LTA (Lymphotoxin-A)

Identity

Other names	TNFb Tumor Necrosis Factor-b
	TNFSF1 TNF Superfamily member 1
Hugo	LTA
Location	6p21.3

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
Hugo	LTA
GDB	LTA
Entrez_Gene	LTA  4049  lymphotoxin alpha (TNF superfamily, member 1)
	Cards
Atlas	LTAID41209ch6p21
GeneCards	LTA
Ensembl	LTA [Search_View]   ENSG00000204496 [Gene_View]
Genatlas	LTA
GeneLynx	LTA
eGenome	LTA
euGene	4049
	Genomic and cartography
GoldenPath	LTA  -  6p21.3   chr6:31648072-31650077 +  6p21.3   [Description]    (hg18-Mar_2006)
Ensembl	LTA - 6p21.3 [CytoView]
NCBI	Mapview
OMIM	Disease map [OMIM]
HomoloGene	LTA
	Gene and transcription
Genbank	A06316 [ ENTREZ ]
Genbank	BC034729 [ ENTREZ ]
Genbank	CR542253 [ ENTREZ ]
Genbank	CR542273 [ ENTREZ ]
Genbank	CR603193 [ ENTREZ ]
RefSeq	NM_000595 [ SRS ]    NM_000595 [ ENTREZ ]
RefSeq	AC_000049 [ SRS ]    AC_000049 [ ENTREZ ]
RefSeq	NC_000006 [ SRS ]    NC_000006 [ ENTREZ ]
RefSeq	NT_007592 [ SRS ]    NT_007592 [ ENTREZ ]
RefSeq	NT_113891 [ SRS ]    NT_113891 [ ENTREZ ]
RefSeq	NT_113894 [ SRS ]    NT_113894 [ ENTREZ ]
RefSeq	NW_923073 [ SRS ]    NW_923073 [ ENTREZ ]
AceView	LTA AceView - NCBI
Unigene	Hs.36 [ SRS ]    Hs.36 [ NCBI ]     HS36 [ spliceNest ]
Fast-db	5870 (alternative variants)
	Protein : pattern, domain, 3D structure
SwissProt	P01374 [ SRS]    P01374 [ EXPASY ]     P01374 [ INTERPRO ]
Prosite	PS00251 TNF_1 [ SRS ]    PS00251 TNF_1 [ Expasy ]
Prosite	PS50049 TNF_2 [ SRS ]    PS50049 TNF_2 [ Expasy ]
Interpro	IPR006053 TNF_abc [ SRS ]    IPR006053 TNF_abc [ EBI ]
Interpro	IPR002960 TNF_beta [ SRS ]    IPR002960 TNF_beta [ EBI ]
Interpro	IPR006052 TNF_family [ SRS ]    IPR006052 TNF_family [ EBI ]
Interpro	IPR003636 TNF_subf [ SRS ]    IPR003636 TNF_subf [ EBI ]
Interpro	IPR008983 Tumour_necrosis_fac-like [ SRS ]    IPR008983 Tumour_necrosis_fac-like [ EBI ]
CluSTr	P01374
Pfam	PF00229 TNF [ SRS ]    PF00229 TNF [ Sanger ]    pfam00229 [ NCBI-CDD ]
Smart	SM00207 TNF [EMBL]
Prodom	PD002012 TNF_subf[INRA-Toulouse]
Prodom	P01374 TNFB_HUMAN [ Domain structure ]   P01374 TNFB_HUMAN  [ sequences sharing at least 1 domain ]
Blocks	P01374
PDB	1TNR [ SRS ]    1TNR [ PdbSum ],   1TNR [ IMB ]   1TNR [ RSDB ]
HPRD	01084
	Protein Interaction databases
DIP	P01374
IntAct	P01374
	Polymorphism : SNP, mutations, diseases
OMIM	153440    [ map ]
GENECLINICS	153440
SNP	LTA [dbSNP-NCBI]
SNP	NM_000595 [SNP-NCI]
SNP	LTA [GeneSNPs - Utah]  LTA] [HGBASE - SRS]
HAPMAP	LTA [HAPMAP]
HGMD	LTA
	General knowledge
Family Browser	LTA [UCSC Family Browser]
SOURCE	NM_000595
SMD	Hs.36
SAGE	Hs.36
GO	cell activation [Amigo]  cell activation
GO	negative regulation of L-glutamate transport [Amigo]  negative regulation of L-glutamate transport
GO	cysteine-type endopeptidase activity [Amigo]  cysteine-type endopeptidase activity
GO	cytokine activity [Amigo]  cytokine activity
GO	tumor necrosis factor receptor binding [Amigo]  tumor necrosis factor receptor binding
GO	extracellular region [Amigo]  extracellular region
GO	extracellular space [Amigo]  extracellular space
GO	proteolysis [Amigo]  proteolysis
GO	apoptosis [Amigo]  apoptosis
GO	induction of apoptosis [Amigo]  induction of apoptosis
GO	immune response [Amigo]  immune response
GO	humoral immune response [Amigo]  humoral immune response
GO	signal transduction [Amigo]  signal transduction
GO	cell-cell signaling [Amigo]  cell-cell signaling
GO	negative regulation of cell proliferation [Amigo]  negative regulation of cell proliferation
GO	response to mechanical stimulus [Amigo]  response to mechanical stimulus
GO	membrane [Amigo]  membrane
GO	integral to membrane [Amigo]  integral to membrane
GO	calcium-mediated signaling [Amigo]  calcium-mediated signaling
GO	positive regulation of I-kappaB kinase/NF-kappaB cascade [Amigo]  positive regulation of I-kappaB kinase/NF-kappaB cascade
GO	positive regulation of neuron apoptosis [Amigo]  positive regulation of neuron apoptosis
GO	positive regulation of mitosis [Amigo]  positive regulation of mitosis
GO	negative regulation of glucose import [Amigo]  negative regulation of glucose import
GO	lymph node development [Amigo]  lymph node development
GO	positive regulation of synaptic transmission [Amigo]  positive regulation of synaptic transmission
GO	positive regulation of protein transport [Amigo]  positive regulation of protein transport
BIOCARTA	Cytokine Network    [Genes]
BIOCARTA	Cytokines and Inflammatory Response    [Genes]
BIOCARTA	TNF/Stress Related Signaling    [Genes]
BIOCARTA	TNFR2 Signaling Pathway    [Genes]
KEGG	Cytokine-cytokine receptor interaction
KEGG	Antigen processing and presentation
KEGG	Type I diabetes mellitus
PubGene	LTA
TreeFam	LTA
CTD	4049 [Comparative ToxicoGenomics Database]
	Other databases
	Probes
Probe	LTA Related clones (RZPD - Berlin)
	PubMed
PubMed	105 Pubmed reference(s) in LocusLink

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

© Atlas of Genetics and Cytogenetics in Oncology and Haematology

indexed on : Wed Jul 2 08:24:44 2008