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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

LTA Gene

protein-coding GIFtS: 64
GCID: GC06P031541

lymphotoxin alpha (TNF superfamily, member 1)

(Previous symbol: TNFB)

Explore 230 diseases affiliated with
LTA via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Lymphotoxin Alpha (TNF Superfamily, Member 1)¹ ²		LT-Alpha¹
TNFB¹ ² ³ ⁵		TNF-Beta¹
TNFSF1¹ ² ³		Lymphotoxin-Alpha¹
LT¹ ²		Tumor Necrosis Factor Beta²
Tumor Necrosis Factor Ligand Superfamily Member 1² ³

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:

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)

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)

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000006.11 NC_018917.1 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+,ALT_REF_LOCI_5 31,531,003-31,533,227	Chr6+,ALT_REF_LOCI_4 31,502,419-31,504,641	Chr6+,ALT_REF_LOCI_6 31,530,070-31,567,920
Chr6+,ALT_REF_LOCI_3 31,521,973-31,535,280	Chr6+,ALT_REF_LOCI_2 31,527,243-31,568,698	Chr6+,ALT_REF_LOCI_7 31,460,142-31,462,364

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

LTA Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins (2 alternative transcripts):

NP_000586.2 NP_001153212.1

ENSEMBL proteins:

ENSP00000403495 ENSP00000413450

Human Recombinant Protein Products:

	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 (see all 2): LTA OriGene Protein Over-expression Lysate (see all 2): LTA OriGene Custom Protein Services for LTA
	GenScript Custom Purified and Recombinant Proteins Services for LTA
	Novus Biologicals LTA Proteins Novus Biologicals LTA Lysate
	Browse Sino Biological Recombinant Proteins
	ProSpec Recombinant Protein for LTA
	Browse Proteins at Uscn

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005615	extracellular space	IEA	--
GO:0016020	membrane	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 (see all 2): LTA OriGene Custom Antibody Services for LTA
	GenScript Superior Antibodies for LTA
	Novus Biologicals LTA Antibodies
	Abcam antibodies for LTA
	Browse Antibodies at Uscn
	Search ThermoFisher Antibodies for LTA

Assay Products for LTA:

	Browse Kits and Assays available from EMD Millipore
	OriGene Custom Immunoassay Development Browse OriGene Fluorogenic Cell Assay Kits
	R&D Systems ELISAs for LTA (TNF-beta/TNFSF1B)
	GenScript Custom Assay Services for LTA
	Browse Enzo Life Sciences for kits & assays
	Browse ELISAs and CLIAs at Uscn

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

LTA for domains About GeneDecksing

5 InterPro domains/families:

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 families:

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

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

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

Genatlas biochemistry entry for LTA:

lymphotoxin alpha,expressed in T cells,tumors necrosis factor (ligand) superfamily,member 1

miRNA Products:		Browse 3'-UTR reporter clones for miRNA target validation Browse MicroRNA Expression Plasmids
		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 plasmid: LTA 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for LTA (see all 7) OriGene shRNA RFP: LTA OriGene siRNA: LTA
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat LTA

Gene Editing
Products:

DNA2.0 Custom Protein Engineering Service for LTA

Clone Products:		Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for LTA (see all 4) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for LTA (see all 2) 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
		Search LifeMap BioReagents cell lines for LTA

In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LTA

Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005102	receptor binding	TAS	3001529
GO:0005125	cytokine activity	IEA	--
GO:0005164	tumor necrosis factor receptor binding	IEA	--

LTA for ontologies About GeneDecksing

1 GenomeRNAi human phenotype for LTA:

Increased G1 DNA content

Animal Models:
     Mouse knock-outs for LTA: Lta/Tnf^Lta/tm1Fda Lta^tm1.1Sned Lta/Tnf^Lta/tm1Eug Lta/Tnf^Lta/tm1Jods Lta^tm1Jods Lta^tm1Tab
                                               Ltb/Tnf/Lta^{Ltb/Tnf/tm1Dvk} Lta^tm1Dch
     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

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
About This Section

Unified GeneCards pathways - 5/23 super-pathways (see all 23) About this table

See pathways by source

Super-pathway

contained gene-specific pathways

PEDF Induced Signaling

8/9 pathways (see all 9)
PEDF Induced Signaling	1.00	RAR-Gamma-RXR-Alpha Degradation	0.54
MIF Mediated Glucocorticoid Regulation	0.73	STAT3 Pathway	0.47
MIF Regulation of Innate Immune Cells	0.71	Endothelin-1 Signaling Pathway	0.44
IL-6 Pathway	0.61	Cytokine-cytokine receptor interaction	0.26

