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

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
  • Lymphotoxin-Beta 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
  • GC06M031600
  • GC06M031767
  • GC06M031811

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. Among its related pathways are TRAF Pathway and Innate 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 CIViC summary , 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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G031557 1.3 Ensembl ENCODE 13.1 +22.9 22932 4.2 HDGF PKNOX1 AGO1 WRNIP1 ZNF2 ZNF143 ZNF207 FOS KLF13 ZNF263 CSNK2B DDX39B LST1 NCR3 UQCRHP1 LTB AIF1 SNORD117 PSORS1C2 C6orf47
GH06G031614 1.1 Ensembl ENCODE 12.4 -33.3 -33313 3.7 HDAC1 ELF3 HDGF TBP ZNF121 RELB ETV6 IKZF2 CREM TBX21 BAG6 LY6G5B HLA-DRB1 SKIV2L LY6G5C LST1 LTB C4A DDX39B DDX39B-AS1
GH06G031269 1.6 FANTOM5 ENCODE dbSUPER 1.6 +311.1 311061 4.4 HDGF PKNOX1 ATF1 WRNIP1 ARID4B SIN3A GLI4 ZNF2 YY1 ZNF121 HLA-C PSORS1C3 PPT2 DDX39B LY6G5B TCF19 LSM2 PSORS1C2 ATF6B HCG18
GH06G031567 2.1 FANTOM5 Ensembl ENCODE dbSUPER 0.7 +4.1 4104 22.2 CREB3L1 MLX AGO1 ZFP64 DMAP1 FEZF1 YBX1 YY1 SLC30A9 ZNF143 DDX39B TNF LY6G5B LSM2 DHX16 ATF6B TCF19 PPP1R10 VARS CSNK2B
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000195564 1122 1601 HDGF MLX AGO1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B SLC30A9

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

Post-translational modifications for LTB Gene

  • Glycosylation at posLast=222222
  • Modification sites at PhosphoSitePlus

Other Protein References for LTB Gene

ENSEMBL proteins:
REFSEQ proteins:

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:0005102 receptor binding TAS 7916655
GO:0005125 cytokine activity IEA --
GO:0005164 tumor necrosis factor receptor 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

CRISPR Products

Inhibitory RNA Products

Clone 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LTB gene
Compartment Confidence
plasma membrane 5
extracellular 4
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1
lysosome 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:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LTB: view

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:0006955 immune response IEA --
GO:0007165 signal transduction TAS 7916655
GO:0007267 cell-cell signaling TAS 7916655
GO:0010467 gene expression IEA --
GO:0033209 tumor necrosis factor-mediated signaling pathway TAS --
genes like me logo Genes that share ontologies with LTB: view

Drugs & Compounds for LTB Gene

(16) 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 214
Isoniazid Approved Pharma 155
Rifampin Approved Pharma Agonist 348
Rifapentine Approved Pharma 31
Simvastatin Approved Pharma Competitive, Inhibitor HMG-CoA reductase inhibitor 519

(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:

CRISPR Products

Inhibitory RNA Products

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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).

NURSA nuclear receptor signaling pathways regulating expression of LTB Gene:

LTB

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.

Evidence on tissue expression from TISSUES for LTB Gene

  • Intestine(4.6)
  • Spleen(4.6)
  • Blood(4.3)
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 , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia LTB 34 35
  • 99.73 (n)
dog
(Canis familiaris)
Mammalia LTB 34 35
  • 84.56 (n)
cow
(Bos Taurus)
Mammalia LTB 34 35
  • 84.29 (n)
rat
(Rattus norvegicus)
Mammalia Ltb 34
  • 80.83 (n)
mouse
(Mus musculus)
Mammalia Ltb 34 16 35
  • 79.66 (n)
oppossum
(Monodelphis domestica)
Mammalia LTB 35
  • 52 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 44 (a)
OneToMany
-- 35
  • 38 (a)
OneToMany
Species where no ortholog for LTB was found in the sources mined by GeneCards:
  • 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
rs1001191370 -- 31,580,937(+) CCGTA(A/G)GCGCC reference, synonymous-codon, utr-variant-3-prime
rs1001470507 -- 31,580,302(+) TGGCC(C/T)TGAAA downstream-variant-500B
rs1002865202 -- 31,582,561(+) TGGGG(G/T)GGGGC upstream-variant-2KB
rs1005203493 -- 31,583,963(+) ATCTG(C/T)CCGTG upstream-variant-2KB
rs1005671968 -- 31,583,514(+) CTGGG(C/G)AACAG upstream-variant-2KB

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

Variant ID Type Subtype PubMed ID
dgv10403n54 CNV loss 21841781
dgv10404n54 CNV loss 21841781
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1126749 CNV deletion 24896259
nsv830627 CNV loss 17160897

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)

Relevant External Links for LTB Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LTB

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LTB Gene

Disorders for LTB Gene

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

No disorders were found for LTB Gene.

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

Publications for LTB Gene

  1. 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 22 46 64
  2. 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 22 46 64
  3. 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 22 64
  4. 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 64
  5. 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 22 64

Products for LTB Gene

Sources for LTB Gene

Content
Loading form....