Human Gene LTA (uc011gyg.2) Description and Page Index
  Description: Homo sapiens lymphotoxin alpha (TNF superfamily, member 1) (LTA), transcript variant 2, mRNA.
RefSeq Summary (NM_000595): 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_hap4:2,883,589-2,884,513 Size: 925 Total Exon Count: 2 Strand: +


Page IndexSequence and LinksGenetic AssociationsCTDMicroarrayOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

+  Sequence and Links to Tools and Databases
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-  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.
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-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  Microarray Expression Data
 
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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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-  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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  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.
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: DQ123827
UCSC ID: uc011gyg.2
RefSeq Accession: NM_000595

-  Gene Model Information
 
category: nearCoding nonsense-mediated-decay: no RNA accession: DQ123827.1
exon count: 2CDS single in 3' UTR: no RNA size: 139
ORF size: 0CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 402.00frame shift in genome: no % Coverage: 100.00
has start codon: no stop codon in genome: no # of Alignments: 7
has end codon: no retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.