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Aliases for LTA Gene

Aliases for LTA Gene

  • Lymphotoxin Alpha 2 3 5
  • Tumor Necrosis Factor Ligand Superfamily Member 1 3 4
  • LT-Alpha 3 4
  • TNF-Beta 3 4
  • TNFSF1 3 4
  • TNFB 3 4
  • Lymphotoxin Alpha (TNF Superfamily, Member 1) 2
  • Tumor Necrosis Factor Ligand 1E 3
  • Tumor Necrosis Factor Beta 3
  • TNF Superfamily, Member 1 3
  • TNF Superfamily Member 1 2
  • Lymphotoxin-Alpha 3
  • TNLG1E 3
  • LT 3

External Ids for LTA Gene

Previous HGNC Symbols for LTA Gene

  • TNFB

Previous GeneCards Identifiers for LTA Gene

  • GC06P031603
  • GC06P031593
  • GC06P031310
  • GC06P031644
  • GC06P031648
  • GC06P031540
  • GC06P031541
  • GC06P031326

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 Psoriatic Arthritis and Leprosy 4. Among its related pathways are TRAF Pathway and 4-1BB 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 CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LTA Gene

Genomics for LTA Gene

Regulatory Elements for LTA Gene

Enhancers for LTA Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G031563 1.6 FANTOM5 Ensembl ENCODE 0.7 +2.9 2928 1.6 HDGF ATF1 ARNT TCF12 GATA2 FOS PAF1 MEF2D SMARCA4 NBN TNF MICB ATP6V1G2 HLA-C HCG23 HLA-B STK19 CLIC1 LST1 LTA
GH06G031557 1.3 Ensembl ENCODE 0.7 -1.0 -960 4.2 HDGF PKNOX1 AGO1 WRNIP1 ZNF2 ZNF143 ZNF207 FOS KLF13 ZNF263 CSNK2B DDX39B LST1 NCR3 UQCRHP1 LTB AIF1 SNORD117 PSORS1C2 C6orf47
GH06G031562 0.9 FANTOM5 0.7 +1.7 1690 0.4 TBL1XR1 DNMT3B ZNF48 ZNF2 RELB ETV6 IKZF2 CREM EGR2 PAF1 TNF ATP6V1G2 STK19 HLA-B LST1 HSPA1B LTA LOC100287329
GH06G031551 0.7 ENCODE 0.4 -9.0 -9002 0.2 CTCF ZNF654 FOXA3 TRIM22 GATAD2B REST RAD21 FOXA1 FOXK2 EED MICB HLA-C LY6G5C ATP6V1G2 LTA
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LTA on UCSC Golden Path with GeneCards custom track

Genomic Location for LTA Gene

Chromosome:
6
Start:
31,560,550 bp from pter
End:
31,574,324 bp from pter
Size:
13,775 bases
Orientation:
Plus strand

Genomic View for LTA Gene

Genes around LTA on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LTA Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LTA Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

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

Post-translational modifications for LTA Gene

  • Glycosylation at posLast=4141 and posLast=9696

Other Protein References for LTA Gene

Antibody Products

  • R&D Systems Antibodies for LTA (Lymphotoxin-alpha/TNF-beta)
  • R&D Systems Antibodies for LTA (Lymphotoxin)

Assay Products

  • Cloud-Clone Corp. Assay Kits for LTA

No data available for DME Specific Peptides for LTA Gene

Domains & Families for LTA Gene

Gene Families for LTA Gene

Graphical View of Domain Structure for InterPro Entry

P01374

UniProtKB/Swiss-Prot:

TNFB_HUMAN :
  • Belongs to the tumor necrosis factor family.
Family:
  • Belongs to the tumor necrosis factor family.
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 --
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:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LTA gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytosol 2
nucleus 1
lysosome 1

Gene Ontology (GO) - Cellular Components for LTA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IEA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with LTA: view

Pathways & Interactions for LTA Gene

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

SIGNOR curated interactions for LTA Gene

Activates:

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 IEA --
genes like me logo Genes that share ontologies with LTA: view

Drugs & Compounds for LTA Gene

(34) Drugs for LTA Gene - From: DrugBank, PharmGKB, DGIdb, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Etanercept Approved, Investigational Pharma Target 403
Abacavir Approved, Investigational Pharma 214
Carbamazepine Approved, Investigational Pharma 132
BAMINERCEPT Pharma 0

(30) Additional Compounds for LTA Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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:

