Set Analyses:
Advanced Search

Advanced Search

 
Search By
Section (entire)
for


 
or upload a file of gene symbols


Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

LTA Gene

protein-coding   GIFtS: 63
GCID: GC06P031541

Lymphotoxin Alpha

(Previous names: lymphotoxin alpha (TNF superfamily, member 1))
(Previous symbol: TNFB)
Microbiology & Infectious Diseases Congress
  See 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)
About This Section

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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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, and among its related super-pathways are MIF Mediated Glucocorticoid Regulation and TNF Signaling. 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.2  NT_007592.15  NT_113891.2  NT_167245.1  NT_167246.1  NT_167247.1  NT_167248.1  
NT_167249.1  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for LTA

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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_113891.2 3,049,492-3,051,714      Chr6+,NT_167246 2,882,760-2,884,982      Chr6+,NT_167248 2,833,512-2,835,736     
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     

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

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
Subcellular location: Secreted. Membrane. Note=The homotrimer is secreted. The heterotrimer is membrane-associated
1 PDB 3D structure from and Proteopedia for LTA:
1TNR (3D)    
Secondary accessions: Q8N4C3 Q9UKS8

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

Explore proteomics data for LTA at MOPED 

LTA Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

LTA Protein Expression

REFSEQ proteins (2 alternative transcripts): 
NP_000586.2  NP_001153212.1  

ENSEMBL proteins: 
 ENSP00000403495   ENSP00000413450  

Human Recombinant Protein Products for LTA: 
Browse Purified and Recombinant Proteins at EMD Millipore
R&D Systems Recombinant & Natural Proteins for LTA (Lymphotoxin, TNF-beta/TNFSF1B)
Enzo Life Sciences proteins for LTA
OriGene Purified Proteins for LTA
OriGene Protein Over-expression Lysate for LTA
OriGene MassSpec for LTA 
OriGene Custom Protein Services for LTA
GenScript Custom Purified and Recombinant Proteins Services for LTA
Novus Biologicals LTA Proteins
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. 

Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

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

LTA for ontologies           About GeneDecksing



LTA Antibody Products: 
EMD Millipore Mono- and Polyclonal Antibodies for the study of LTA
R&D Systems Antibodies for LTA (Lymphotoxin, TNF-beta/TNFSF1B)
OriGene Antibodies for LTA
OriGene Custom Antibody Services for LTA
GenScript Superior Antibodies for LTA
Novus Biologicals LTA Antibodies
Abcam antibodies for LTA
Browse Antibodies at Cloud-Clone Corp. 
ThermoFisher Antibodies for LTA
LSBio Antibodies in human, mouse, rat for LTA 

Assay Products for LTA: 
Browse Kits and Assays available from EMD Millipore
OriGene Custom Assay Services for LTA
R&D Systems ELISAs for LTA (TNF-beta/TNFSF1B)
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.


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

5 InterPro protein domains:
 IPR021184 TNF_CS
 IPR006052 TNF
 IPR002960 TNF_beta
 IPR006053 TNF_a/b/c
 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


LTA for domains           About GeneDecksing


(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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

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 (GO ID links to tree view):    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 ----
     
LTA for ontologies           About GeneDecksing


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

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

LTA for phenotypes           About GeneDecksing

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 - Custom generated mouse model solutions for LTA 
   inGenious Targeting Laboratory - Custom generated inducible mouse model solutions 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
Products:
    
QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat LTA
7 QIAGEN miScript miRNA 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:
    
Browse for Gene Knock-down Tools from EMD Millipore
OriGene RNAi products in human, mouse, rat for LTA
QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat LTA

Gene Editing
Products:
DNA2.0 Custom Protein Engineering Service for LTA
Sirion Biotech Customized adenovirus for overexpression of LTA

Clone
Products:
     
Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
OriGene clones in human, mouse for LTA (see all 11)
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
Sirion Biotech Customized lentivirus for stable overexpression of LTA 
                     Customized lentivirus expression plasmids for stable overexpression of LTA 

Cell Line
Products:
     
GenScript Custom overexpressing Cell Line Services for LTA
Search LifeMap BioReagents cell lines for LTA
In Situ Assay
Products:
   

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LTA


(Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
About This Section

SuperPaths for LTA About   (see all 28)                                                                                              See pathways by source

SuperPathSelected contained pathways About (see all per SuperPath)
1PEDF Induced Signaling
MIF Mediated Glucocorticoid Regulation0.94
IL-6 Pathway0.61
MIF Regulation of Innate Immune Cells0.94
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 & their Associated Functions0.49
Death Receptor Signaling0.50
NF-kB (NFkB) Pathway0.46
3Apoptosis and survival Lymphotoxin-beta receptor signaling
Apoptosis and survival Lymphotoxin-beta receptor signaling0.46
LT-BetaR Pathway0.46
4Rho Family GTPases
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

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways

2 EMD Millipore Pathways for LTA
    Transcription NF-kB signaling pathway
Apoptosis and survival Lymphotoxin-beta receptor signaling

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

5/33 Downloadable PowerPoint Slides of QIAGEN 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


