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LTBR lymphotoxin beta receptor [ Homo sapiens (human) ]

Gene ID: 4055, updated on 15-Apr-2019

Summary

Official Symbol
LTBRprovided by HGNC
Official Full Name
lymphotoxin beta receptorprovided by HGNC
Primary source
HGNC:HGNC:6718
See related
Ensembl:ENSG00000111321 MIM:600979
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
TNFCR; TNFR3; D12S370; TNFR-RP; TNFRSF3; TNFR2-RP; LT-BETA-R; TNF-R-III
Summary
This gene encodes a member of the tumor necrosis factor receptor superfamily. The major ligands of this receptor include lymphotoxin alpha/beta and tumor necrosis factor ligand superfamily member 14. The encoded protein plays a role in signalling during the development of lymphoid and other organs, lipid metabolism, immune response, and programmed cell death. Activity of this receptor has also been linked to carcinogenesis. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Aug 2012]
Expression
Ubiquitous expression in prostate (RPKM 23.4), placenta (RPKM 23.0) and 25 other tissues See more
Orthologs

Genomic context

See LTBR in Genome Data Viewer
Location:
12p13.31
Exon count:
12
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (6375368..6391571)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (6484534..6500737)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984500 Neighboring gene sodium channel epithelial 1 alpha subunit Neighboring gene uncharacterized LOC105369626 Neighboring gene ribosomal protein L31 pseudogene 10 Neighboring gene CD27 antisense RNA 1 Neighboring gene signal recognition particle 14 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 FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

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

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Cytokine Signaling in Immune system, organism-specific biosystem (from REACTOME)
    Cytokine Signaling in Immune system, organism-specific biosystemCytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concen...
  • Cytokine-cytokine receptor interaction, organism-specific biosystem (from KEGG)
    Cytokine-cytokine receptor interaction, organism-specific biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
  • Cytokine-cytokine receptor interaction, conserved biosystem (from KEGG)
    Cytokine-cytokine receptor interaction, conserved biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
  • HIF-1 signaling pathway, organism-specific biosystem (from KEGG)
    HIF-1 signaling pathway, organism-specific biosystemHypoxia-inducible factor 1 (HIF-1) is a transcription factor that functions as a master regulator of oxygen homeostasis. It consists of two subunits: an inducibly-expressed HIF-1alpha subunit and a c...
  • HTLV-I infection, organism-specific biosystem (from KEGG)
    HTLV-I infection, organism-specific biosystemHuman T-lymphotropic virus type 1 (HTLV-1) is a pathogenic retrovirus that is associated with adult T-cell leukemia/lymphoma (ATL). It is also strongly implicated in non-neoplastic chronic inflammato...
  • HTLV-I infection, conserved biosystem (from KEGG)
    HTLV-I infection, conserved biosystemHuman T-lymphotropic virus type 1 (HTLV-1) is a pathogenic retrovirus that is associated with adult T-cell leukemia/lymphoma (ATL). It is also strongly implicated in non-neoplastic chronic inflammato...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Intestinal immune network for IgA production, organism-specific biosystem (from KEGG)
    Intestinal immune network for IgA production, organism-specific biosystemThe intestine is the largest lymphoid tissue in the body. One striking feature of intestinal immunity is its ability to generate great amounts of noninflammatory immunoglobulin A (IgA) antibodies tha...
  • Intestinal immune network for IgA production, conserved biosystem (from KEGG)
    Intestinal immune network for IgA production, conserved biosystemThe intestine is the largest lymphoid tissue in the body. One striking feature of intestinal immunity is its ability to generate great amounts of noninflammatory immunoglobulin A (IgA) antibodies tha...
  • NF-kappa B signaling pathway, organism-specific biosystem (from KEGG)
    NF-kappa B signaling pathway, organism-specific biosystemNuclear factor-kappa B (NF-kappa B) is the generic name of a family of transcription factors that function as dimers and regulate genes involved in immunity, inflammation and cell survival. There are...
  • NF-kappa B signaling pathway, conserved biosystem (from KEGG)
    NF-kappa B signaling pathway, conserved biosystemNuclear factor-kappa B (NF-kappa B) is the generic name of a family of transcription factors that function as dimers and regulate genes involved in immunity, inflammation and cell survival. There are...
  • TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway, organism-specific biosystem (from REACTOME)
    TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway, organism-specific biosystemActivation of NF-kB is fundamental to signal transduction by members of the TNFRSF. Expression of NF-kB target genes is essential for mounting innate immune responses to infectious microorganisms but...
  • TNFR2 non-canonical NF-kB pathway, organism-specific biosystem (from REACTOME)
    TNFR2 non-canonical NF-kB pathway, organism-specific biosystemTumor necrosis factor-alpha (TNFA) exerts a wide range of biological effects through TNF receptor 1 (TNFR1) and TNF receptor 2 (TNFR2). Under normal physiological conditions TNFR2 exhibits more restr...
  • Viral carcinogenesis, organism-specific biosystem (from KEGG)
    Viral carcinogenesis, organism-specific biosystemThere is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C vi...
  • Viral carcinogenesis, conserved biosystem (from KEGG)
    Viral carcinogenesis, conserved biosystemThere is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C vi...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
identical protein binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
apoptotic process IEA
Inferred from Electronic Annotation
more info
 
