Format

Send to:

Choose Destination

LTA lymphotoxin alpha [ Homo sapiens (human) ]

Gene ID: 4049, updated on 13-Mar-2020

Summary

Official Symbol
LTAprovided by HGNC
Official Full Name
lymphotoxin alphaprovided by HGNC
Primary source
HGNC:HGNC:6709
See related
Ensembl:ENSG00000226979 MIM:153440
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
LT; TNFB; TNFSF1; TNLG1E
Summary
The encoded protein, a member of the tumor necrosis factor family, is a cytokine produced by lymphocytes. The protein is highly inducible, secreted, and forms heterotrimers with lymphotoxin-beta which anchor lymphotoxin-alpha to the cell surface. This protein also mediates a large variety of inflammatory, immunostimulatory, and antiviral responses, is involved in the formation of secondary lymphoid organs during development and plays a role in apoptosis. Genetic variations in this gene are associated with susceptibility to leprosy type 4, myocardial infarction, non-Hodgkin's lymphoma, and psoriatic arthritis. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012]
Expression
Biased expression in lymph node (RPKM 3.5), appendix (RPKM 1.7) and 7 other tissues See more
Orthologs

Genomic context

See LTA in Genome Data Viewer
Location:
6p21.33
Exon count:
8
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (31560550..31574324)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31539876..31542101)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATP6V1G2-DDX39B readthrough (NMD candidate) Neighboring gene ATPase H+ transporting V1 subunit G2 Neighboring gene NFKB inhibitor like 1 Neighboring gene uncharacterized LOC100287329 Neighboring gene tumor necrosis factor Neighboring gene lymphotoxin beta

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
Leprosy 4
MedGen: C1970254 OMIM: 610988 GeneReviews: Not available
Compare labs
Myocardial infarction 1
MedGen: C1832662 OMIM: 608446 GeneReviews: Not available
Compare labs
Psoriatic arthritis, susceptibility to
MedGen: C1835223 OMIM: 607507 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
NHGRI GWA Catalog
Identification of candidate loci at 6p21 and 21q22 in a genome-wide association study of cardiac manifestations of neonatal lupus.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env In endometrial epithelium-derived cells, gp120 from CCR5-tropic HIV-1 increases the release of monocytes/chemokines-attracting chemokines (IL-8 and GRO) and proinflammatory cytokines (TNF-beta and IL-1alpha) PubMed
Tat tat HIV-1 Tat101 upregulates the expression of lymphotoxin alpha (LTA; TNFB) in Jurkat cells PubMed
tat HIV-1 Tat downregulates TNF-beta expression in central nervous system-derived glial cells, suggesting a novel mechanism whereby HIV-1 is able to establish latent infection of glial cells PubMed
tat HIV-1 Tat upregulates TNF-beta expression through binding to a TAR-like RNA structure in the TNF-beta promoter PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cytokine activity IEA
Inferred from Electronic Annotation
more info
 
signaling receptor binding TAS
Traceable Author Statement
more info
PubMed 
tumor necrosis factor receptor binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
apoptotic process TAS
Traceable Author Statement
more info
PubMed 
cell-cell signaling TAS
Traceable Author Statement
more info
PubMed 
defense response to Gram-positive bacterium IEA
Inferred from Electronic Annotation
more info
 
humoral immune response IEA
Inferred from Electronic Annotation
more info
 
lymph node development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of fibroblast proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of chronic inflammatory response to antigenic stimulus IEA
Inferred from Electronic Annotation
more info
 
positive regulation of glial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of humoral immune response mediated by circulating immunoglobulin IEA
Inferred from Electronic Annotation
more info
 
positive regulation of interferon-gamma production IEA
Inferred from Electronic Annotation
more info
 
response to drug IEA
Inferred from Electronic Annotation
more info
 
response to hypoxia IEA
Inferred from Electronic Annotation
more info
 
response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
 
response to nutrient IEA
Inferred from Electronic Annotation
more info
 
signal transduction TAS
Traceable Author Statement
more info
PubMed 
tumor necrosis factor-mediated signaling pathway TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
extracellular space IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
lymphotoxin-alpha
Names
LT-alpha
TNF superfamily, member 1
TNF-beta
truncated lymphotoxin alpha
tumor necrosis factor beta
tumor necrosis factor ligand 1E
tumor necrosis factor ligand superfamily member 1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_012010.1 RefSeqGene

    Range
    5001..7226
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000595.4NP_000586.2  lymphotoxin-alpha precursor

    See identical proteins and their annotated locations for NP_000586.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AL662801, BG685356, BX108399, D12614
    Consensus CDS
    CCDS4701.1
    UniProtKB/Swiss-Prot
    P01374
    UniProtKB/TrEMBL
    Q5STV3
    Related
    ENSP00000413450.2, ENST00000418386.2
    Conserved Domains (1) summary
    cd00184
    Location:63203
    TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...
  2. NM_001159740.2NP_001153212.1  lymphotoxin-alpha precursor

    See identical proteins and their annotated locations for NP_001153212.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    BP338937, BX108399, D12614
    Consensus CDS
    CCDS4701.1
    UniProtKB/Swiss-Prot
    P01374
    UniProtKB/TrEMBL
    Q5STV3
    Related
    ENSP00000403495.1, ENST00000454783.5
    Conserved Domains (1) summary
    cd00184
    Location:63203
    TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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
    31560550..31574324
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514618.1XP_011512920.1  lymphotoxin-alpha isoform X1

    See identical proteins and their annotated locations for XP_011512920.1

    UniProtKB/Swiss-Prot
    P01374
    UniProtKB/TrEMBL
    Q5STV3
    Conserved Domains (1) summary
    cd00184
    Location:63203
    TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...
  2. XM_011514615.2XP_011512917.1  lymphotoxin-alpha isoform X1

    See identical proteins and their annotated locations for XP_011512917.1

    UniProtKB/Swiss-Prot
    P01374
    UniProtKB/TrEMBL
    Q5STV3
    Conserved Domains (1) summary
    cd00184
    Location:63203
    TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...
  3. XM_011514616.2XP_011512918.1  lymphotoxin-alpha isoform X1

    See identical proteins and their annotated locations for XP_011512918.1

    UniProtKB/Swiss-Prot
    P01374
    UniProtKB/TrEMBL
    Q5STV3
    Conserved Domains (1) summary
    cd00184
    Location:63203
    TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...
  4. XM_011514617.2XP_011512919.1  lymphotoxin-alpha isoform X1

    See identical proteins and their annotated locations for XP_011512919.1

    UniProtKB/Swiss-Prot
    P01374
    UniProtKB/TrEMBL
    Q5STV3
    Conserved Domains (1) summary
    cd00184
    Location:63203
    TNF; Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal ...

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

    Range
    3049386..3051611
    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
    2819830..2822057
    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
    2877140..2879365
    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
    2913995..2916222
    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
    2827916..2830143
    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
    2871379..2873604
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Support Center