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LTB lymphotoxin beta [ Homo sapiens (human) ]

Gene ID: 4050, updated on 3-May-2025
Official Symbol
LTBprovided by HGNC
Official Full Name
lymphotoxin betaprovided by HGNC
Primary source
HGNC:HGNC:6711
See related
Ensembl:ENSG00000227507 MIM:600978; AllianceGenome:HGNC:6711
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
p33; TNFC; TNFSF3; TNLG1C
Summary
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]
Expression
Biased expression in spleen (RPKM 84.6), lymph node (RPKM 56.9) and 8 other tissues See more
Orthologs
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See LTB in Genome Data Viewer
Location:
6p21.33
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (31580558..31582425, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (31433610..31435477, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31548335..31550202, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100287329 Neighboring gene lymphotoxin alpha Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:31545791-31546990 Neighboring gene tumor necrosis factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:31549801-31550555 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:31557557-31558057 Neighboring gene leukocyte specific transcript 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:31561069-31561989 Neighboring gene natural cytotoxicity triggering receptor 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:31565006-31565506 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:31565507-31566007 Neighboring gene ubiquinol-cytochrome c reductase hinge protein pseudogene 1

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

EBI GWAS Catalog

Description
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
EBI GWAS Catalog
Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02).
EBI GWAS Catalog
Identification of candidate loci at 6p21 and 21q22 in a genome-wide association study of cardiac manifestations of neonatal lupus.
EBI GWAS Catalog

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat upregulates the expression of lymphotoxin beta (TNF superfamily, member 3, LTB) gene in mammary epithelial cells PubMed

Go to the HIV-1, Human Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cytokine activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables cytokine activity IEA
Inferred from Electronic Annotation
more info
 
enables signaling receptor binding IEA
Inferred from Electronic Annotation
more info
 
enables signaling receptor binding TAS
Traceable Author Statement
more info
PubMed 
enables tumor necrosis factor receptor binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in cell surface receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cell-cell signaling TAS
Traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within gene expression IEA
Inferred from Electronic Annotation
more info
 
involved_in immune response IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within lymph node development IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of canonical NF-kappaB signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in positive regulation of extrinsic apoptotic signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in positive regulation of interleukin-12 production IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of interleukin-12 production ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in signal transduction TAS
Traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within skin development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in extracellular space IEA
Inferred from Electronic Annotation
more info
 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
Preferred Names
lymphotoxin-beta
Names
LT-beta
TNF superfamily member 3
TNF-C
lymphotoxin beta (TNF superfamily, member 3)
tumor necrosis factor C
tumor necrosis factor ligand 1C
tumor necrosis factor ligand superfamily member 3

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_002341.2NP_002332.1  lymphotoxin-beta isoform a

    See identical proteins and their annotated locations for NP_002332.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript, encodes the longer isoform (a), and can form the heterotrimeric complex with lymphotoxin-alpha.
    Source sequence(s)
    AL662801
    Consensus CDS
    CCDS4703.1
    UniProtKB/Swiss-Prot
    P78370, Q06643, Q52LU8, Q99761
    UniProtKB/TrEMBL
    A8MQV6, Q5STB2
    Related
    ENSP00000410481.3, ENST00000429299.3
    Conserved Domains (1) summary
    pfam00229
    Location:102243
    TNF; TNF(tumor Necrosis Factor) family
  2. NM_009588.1NP_033666.1  lymphotoxin-beta isoform b

    See identical proteins and their annotated locations for NP_033666.1

    Status: REVIEWED

    Description
    Transcript Variant: This splice variant (2) lacks an exon in the coding region, compared to variant 1. The encoded protein (isoform b) has a premature stop codon and lacks the majority of the extracellular domain, compared to isoform a. This loss impairs its ability to complex with lympytoxin-alpha.
    Source sequence(s)
    U89922
    Consensus CDS
    CCDS4704.1
    UniProtKB/Swiss-Prot
    Q06643
    Related
    ENSP00000416113.2, ENST00000446745.2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    31580558..31582425 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    2913137..2915004 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    3057845..3059712 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    2828291..2830158 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    2885599..2887466 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    2922456..2924323 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    2836379..2838246 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    2879838..2881705 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    31433610..31435477 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)