Rho Family GTPases

	Rho Family GTPases	1.00			Molecular Mechanisms of Cancer	0.51
	ERK Signaling	0.61			MAPK Signaling	0.51

TRAF Pathway

	TRAF Pathway	1.00			TNF Superfamily - Human Ligand-Receptor Interactions & their Associated Functions	0.08
	TNF Superfamily Pathway	0.42

Apoptosis and survival_Lymphotoxin-beta receptor signaling

	Apoptosis and survival Lymphotoxin-beta receptor signaling	1.00			LT-BetaR Pathway	0.46
	Apoptosis and survival_Lymphotoxin-beta receptor signaling	1.00

Transcription NF-kB signaling pathway

Transcription NF-kB signaling pathway

1.00

Transcription_NF-kB signaling pathway

0.85

Pathway sources
See GeneCards unified pathways
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

2 Kegg Pathways (Kegg details for LTA):

	Cytokine-cytokine receptor interaction
	Type I diabetes mellitus

LTA for pathways About GeneDecksing

Interactions:

SABiosciences Gene Network Central^TM Interacting Genes and Proteins Network for LTA

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

5/11 Interacting proteins for LTA (P01374^{2, 3} ENSP00000403495⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 11)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
TUBA1A	Q71U36²^,³	MINT-49840 I2D: score=1
LGALS2	P05162²^,³, ENSP00000215886⁴	MINT-49838 MINT-49837 MINT-49836 I2D: score=4 STRING: ENSP00000215886
LTB	Q06643³, ENSP00000410481⁴	I2D: score=4 STRING: ENSP00000410481
TNFRSF14	Q92956³, ENSP00000347948⁴	I2D: score=4 STRING: ENSP00000347948
UMOD	P07911³, ENSP00000306279⁴	I2D: score=3 STRING: ENSP00000306279

About this table

Gene Ontology (GO): 5/16 biological process terms (GO ID links to tree view) (see all 16): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001666	response to hypoxia	IEA	--
GO:0002876	positive regulation of chronic inflammatory response to antigenic stimulus	IEA	--
GO:0002925	positive regulation of humoral immune response mediated by circulating immunoglobulin	IEA	--
GO:0006917	induction of apoptosis	TAS	6334807
GO:0006959	humoral immune response	IEA	--

LTA for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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

1 DrugBank Compound for LTA About this table

Compound	Synonyms	CAS #	Type	Actions	PubMed Ids
Etanercept	CD120b (see all 7)	185243-69-0	target	--	15033655 1328224 15695296 15005015 11302411

10/61 Novoseek 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

Drug/compound	PharmGKB Annotation
carbamazepine	CA

About this table

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

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 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,
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, 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

miRNA Products:		Browse 3'-UTR reporter clones for miRNA target validation Browse OriGene MicroRNA Expression Plasmids
		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 plasmid: LTA 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for LTA (see all 7) OriGene shRNA RFP: LTA OriGene siRNA: LTA
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat LTA

Clone Products:		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for LTA (see all 4) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for LTA (see all 2) 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

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for LTA Browse OriGene validated miRNA SYBR primer pairs
		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 cDNA 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):

W74395 BC034729 BP338937 D12614 NM_000595 CD697300 AI075301 CR603193

X01393 BI832977 CR542273 W72329 BG685356 BF976097 BQ643169 BF796746

CR542253 D00102 CD698103 BI832903 BX370788 BX108399 AI702790 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)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --

About this image
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 genome-wide validated SYBR primer pairs in human, mouse, rat for LTA Browse OriGene validated miRNA SYBR primer pairs
		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 1/7 species (see all 7) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
zebrafish (Danio rerio)	Actinopterygii	tnfa⁶ tnfb⁶	tumor necrosis factor a (TNF superfamily, member 2... tumor necrosis factor b (TNF superfamily, member 2...	24(a) 24(a)	many ↔ many many ↔ many	19(27505097-27509684) 15(33995840-33998916)

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 19 protein entries: TNFB_HUMAN (see all proteins):

LTB TNF

LTA for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, 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]

