Lta lymphotoxin alpha [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Ltaprovided by RGD
Full Name: lymphotoxin alphaprovided by RGD
Primary source: RGD:3020
See related: Ensembl:ENSRNOG00000000838 AllianceGenome:RGD:3020
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Tnfb
Summary: Predicted to enable cytokine activity and tumor necrosis factor receptor binding activity. Involved in several processes, including negative regulation of fibroblast proliferation; positive regulation of glial cell proliferation; and response to lipopolysaccharide. Located in extracellular space. Biomarker of cystitis. 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 (RPKM 15.3), Thymus (RPKM 13.0) and 1 other tissue See more
Orthologs: human mouse all
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Genomic context

Location:: 20p12

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (3622291..3625852)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (3618853..3621324)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (4851889..4854677)

Chromosome 20 - NC_086038.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Lymphotoxin-alpha expression in the meninges causes lymphoid tissue formation and neurodegeneration.
Title: Lymphotoxin-alpha expression in the meninges causes lymphoid tissue formation and neurodegeneration.
Elevated lymphotoxin-alpha (TNFbeta) is associated with intervertebral disc degeneration.
Title: Elevated lymphotoxin-α (TNFβ) is associated with intervertebral disc degeneration.
Adrenomedullin can increase the expression of TNF-beta and TNFR in renal early trauma.
Title: [Experimentation and investigation of the effects of TNF and the acceptor expression in renal early trauma with extraneous adrenomedullin].
TNFbeta-so far only known to be produced by lymphocytes-was demonstrated in alveolar macrophages, bronchial epithelial cells, vascular smooth muscle cells and endothelial cells at the protein and the message level
Title: In situ localization of TNFalpha/beta, TACE and TNF receptors TNF-R1 and TNF-R2 in control and LPS-treated lung tissue.

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables cytokine activity	IEA Inferred from Electronic Annotation more info
enables tumor necrosis factor receptor binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within defense response to Gram-positive bacterium	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within humoral immune response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lymph node development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of fibroblast proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of chronic inflammatory response to antigenic stimulus	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of glial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of humoral immune response mediated by circulating immunoglobulin	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of type II interferon production	ISO Inferred from Sequence Orthology more info
involved_in response to hypoxia	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to lipopolysaccharide	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to nutrient	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in signal transduction	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: lymphotoxin-alpha

Names: LT-alpha; TNF-beta; lymphotoxin A; lymphotoxin alpha (TNF superfamily, member 1); lymphotoxin-alpha-like; tumor necrosis factor beta; 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)

NM_080769.2 → NP_542947.1 lymphotoxin-alpha precursor

See identical proteins and their annotated locations for NP_542947.1

Status: VALIDATED

Source sequence(s)

BX883046

UniProtKB/Swiss-Prot

Q06332

Related

ENSRNOP00000001111.1, ENSRNOT00000001111.3

Conserved Domains (1) summary

pfam00229
Location:74 → 202

TNF; TNF(tumor Necrosis Factor) family

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086038.1 Reference GRCr8

Range

3622291..3625852

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039098430.2 → XP_038954358.1 lymphotoxin-alpha isoform X1

UniProtKB/Swiss-Prot

Q06332

Conserved Domains (1) summary

pfam00229
Location:74 → 202

TNF; TNF(tumor Necrosis Factor) family