cellular response to mechanical stimulus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to mechanical stimulus IEP
Inferred from Expression Pattern
more info
PubMed 
immune response IEA
Inferred from Electronic Annotation
more info
 
myeloid dendritic cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of I-kappaB kinase/NF-kappaB signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of I-kappaB kinase/NF-kappaB signaling IEP
Inferred from Expression Pattern
more info
PubMed 
positive regulation of JNK cascade IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of JNK cascade IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of extrinsic apoptotic signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of extrinsic apoptotic signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
signal transduction TAS
Traceable Author Statement
more info
PubMed 
tumor necrosis factor-mediated signaling pathway TAS
Traceable Author Statement
more info
 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Golgi apparatus IDA
Inferred from Direct Assay
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
tumor necrosis factor receptor superfamily member 3
Names
lymphotoxin B receptor
lymphotoxin beta receptor (TNFR superfamily, member 3)
tumor necrosis factor C receptor
tumor necrosis factor receptor 2-related protein
tumor necrosis factor receptor type III

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_033039.2 RefSeqGene

    Range
    5001..21204
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001270987.1NP_001257916.1  tumor necrosis factor receptor superfamily member 3 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK027080, AK293187, BC026262, DC424721
    Consensus CDS
    CCDS59233.1
    UniProtKB/Swiss-Prot
    P36941
    Related
    ENSP00000440875.1, ENST00000539925.5
    Conserved Domains (3) summary
    cd00185
    Location:151191
    TNFRSF; CRD2 [structural motif]
    cd10578
    Location:4149
    TNFRSF3; Tumor necrosis factor receptor superfamily member 3 (TNFRSF3), also known as lymphotoxin beta receptor (LTBR)
    cl22855
    Location:129191
    TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)
  2. NM_002342.3NP_002333.1  tumor necrosis factor receptor superfamily member 3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_002333.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK027080, BC026262, DA679291, L04270
    Consensus CDS
    CCDS8544.1
    UniProtKB/Swiss-Prot
    P36941
    Related
    ENSP00000228918.4, ENST00000228918.9
    Conserved Domains (4) summary
    cd00185
    Location:170210
    TNFRSF; CRD2 [structural motif]
    cd10578
    Location:11168
    TNFRSF3; Tumor necrosis factor receptor superfamily member 3 (TNFRSF3), also known as lymphotoxin beta receptor (LTBR)
    cl22855
    Location:148210
    TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)
    cl27169
    Location:264342
    ZipA; ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    6375368..6391571
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005253688.2XP_005253745.1  tumor necrosis factor receptor superfamily member 3 isoform X1

    See identical proteins and their annotated locations for XP_005253745.1

    Conserved Domains (3) summary
    cd00185
    Location:170210
    TNFRSF; CRD2 [structural motif]
    cd10578
    Location:11168
    TNFRSF3; Tumor necrosis factor receptor superfamily member 3 (TNFRSF3), also known as lymphotoxin beta receptor (LTBR)
    cl22855
    Location:148210
    TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)
  2. XM_006718983.3XP_006719046.1  tumor necrosis factor receptor superfamily member 3 isoform X2

    See identical proteins and their annotated locations for XP_006719046.1

    Related
    ENSP00000437647.1, ENST00000536876.5
    Conserved Domains (3) summary
    cd00185
    Location:170210
    TNFRSF; CRD2 [structural motif]
    cd10578
    Location:11168
    TNFRSF3; Tumor necrosis factor receptor superfamily member 3 (TNFRSF3), also known as lymphotoxin beta receptor (LTBR)
    cl22855
    Location:148210
    TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)
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