SNP ID	Valid	Clinical significance	Chr 6 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs1041981^1,2	C,F,A,H,	other	31327518(+)	`CAGCAC/ACCTCA`	1	--	us2k¹		59		EA MN NS NA WA CSA EU	13152
rs56277413^1,2	C	--	31324781(+)	`CTCAAA/GTAG`	2	--	int¹ us2k¹		0	--	--	--	--
rs3093539^1,2	C,F,H,	--	31325009(+)	`AAGTTG/AGTATT`	3	--	us2k¹ int¹		7		NS EA WA	624
rs4647189^1,2	F	--	31325154(+)	`gaaacAAAC/- caaat`	1	--	int¹		1		NS	120
rs736160^1,2	C,F	--	31325228(-)	`tttttA/Taaaaa`	1	--	int¹		1		NS	112
rs56127727^1,2	C,	--	31325467(+)	`CTGGGC/TGGTGG`	1	--	int¹		0	--	--	--	--
rs36221456^1,2	C,	--	31325595(-)	`AAGACA/TCTGTC`	1	--	int¹		0	--	--	--	--
rs4647192^1,2	C,	--	31325612(+)	`tccccC/Taggct`	1	--	int¹		1		NS	156
rs111602778^1,2		--	31325619(+)	`GGCTGG/AAATAC`	1	--	int¹		1		CSA	2
rs3093540^1,2	C,F,	--	31325742(+)	`tttttG/Atattt`	1	--	int¹		5		NS WA NA	490

HapMap Linkage Disequilibrium report for LTA (31539831 - 31542101 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for LTA
1 CNV: 2625
Human Gene Mutation Database (HGMD): LTA

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat 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.)
About This Section

LTA for disorders           About GeneDecksing

OMIM gene information: 153440
OMIM disorders: 607507  610988
UniProtKB/Swiss-Prot: TNFB_HUMAN, P01374

Genetic variations in LTA are a cause of susceptibility psoriatic arthritis (PSORAS) [MIM:607507]. PSORAS is

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

rheumatoidlike 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)

20/230 diseases for LTA (see all 230): About MalaCards

non-hodgkin lymphoma myocardial infarction psoriatic arthritis hodgkin's lymphoma

leprosy post-transplant lymphoproliferative disease graft versus host disease monoclonal gammopathy of uncertain significance

arthritis spinal cord injury dengue hemorrhagic fever diffuse large b-cell lymphoma

human t-cell leukemia virus type 1 hypersensitivity reaction type ii disease acute graft versus host disease sympathetic ophthalmia

chronic venous leg ulcers myocardial infarction susceptibility cor pulmonale optic neuritis

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

Cancer

10/95 Novoseek 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 1096):
(articles sorted by number of sources associating them with LTA)

Utopia: connect your pdf to the dynamic
world of online information

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)
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)
[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)
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)
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)
Polymorphisms in the +252(A/G) lymphotoxin-alpha and the -308(A/G) tumor necrosis factor-alpha genes and susceptibility to chronic periodontitis in a Czech population. (PubMed id 12828656)^{1, 4, 9} Fassmann A....Vanek J. (2003)
An association study in essential hypertension using functional polymorphisms in lymphotoxin-alpha gene. (PubMed id 15533732)^{1, 4, 9} Nakayama T....Kokubun S. (2004)
Association of a TNFbeta gene polymorphism with complications after major abdominal operations. (PubMed id 12558135)^{1, 4, 9} Riese J....Haupt W. (2003)
[Polymorphism of angiotensin converting enzyme (ACE) and TNF-beta genes in men with disorders of spermatogenesis--pilot study] (PubMed id 11732226)^{1, 4, 9} Kucera M....Znojil V. (2001)
MHC class II, tumour necrosis factor alpha, and lymphotoxin alpha gene haplotype associations with serological subsets of systemic lupus erythematosus. (PubMed id 16107511)^{1, 4, 9} McHugh N.J....Welsh K. (2006)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
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

Name	Description
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-SNPs	http://egp.gs.washington.edu/data/lta/
SeattleSNPs	http://pga.gs.washington.edu/data/lta/
SHMPD	http://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=LTA

Intellectual Property for LTA gene
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Patent Information for LTA gene:
Search GeneIP for patents involving LTA

GeneCards and IP:
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lymphotoxin alpha (TNF superfamily, member 1)

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