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LTB lymphotoxin beta [ Homo sapiens (human) ]

Gene ID: 4050, updated on 8-Jul-2021

Summary

Official Symbol
LTBprovided by HGNC
Official Full Name
lymphotoxin betaprovided by HGNC
Primary source
HGNC:HGNC:6711
See related
Ensembl:ENSG00000227507 MIM:600978
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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Genomic context

See LTB in Genome Data Viewer
Location:
6p21.33
Exon count:
4
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (31580558..31582425, complement)
105.20201022 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 tumor necrosis factor Neighboring gene leukocyte specific transcript 1 Neighboring gene natural cytotoxicity triggering receptor 3 Neighboring gene ubiquinol-cytochrome c reductase hinge protein pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
GeneReviews: Not available
Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02).
GeneReviews: Not available
Identification of candidate loci at 6p21 and 21q22 in a genome-wide association study of cardiac manifestations of neonatal lupus.
GeneReviews: Not available

HIV-1 interactions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cytokine activity 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-cell signaling TAS
Traceable Author Statement
more info
PubMed 
involved_in gene expression IEA
Inferred from Electronic Annotation
more info
 
involved_in immune response IEA
Inferred from Electronic Annotation
more info
 
involved_in lymph node development 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 
involved_in skin development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
 
located_in extracellular space IEA
Inferred from Electronic Annotation
more info
 
located_in integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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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
    Q06643
    UniProtKB/TrEMBL
    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: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

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

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p13 ALT_REF_LOCI_1

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

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

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

Reference GRCh38.p13 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p13 ALT_REF_LOCI_3

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

Reference GRCh38.p13 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p13 ALT_REF_LOCI_4

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

Reference GRCh38.p13 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p13 ALT_REF_LOCI_5

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

Reference GRCh38.p13 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p13 ALT_REF_LOCI_6

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

Reference GRCh38.p13 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p13 ALT_REF_LOCI_7

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