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Aliases for LTA Gene

Aliases for LTA Gene

  • Lymphotoxin Alpha 2 3
  • TNFB 3 4 6
  • Tumor Necrosis Factor Ligand Superfamily Member 1 3 4
  • LT-Alpha 3 4
  • TNF-Beta 3 4
  • TNFSF1 3 4
  • Lymphotoxin Alpha (TNF Superfamily, Member 1) 2
  • Tumor Necrosis Factor Beta 3
  • TNF Superfamily, Member 1 3
  • TNF Superfamily Member 1 2
  • Lymphotoxin-Alpha 3
  • LT 3

External Ids for LTA Gene

Previous Symbols for LTA Gene

  • TNFB

Summaries for LTA Gene

Entrez Gene Summary for LTA Gene

  • 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]

GeneCards Summary for LTA Gene

LTA (Lymphotoxin Alpha) is a Protein Coding gene. Diseases associated with LTA include dengue hemorrhagic fever and spondylarthropathy. Among its related pathways are NF-KappaB Family Pathway and NF-KappaB Family Pathway. GO annotations related to this gene include receptor binding and tumor necrosis factor receptor binding. An important paralog of this gene is TNF.

UniProtKB/Swiss-Prot for LTA Gene

  • 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

Gene Wiki entry for LTA Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LTA Gene

Genomics for LTA Gene

Genomic Location for LTA Gene

Start:
31,572,054 bp from pter
End:
31,574,324 bp from pter
Size:
2,271 bases
Orientation:
Plus strand

Genomic View for LTA Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for LTA Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Regulatory Elements for LTA Gene

Proteins for LTA Gene

  • Protein details for LTA Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P01374-TNFB_HUMAN
    Recommended name:
    Lymphotoxin-alpha
    Protein Accession:
    P01374
    Secondary Accessions:
    • Q8N4C3
    • Q9UKS8

    Protein attributes for LTA Gene

    Size:
    205 amino acids
    Molecular mass:
    22297 Da
    Quaternary structure:
    • Homotrimer, and heterotrimer of either two LTB and one LTA subunits or (less prevalent) two LTA and one LTB subunits

    Three dimensional structures from OCA and Proteopedia for LTA Gene

neXtProt entry for LTA Gene

Proteomics data for LTA Gene at MOPED

Post-translational modifications for LTA Gene

Other Protein References for LTA Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LTA Gene

Domains for LTA Gene

Gene Families for LTA Gene

HGNC:
  • TNFSF :Tumor necrosis factor (ligand) superfamily

UniProtKB/Swiss-Prot:

TNFB_HUMAN
Family:
  • Belongs to the tumor necrosis factor family.:
    • P01374
genes like me logo Genes that share domains with LTA: view

Function for LTA Gene

Molecular function for LTA Gene

GENATLAS Biochemistry: lymphotoxin alpha,expressed in T cells,tumors necrosis factor (ligand) superfamily,member 1
UniProtKB/Swiss-Prot 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

Gene Ontology (GO) - Molecular Function for LTA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 receptor binding TAS 3001529
GO:0005125 cytokine activity IEA --
GO:0005164 tumor necrosis factor receptor binding IEA --
GO:0005515 protein binding --
genes like me logo Genes that share ontologies with LTA: view
genes like me logo Genes that share phenotypes with LTA: view

Animal Models for LTA Gene

MGI Knock Outs for LTA:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for LTA Gene

Localization for LTA Gene

Subcellular locations from UniProtKB/Swiss-Prot for LTA Gene

Secreted. Membrane. Note=The homotrimer is secreted. The heterotrimer is membrane-associated.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LTA Gene COMPARTMENTS Subcellular localization image for LTA gene
Compartment Confidence
extracellular 5
nucleus 2
plasma membrane 2

Gene Ontology (GO) - Cellular Components for LTA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with LTA: view

Pathways for LTA Gene

genes like me logo Genes that share pathways with LTA: view

Gene Ontology (GO) - Biological Process for LTA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IEA --
GO:0002876 positive regulation of chronic inflammatory response to antigenic stimulus IEA --
GO:0002925 positive regulation of humoral immune response mediated by circulating immunoglobulin IEA --
GO:0006915 apoptotic process TAS 6334807
GO:0006955 immune response --
genes like me logo Genes that share ontologies with LTA: view

Compounds for LTA Gene

(1) Drugbank Compounds for LTA Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Etanercept
  • CD120b
185243-69-0 target

(61) Novoseek inferred chemical compound relationships for LTA Gene

Compound -log(P) Hits PubMed IDs
il 10 53.8 7
rantes 47.3 14
toxin-1 45.7 2
lipoteichoic acid 36.2 2
ionomycin 34.7 4

(3) PharmGKB related drug/compound annotations for LTA Gene

Drug/compound Annotation
carbamazepine CA
cyclosporine CA
mycophenolate mofetil CA
genes like me logo Genes that share compounds with LTA: view

Transcripts for LTA Gene

Unigene Clusters for LTA Gene

Lymphotoxin alpha (TNF superfamily, member 1):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for LTA Gene

No ASD Table

Relevant External Links for LTA Gene

GeneLoc Exon Structure for
LTA
ECgene alternative splicing isoforms for
LTA

Expression for LTA Gene

mRNA expression in normal human tissues for LTA Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

SOURCE GeneReport for Unigene cluster for LTA Gene Hs.36

genes like me logo Genes that share expressions with LTA: view

Orthologs for LTA Gene

This gene was present in the common ancestor of chordates.

