Free for academic non-profit institutions. Other users need a Commercial license

Aliases for LTB Gene

Aliases for LTB Gene

  • Lymphotoxin Beta (TNF Superfamily, Member 3) 2 3
  • TNFC 3 4 6
  • Tumor Necrosis Factor Ligand Superfamily Member 3 3 4
  • Tumor Necrosis Factor C 3 4
  • LT-Beta 3 4
  • TNFSF3 3 4
  • TNF-C 3 4
  • Lymphotoxin-Beta 3
  • P33 3

External Ids for LTB Gene

Previous Symbols for LTB Gene

  • TNFC

Summaries for LTB Gene

Entrez Gene Summary for LTB Gene

  • Lymphotoxin beta is a type II membrane protein of the TNF family. It anchors lymphotoxin-alpha to the cell surface through heterotrimer formation. The predominant form on the lymphocyte surface is the lymphotoxin-alpha 1/beta 2 complex (e.g. 1 molecule alpha/2 molecules beta) and this complex is the primary ligand for the lymphotoxin-beta receptor. The minor complex is lymphotoxin-alpha 2/beta 1. LTB is an inducer of the inflammatory response system and involved in normal development of lymphoid tissue. Lymphotoxin-beta isoform b is unable to complex with lymphotoxin-alpha suggesting a function for lymphotoxin-beta which is independent of lympyhotoxin-alpha. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

GeneCards Summary for LTB Gene

LTB (Lymphotoxin Beta (TNF Superfamily, Member 3)) is a Protein Coding gene. Among its related pathways are NF-KappaB Family Pathway and Spinal Cord Injury. GO annotations related to this gene include receptor binding and tumor necrosis factor receptor binding.

UniProtKB/Swiss-Prot for LTB Gene

  • Cytokine that binds to LTBR/TNFRSF3. May play a specific role in immune response regulation. Provides the membrane anchor for the attachment of the heterotrimeric complex to the cell surface. Isoform 2 is probably non-functional

Gene Wiki entry for LTB Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LTB Gene

Genomics for LTB Gene

Genomic Location for LTB Gene

Start:
31,580,525 bp from pter
End:
31,582,522 bp from pter
Size:
1,998 bases
Orientation:
Minus strand

Genomic View for LTB Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for LTB Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Regulatory Elements for LTB Gene

Proteins for LTB Gene

  • Protein details for LTB Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q06643-TNFC_HUMAN
    Recommended name:
    Lymphotoxin-beta
    Protein Accession:
    Q06643
    Secondary Accessions:
    • P78370
    • Q52LU8
    • Q99761

    Protein attributes for LTB Gene

    Size:
    244 amino acids
    Molecular mass:
    25390 Da
    Quaternary structure:
    • Heterotrimer of either two LTB and one LTA subunits or (less prevalent) one LTB and two LTA subunits

    Three dimensional structures from OCA and Proteopedia for LTB Gene

    Alternative splice isoforms for LTB Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LTB Gene

Proteomics data for LTB Gene at MOPED

Post-translational modifications for LTB Gene

Other Protein References for LTB Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LTB Gene

Domains for LTB Gene

Gene Families for LTB Gene

HGNC:
  • TNFSF :Tumor necrosis factor (ligand) superfamily

UniProtKB/Swiss-Prot:

TNFC_HUMAN
Family:
  • Belongs to the tumor necrosis factor family.:
    • Q06643
genes like me logo Genes that share domains with LTB: view

Function for LTB Gene

Molecular function for LTB Gene

GENATLAS Biochemistry: lymphotoxin beta,expressed in macrophages,,tumors necrosis factor (ligand) superfamily,member 3
UniProtKB/Swiss-Prot Function: Cytokine that binds to LTBR/TNFRSF3. May play a specific role in immune response regulation. Provides the membrane anchor for the attachment of the heterotrimeric complex to the cell surface. Isoform 2 is probably non-functional

Gene Ontology (GO) - Molecular Function for LTB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 receptor binding TAS 7916655
GO:0005125 cytokine activity IEA --
GO:0005164 tumor necrosis factor receptor binding IEA --
GO:0005515 protein binding --
genes like me logo Genes that share ontologies with LTB: view
genes like me logo Genes that share phenotypes with LTB: view

Animal Models for LTB Gene

MGI Knock Outs for LTB:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for LTB Gene

Localization for LTB Gene

Subcellular locations from UniProtKB/Swiss-Prot for LTB Gene

Membrane; Single-pass type II membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LTB Gene COMPARTMENTS Subcellular localization image for LTB gene
Compartment Confidence
extracellular 3
plasma membrane 3
cytosol 1
endoplasmic reticulum 1
lysosome 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for LTB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005615 extracellular space IEA --
GO:0016020 membrane --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LTB: view

Pathways for LTB Gene

genes like me logo Genes that share pathways with LTB: view

Pathways by source for LTB Gene

3 Sino Biological pathways for LTB Gene
1 GeneGo (Thomson Reuters Life Sciences Research) pathway for LTB Gene

Gene Ontology (GO) - Biological Process for LTB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006955 immune response IEA --
GO:0007165 signal transduction TAS 7916655
GO:0007267 cell-cell signaling TAS 7916655
GO:0010467 gene expression IEA --
GO:0043588 skin development IEA --
genes like me logo Genes that share ontologies with LTB: view

