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LTA (Lymphotoxin-A)

Written2005-02Fei Chen
Health Effects Laboratory Division, NIOSH, 1095 Willowdale Rd, Morgantown, WV 26505, USA

(Note : for Links provided by Atlas : click)

Identity

Alias_namesTNFB
lymphotoxin alpha (TNF superfamily
Alias_symbol (synonym)TNFSF1
LT
Other aliasTNFb Tumor Necrosis Factor-b
TNFSF1 TNF Superfamily member 1
HGNC (Hugo) LTA
LocusID (NCBI) 4049
Atlas_Id 41209
Location 6p21.33  [Link to chromosome band 6p21]
Location_base_pair Starts at 31572294 and ends at 31574323 bp from pter ( according to hg19-Feb_2009)  [Mapping LTA.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)

DNA/RNA

Description The human TNFb gene is located next to HLA-C and HLA-B loci in chromosome 6 (6p21.3). The gene spans 2005bp with 4 exons, which transcribes a TNFb mRNA with size of 1386nt.

Protein

 
Description The human TNFb protein contains 205 amino acids. The soluble form of TNFb is usually a homotrimer with a relative molecular mass of 60 to 70 kDa, whereas the membrane form of TNFb is a heteromeric complex with lymphotoxin b (TNFc, LTb, TNFSF3). The human TNFb shares 35% identity and 50% homology in amino acid sequence with the human TNFa. The biological function of TNFb is mediated largely by TNFa receptor 1 and TNFa receptor 2. Recent studies suggested that TNFb can also recognize LIGHT ( TNFSF14) receptor.
Expression The main cellular source of TNFb is the activated lymphocytes in immune response.
Localisation Cell membrane, extracellular soluble form, blood stream, and biological fluids.
Function The human TNFb is an important cytokine involved in the development of secondary lymphoid organs and inflammatory responses.

Implicated in

Note
Disease The polymorphism of TNFb gene in either the coding region or the promoter region has been associated with Crohn disease and myocardial infarction.
  

Bibliography

Signalling pathways of the TNF superfamily: a double-edged sword.
Aggarwal BB
Nature reviews. Immunology. 2003 ; 3 (9) : 745-756.
PMID 12949498
 
Lymphotoxin/light, lymphoid microenvironments and autoimmune disease.
Gommerman JL, Browning JL
Nature reviews. Immunology. 2003 ; 3 (8) : 642-655.
PMID 12974479
 

Citation

This paper should be referenced as such :
Chen, F
LTA (lymphotoxin-A)
Atlas Genet Cytogenet Oncol Haematol. 2005;9(2):119-119.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/LTAID41209ch6p21.html