Orthologs for LTA Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LTA 36
  • 99.51 (n)
  • 99.51 (a)
LTA 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LTA 36
  • 82.03 (n)
  • 72.55 (a)
LTA 37
  • 74 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LTA 36
  • 83.5 (n)
  • 75 (a)
LTA 37
  • 77 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lta 36
  • 78.88 (n)
  • 72.28 (a)
Lta 16
Lta 37
  • 73 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LTA 37
  • 61 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lta 36
  • 78.88 (n)
  • 72.77 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lta 36
  • 46.15 (n)
  • 39.05 (a)
zebrafish
(Danio rerio)
Actinopterygii tnfa 37
  • 25 (a)
ManyToMany
tnfb 37
  • 24 (a)
ManyToMany
Species with no ortholog for LTA:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LTA Gene

ENSEMBL:
Gene Tree for LTA (if available)
TreeFam:
Gene Tree for LTA (if available)

Paralogs for LTA Gene

Paralogs for LTA Gene

genes like me logo Genes that share paralogs with LTA: view

Variants for LTA Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for LTA Gene

P01374-TNFB_HUMAN
A polymorphism in LTA accounts, in part, for susceptibility to leprosy linked to chromosome 6p21.3 (LPRS4) [MIM:610988]

Sequence variations from dbSNP and Humsavar for LTA Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type MAF
rs746868 -- 31,572,652(-) GGAGA(C/G)AGCAC intron-variant
rs909253 other 31,572,536(-) AGGAA(C/T)CATGG intron-variant
rs915654 -- 31,570,720(-) TTTTT(A/T)AAAAA upstream-variant-2KB
rs1041981 other, - 31,573,007(+) CAGCA(A/C)CCTCA missense, reference
rs1800683 -- 31,572,294(+) GCTCC(A/G)CACAG utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for LTA Gene

Variant ID Type Subtype PubMed ID
esv690 CNV CNV 17122850
essv13266 CNV CNV 17122850
nsv830627 CNV Loss 17160897
nsv470809 CNV Loss 18288195
nsv884418 CNV Gain 21882294
nsv462870 CNV Loss 19166990

Relevant External Links for LTA Gene

HapMap Linkage Disequilibrium report
LTA
Human Gene Mutation Database (HGMD)
LTA

Disorders for LTA Gene

(3) OMIM Diseases for LTA Gene (153440)

UniProtKB/Swiss-Prot

TNFB_HUMAN
  • 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). {ECO:0000269 PubMed:12746914}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

(1) University of Copenhagen DISEASES for LTA Gene

(95) Novoseek inferred disease relationships for LTA Gene

Disease -log(P) Hits PubMed IDs
necrosis 87.9 147
tumors 73.9 152
tonsillar hypertrophy 50 1
leukemia t-cell 46.5 3
toxic shock syndrome 46.3 4

Relevant External Links for LTA

Genetic Association Database (GAD)
LTA
Human Genome Epidemiology (HuGE) Navigator
LTA
genes like me logo Genes that share disorders with LTA: view

Publications for LTA Gene

  1. Cytokine gene polymorphisms: association with psoriatic arthritis susceptibility and severity. (PMID: 12746914) Balding J. … FitzGerald O. (Arthritis Rheum. 2003) 3 4 23 49
  2. Polymorphisms of tumor necrosis factor (TNF) alpha and beta genes in Korean patients with psoriasis. (PMID: 12709814) Kim T.G. … Kim T.Y. (Arch. Dermatol. Res. 2003) 3 23 49
  3. Association of plasma levels of tumor necrosis factor (TNF)-alpha and its soluble receptors, two polymorphisms of the TNF gene, with acute severe pancreatitis and early septic shock due to it. (PMID: 12717265) Dianliang Z. … Baojun Y. (Pancreas 2003) 3 23 49
  4. TNF-alpha and -beta gene polymorphisms in multiple sclerosis: a highly significant role for determinants in the first intron of the TNF-beta gene. (PMID: 12568117) Fernandes Filho J.A. … Pandey J.P. (Autoimmunity 2002) 3 23 49
  5. TNFB polymorphism may be associated with schizophrenia in the Korean population. (PMID: 12648734) Jun T.Y. … Serretti A. (Schizophr. Res. 2003) 3 23 49

Products for LTA Gene

Sources for LTA Gene

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