Cd40 CD40 molecule [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cd40provided by RGD
Official Full Name: CD40 moleculeprovided by RGD
Primary source: RGD:619830
See related: EnsemblRapid:ENSRNOG00000018488 AllianceGenome:RGD:619830
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: Tnfrsf5
Summary: Enables antigen binding activity and protein domain specific binding activity. Involved in several processes, including cellular response to cytokine stimulus; cellular response to lipopolysaccharide; and response to type II interferon. 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, Nov 2024]
Expression: Biased expression in Spleen (RPKM 76.6), Thymus (RPKM 46.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3q42

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (174209113..174224592)
RS_2023_06	previous assembly	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_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

Renal Fibrosis Is Significantly Attenuated Following Targeted Disruption of Cd40 in Experimental Renal Ischemia.
Title: Renal Fibrosis Is Significantly Attenuated Following Targeted Disruption of Cd40 in Experimental Renal Ischemia.
CD40 was a direct target of miR-16 and was negatively regulated by miR-16 in H9c2 cells stimulated by LPS. The ablation of CD40 aggravated the biological activities of miR-16 in LPS-induced H9c2 cells.
Title: MiR-16, as a potential NF-κB-related miRNA, exerts anti-inflammatory effects on LPS-induced myocarditis via mediating CD40 expression: A preliminary study.
Transient middle cerebral artery occlusion (MCAO) rats yielded an acceleration of thrombus formation that was accompanied by increased CD40 levels in serum. The brain infarction was significantly decreased in CD40 antagonist treatment group compared to MCAO model group. The mTOR/S6K signaling was activated in MACO model than that of CD40 antagonist treatment group.
Title: The CD40/CD40L system regulates rat cerebral microvasculature after focal ischemia/reperfusion via the mTOR/S6K signaling pathway.
Cd40 plays a crucial role in the development of hypertensive renal disease via development of renal fibrosis.
Title: Targeted disruption of Cd40 in a genetically hypertensive rat model attenuates renal fibrosis and proteinuria, independent of blood pressure.
SIRT1 inhibits LPS-induced CD40 expression in renal medullary collecting duct cells by suppressing the TLR4-NF-kappaB signaling pathway
Title: SIRT1 regulates lipopolysaccharide-induced CD40 expression in renal medullary collecting duct cells by suppressing the TLR4-NF-κB signaling pathway.
Suggest that CD154-CD40 T-cell co-stimulation pathway is a key mechanism in kidney ischemia-reperfusion injury.
Title: CD154-CD40 T-cell co-stimulation pathway is a key mechanism in kidney ischemia-reperfusion injury.
Regulatory B Cells with a Partial Defect in CD40 Signaling and Overexpressing Granzyme B Transfer Allograft Tolerance in Rodents
Title: Regulatory B Cells with a Partial Defect in CD40 Signaling and Overexpressing Granzyme B Transfer Allograft Tolerance in Rodents.
Migrating lymph dendritic cells contain stores of CD40 that can be mobilized rapidly to sites of interaction with antigen-specific T cells; the disappearance of CD40 by 24 hours may help regulate T cell activation.
Title: Migrating lymph dendritic cells contain intracellular CD40 that is mobilized to the immunological synapse during interactions with antigen-specific T lymphocytes.
CD40/CD40L and IkappaB/NF-kappaB pathways could effectively extend the survival of islet grafts
Title: Simultaneous blockade of the CD40/CD40L and NF-κB pathways prolonged islet allograft survival.
The intra-renal effective blockade of the CD40/CD40L signal reduces graft inflammation as well as the incidence of humoral vascular acute rejection in transplanted kidneys.
Title: In vivo therapeutic efficacy of intra-renal CD40 silencing in a model of humoral acute rejection.

Submit: New GeneRIF Correction See all GeneRIFs (15)

General gene information

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Markers

AW433947 (e-PCR)
- UniSTS:248674

BF403631 (e-PCR)
- UniSTS:246490

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
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	ISO Inferred from Sequence Orthology 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
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	ISO Inferred from Sequence Orthology more info
involved_in cell surface receptor signaling pathway via JAK-STAT	ISO Inferred from Sequence Orthology more info
involved_in cellular response to erythropoietin	IEP Inferred from Expression Pattern 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	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within defense response to protozoan	ISO Inferred from Sequence Orthology more info
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
acts_upstream_of_or_within immune response-regulating cell surface receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in intracellular calcium ion homeostasis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of B cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of MAPK cascade	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of blood vessel endothelial cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of endothelial cell apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of interleukin-12 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-4-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
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 transcription by RNA polymerase II	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	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
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
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
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

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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)

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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_001431500.1 → NP_001418429.1 tumor necrosis factor receptor superfamily member 5 isoform 1 precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000003

UniProtKB/TrEMBL

A0A8I6AHI1
NM_134360.2 → NP_599187.1 tumor necrosis factor receptor superfamily member 5 isoform 2 precursor

See identical proteins and their annotated locations for NP_599187.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000003

UniProtKB/TrEMBL

A0A8I6A2T5, A0A8I6A4J5, A6JXD6, A6JXD7, Q4QQW2

Related

ENSRNOP00000076770.2, ENSRNOT00000114607.2

Conserved Domains (1) summary

cd13407
Location:26 → 186

TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40

RNA

NR_197228.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

JAXUCZ010000003

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_086021.1 Reference GRCr8

Range

174209113..174224592

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039104199.2 → XP_038960127.1 tumor necrosis factor receptor superfamily member 5 isoform X4

UniProtKB/TrEMBL

A6JXD9

Conserved Domains (1) summary

cd13407
Location:26 → 186

TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40
XM_008762463.4 → XP_008760685.1 tumor necrosis factor receptor superfamily member 5 isoform X2

Conserved Domains (1) summary

cd13407
Location:26 → 166

TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40
XM_006235511.4 → XP_006235573.1 tumor necrosis factor receptor superfamily member 5 isoform X1

Related

ENSRNOP00000092907.1, ENSRNOT00000109324.2

Conserved Domains (1) summary

cd13407
Location:26 → 186

TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40
XM_039104200.2 → XP_038960128.1 tumor necrosis factor receptor superfamily member 5 isoform X5

Conserved Domains (2) summary

cd00185
Location:26 → 59

TNFRSF; CRD1 [structural motif]

cl22855
Location:26 → 166

TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)
XM_039104201.2 → XP_038960129.1 tumor necrosis factor receptor superfamily member 5 isoform X6

Conserved Domains (2) summary

cd00185
Location:26 → 59

TNFRSF; CRD1 [structural motif]

cl22855
Location:26 → 166

TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)
XM_008762464.3 → XP_008760686.1 tumor necrosis factor receptor superfamily member 5 isoform X3

UniProtKB/TrEMBL

A6JXD9

Conserved Domains (1) summary

cd13407
Location:26 → 186

TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40
XM_008762465.3 → XP_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, A6JXD8, Q9JKE0

Related

ENSRNOP00000087215.2, ENSRNOT00000119493.2

Conserved Domains (2) summary

cd00185
Location:62 → 103

TNFRSF; CRD2 [structural motif]

cl22855
Location:26 → 166

TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)
XM_063283043.1 → XP_063139113.1 tumor necrosis factor receptor superfamily member 5 isoform X8