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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CD40 Gene

protein-coding   GIFtS: 69
GCID: GC20P044746

CD40 Molecule, TNF Receptor Superfamily Member 5

(Previous names: tumor necrosis factor receptor superfamily, member 5)
(Previous symbol: TNFRSF5)
Microbiology & Infectious Diseases Congress
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
CD40 Molecule, TNF Receptor Superfamily Member 51 2     B Cell-Associated Molecule2
TNFRSF51 2 3 5     CD40 Antigen (TNF Receptor Superfamily Member 5)2
Tumor Necrosis Factor Receptor Superfamily, Member 51 2     CD40 Type II Isoform2
Bp502 3     Nerve Growth Factor Receptor-Related B-Lymphocyte Activation Molecule2
B-Cell Surface Antigen CD402 3     p502
CD40L Receptor2 3     Tumor Necrosis Factor Receptor Superfamily Member 52
CDW402     CDw403
B Cell Surface Antigen CD402     CD40 Antigen3

External Ids:    HGNC: 119191   Entrez Gene: 9582   Ensembl: ENSG000001010177   OMIM: 1095355   UniProtKB: P259423   

Export aliases for CD40 gene to outside databases

Previous GC identifers: GC20P044181 GC20P041488


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for CD40 Gene:
The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor has been found to be
essential in mediating a broad variety of immune and inflammatory responses including T cell-dependent
immunoglobulin class switching, memory B cell development, and germinal center formation. AT-hook transcription
factor AKNA is reported to coordinately regulate the expression of this receptor and its ligand, which may be
important for homotypic cell interactions. Adaptor protein TNFR2 interacts with this receptor and serves as a
mediator of the signal transduction. The interaction of this receptor and its ligand is found to be necessary for
amyloid-beta-induced microglial activation, and thus is thought to be an early event in Alzheimer disease
pathogenesis. Two alternatively spliced transcript variants of this gene encoding distinct isoforms have been
reported. (provided by RefSeq, Jul 2008)

GeneCards Summary for CD40 Gene: 
CD40 (CD40 molecule, TNF receptor superfamily member 5) is a protein-coding gene. Diseases associated with CD40 include cd40 deficiency, and chromosome 20q deletion, and among its related super-pathways are TNF Signaling and Toll-like receptor signaling pathway. GO annotations related to this gene include receptor activity and signal transducer activity. An important paralog of this gene is TNFRSF21.

UniProtKB/Swiss-Prot: TNR5_HUMAN, P25942
Function: Receptor for TNFSF5/CD40LG

Gene Wiki entry for CD40 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000020.10  NT_011362.10  NC_018931.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CD40 gene promoter:
         c-Fos   AP-1   ATF-2   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): CD40 promoter sequence
   Search SABiosciences Chromatin IP Primers for CD40

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CD40


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 20q12-q13.2   Ensembl cytogenetic band:  20q13.12   HGNC cytogenetic band: 20q12-q13.2

CD40 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CD40 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P044746:  view genomic region     (about GC identifiers)

Start:
44,746,906 bp from pter      End:
44,758,502 bp from pter
Size:
11,597 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: TNR5_HUMAN, P25942 (See protein sequence)
Recommended Name: Tumor necrosis factor receptor superfamily member 5 precursor  
Size: 277 amino acids; 30619 Da
Subunit: Monomer and homodimer. The variant form found in the bladder carcinoma cell line Hu549 does not form
homodimers. Interacts with TRAF1, TRAF2, TRAF3, TRAF5 and TRAF6
Subcellular location: Isoform I: Cell membrane; Single-pass type I membrane protein
Subcellular location: Isoform II: Secreted
6 PDB 3D structures from and Proteopedia for CD40:
1CDF (3D)        1CZZ (3D)        1D00 (3D)        1FLL (3D)        1LB6 (3D)        3QD6 (3D)    
Secondary accessions: E1P5S9 Q53GN5 Q5JY15 Q5U007 Q7M4Q8 Q86YK5 Q9BYU0
Alternative splicing: 2 isoforms:  P25942-1   P25942-2   

Explore the universe of human proteins at neXtProt for CD40: NX_P25942

Explore proteomics data for CD40 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P25942

  • CD40 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CD40 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001241.1  NP_690593.1  

    ENSEMBL proteins: 
     ENSP00000361359   ENSP00000361350   ENSP00000434825  
    Reactome Protein details: P25942
    Human Recombinant Protein Products for CD40: 
    Browse Purified and Recombinant Proteins at EMD Millipore
    R&D Systems Recombinant & Natural Proteins for CD40 (CD40/TNFRSF5)
    Enzo Life Sciences proteins for CD40
    Browse OriGene full length recombinant human proteins expressed in human HEK293 cells
    OriGene Protein Over-expression Lysate for OriGene Protein Over-expression Lysate for CD40 (NM_001250  NM_152854  NM_152854  )
    OriGene Custom MassSpec 
    OriGene Custom Protein Services for CD40
    GenScript Purified and Recombinant Proteins for CD40
    Novus Biologicals CD40 Proteins
    Novus Biologicals CD40 Lysates
    Sino Biological Recombinant Protein for CD40
    Sino Biological Cell Lysate for CD40 
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 5/7 cellular component terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--
    GO:0005886plasma membrane TAS--
    GO:0005887integral to plasma membrane TAS10748139
    GO:0009897external side of plasma membrane IEA--
    GO:0009986cell surface ----

