U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Cd40 CD40 molecule [ Rattus norvegicus (Norway rat) ]

Gene ID: 171369, updated on 5-Jan-2023

Summary

Official Symbol
Cd40provided by RGD
Official Full Name
CD40 moleculeprovided by RGD
Primary source
RGD:619830
See related
Ensembl:ENSRNOG00000018488 AllianceGenome:RGD:619830
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Tnfrsf5
Summary
Enables antigen binding activity and protein domain specific binding activity. Involved in several processes, including cellular response to cytokine stimulus; response to cobalamin; and response to interferon-gamma. Located in several cellular components, including cell surface; neuronal cell body; and varicosity. Used to study several diseases, including Ehrlich tumor carcinoma; artery disease (multiple); colitis; membranous glomerulonephritis; and obesity. Biomarker of asthma; atherosclerosis; and perinatal necrotizing enterocolitis. Human ortholog(s) of this gene implicated in several diseases, including Kawasaki disease; autoimmune disease (multiple); end stage renal disease; hyperimmunoglobulin syndrome (multiple); and non-Hodgkin lymphoma (multiple). Orthologous to human CD40 (CD40 molecule). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Spleen (RPKM 76.6), Thymus (RPKM 46.3) and 9 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See Cd40 in Genome Data Viewer
Location:
3q42
Exon count:
11
Annotation release Status Assembly Chr Location
108 current mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (153790372..153805279)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (161519789..161534943)

Chromosome 3 - NC_051338.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108350521 Neighboring gene solute carrier family 12 member 5 Neighboring gene nuclear receptor coactivator 5 Neighboring gene uncharacterized LOC120101785 Neighboring gene cadherin 22 Neighboring gene translation initiation factor IF-2-like Neighboring gene solute carrier family 35 member C2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables antigen binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables antigen binding IDA
Inferred from Direct Assay
more info
PubMed 
enables enzyme binding ISO
Inferred from Sequence Orthology
more info
 
enables protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables signaling receptor activity IEA
Inferred from Electronic Annotation
more info
 
enables ubiquitin protein ligase binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in B cell activation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in B cell activation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within B cell activation ISO
Inferred from Sequence Orthology
more info
 
involved_in B cell mediated immunity ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of B cell proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in CD40 signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in CD40 signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in TRIF-dependent toll-like receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cellular response to erythropoietin IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in cellular response to interleukin-1 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cellular response to interleukin-1 IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in cellular response to lipopolysaccharide IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in cellular response to mechanical stimulus ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to tumor necrosis factor IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cellular response to tumor necrosis factor IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in defense response to protozoan IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within defense response to protozoan ISO
Inferred from Sequence Orthology
more info
 
involved_in defense response to virus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within defense response to virus ISO
Inferred from Sequence Orthology
more info
 
involved_in immune response-regulating cell surface receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within immune response-regulating cell surface receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in inflammatory response IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in inflammatory response IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in intracellular calcium ion homeostasis ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of B cell proliferation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within positive regulation of B cell proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of GTPase activity ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of I-kappaB kinase/NF-kappaB signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of I-kappaB kinase/NF-kappaB signaling ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of MAP kinase activity ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of NF-kappaB transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of NF-kappaB transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of angiogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of angiogenesis ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of blood vessel endothelial cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of blood vessel endothelial cell migration ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of endothelial cell apoptotic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of endothelial cell apoptotic process ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of interleukin-12 production IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within positive regulation of interleukin-12 production ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of isotype switching to IgG isotypes IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within positive regulation of isotype switching to IgG isotypes ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of protein kinase C signaling ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of protein phosphorylation ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of tyrosine phosphorylation of STAT protein IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of tyrosine phosphorylation of STAT protein ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within protein kinase B signaling ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of immune response ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of immunoglobulin production ISO
Inferred from Sequence Orthology
more info
 
involved_in response to bacterium IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to cobalamin IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to nutrient levels IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to peptide IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to type II interferon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in response to type II interferon IEP
Inferred from Expression Pattern
more info
PubMed 
Component Evidence Code Pubs
part_of CD40 receptor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of CD40 receptor complex ISO
Inferred from Sequence Orthology
more info
 
located_in cell surface IDA
Inferred from Direct Assay
more info
PubMed 
located_in cell surface ISO
Inferred from Sequence Orthology
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in external side of plasma membrane ISO
Inferred from Sequence Orthology
more info
 
located_in extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
located_in intracellular membrane-bounded organelle ISO
Inferred from Sequence Orthology
more info
 
located_in neuronal cell body IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
 
located_in varicosity IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
tumor necrosis factor receptor superfamily member 5
Names
CD40 antigen, TNF receptor superfamily member 5
CD40 molecule, TNF receptor superfamily member 5
tumor necrosis factor receptor superfamily, member 5

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_134360.1NP_599187.1  tumor necrosis factor receptor superfamily member 5 precursor

    See identical proteins and their annotated locations for NP_599187.1

    Status: PROVISIONAL

    Source sequence(s)
    BC097949
    UniProtKB/TrEMBL
    Q4QQW2
    Related
    ENSRNOP00000087215.1, ENSRNOT00000119493.1
    Conserved Domains (1) summary
    cd13407
    Location:26186
    TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

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

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051338.1 Reference mRatBN7.2 Primary Assembly

    Range
    153790372..153805279
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_008762463.3XP_008760685.1  tumor necrosis factor receptor superfamily member 5 isoform X2

    Conserved Domains (1) summary
    cd13407
    Location:26166
    TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40
  2. XM_006235511.3XP_006235573.1  tumor necrosis factor receptor superfamily member 5 isoform X1

    UniProtKB/TrEMBL
    A0A8I6AHI1
    Related
    ENSRNOP00000092907.1, ENSRNOT00000109324.1
    Conserved Domains (1) summary
    cd13407
    Location:26186
    TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40
  3. XM_008762464.2XP_008760686.1  tumor necrosis factor receptor superfamily member 5 isoform X3

    Conserved Domains (1) summary
    cd13407
    Location:26186
    TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40
  4. XM_039104199.1XP_038960127.1  tumor necrosis factor receptor superfamily member 5 isoform X4

    Conserved Domains (1) summary
    cd13407
    Location:26186
    TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40
  5. XM_008762465.2XP_008760687.1  tumor necrosis factor receptor superfamily member 5 isoform X7

    See identical proteins and their annotated locations for XP_008760687.1

    UniProtKB/TrEMBL
    A0A8I5XVD8
    Related
    ENSRNOP00000076770.1, ENSRNOT00000114607.1
    Conserved Domains (2) summary
    cd00185
    Location:62103
    TNFRSF; CRD2 [structural motif]
    cl22855
    Location:26166
    TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)
  6. XM_039104200.1XP_038960128.1  tumor necrosis factor receptor superfamily member 5 isoform X5

    Conserved Domains (2) summary
    cd00185
    Location:2659
    TNFRSF; CRD1 [structural motif]
    cl22855
    Location:26166
    TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)
  7. XM_039104201.1XP_038960129.1  tumor necrosis factor receptor superfamily member 5 isoform X6

    Conserved Domains (2) summary
    cd00185
    Location:2659
    TNFRSF; CRD1 [structural motif]
    cl22855
    Location:26166
    TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)
  8. XM_039104202.1XP_038960130.1  tumor necrosis factor receptor superfamily member 5 isoform X8

    Conserved Domains (2) summary
    cd00185
    Location:1353
    TNFRSF; CRD4 [structural motif]
    cl22855
    Location:153
    TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)

RNA

  1. XR_591833.2 RNA Sequence

  2. XR_591835.3 RNA Sequence