5/6         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


LTA for pathways           About GeneDecksing

Interactions:

    SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for LTA

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

5/18 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): 5/17 biological process terms (GO ID links to tree view) (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 ----

LTA for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

LTA for compounds           About GeneDecksing

Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

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

10/61 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)

1 PharmGKB related drug/compound annotation for LTA gene    About this table
Drug/compound PharmGKB Annotation
carbamazepineCA  

Search CenterWatch for drugs/clinical trials and news about LTA / TNFB

(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,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

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
Congresses - knowledge worth sharing:  
European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

miRNA
Products:
     
QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat LTA
7 QIAGEN miScript miRNA 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:
     
Browse for Gene Knock-down Tools from EMD Millipore
OriGene RNAi products in human, mouse, rat for LTA
QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat LTA
Clone
Products:
     
OriGene clones in human, mouse for LTA (see all 11)
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)
DNA2.0 Custom Codon Optimized Gene Synthesis Service for LTA
Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LTA
Sirion Biotech Customized lentivirus for stable overexpression of LTA 
                     Customized lentivirus expression plasmids for stable overexpression of LTA 
Primer
Products:
    
OriGene qSTAR qPCR primer pairs in human, mouse for LTA
SABiosciences RT2 qPCR Primer Assay in human, mouse, rat LTA
  QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat LTA
  QIAGEN 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 

24/28 AceView cDNA sequences (see all 28):

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

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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

LTA expression in normal human tissues (normalized intensities)      LTA embryonic expression: see
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 
 5/3 selected tissues (see all 3) fully expand
 
 Blood (Hematopoietic System)    fully expand to see all 2 entries
         b cells   
 
 Eye (Sensory Organs)
         Glycinergic Amacrine Cells Inner Nuclear Layer
 
 Spleen (Hematopoietic System)
         splenocytes   

See LTA Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for LTA

SOURCE GeneReport for Unigene cluster: Hs.36
    SABiosciences Expression via Pathway-Focused 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
Products:
OriGene qSTAR qPCR primer pairs in human, mouse for LTA
SABiosciences RT2 qPCR Primer Assay in human, mouse, rat LTA
QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat LTA
QIAGEN QuantiFast Probe-based Assays in human, mouse, rat LTA
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

This gene was present in the common ancestor of chordates.

Orthologs for LTA gene from 2/7 species (see all 7)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Lta1 , 5 lymphotoxin A1, 5 80.03(n)1
73.27(a)1
  17 (18.59 cM)5
169921  NM_010735.21  NP_034865.11 
 352031655 
zebrafish
(Danio rerio)
Actinopterygii tnfb6
tnfa6
tumor necrosis factor b (TNF superfamily, member 2...
tumor necrosis factor a (TNF superfamily, member 2...
23(a)
23(a)
many ↔ many
many ↔ many
15(33995840-33998916)
19(27505097-27509684)


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)
About This Section
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

LTA for paralogs           About GeneDecksing



(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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

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


4 SNPs in LTA are shown    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
VAR_0130244
----see VAR_0130242 H P mis40--------
VAR_0075124
----see VAR_0075122 T P mis40--------
VAR_0075114
----see VAR_0075112 T N mis40--------
VAR_0130234
----see VAR_0130232 C R 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
SABiosciences Cancer Mutation 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, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
OMIM gene information: 153440   
OMIM disorders: 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

  • 20/211 diseases for LTA (see all 211):    About MalaCards
    psoriatic arthritis    leprosy    transient hypogammaglobulinemia    non-hodgkin lymphoma
    sympathetic ophthalmia    monoclonal gammopathy of uncertain significance    shigellosis    streptococcal toxic-shock syndrome
    dengue hemorrhagic fever    sarcoidosis    posterior uveitis    hodgkin's lymphoma
    toxic shock syndrome    post-transplant lymphoproliferative disease    coronary aneurysm    myocardial infarction
    uveitis    cardiac sarcoidosis    obstructive lung disease    castleman's disease

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

    LTA for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:  
    The International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD) 9 - 13 March 2014
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

    10/95 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)
    About This Section

    PubMed articles for LTA gene, integrated from 9 sources (see all 1116):
    (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. (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. (2005)
    3. Relationship between tumor necrosis factor beta gene polymorphism and acute respiratory distress syndrome after operation for esopha geal carcinoma. (PubMed id 19958618)1, 4, 9 Liu L.X....Hu Z.J. (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. (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. (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. (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. (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....Vacha J. (2001)
    9. Association between LTA, TNF and AGER polymorphisms and late diabetic complications. (PubMed id 18575614)1, 4, 9 Lindholm E....Agardh C.D. (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. (2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 4049 HGNC: 6709 AceView: LTA Ensembl:ENSG00000226979 euGenes: HUgn4049
    ECgene: LTA Kegg: 4049 H-InvDB: LTA

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    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.)
    About This Section
    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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     Browse Kits and Assays available from EMD Millipore
     EMD Millipore Mono- and Polyclonal Antibodies for the study of LTA
     Browse Purified and Recombinant Proteins at EMD Millipore
     Browse for Gene Knock-down Tools from EMD Millipore
     Browse Small Molecules at EMD Millipore
     Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
     
