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    Cd40 CD40 antigen [ Mus musculus (house mouse) ]

    Gene ID: 21939, updated on 9-Dec-2024

    Summary

    Official Symbol
    Cd40provided by MGI
    Official Full Name
    CD40 antigenprovided by MGI
    Primary source
    MGI:MGI:88336
    See related
    Ensembl:ENSMUSG00000017652 AllianceGenome:MGI:88336
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    IGM; p50; Bp50; GP39; IMD3; TRAP; HIGM1; T-BAM; Tnfrsf5
    Summary
    Predicted to enable antigen binding activity; protein domain specific binding activity; and ubiquitin protein ligase binding activity. Involved in B cell mediated immunity; CD40 signaling pathway; and intracellular calcium ion homeostasis. Acts upstream of or within several processes, including defense response to other organism; phosphatidylinositol 3-kinase/protein kinase B signal transduction; and positive regulation of B cell activation. Located in external side of plasma membrane and intracellular membrane-bounded organelle. Part of CD40 receptor complex. Is expressed in several structures, including alimentary system; brain; hemolymphoid system gland; limb; and reproductive system. 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, Dec 2024]
    Expression
    Broad expression in spleen adult (RPKM 16.5), lung adult (RPKM 9.0) and 19 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Cd40 in Genome Data Viewer
    Location:
    2 H3; 2 85.38 cM
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (164897535..164913574)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (165055614..165071654)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene solute carrier family 12, member 5 Neighboring gene nuclear receptor coactivator 5 Neighboring gene heat shock protein 90, alpha (cytosolic), class A member 1 pseudogene Neighboring gene STARR-seq mESC enhancer starr_06346 Neighboring gene STARR-positive B cell enhancer ABC_E2060 Neighboring gene STARR-positive B cell enhancer ABC_E4518 Neighboring gene RIKEN cDNA 1700025C18 gene Neighboring gene STARR-seq mESC enhancer starr_06347 Neighboring gene predicted gene, 36690

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables antigen binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables enzyme binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein domain specific binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables signaling receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ubiquitin protein ligase binding 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
     
    acts_upstream_of_or_within B cell activation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in B cell activation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in B cell mediated immunity IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of B cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of B cell proliferation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in CD40 signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in CD40 signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cell surface receptor signaling pathway via JAK-STAT IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to mechanical stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within defense response to protozoan IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within defense response to virus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in immunoglobulin production IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of interleukin-12 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in intracellular calcium ion homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of B cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of B cell proliferation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of GTPase activity 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 MAPK cascade IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of NF-kappaB transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of angiogenesis IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of endothelial cell apoptotic process IEA
    Inferred from Electronic Annotation
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of interleukin-4-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within positive regulation of isotype switching to IgG isotypes IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of protein kinase C signaling IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    more info
     
    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 ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of immune response IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within regulation of immunoglobulin production IDA
    Inferred from Direct Assay
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular space ISO
    Inferred from Sequence Orthology
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in neuronal cell body ISO
    Inferred from Sequence Orthology
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in varicosity ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    tumor necrosis factor receptor superfamily member 5
    Names
    B-cell surface antigen CD40
    CD40L receptor
    T-cell differentiation antigen

    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_011611.3NP_035741.2  tumor necrosis factor receptor superfamily member 5 isoform 1 precursor

      See identical proteins and their annotated locations for NP_035741.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL591411, AL591495
      Consensus CDS
      CCDS17069.1
      UniProtKB/Swiss-Prot
      P27512, Q3TS33, Q3TSL2, Q3U799, Q3U7C9, Q3UBH3, Q542B1, Q8K2X6, Q99NE0, Q99NE1, Q99NE2, Q99NE3
      Related
      ENSMUSP00000017799.6, ENSMUST00000017799.12
      Conserved Domains (1) summary
      cd13407
      Location:26186
      TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40
    2. NM_170702.3NP_733803.2  tumor necrosis factor receptor superfamily member 5 isoform 5 precursor

      See identical proteins and their annotated locations for NP_733803.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting isoform (5), also known as type V, lacks an internal segment near the C-terminus, compared to isoform 1.
      Source sequence(s)
      AL591411, AL591495
      Consensus CDS
      CCDS17070.1
      UniProtKB/Swiss-Prot
      P27512
      Related
      ENSMUSP00000073386.3, ENSMUST00000073707.9
      Conserved Domains (1) summary
      cd13407
      Location:26186
      TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40
    3. NM_170703.3NP_733804.1  tumor necrosis factor receptor superfamily member 5 isoform 2 precursor

      See identical proteins and their annotated locations for NP_733804.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting isoform (2), also known as type II, lacks an internal segment near the C-terminus, compared to isoform 1.
      Source sequence(s)
      AL591411, AL591495
      Consensus CDS
      CCDS17071.1
      UniProtKB/Swiss-Prot
      P27512
      Related
      ENSMUSP00000080059.5, ENSMUST00000081310.11
      Conserved Domains (2) summary
      cd00185
      Location:62103
      TNFRSF; CRD2 [structural motif]
      cl22855
      Location:26166
      TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)
    4. NM_170704.3NP_733805.1  tumor necrosis factor receptor superfamily member 5 isoform 4 precursor

      See identical proteins and their annotated locations for NP_733805.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site in the 3' coding region that results in a frameshift, compared to variant 1. The resulting isoform (4), also known as type IV, has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL591411, AL591495
      UniProtKB/Swiss-Prot
      P27512
      Related
      ENSMUSP00000139193.2, ENSMUST00000184221.2
      Conserved Domains (1) summary
      cd13407
      Location:26186
      TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40

    RNA

    1. NR_027852.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) retains an intron, compared to variant 1. This variant is represented as non-coding because it is a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL591411, AL591495

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000068.8 Reference GRCm39 C57BL/6J

      Range
      164897535..164913574
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006499155.5XP_006499218.1  tumor necrosis factor receptor superfamily member 5 isoform X2

      Conserved Domains (2) summary
      cd00185
      Location:1555
      TNFRSF; CRD4 [structural motif]
      cl22855
      Location:155
      TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)
    2. XM_006499154.4XP_006499217.1  tumor necrosis factor receptor superfamily member 5 isoform X1

      Conserved Domains (1) summary
      cd13407
      Location:26166
      TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40