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LTA Gene

protein-coding   GIFtS: 64
GCID: GC06P031541

Lymphotoxin Alpha

(Previous names: lymphotoxin alpha (TNF superfamily, member 1))
(Previous symbol: TNFB)
  See LTA-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Lymphotoxin Alpha1 2     Lymphotoxin Alpha (TNF Superfamily, Member 1)1
TNFB1 2 3 5     TNF Superfamily Member 11
Tumor Necrosis Factor Ligand Superfamily Member 12 3     LT2
LT-alpha2 3     lymphotoxin-alpha2
TNF-beta2 3     TNF Superfamily, Member 12
TNFSF12 3     Tumor Necrosis Factor Beta2

External Ids:    HGNC: 67091   Entrez Gene: 40492   Ensembl: ENSG000002269797   OMIM: 1534405   UniProtKB: P013743   

Export aliases for LTA gene to outside databases

Previous GC identifers: GC06P031603 GC06P031593 GC06P031310 GC06P031644 GC06P031648 GC06P031540 GC06P031326


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 leprosy 4, and dengue hemorrhagic fever. GO annotations related to this gene include tumor necrosis factor receptor binding and receptor binding. An important paralog of this gene is FASLG.

UniProtKB/Swiss-Prot: TNFB_HUMAN, P01374
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 Wiki entry for LTA (Lymphotoxin alpha) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000006.11  NC_018917.2  NT_007592.16  NT_113891.3  NT_167245.2  NT_167246.2  NT_167247.2  NT_167248.2  
NT_167249.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the LTA gene promoter:
         c-Fos   p53   AP-1   ATF-2   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 4): LTA promoter sequence
   Search Chromatin IP Primers for LTA

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LTA


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6p21.3   Ensembl cytogenetic band:  6p21.33   HGNC cytogenetic band: 6p21.3

LTA Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LTA gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P031541:  view genomic region     (about GC identifiers)

Start:
31,539,831 bp from pter      End:
31,542,101 bp from pter
Size:
2,271 bases      Orientation:
plus strand

6 alternative locations:
Chr6+,NT_167249 2,870,677-2,872,899      Chr6+,NT_167245 2,825,415-2,827,639      Chr6+,NT_167247 2,919,580-2,921,804     
Chr6+,NT_167246 2,882,760-2,884,982      Chr6+,NT_113891.2 3,049,492-3,051,714      Chr6+,NT_167248 2,833,512-2,835,736     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: TNFB_HUMAN, P01374 (See protein sequence)
Recommended Name: Lymphotoxin-alpha precursor  
Size: 205 amino acids; 22297 Da
Subunit: Homotrimer, and heterotrimer of either two LTB and one LTA subunits or (less prevalent) two LTA and one
LTB subunits
3 PDB 3D structures from and Proteopedia for LTA:
1TNR (3D)        4MXV (3D)        4MXW (3D)    
Secondary accessions: Q8N4C3 Q9UKS8

Explore the universe of human proteins at neXtProt for LTA: NX_P01374

Post-translational modifications: 

  • Glycosylation2 at Thr41, Asn96
  • REFSEQ proteins (2 alternative transcripts): 
    NP_000586.2  NP_001153212.1  

    ENSEMBL proteins: 
     ENSP00000403495   ENSP00000413450  

    LTA Human Recombinant Protein Products:

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    Novus Biologicals LTA Lysate
    Sino Biological Recombinant Protein for LTA
    Browse Sino Biological Cell Lysates
    ProSpec Recombinant Protein for LTA
    Browse Proteins at Cloud-Clone Corp.

     
    eBioscience Proteins for LTA:  
                        Recombinant Human TNF-beta 10 ug

    LTA Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of LTA
    R&D Systems Antibodies for LTA (Lymphotoxin, TNF-beta/TNFSF1)
    OriGene Antibodies for LTA
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    Novus Biologicals LTA Antibodies
    Abcam antibodies for LTA (Q06643, P01374)
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    ThermoFisher Antibodies for LTA
    LSBio Antibodies in human, mouse, rat for LTA

    LTA Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    R&D Systems ELISAs for LTA (TNF-beta/TNFSF1)
    GenScript Custom Assay Services for LTA
    Browse Enzo Life Sciences for kits & assays
    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.
    eBioscience ELISAs for LTA: (see all 4
                        Human TNF-beta Platinum ELISA 10 x 96 tests


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    TNFSF: Tumor necrosis factor (ligand) superfamily

    5 InterPro protein domains:
     IPR021184 TNF_CS
     IPR006052 TNF_dom
     IPR002960 TNF_beta
     IPR006053 TNF
     IPR008983 Tumour_necrosis_fac-like_dom

