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Lta lymphotoxin A [ Mus musculus (house mouse) ]

Gene ID: 16992, updated on 18-Apr-2024

Summary

Official Symbol
Ltaprovided by MGI
Official Full Name
lymphotoxin Aprovided by MGI
Primary source
MGI:MGI:104797
See related
Ensembl:ENSMUSG00000024402 AllianceGenome:MGI:104797
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
LT; Ltx; Tnfb; LT[a]; LT-[a]; TNFSF1; Tnlg1e; hlb382; LTalpha; Tnfsf1b; LT-alpha; TNF-beta
Summary
Predicted to enable tumor necrosis factor receptor binding activity. Acts upstream of or within several processes, including lymph node development; positive regulation of immune response; and positive regulation of interferon-gamma production. Predicted to be located in extracellular space. Is expressed in several structures, including extraembryonic component; gut; hemolymphoid system; liver; and reproductive system. Human ortholog(s) of this gene implicated in several diseases, including artery disease (multiple); autoimmune disease (multiple); glucose metabolism disease (multiple); leishmaniasis (multiple); and lung disease (multiple). Orthologous to human LTA (lymphotoxin alpha). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in spleen adult (RPKM 15.0), mammary gland adult (RPKM 7.3) and 2 other tissues See more
Orthologs
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Genomic context

Location:
17 B1; 17 18.59 cM
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (35422141..35424568, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (35203165..35205578, complement)

Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene microRNA 6973a Neighboring gene CapStarr-seq enhancer MGSCv37_chr17:35337508-35337695 Neighboring gene lymphotoxin B Neighboring gene tumor necrosis factor Neighboring gene microRNA 6974 Neighboring gene STARR-positive B cell enhancer ABC_E11642 Neighboring gene nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor like 1 Neighboring gene STARR-positive B cell enhancer ABC_E5601 Neighboring gene STARR-positive B cell enhancer ABC_E7528 Neighboring gene STARR-positive B cell enhancer ABC_E1942 Neighboring gene ATPase, H+ transporting, lysosomal V1 subunit G2 Neighboring gene STARR-positive B cell enhancer ABC_E10948 Neighboring gene DEAD box helicase 39b Neighboring gene predicted gene, 22589

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (11)  1 citation
  • Chemically induced (ENU) (1) 
  • Endonuclease-mediated (3) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC117668

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables cytokine activity IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables tumor necrosis factor receptor binding TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within defense response to Gram-positive bacterium IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within humoral immune response IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in immune response IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within inflammatory response TAS
Traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within lymph node development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of fibroblast proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of apoptotic process ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of cell population proliferation TAS
Traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within positive regulation of chronic inflammatory response to antigenic stimulus IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of glial cell proliferation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of humoral immune response mediated by circulating immunoglobulin IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within positive regulation of type II interferon production IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of type II interferon production IGI
Inferred from Genetic Interaction
more info
PubMed 
Component Evidence Code Pubs
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular space ISO
Inferred from Sequence Orthology
more info
 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
lymphotoxin-alpha
Names
TNF beta
tumor necrosis factor ligand 1e
tumor necrosis factor ligand superfamily member 1

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_010735.2NP_034865.1  lymphotoxin-alpha precursor

    See identical proteins and their annotated locations for NP_034865.1

    Status: VALIDATED

    Source sequence(s)
    BC099464
    Consensus CDS
    CCDS28692.1
    UniProtKB/Swiss-Prot
    P09225
    UniProtKB/TrEMBL
    Q542S2
    Related
    ENSMUSP00000025266.6, ENSMUST00000025266.6
    Conserved Domains (1) summary
    pfam00229
    Location:76202
    TNF; TNF(tumor Necrosis Factor) family

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000083.7 Reference GRCm39 C57BL/6J

    Range
    35422141..35424568 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006523731.5XP_006523794.1  lymphotoxin-alpha isoform X1

    See identical proteins and their annotated locations for XP_006523794.1

    UniProtKB/Swiss-Prot
    P09225
    UniProtKB/TrEMBL
    Q542S2
    Conserved Domains (1) summary
    pfam00229
    Location:76202
    TNF; TNF(tumor Necrosis Factor) family