, Q9UKS8, TNFB, TNFB_HUMAN, TNFSF1, uc011gye.1
UCSC ID: uc011gye.2
RefSeq Accession: NM_001159740
Protein: P01374 (aka TNFB_HUMAN