External links

Nomenclature
HGNC (Hugo)LTA   6709
Cards
AtlasLTAID41209ch6p21
Entrez_Gene (NCBI)LTA  4049  lymphotoxin alpha
AliasesLT; TNFB; TNFSF1; TNLG1E
GeneCards (Weizmann)LTA
Ensembl hg19 (Hinxton)ENSG00000226979 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000226979 [Gene_View]  chr6:31572294-31574323 [Contig_View]  LTA [Vega]
ICGC DataPortalENSG00000226979
TCGA cBioPortalLTA
AceView (NCBI)LTA
Genatlas (Paris)LTA
WikiGenes4049
SOURCE (Princeton)LTA
Genetics Home Reference (NIH)LTA
Genomic and cartography
GoldenPath hg38 (UCSC)LTA  -     chr6:31572294-31574323 +  6p21.33   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)LTA  -     6p21.33   [Description]    (hg19-Feb_2009)
EnsemblLTA - 6p21.33 [CytoView hg19]  LTA - 6p21.33 [CytoView hg38]
Mapping of homologs : NCBILTA [Mapview hg19]  LTA [Mapview hg38]
OMIM153440   607507   608446   610988   
Gene and transcription
Genbank (Entrez)A06316 BC034729 BG685356 BP338937 BX108399
RefSeq transcript (Entrez)NM_000595 NM_001159740
RefSeq genomic (Entrez)NC_000006 NC_018917 NG_007462 NG_012010 NT_113891 NT_167245 NT_167246 NT_167247 NT_167248 NT_167249
Consensus coding sequences : CCDS (NCBI)LTA
Cluster EST : UnigeneHs.36 [ NCBI ]
CGAP (NCI)Hs.36
Alternative Splicing GalleryENSG00000226979
Gene ExpressionLTA [ NCBI-GEO ]   LTA [ EBI - ARRAY_EXPRESS ]   LTA [ SEEK ]   LTA [ MEM ]
Gene Expression Viewer (FireBrowse)LTA [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)4049
GTEX Portal (Tissue expression)LTA
Human Protein AtlasENSG00000226979-LTA [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP01374   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP01374  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP01374
Splice isoforms : SwissVarP01374
PhosPhoSitePlusP01374
Domaine pattern : Prosite (Expaxy)TNF_1 (PS00251)    TNF_2 (PS50049)   
Domains : Interpro (EBI)TNF    TNF_beta    TNF_CS    TNF_dom    Tumour_necrosis_fac-like_dom   
Domain families : Pfam (Sanger)TNF (PF00229)   
Domain families : Pfam (NCBI)pfam00229   
Domain families : Smart (EMBL)TNF (SM00207)  
Conserved Domain (NCBI)LTA
DMDM Disease mutations4049
Blocks (Seattle)LTA
PDB (SRS)1TNR    4MXV    4MXW   
PDB (PDBSum)1TNR    4MXV    4MXW   
PDB (IMB)1TNR    4MXV    4MXW   
PDB (RSDB)1TNR    4MXV    4MXW   
Structural Biology KnowledgeBase1TNR    4MXV    4MXW   
SCOP (Structural Classification of Proteins)1TNR    4MXV    4MXW   
CATH (Classification of proteins structures)1TNR    4MXV    4MXW   
SuperfamilyP01374
Human Protein Atlas [tissue]ENSG00000226979-LTA [tissue]
Peptide AtlasP01374
HPRD01084
IPIIPI00001670   IPI00941920   IPI01022808   IPI00815722   IPI00815880   IPI00816250   IPI00640229   IPI00645121   IPI00643970   
Protein Interaction databases
DIP (DOE-UCLA)P01374
IntAct (EBI)P01374
FunCoupENSG00000226979
BioGRIDLTA
STRING (EMBL)LTA
ZODIACLTA
Ontologies - Pathways
QuickGOP01374
Ontology : AmiGOresponse to hypoxia  positive regulation of chronic inflammatory response to antigenic stimulus  positive regulation of humoral immune response mediated by circulating immunoglobulin  receptor binding  cytokine activity  tumor necrosis factor receptor binding  extracellular space  plasma membrane  apoptotic process  humoral immune response  signal transduction  cell-cell signaling  response to nutrient  response to lipopolysaccharide  positive regulation of interferon-gamma production  tumor necrosis factor-mediated signaling pathway  response to drug  positive regulation of apoptotic process  negative regulation of growth of symbiont in host  negative regulation of fibroblast proliferation  lymph node development  defense response to Gram-positive bacterium  positive regulation of glial cell proliferation  
Ontology : EGO-EBIresponse to hypoxia  positive regulation of chronic inflammatory response to antigenic stimulus  positive regulation of humoral immune response mediated by circulating immunoglobulin  receptor binding  cytokine activity  tumor necrosis factor receptor binding  extracellular space  plasma membrane  apoptotic process  humoral immune response  signal transduction  cell-cell signaling  response to nutrient  response to lipopolysaccharide  positive regulation of interferon-gamma production  tumor necrosis factor-mediated signaling pathway  response to drug  positive regulation of apoptotic process  negative regulation of growth of symbiont in host  negative regulation of fibroblast proliferation  lymph node development  defense response to Gram-positive bacterium  positive regulation of glial cell proliferation  
Pathways : KEGGCytokine-cytokine receptor interaction    NF-kappa B signaling pathway    TNF signaling pathway    Type I diabetes mellitus    HTLV-I infection    Herpes simplex infection   
REACTOMEP01374 [protein]
REACTOME PathwaysR-HSA-5676594 [pathway]   
NDEx NetworkLTA
Atlas of Cancer Signalling NetworkLTA
Wikipedia pathwaysLTA
Orthology - Evolution
OrthoDB4049
GeneTree (enSembl)ENSG00000226979
Phylogenetic Trees/Animal Genes : TreeFamLTA
HOVERGENP01374
HOGENOMP01374
Homologs : HomoloGeneLTA
Homology/Alignments : Family Browser (UCSC)LTA
Gene fusions - Rearrangements
Tumor Fusion PortalLTA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLTA [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LTA
dbVarLTA
ClinVarLTA
1000_GenomesLTA 
Exome Variant ServerLTA
ExAC (Exome Aggregation Consortium)ENSG00000226979
GNOMAD BrowserENSG00000226979
Genetic variants : HAPMAP4049
Genomic Variants (DGV)LTA [DGVbeta]
DECIPHERLTA [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisLTA 
Mutations
ICGC Data PortalLTA 
TCGA Data PortalLTA 
Broad Tumor PortalLTA
OASIS PortalLTA [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLTA  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDLTA
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)TBsLVD Tuberculosis susceptibility Locus Variation Database
BioMutasearch LTA
DgiDB (Drug Gene Interaction Database)LTA
DoCM (Curated mutations)LTA (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LTA (select a term)
intoGenLTA
NCG5 (London)LTA
Cancer3DLTA(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM153440    607507    608446    610988   
Orphanet
DisGeNETLTA
MedgenLTA
Genetic Testing Registry LTA
NextProtP01374 [Medical]
TSGene4049
GENETestsLTA
Target ValidationLTA
Huge Navigator LTA [HugePedia]
snp3D : Map Gene to Disease4049
BioCentury BCIQLTA
ClinGenLTA
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD4049
Chemical/Pharm GKB GenePA30474
Clinical trialLTA
Miscellaneous
canSAR (ICR)LTA (select the gene name)
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLTA
EVEXLTA
GoPubMedLTA
iHOPLTA
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 14:54:49 CET 2017

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