    Graphical View of Domain Structure for InterPro Entry P01374

    ProtoNet protein and cluster: P01374

    3 Blocks protein domains:
    IPB002960 Tumour necrosis factor beta (lymphotoxin-alpha) signature
    IPB006052 Tumor Necrosis Factor
    IPB006053 Tumour necrosis factor family signature


    UniProtKB/Swiss-Prot: TNFB_HUMAN, P01374
    Similarity: Belongs to the tumor necrosis factor family


    Find genes that share domains with LTA           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TNFB_HUMAN, P01374
    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

         Genatlas biochemistry entry for LTA:
    lymphotoxin alpha,expressed in T cells,tumors necrosis factor (ligand) superfamily,member 1

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005102receptor binding TAS3001529
    GO:0005125cytokine activity IEA--
    GO:0005164tumor necrosis factor receptor binding IEA--
    GO:0005515protein binding ----
         
    Find genes that share ontologies with LTA           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for LTA:
     Increased G1 DNA content 

         14 MGI mutant phenotypes (inferred from 9 alleles(MGI details for Lta):
     behavior/neurological  cardiovascular system  endocrine/exocrine gland  growth/size/body  hematopoietic system 
     homeostasis/metabolism  immune system  limbs/digits/tail  liver/biliary system  mortality/aging 
     nervous system  respiratory system  skeleton  vision/eye 

    Find genes that share phenotypes with LTA           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for LTA: Lta/TnfLta/tm1Fda Ltatm1.1Sned Lta/TnfLta/tm1Eug Lta/TnfLta/tm1Jods Ltatm1Jods Ltatm1Tab
                                                         Ltb/Tnf/LtaLtb/Tnf/tm1Dvk Ltatm1Dch

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for LTA
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for LTA

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for LTA
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for LTA

    miRNA
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    7 qRT-PCR Assays for microRNAs that regulate LTA:
    hsa-miR-1290 hsa-miR-331-3p hsa-miR-32* hsa-miR-3175 hsa-miR-3612 hsa-miR-650 hsa-miR-1248
    SwitchGear 3'UTR luciferase reporter plasmidLTA 3' UTR sequence
    Inhib. RNA
    Products:
        
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    Predesigned siRNA for gene silencing in human, mouse, rat LTA

    Gene Editing
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    Clone
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    OriGene clones in human, mouse for LTA (see all 10)
    OriGene ORF clones in mouse, rat for LTA
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 6): LTA (NM_001833)
    Sino Biological Human cDNA Clone for LTA
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for LTA
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LTA

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for LTA
    Browse ESI BIO Cell Lines and PureStem Progenitors for LTA 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LTA


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    TNFB_HUMAN, P01374: Secreted. Membrane. Note=The homotrimer is secreted. The heterotrimer is membrane-associated
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    nucleus2
    plasma membrane2

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005615extracellular space IEA--
    GO:0016020membrane IEA--

    Find genes that share ontologies with LTA           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for LTA About   (see all 28)  
    See pathways by source

    SuperPathSelected contained pathways About (see all per SuperPath)
    1PEDF Induced Signaling
    MIF Regulation of Innate Immune Cells0.94
    IL-6 Pathway0.61
    MIF Mediated Glucocorticoid Regulation0.94
    STAT3 Pathway0.47
    PEDF Induced Signaling0.73
    Endothelin-1 Signaling Pathway0.46
    all-trans-Retinoic Acid Signaling in Brain0.71
    Cytokine-cytokine receptor interaction0.43
    2TNF Signaling
    TNF Signaling0.50
    TNF Superfamily - Human Ligand-Receptor Interactions and their Associated Functions0.49
    Death Receptor Signaling0.50
    NF-kB (NFkB) Pathway0.46
    3LT-BetaR Pathway
    Apoptosis and survival Lymphotoxin beta receptor signaling0.46
    LT-BetaR Pathway0.46
    4ERK Signaling
    Rho Family GTPases0.61
    MAPK Signaling0.58
    ERK Signaling0.61
    Molecular Mechanisms of Cancer0.51
    5NF-KappaB Family Pathway
    NF-KappaB (p50-p65) Pathway0.72
    NF-KappaB Family Pathway0.72


    Find genes that share SuperPaths with LTA           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 R&D Systems Pathways for LTA
        TNF Superfamily - Human Ligand-Receptor Interactions & their Associated Functions
    Th1 Differentiation

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for LTA (see all 33)
        Caspase Cascade
    14-3-3 Induced Apoptosis
    LT-BetaR Pathway
    Molecular Mechanisms of Cancer
    Antioxidant Action of Vitamin-C

