Human Gene LTBR (ENST00000228918.9_10) from GENCODE V47lift37
  Description: Receptor for the heterotrimeric lymphotoxin containing LTA and LTB, and for TNFS14/LIGHT. Promotes apoptosis via TRAF3 and TRAF5. May play a role in the development of lymphoid organs. (from UniProt P36941)
Gencode Transcript: ENST00000228918.9_10
Gencode Gene: ENSG00000111321.11_15
Transcript (Including UTRs)
   Position: hg19 chr12:6,493,328-6,500,732 Size: 7,405 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr12:6,493,525-6,500,103 Size: 6,579 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:6,493,328-6,500,732)mRNA (may differ from genome)Protein (435 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsHGNC
MGIPubMedReactomeUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: TNR3_HUMAN
DESCRIPTION: RecName: Full=Tumor necrosis factor receptor superfamily member 3; AltName: Full=Lymphotoxin-beta receptor; AltName: Full=Tumor necrosis factor C receptor; AltName: Full=Tumor necrosis factor receptor 2-related protein; AltName: Full=Tumor necrosis factor receptor type III; Short=TNF-RIII; Short=TNFR-III; Flags: Precursor;
FUNCTION: Receptor for the heterotrimeric lymphotoxin containing LTA and LTB, and for TNFS14/LIGHT. Promotes apoptosis via TRAF3 and TRAF5. May play a role in the development of lymphoid organs.
SUBUNIT: Self-associates. Associates with TRAF3, TRAF4 and TRAF5. Interacts with HCV core protein.
INTERACTION: Self; NbExp=2; IntAct=EBI-3509981, EBI-3509981; Q15326:ZMYND11; NbExp=5; IntAct=EBI-3509981, EBI-2799565;
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein.
SIMILARITY: Contains 4 TNFR-Cys repeats.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 66.41 RPKM in Cells - Cultured fibroblasts
Total median expression: 1477.23 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -94.00197-0.477 Picture PostScript Text
3' UTR -235.90629-0.375 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001368 - TNFR/NGFR_Cys_rich_reg
IPR017349 - TNFR_3_LTBR

Pfam Domains:
PF00020 - TNFR/NGFR cysteine-rich region

SCOP Domains:
57586 - TNF receptor-like
57184 - Growth factor receptor domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1RF3 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P36941
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005031 tumor necrosis factor-activated receptor activity
GO:0005515 protein binding
GO:0031625 ubiquitin protein ligase binding
GO:0042802 identical protein binding

Biological Process:
GO:0006915 apoptotic process
GO:0006954 inflammatory response
GO:0006955 immune response
GO:0007165 signal transduction
GO:0007275 multicellular organism development
GO:0016032 viral process
GO:0032496 response to lipopolysaccharide
GO:0033209 tumor necrosis factor-mediated signaling pathway
GO:0042127 regulation of cell proliferation
GO:0043011 myeloid dendritic cell differentiation
GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0046330 positive regulation of JNK cascade
GO:0048534 hematopoietic or lymphoid organ development
GO:0071260 cellular response to mechanical stimulus
GO:2001238 positive regulation of extrinsic apoptotic signaling pathway

Cellular Component:
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  L04489 - Homo sapiens (clone NCD18) tumor necrosis factor receptor related protein mRNA, complete exon and repeat region.
AK293187 - Homo sapiens cDNA FLJ55950 complete cds, highly similar to Tumor necrosis factor receptor superfamily member 3 precursor.
AK095418 - Homo sapiens cDNA FLJ38099 fis, clone D3OST1000238, highly similar to Tumor necrosis factor receptor superfamily member 3 precursor.
BC026262 - Homo sapiens lymphotoxin beta receptor (TNFR superfamily, member 3), mRNA (cDNA clone MGC:22593 IMAGE:4703362), complete cds.
AK027080 - Homo sapiens cDNA: FLJ23427 fis, clone HRC04788, highly similar to HUMTNFRRP Homo sapiens tumor necrosis factor receptor 2 related protein mRNA.
L04270 - Homo sapiens (clone CD18) tumor necrosis factor receptor 2 related protein mRNA, complete cds.
JD158149 - Sequence 139173 from Patent EP1572962.
JD401118 - Sequence 382142 from Patent EP1572962.
JD079745 - Sequence 60769 from Patent EP1572962.
JD464995 - Sequence 446019 from Patent EP1572962.
JD257138 - Sequence 238162 from Patent EP1572962.
JD195365 - Sequence 176389 from Patent EP1572962.
JD129331 - Sequence 110355 from Patent EP1572962.
AB527559 - Synthetic construct DNA, clone: pF1KB6620, Homo sapiens LTBR gene for lymphotoxin beta receptor, without stop codon, in Flexi system.
DQ891995 - Synthetic construct clone IMAGE:100004625; FLH182159.01X; RZPDo839D03138D lymphotoxin beta receptor (TNFR superfamily, member 3) (LTBR) gene, encodes complete protein.
DQ895185 - Synthetic construct Homo sapiens clone IMAGE:100009645; FLH182156.01L; RZPDo839D03137D lymphotoxin beta receptor (TNFR superfamily, member 3) (LTBR) gene, encodes complete protein.
CU693188 - Synthetic construct Homo sapiens gateway clone IMAGE:100022265 5' read LTBR mRNA.
KJ897148 - Synthetic construct Homo sapiens clone ccsbBroadEn_06542 LTBR gene, encodes complete protein.
AK128019 - Homo sapiens cDNA FLJ46138 fis, clone TESTI2052525, highly similar to Lymphotoxin-beta receptor precursor.
BX648074 - Homo sapiens mRNA; cDNA DKFZp686M07210 (from clone DKFZp686M07210).
JD345802 - Sequence 326826 from Patent EP1572962.
JD372799 - Sequence 353823 from Patent EP1572962.
JD418456 - Sequence 399480 from Patent EP1572962.
JD365694 - Sequence 346718 from Patent EP1572962.
JD218335 - Sequence 199359 from Patent EP1572962.
JD176837 - Sequence 157861 from Patent EP1572962.
JD500118 - Sequence 481142 from Patent EP1572962.
JD226322 - Sequence 207346 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P36941 (Reactome details) participates in the following event(s):

R-HSA-5668789 LA,TNFSF14 binds LTBR
R-HSA-5676591 2xLTBR binds LTBR:lymphotoxin,TNFSF14 trimer
R-HSA-5676593 TRAF2:TRAF1:cIAP1,2:TRAF3:NIK regulatory complex binds LTBR
R-HSA-5676594 TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway
R-HSA-5668541 TNFR2 non-canonical NF-kB pathway
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B7Z1D2, D12S370, D3DUR2, ENST00000228918.1, ENST00000228918.2, ENST00000228918.3, ENST00000228918.4, ENST00000228918.5, ENST00000228918.6, ENST00000228918.7, ENST00000228918.8, F5GXE7, NR_182273, P36941, TNFCR, TNFR3, TNFRSF3, TNR3_HUMAN, uc317dpd.1, uc317dpd.2
UCSC ID: ENST00000228918.9_10
RefSeq Accession: NM_002342.3
Protein: P36941 (aka TNR3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.