     EMD Millipore Custom Antibody & Bulk Services
     EMD Millipore Preclinical / Clinical Development Services
     EMD Millipore Immunoassay Services
     EMD Millipore Target Screening & Profiling Services

      
     Antibodies for LTA (Lymphotoxin)   Browse Cell Culture Products  
     ELISAs for LTA (TNF-beta/TNFSF1B)   Browse Flow Cytometry Kits  
     Browse Primer Pairs   Browse Kinase Activity Assays/Reagents  
     Browse ELISpot Kits/Development Modules   Browse TFB/Immunoprecipitation Assays  
     Browse Apoptosis Detection Kits/Reagents   Browse Ubiquitin Proteasome Pathway (UPP) Assay Kits/Reagents  
     Browse DNA Damage/Repair Kits/Reagents   Browse Multiplex/Array Assay Kits/Reagents  
     Browse Cell Selection/Detection Kits/Reagents   Browse Secondary Antibodies/Controls/Staining Reagents  
     Browse Protease Activity Assays and Reagents   Recombinant/Natural Proteins for LTA (Lymphotoxin)  
     Browse Stem Cell Products   Browse Tocris Biochemicals & Compounds  
     Browse cDNA Clones   Browse Proteome Profiler Antibody Arrays  
     OriGene Antibodies for LTA   OriGene RNAi products in human, mouse, rat for LTA  
     Browse OriGene qPCR primer pairs and template standards   OriGene Protein Over-expression Lysate for LTA  
     OriGene MassSpec something-or-other for LTA   OriGene clones in human, mouse for LTA  
     OriGene qSTAR qPCR primer pairs in human, mouse for LTA   OriGene Purified Protein for LTA  
     OriGene ORF clones in mouse, rat for LTA   OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling  
     OriGene Custom Antibody Services for LTA   OriGene Custom Protein Services for LTA  

     
     
     QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat LTA
     QIAGEN SeqTarget long-range PCR primers for resequencing LTA
     QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat LTA
     QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat LTA
     QIAGEN QuantiFast Probe-based Assays in human, mouse, rat LTA
     QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat LTA
     GenScript Custom Purified and Recombinant Proteins Services for LTA GenScript cDNA clones with any tag delivered in your preferred vector for LTA
     GenScript Custom Assay Services for LTA GenScript Superior Antibodies for LTA
     GenScript Custom overexpressing Cell Line Services for LTA CloneReady with Over 120,000 Genes
     Gene Synthesis: Any Gene in Any Vector Vector-based siRNA and miRNA, Ready for Transfection
     Gene Mutant Library, Variants up to 10^11 Plasmid Preparation
     Custom Peptide Services
     Search for Antibodies & Assays

     Regulatory tfbs in LTA promoter
     Search Chromatin IP Primers for LTA
     RT2 qPCR Primer Assay in human, mouse, rat LTA
     GNC Network for LTA
     SABiosciences PCR Arrays including human, mouse, rat LTA
     Search Tocris compounds for LTA (TNFB)
     Proteins and Antibodies for LTA
     Browse Sino Biological Cell Lysates
     cDNA Clones for LTA
     4000+ Proteins
     Search Sino Biological for antibodies, proteins & pathways
     Protein Production Services
     Transfection Reagents
     Protein A/G/L resins
     Isotyping reagents
     Proteins for LTA
     Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies
     Novus Tissue Slides
     LTA antibodies
     LTA proteins
     LTA lysates
     Antibodies for LTA
     See all of Abcam's Antibodies, Kits and Proteins for LTA
     Custom Antibody / Protein Production Service
     Bulk Purchasing
     Advantages of Rabbit Monoclonal antibodies
     Abcam protocols and scientific support
     Recombinant Protein for LTA




     Browse Proteins at Cloud-Clone Corp.
     Browse Antibodies at Cloud-Clone Corp.
     Browse ELISAs at Cloud-Clone Corp.
     Browse CLIAs at Cloud-Clone Corp.
     Search LifeMap BioReagents cell lines for LTA
     Gene Synthesis
     Protein Engineering
     Variant Library Synthesis
     Codon Optimization
     Protein Production and Purification
     Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LTA
     SwitchGear 3'UTR luciferase reporter plasmids for LTA
     SwitchGear Promoter luciferase reporter plasmids for LTA
     ThermoFisher Antibodies for LTA
     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LTA
     inGenious Targeting Laboratory - Custom generated mouse model solutions for LTA
     inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for LTA
    Customized:
     lentivirus for stable overexpression of LTA
     lentivirus expression plasmids for stable overexpression of LTA
     adenovirus for overexpression of LTA
     LSBio Antibodies in human, mouse, rat for LTA
    Customized transgenic rodents for:
     Humanization
     Biomarker expression
     Off-target effect monitoring
     Translational medicine
     Tissue-specific gene expresssion
     Time-controlled gene expresssion
           
    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

    View Random Gene

    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


    Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

    Hot genes      Disease genes      LTA gene at Home site.
    hostname: 356980-web2.xennexinc.com index build: 106 solr: 1.4