    2 GeneGo (Thomson Reuters) Pathways for LTA
        Transcription NF-kB signaling pathway
    Apoptosis and survival Lymphotoxin-beta receptor signaling

    3 BioSystems Pathways for LTA
        Apoptosis
    IL4-mediated signaling events
    IL2 signaling events mediated by STAT5

    3 Sino Biological Pathways for LTA
        TNF Signaling
    Death Receptor Signaling
    NF-kB (NFkB) Pathway


    Selected Kegg Pathways  (Kegg details for LTA) (see all 6):
        Cytokine-cytokine receptor interaction
    NF-kappa B signaling pathway
    TNF signaling pathway
    Type I diabetes mellitus
    HTLV-I infection

        Pathway & Disease-focused RT2 Profiler PCR Arrays including LTA (see all 16): 
              NFKB Signaling Targets in human mouse rat
              Multiple Sclerosis in human mouse rat
              Toll-Like Receptor Signaling Pathway in human mouse rat
              Inflammatory Response & Autoimmunity in human mouse rat
              Apoptosis in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for LTA

    STRING Interaction Network Preview (showing 5 interactants - click image to see 9)

    Selected Interacting proteins for LTA (P013742, 3 ENSP000004034954) via UniProtKB, MINT, STRING, and/or I2D (see all 18)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    TUBA1AQ71U362, 3MINT-49840 I2D: score=1 
    LTBQ066433, ENSP000004104814I2D: score=4 STRING: ENSP00000410481
    ENSG00000204487Q066433I2D: score=4 
    ENSG00000206437Q066433I2D: score=4 
    ENSG00000223448Q066433I2D: score=4 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 17):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001666response to hypoxia IEA--
    GO:0002876positive regulation of chronic inflammatory response to antigenic stimulus IEA--
    GO:0002925positive regulation of humoral immune response mediated by circulating immunoglobulin IEA--
    GO:0006915apoptotic process TAS6334807
    GO:0006955immune response ----

    Find genes that share ontologies with LTA           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for LTA (TNFB)

    1 DrugBank Compound for LTA    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    EtanerceptCD120b (see all 7)185243-69-0target--15033655 1328224 15695296 15005015 11302411

    Selected Novoseek inferred chemical compound relationships for LTA gene (see all 61)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    il 10 53.8 8 16389181 (1), 8621762 (1), 7521890 (1), 9924213 (1) (see all 7)
    rantes 47.3 14 10366103 (2), 12620497 (2), 9764576 (1), 14693736 (1) (see all 12)
    toxin-1 45.7 2 7911750 (1), 8515117 (1)
    lipoteichoic acid 36.2 2 16175622 (1), 12439617 (1)
    ionomycin 34.7 4 8625537 (1), 12176893 (1), 7631148 (1), 8647171 (1)
    actinomycin d 26.5 4 1707879 (1), 7535097 (1), 10721723 (1), 16280692 (1)
    etanercept 25.3 4 15005015 (1), 18473978 (1), 12749755 (1), 11458980 (1)
    neopterin 25 4 8304116 (1), 1825941 (1), 8148443 (1)
    okt3 18.9 1 7993789 (1)
    pge2 14.3 11 8442433 (3), 8777276 (2), 1707006 (1), 1815239 (1) (see all 5)

    3 PharmGKB related drug/compound annotations for LTA gene    About this table
    Drug/compound PharmGKB Annotation
    carbamazepineCA  
    cyclosporineCA  
    mycophenolate mofetilCA  



    Find genes that share compounds with LTA           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for LTA gene (2 alternative transcripts): 
    NM_000595.3  NM_001159740.2  

    Unigene Cluster for LTA:

    Lymphotoxin alpha (TNF superfamily, member 1)
    Hs.36  [show with all ESTs]
    Unigene Representative Sequence: NM_001159740
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000454783(uc011dnu.1) ENST00000489638(uc003nuf.3 uc003nuh.3 uc003nug.3 uc010jsr.3)
    ENST00000418386(uc003nue.1) ENST00000471842
    miRNA
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    7 qRT-PCR Assays for microRNAs that regulate LTA:
    hsa-miR-1290 hsa-miR-331-3p hsa-miR-32* hsa-miR-3175 hsa-miR-3612 hsa-miR-650 hsa-miR-1248
    SwitchGear 3'UTR luciferase reporter plasmidLTA 3' UTR sequence
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector (see all 6): LTA (NM_001833)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LTA
    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat LTA
      QuantiTect SYBR Green Assays in human, mouse, rat LTA
      QuantiFast Probe-based Assays in human, mouse, rat LTA

