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Aliases for LTB Gene

Aliases for LTB Gene

  • Lymphotoxin Beta 2 3 5
  • Tumor Necrosis Factor Ligand Superfamily Member 3 3 4
  • TNF Superfamily Member 3 2 3
  • Tumor Necrosis Factor C 3 4
  • LT-Beta 3 4
  • TNFSF3 3 4
  • TNF-C 3 4
  • TNFC 3 4
  • Lymphotoxin Beta (TNF Superfamily, Member 3) 3
  • Tumor Necrosis Factor Ligand 1C 3
  • TNLG1C 3
  • P33 3

External Ids for LTB Gene

Previous HGNC Symbols for LTB Gene

  • TNFC

Previous GeneCards Identifiers for LTB Gene

  • GC06M031611
  • GC06M031602
  • GC06M031319
  • GC06M031652
  • GC06M031656
  • GC06M031549
  • GC06M031335
  • GC06M031582
  • GC06M031583

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) is a Protein Coding gene. Diseases associated with LTB include Rheumatoid Arthritis. Among its related pathways are TNF Signaling (sino) and Immune System. 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

Regulatory Elements for LTB Gene

Enhancers for LTB Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around LTB on UCSC Golden Path with GeneCards custom track

Promoters for LTB Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around LTB on UCSC Golden Path with GeneCards custom track

Genomic Location for LTB Gene

Chromosome:
6
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

Genes around LTB on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LTB Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LTB Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

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

  • Glycosylation at Asn 222
  • Modification sites at PhosphoSitePlus

Other Protein References for LTB Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • R&D Systems Antibodies for LTB (Lymphotoxin beta/TNFSF3)

No data available for DME Specific Peptides for LTB Gene

Domains & Families for LTB Gene

Gene Families for LTB Gene

Graphical View of Domain Structure for InterPro Entry

Q06643

UniProtKB/Swiss-Prot:

TNFC_HUMAN :
  • Belongs to the tumor necrosis factor family.
Family:
  • Belongs to the tumor necrosis factor family.
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:0005515 protein binding IEA --
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:

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets 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
plasma membrane 5
extracellular 4
cytosol 1
endoplasmic reticulum 1
lysosome 1
mitochondrion 1
peroxisome 1
vacuole 1

No data available for Gene Ontology (GO) - Cellular Components for LTB Gene

Pathways & Interactions for LTB Gene

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

SIGNOR curated interactions for LTB Gene

Activates:

Gene Ontology (GO) - Biological Process for LTB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043588 skin development IEA --
GO:0045084 positive regulation of interleukin-12 biosynthetic process ISS --
genes like me logo Genes that share ontologies with LTB: view

Drugs & Compounds for LTB Gene

(12) Drugs for LTB Gene - From: PharmGKB, ClinicalTrials, DGIdb, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Abacavir Approved, Investigational Pharma 205
Isoniazid Approved Pharma 144
Rifapentine Approved Pharma 29
Simvastatin Approved Pharma Competitive, Inhibitor HMG-CoA reductase inhibitor 499
Anti-Bacterial Agents Pharma 10427

(1) Additional Compounds for LTB Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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 (x26.2), Spleen (x14.1), and Small Intestine - Terminal Ileum (x4.5).

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 expression patterns with LTB: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for LTB Gene

Orthologs for LTB Gene

This gene was present in the common ancestor of mammals.

Orthologs for LTB Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia LTB 35
  • 84.29 (n)
  • 80.33 (a)
LTB 36
  • 79 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LTB 35
  • 84.56 (n)
  • 81.15 (a)
LTB 36
  • 78 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ltb 35
  • 79.66 (n)
  • 74.41 (a)
Ltb 16
Ltb 36
  • 61 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia LTB 35
  • 99.73 (n)
  • 99.59 (a)
LTB 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ltb 35
  • 80.83 (n)
  • 76.25 (a)
oppossum
(Monodelphis domestica)
Mammalia LTB 36
  • 52 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 38 (a)
OneToMany
-- 36
  • 44 (a)
OneToMany
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

(1) 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
rs3093554 - 31,581,630(-) TCCAG(A/G)GTTTC reference, missense
rs3093555 - 31,581,113(-) AACAG(C/G)CGTTT reference, missense, utr-variant-3-prime
rs4647186 - 31,581,587(+) CTCAG(A/C/G)CCCGG reference, synonymous-codon, missense
rs4647187 - 31,581,580(-) CCGGG(C/G/T)TCCCA reference, synonymous-codon, missense
rs2229699 - 31,581,079(-) GGACG(A/C/T)CGAGG reference, missense, 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

Variation tolerance for LTB Gene

Residual Variation Intolerance Score: 64.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.36; 41.97% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for LTB Gene

Disorders for LTB Gene

MalaCards: The human disease database

(1) MalaCards diseases for LTB Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
rheumatoid arthritis
  • rheumatoid arthritis, progression of
- elite association - COSMIC cancer census association via MalaCards
Search LTB in MalaCards View complete list of genes associated with diseases

Relevant External Links for LTB

Genetic Association Database (GAD)
LTB
Human Genome Epidemiology (HuGE) Navigator
LTB
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LTB
genes like me logo Genes that share disorders with LTB: view

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

Publications for LTB Gene

  1. 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 67
  2. 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
  3. Accelerated thymic atrophy as a result of elevated homeostatic expression of the genes encoded by the TNF/lymphotoxin cytokine locus. (PMID: 19735075) Liepinsh D.J. … Nedospasov S.A. (Eur. J. Immunol. 2009) 3 23
  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
  5. Lymphotoxin-alpha 1 beta 2 and LIGHT induce classical and noncanonical NF-kappa B-dependent proinflammatory gene expression in vascular endothelial cells. (PMID: 18292573) Madge L.A. … May M.J. (J. Immunol. 2008) 3 23

Products for LTB Gene

Sources for LTB Gene

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