CRISPR Products

Inhibitory RNA Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE for LTA Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of LTA Gene:

LTA

SOURCE GeneReport for Unigene cluster for LTA Gene:

Hs.36

Evidence on tissue expression from TISSUES for LTA Gene

  • Blood(3.2)
  • Spleen(2)
genes like me logo Genes that share expression patterns with LTA: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LTA Gene

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 34 35
  • 99.51 (n)
dog
(Canis familiaris)
Mammalia LTA 34 35
  • 83.5 (n)
cow
(Bos Taurus)
Mammalia LTA 34 35
  • 82.03 (n)
mouse
(Mus musculus)
Mammalia Lta 34 16 35
  • 78.88 (n)
rat
(Rattus norvegicus)
Mammalia Lta 34
  • 78.88 (n)
oppossum
(Monodelphis domestica)
Mammalia LTA 35
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lta 34
  • 46.15 (n)
zebrafish
(Danio rerio)
Actinopterygii tnfa 35
  • 25 (a)
ManyToMany
tnfb 35
  • 24 (a)
ManyToMany
Species where no ortholog for LTA was found in the sources mined by GeneCards:
  • 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

TNFB_HUMAN-P01374
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
rs1041981 other 31,573,007(+) CAGCA(A/C)CCTCA upstream-variant-2KB, reference, missense
rs909253 other 31,572,536(-) AGGAA(C/T)CATGG intron-variant
rs1000033668 -- 31,564,237(+) AGAGG(A/C)CAGAC intron-variant
rs1000136608 -- 31,573,328(+) CGGAC(C/T)GTGCC upstream-variant-2KB, reference, missense
rs1000151653 -- 31,564,442(+) GCCCA(A/G)CTAAT intron-variant

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

Variant ID Type Subtype PubMed ID
dgv10403n54 CNV loss 21841781
dgv10404n54 CNV loss 21841781
esv2759414 CNV gain+loss 17122850
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1126749 CNV deletion 24896259
nsv462870 CNV loss 19166990
nsv470809 CNV loss 18288195
nsv601941 CNV loss 21841781
nsv830627 CNV loss 17160897

Variation tolerance for LTA Gene

Residual Variation Intolerance Score: 79.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 14.26; 96.25% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LTA Gene

Human Gene Mutation Database (HGMD)
LTA
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LTA

Disorders for LTA Gene

MalaCards: The human disease database

(39) MalaCards diseases for LTA Gene - From: OMIM, ClinVar, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
psoriatic arthritis
  • arthritis psoriatica
leprosy 4
  • leprosy, susceptibility to, 4
myocardial infarction
  • myocardial infarction, protection against
transient hypogammaglobulinemia
toxic shock syndrome
  • toxic shock
- elite association - COSMIC cancer census association via MalaCards
Search LTA in MalaCards View complete list of genes associated with diseases

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.

Relevant External Links for LTA

Genetic Association Database (GAD)
LTA
Human Genome Epidemiology (HuGE) Navigator
LTA
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LTA
genes like me logo Genes that share disorders with LTA: view

No data available for Genatlas for LTA Gene

Publications for LTA Gene

  1. Association of LT-alpha Ala252Gly gene polymorphism and the genetic predisposition of coronary heart disease in Chinese. (PMID: 19365711) Gao H. … Bai M. (Mol. Biol. Rep. 2010) 3 22 46 64
  2. [Relationship between tumor necrosis factor beta gene polymorphism and acute respiratory distress syndrome after operation for esophageal carcinoma]. (PMID: 19958618) Liu L.X. … Hu Z.J. (Ai Zheng 2009) 3 22 46 64
  3. Genetic variation in TNF and IL10 and risk of non-Hodgkin lymphoma: a report from the InterLymph Consortium. (PMID: 16389181) Rothman N. … Nieters A. (Lancet Oncol. 2006) 3 22 46 64
  4. Association between vitamin D receptor, CCR5, TNF-alpha and TNF-beta gene polymorphisms and HBV infection and severity of liver disease. (PMID: 16545485) Suneetha P.V. … Hissar S. (J. Hepatol. 2006) 3 22 46 64
  5. Lymphotoxin alpha gene in Crohn's disease patients: absence of implication in the response to infliximab in a large cohort study. (PMID: 16609369) Dideberg V. … Bours V. (Pharmacogenet. Genomics 2006) 3 22 46 64

Products for LTA Gene

Sources for LTA Gene

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