    Additional mRNA sequence: 

    BC034729.1 CR542253.1 CR542273.1 D00102.1 D12614.1 DQ123821.1 DQ123822.1 DQ123823.1 
    DQ123824.1 DQ123825.2 DQ123826.1 DQ123827.1 X01393.1 

    3 DOTS entries:

    DT.411032  DT.100746901  DT.91679243 

    Selected AceView cDNA sequences (see all 28):

    BC034729 D12614 NM_000595 BP338937 W74395 X01393 CD697300 BG685356 
    BI832977 BF976097 AI075301 CR542273 BF796746 W72329 CR603193 BQ643169 
    CR542253 AI702790 AA910185 D00102 CD698103 BI832903 BX108399 BX370788 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    LTA expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    LTA Expression
    About this image


    LTA expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Neurons
             Glycinergic Amacrine Cells Inner Nuclear Layer
     
     Eye (Sensory Organs)
             Glycinergic Amacrine Cells Inner Nuclear Layer
    LTA Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

    SOURCE GeneReport for Unigene cluster: Hs.36
        Pathway & Disease-focused RT2 Profiler PCR Arrays including LTA (see all 16): 
              NFKB Signaling Targets in human mouse rat
              Multiple Sclerosis in human mouse rat
              Toll-Like Receptor Signaling Pathway in human mouse rat
              Inflammatory Response & Autoimmunity in human mouse rat
              Apoptosis in human mouse rat

    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LTA

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

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    This gene was present in the common ancestor of chordates.

    Orthologs for LTA gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Lta1 , 5 lymphotoxin A1, 5 78.88(n)1
    72.28(a)1
      17 (18.59 cM)5
    169921  NM_010735.21  NP_034865.11 
     352031655 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia lta1 lymphotoxin alpha 46.15(n)
    39.05(a)
      100135001  NM_001113678.1  NP_001107150.1 
    zebrafish
    (Danio rerio)
    Actinopterygii tnfa6
    tnfb6
    tumor necrosis factor a (TNF superfamily, member 2...
    tumor necrosis factor b (TNF superfamily, member 2...
    25(a)
    24(a)
    many ↔ many
    many ↔ many
    19(27505097-27509684) ENSDARG00000009511
    15(33995840-33998916) ENSDARG00000013598


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for LTA gene
    FASLG2  TNFSF152  TNFSF142  TNF2  
    2 SIMAP similar genes for LTA using alignment to 16 protein entries:     TNFB_HUMAN (see all proteins):
    LTB    TNF

    Find genes that share paralogs with LTA           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Polymorphic Variants from UniProtKB/Swiss-Prot
    TNFB_HUMAN, P01374: A polymorphism in LTA accounts, in part, for susceptibility to leprosy linked to chromosome 6p21.3
    (LPRS4) [MIM:610988]


    4 SNPs for LTA    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs22290921,2,4
    ----see VAR_0130242 mis40--------
    VAR_0075124
    ----see VAR_0075122 T P mis40--------
    rs10419811,2,4
    ----see VAR_0075112 mis40--------
    rs22290941,2,4
    ----see VAR_0130232 mis40--------

    HapMap Linkage Disequilibrium report for LTA (31539831 - 31542101 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for LTA:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv830627CNV Loss17160897
    nsv462870CNV Loss19166990
    nsv470809CNV Loss18288195
    nsv884418CNV Gain21882294
    esv690CNV CNV17122850
    essv13266CNV CNV17122850

    Human Gene Mutation Database (HGMD): LTA
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing LTA
    DNA2.0 Custom Variant and Variant Library Synthesis for LTA

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 153440   
    OMIM disorders: 608446  607507  610988  
    UniProtKB/Swiss-Prot: TNFB_HUMAN, P01374
  • 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

  • Selected diseases for LTA (see all 35):    
    About MalaCards
    leprosy 4    dengue hemorrhagic fever    spondylarthropathy    psoriatic arthritis
    monoclonal gammopathy of uncertain significance    chronic venous leg ulcers    shigellosis    transient hypogammaglobulinemia
    sarcoidosis    coronary aneurysm    toxic shock syndrome    leprosy
    cardiac sarcoidosis    post-transplant lymphoproliferative disease    sympathetic ophthalmia    myocardial infarction
    posterior uveitis    obstructive lung disease    tonsillitis    optic neuritis

    1 disease from the University of Copenhagen DISEASES database for LTA:
    Cancer