Compounds for LTB Gene

(1) HMDB Compounds for LTB Gene

Compound Synonyms Cas Number PubMed IDs
Simvastatin
  • (+)-Simvastatin
79902-63-9

(2) Novoseek inferred chemical compound relationships for LTB Gene

Compound -log(P) Hits PubMed IDs
rantes 38.6 3
cyclosporin a 0 3

(1) PharmGKB related drug/compound annotations for LTB Gene

Drug/compound Annotation
abacavir CA
genes like me logo Genes that share compounds with LTB: view

Transcripts for LTB Gene

mRNA/cDNA for LTB Gene

(2) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(13) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LTB Gene

Lymphotoxin beta (TNF superfamily, member 3):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for LTB Gene

No ASD Table

Relevant External Links for LTB Gene

GeneLoc Exon Structure for
LTB
ECgene alternative splicing isoforms for
LTB

Expression for LTB Gene

mRNA expression in normal human tissues for LTB Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LTB Gene

This gene is overexpressed in Whole Blood (26.2), Spleen (14.1), and Small Intestine - Terminal Ileum (4.5).

SOURCE GeneReport for Unigene cluster for LTB Gene Hs.376208

mRNA Expression by UniProt/SwissProt for LTB Gene

Q06643-TNFC_HUMAN
Tissue specificity: Spleen and thymus
genes like me logo Genes that share expressions with LTB: view

Orthologs for LTB Gene

This gene was present in the common ancestor of mammals.

Orthologs for LTB Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LTB 36
  • 99.73 (n)
  • 99.59 (a)
LTB 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LTB 36
  • 84.29 (n)
  • 80.33 (a)
LTB 37
  • 79 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LTB 36
  • 84.56 (n)
  • 81.15 (a)
LTB 37
  • 78 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ltb 36
  • 79.66 (n)
  • 74.41 (a)
Ltb 16
Ltb 37
  • 61 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LTB 37
  • 52 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 37
  • 38 (a)
OneToMany
-- 37
  • 44 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Ltb 36
  • 80.83 (n)
  • 76.25 (a)
Species with no ortholog for LTB:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for LTB Gene

ENSEMBL:
Gene Tree for LTB (if available)
TreeFam:
Gene Tree for LTB (if available)

Paralogs for LTB Gene

Selected SIMAP similar genes for LTB Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with LTB: view

No data available for Paralogs for LTB Gene

Variants for LTB Gene

Sequence variations from dbSNP and Humsavar for LTB Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type MAF
rs769174 -- 31,583,289(-) ccaaa(C/G)tgttg upstream-variant-2KB
rs769175 -- 31,580,591(-) TGAAA(A/G)TAAAG utr-variant-3-prime
rs2022045 -- 31,582,783(-) TTGAG(A/G)GTATA upstream-variant-2KB
rs2229698 -- 31,581,093(-) GGGAC(G/T)CAGTT reference, synonymous-codon, utr-variant-3-prime
rs2229699 - 31,581,079(-) GGACG(A/C/T)CGAGG missense, reference, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for LTB Gene

Variant ID Type Subtype PubMed ID
nsv830627 CNV Loss 17160897
nsv884418 CNV Gain 21882294

Relevant External Links for LTB Gene

HapMap Linkage Disequilibrium report
LTB

Disorders for LTB Gene

(1) University of Copenhagen DISEASES for LTB Gene

(10) Novoseek inferred disease relationships for LTB Gene

Disease -log(P) Hits PubMed IDs
necrosis 58.5 13
synovitis 40.3 1
tumors 38.5 14
herpes 25.6 1
inflammation 18.1 3

Relevant External Links for LTB

Genetic Association Database (GAD)
LTB
Human Genome Epidemiology (HuGE) Navigator
LTB
genes like me logo Genes that share disorders with LTB: view

No data available for UniProtKB/Swiss-Prot for LTB Gene

Publications for LTB Gene

  1. Lymphotoxin and an associated 33-kDa glycoprotein are expressed on the surface of an activated human T cell hybridoma. (PMID: 1714477) Browning J.L. … Ware C.F. (J. Immunol. 1991) 2 3 23
  2. Identification of two lymphotoxin beta isoforms expressed in human lymphoid cell lines and non-Hodgkin's lymphomas. (PMID: 9299492) Warzocha K. … Salles G. (Biochem. Biophys. Res. Commun. 1997) 3 4 23
  3. 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. (PMID: 15969671) Migita O. … Arinami T. (Clin. Exp. Allergy 2005) 3 23 49
  4. Variation in inflammation-related genes and risk of incident nonfatal myocardial infarction or ischemic stroke. (PMID: 17981284) Bis J.C. … Psaty B.M. (Atherosclerosis 2008) 3 23 49
  5. Lymphotoxin beta, a novel member of the TNF family that forms a heteromeric complex with lymphotoxin on the cell surface. (PMID: 7916655) Browning J.L. … Ware C.F. (Cell 1993) 2 3 4

Products for LTB Gene

Sources for LTB Gene

Back to Top

Content