LTA (Lymphotoxin-A)

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LTA (Lymphotoxin-A)

Identity

Other names	TNFb Tumor Necrosis Factor-b
	TNFSF1 TNF Superfamily member 1
HGNC (Hugo)	LTA
LocusID (NCBI)	4049
Location	6p21.3
Location_base_pair	Starts at 3049709 and ends at 3051714 bp from pter ( according to hg19-Feb_2009) [Mapping]

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

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

External links

	Nomenclature
HGNC (Hugo)	LTA 6709
Entrez_Gene (NCBI)	LTA 4049 lymphotoxin alpha (TNF superfamily, member 1)
	Cards
Atlas	LTAID41209ch6p21
GeneCards (Weizmann)	LTA
Ensembl (Hinxton)	ENSG00000226979 [Gene_View] chr6_cox_hap2:3049709-3051714 [Contig_View] LTA [Vega]
AceView (NCBI)	LTA
Genatlas (Paris)	LTA
euGene (Indiana)	4049
SOURCE (Stanford)	NM_000595 NM_001159740
	Genomic and cartography
GoldenPath (UCSC)	LTA - 6p21.3 chr6_cox_hap2:3049709-3051714 + 6p21.3 [Description] (hg19-Feb_2009)
Ensembl	LTA - 6p21.3 [CytoView]
Mapping of homologs : NCBI	LTA [Mapview]
OMIM	153440 607507 608446 610988
	Gene and transcription
Genbank (Entrez)	A06316 BC034729 BP338937 CR542253 CR542273
RefSeq transcript (SRS)	NM_000595 NM_001159740
RefSeq transcript (Entrez)	NM_000595 NM_001159740
RefSeq genomic (SRS)	AC_000138 NC_000006 NG_007462 NG_012010 NT_007592 NT_113891 NT_167245 NT_167246 NT_167247 NT_167248 NT_167249 NW_001838980
RefSeq genomic (Entrez)	AC_000138 NC_000006 NG_007462 NG_012010 NT_007592 NT_113891 NT_167245 NT_167246 NT_167247 NT_167248 NT_167249 NW_001838980
Consensus coding sequences : CCDS (NCBI)	LTA
Cluster EST : Unigene	Hs.36 [ SRS ] Hs.36 [ NCBI ]
Alternative Splicing : Fast-db (Paris)	5870
Alternative Splicing Gallery	ENSG00000226979
Gene Expression	LTA [ NCBI-GEO ] LTA [ EBI - ARRAY_EXPRESS ]
	Protein : pattern, domain, 3D structure
UniProt/SwissProt	P01374 (SRS) P01374 (Uniprot)
With graphics : InterPro	P01374
Splice isoforms : SwissVar	P01374(Swissvar)
Domaine pattern : Prosite (SRS)	TNF_1 (PS00251) TNF_2 (PS50049)
Domaine pattern : Prosite (Expaxy)	TNF_1 (PS00251) TNF_2 (PS50049)
Domains : Interpro (SRS)	TNF TNF_a/b/c TNF_beta TNF_CS Tumour_necrosis_fac-like
Domains : Interpro (EBI)	TNF TNF_a/b/c TNF_beta TNF_CS Tumour_necrosis_fac-like
Related proteins : CluSTr	P01374
Domain families : Pfam (SRS)	TNF (PF00229)
Domain families : Pfam (Sanger)	TNF (PF00229)
Domain families : Pfam (NCBI)	pfam00229
Domain families : Smart (EMBL)	TNF (SM00207)
Blocks (Seattle)	P01374
PDB (SRS)	1TNR
PDB (PDBSum)	1TNR
PDB (IMB)	1TNR
PDB (RSDB)	1TNR
Human Protein Atlas	ENSG00000226979
HPRD	01084
IPI	IPI00001670 IPI00941920 IPI01022808 IPI00815722 IPI00815880 IPI00816250 IPI00640229 IPI00645121 IPI00643970
	Protein Interaction databases
DIP (DOE-UCLA)	P01374
IntAct (EBI)	P01374
FunCoup	ENSG00000226979
REACTOME	LTA
BioGRID	LTA
InParanoid	P01374
Interologous Interaction database	P01374
	Polymorphism : SNP, mutations, diseases
SNP Single Nucleotide Polymorphism (NCBI)	LTA
SNP (GeneSNP Utah)	LTA
SNP : HGBase	LTA
Genetic variants : HAPMAP	LTA
Somatic Mutations in Cancer : COSMIC	LTA
CONAN: Copy Number Analysis	LTA
Mutations and Diseases : HGMD	LTA
OMIM	153440 607507 608446 610988
GENETests	153440 607507 608446 610988
Disease Genetic Association	LTA
Huge Navigator	LTA [HugePedia] LTA [HugeCancerGEM]
Genomic Variants	LTA
snp3D : Map Gene to Disease	4049
	General knowledge
Homologs : HomoloGene	LTA
Homology/Alignments : Family Browser (UCSC)	LTA
Phylogenetic Trees/Animal Genes : TreeFam	LTA
Chemical/Protein Interactions : CTD	4049
Chemical/Pharm GKB Gene	PA30474
Clinical trial	LTA
Cancer Resource (Charite)	ENSG00000226979
Ontology : AmiGO	response 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 region extracellular space induction of apoptosis immune response humoral immune response signal transduction cell-cell signaling response to nutrient membrane response to lipopolysaccharide positive regulation of interferon-gamma production response to drug negative regulation of growth of symbiont in host negative regulation of fibroblast proliferation lymph node development defense response to Gram-positive bacterium
Ontology : EGO-EBI	response 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 region extracellular space induction of apoptosis immune response humoral immune response signal transduction cell-cell signaling response to nutrient membrane response to lipopolysaccharide positive regulation of interferon-gamma production response to drug negative regulation of growth of symbiont in host negative regulation of fibroblast proliferation lymph node development defense response to Gram-positive bacterium
Pathways : KEGG	Antigen processing and presentation Cytokine-cytokine receptor interaction Type I diabetes mellitus
	Other databases
	Probes
Probes : Imagenes	LTA Related clones (RZPD - Berlin)
	Litterature
PubMed	467 Pubmed reference(s) in Entrez
PubGene	LTA
iHOP	LTA

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

REVIEW articles	automatic search in PubMed
Last year publications	automatic search in PubMed

Search in all EBI NCBI

Contributor(s)

Written	02-2005	Fei Chen
		NIOSH, 1095 Willowdale Rd, Morgantown, WV 26505, USA

Citation
This paper should be referenced as such :
Chen F . LTA (Lymphotoxin-A). Atlas Genet Cytogenet Oncol Haematol. February 2005 .
URL : http://AtlasGeneticsOncology.org/Genes/LTAID41209ch6p21.html

This paper is referenced by INIST as such :
http://documents.irevues.inist.fr/bitstream/2042/38178/1/02-2005-LTAID41209ch6p21.pdf [ Bibliographic record ]

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Apr 28 15:06:39 CEST 2012

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