    Find genes that share disorders with LTA           About GenesLikeMe

    Selected Novoseek inferred disease relationships for LTA gene (see all 95)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    necrosis 87.9 723 9798700 (5), 15224026 (3), 12620497 (3), 8509747 (2) (see all 99)
    tumors 73.9 627 9798700 (5), 15224026 (3), 12620497 (3), 19022528 (2) (see all 99)
    tonsillar hypertrophy 50 1 8860357 (1)
    leukemia t-cell 46.5 3 2039827 (1), 1976820 (1), 7696918 (1)
    toxic shock syndrome 46.3 4 8515117 (3), 7911750 (1)
    genetic susceptibility 46.1 4 11037831 (1), 17767060 (1), 16939911 (1)
    autoimmune diseases 41.1 8 10600011 (1), 9098447 (1), 12568117 (1), 14617046 (1) (see all 8)
    miscarriage recurrent 40.9 5 11737072 (3), 18299433 (1), 18394614 (1)
    inflammation 40.7 18 16770523 (3), 2133280 (1), 7590816 (1), 10923599 (1) (see all 15)
    multiple sclerosis 40.1 19 8624683 (5), 12568117 (2), 17295710 (2), 9098447 (1) (see all 8)

    Genetic Association Database (GAD): LTA
    Human Genome Epidemiology (HuGE) Navigator: LTA (450 documents)

    Export disorders for LTA gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for LTA gene, integrated from 10 sources (see all 1122):
    (articles sorted by number of sources associating them with LTA)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cytokine gene polymorphisms: association with psoriatic arthritis susceptibility and severity. (PubMed id 12746914)1, 2, 4, 9 Balding J.... FitzGerald O. (Arthritis Rheum. 2003)
    2. The influence of a polymorphism at position -857 of the tumour necrosis factor alpha gene on clinical response to etanercept therapy in rheumatoid arthritis. (PubMed id 15695296)1, 4, 7 Kang C.P....Bae S.C. (Rheumatology (Oxford) 2005)
    3. [Relationship between tumor necrosis factor beta gene polymorphism and acute respiratory distress syndrome after operation for esophageal carcinoma]. (PubMed id 19958618)1, 4, 9 Liu L.X....Hu Z.J. (Ai Zheng 2009)
    4. Polymorphic structure of the tumor necrosis factor (TNF) locus: an NcoI polymorphism in the first intron of the human TNF-beta gene correlates with a variant amino acid in position 26 and a reduced level of TNF-beta production. (PubMed id 1670638)1, 2, 9 Messer G.... Weiss E.H. (J. Exp. Med. 1991)
    5. Haplotype analysis of a 100 kb region spanning TNF-LTA identifies a polymorphism in the LTA promoter region that is associated with atopic asthma susceptibility in Japan. (PubMed id 15969671)1, 4, 9 Migita O....Arinami T. (Clin. Exp. Allergy 2005)
    6. [Association between tumor necrosis factor-beta polymorphisms and coronary heart disease in a Chinese population]. (PubMed id 15583987)1, 4, 9 Li Y....Huang C.X. (Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2004)
    7. The interaction of the polymorphisms in transporter of antigen peptides (TAP) and lymphotoxin alpha (LT-alpha) genes and atopic diseases in the Czech population. (PubMed id 11591192)1, 4, 9 IzakovicovA! HollA! L....Znojil V. (Clin. Exp. Allergy 2001)
    8. Interactions of lymphotoxin alpha (TNF-beta), angiotensin-converting enzyme (ACE), and endothelin-1 (ET-1) gene polymorphisms in adult periodontitis. (PubMed id 11210078)1, 4, 9 HollA! L.I....VA!cha J. (J. Periodontol. 2001)
    9. Association between LTA, TNF and AGER polymorphisms and late diabetic complications. (PubMed id 18575614)1, 4, 9 Lindholm E....Agardh C.D. (PLoS ONE 2008)
    10. Functional variants in the lymphotoxin-alpha gene predict cardiovascular disease in dialysis patients. (PubMed id 16988060)1, 4, 9 Liu Y....Coresh J. (J. Am. Soc. Nephrol. 2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 4049 HGNC: 6709 AceView: LTA Ensembl:ENSG00000226979 euGenes: HUgn4049
    ECgene: LTA Kegg: 4049 H-InvDB: LTA

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for LTA Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for LTA Genetics and Cytogenetics in Oncology and Haematology
    Wikipedia http://en.wikipedia.org/wiki/Lymphotoxin
    NIEHS-SNPshttp://egp.gs.washington.edu/data/lta/
    SeattleSNPshttp://pga.gs.washington.edu/data/lta/
    SHMPDhttp://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=LTA

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for LTA gene:
    Search GeneIP for patents involving LTA

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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