    CD40 for ontologies           About GeneDecksing



    CD40 Antibody Products: 
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    Novus Biologicals CD40 Antibodies
    Abcam antibodies for CD40
    Browse Antibodies at Cloud-Clone Corp. 
    ThermoFisher Antibodies for CD40
    LSBio Antibodies in human, mouse, rat for CD40 

    Assay Products for CD40: 
    Browse Kits and Assays available from EMD Millipore
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    R&D Systems ELISAs for CD40 (CD40/TNFRSF5)         (see all)
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    Enzo Life Sciences assays for CD40
    Browse ELISAs at Cloud-Clone Corp. 
    Browse CLIAs at Cloud-Clone Corp.


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    CD: CD molecules
    TNFRSF: Tumor necrosis factor receptor superfamily

    IUPHAR Guide to PHARMACOLOGY protein family classification: CD40 
    Tumour necrosis factor (TNF) receptor family

    2 InterPro protein domains:
     IPR020435 TNFR_5
     IPR001368 TNFR/NGFR_Cys_rich_reg

    Graphical View of Domain Structure for InterPro Entry P25942

    ProtoNet protein and cluster: P25942

    2 Blocks protein domains:
    IPB001368 TNFR/CD27/30/40/95 cysteine-rich region
    IPB008063 FAS/CD95 receptor family signature


    UniProtKB/Swiss-Prot: TNR5_HUMAN, P25942
    Similarity: Contains 4 TNFR-Cys repeats


    CD40 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TNR5_HUMAN, P25942
    Function: Receptor for TNFSF5/CD40LG

         Gene Ontology (GO): 5 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004871signal transducer activity TAS9671306
    GO:0004872receptor activity TAS10092834
    GO:0005515protein binding IPI12140561
    GO:0019899enzyme binding IPI12223522
    GO:0031625ubiquitin protein ligase binding IPI11279055
         
    CD40 for ontologies           About GeneDecksing


    Phenotypes:
         8 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Cd40):
     cellular  hematopoietic system  homeostasis/metabolism  immune system  nervous system 
     normal  renal/urinary system  skeleton 

    CD40 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for CD40: Cd40tm1Geha Cd40tm1Kik Cd40tm1Arah

       inGenious Targeting Laboratory - Custom generated mouse model solutions for CD40 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for CD40

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CD40 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for CD40 

    miRNA
    Products:
        
    miRTarBase miRNAs that target CD40:
    hsa-mir-486-5p (MIRT004620), hsa-mir-224 (MIRT003393)

    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat CD40
    8 QIAGEN miScript miRNA Assays for microRNAs that regulate CD40:
    hsa-miR-30c-2* hsa-miR-30c-1* hsa-miR-575 hsa-miR-145 hsa-miR-3165 hsa-miR-3155 hsa-miR-3155b hsa-miR-484
    SwitchGear 3'UTR luciferase reporter plasmidCD40 3' UTR sequence
    Inhib. RNA
    Products:
        
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for CD40
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat CD40

    Gene Editing
    Products:
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    Sirion Biotech Customized adenovirus for overexpression of CD40

    Clone
    Products:
         
    Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
    OriGene clones in human, mouse for CD40 (see all 16)
    OriGene ORF clones in mouse, rat for CD40
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): CD40 (NM_152854)
    Sino Biological Human cDNA Clone for CD40
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CD40
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CD40
    Sirion Biotech Customized lentivirus for stable overexpression of CD40 
                         Customized lentivirus expression plasmids for stable overexpression of CD40 

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for CD40
    Search LifeMap BioReagents cell lines for CD40
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CD40


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for CD40 About   (see all 21)                                                                                              See pathways by source

    SuperPathContained pathways About
    1TNF Signaling
    TNF Signaling0.50
    TNF Superfamily - Human Ligand-Receptor Interactions & their Associated Functions0.49
    Death Receptor Signaling0.50
    NF-kB (NFkB) Pathway0.46
    2Toll-like receptor signaling pathway
    Toll-like receptor signaling pathway0.93
    Toll-like receptor signaling pathway0.93
    3Allograft rejection
    Allograft rejection0.69
    Intestinal immune network for IgA production0.42
    Autoimmune thyroid disease0.62
    Viral myocarditis0.35
    Asthma0.47
    4Immune System
    Immune System0.56
    Adaptive Immune System0.56
    5Apoptosis and survival Anti-apoptotic TNFs/NF-kB/Bcl-2 pathway
    Apoptosis and survival Anti-apoptotic TNFs/NF-kB/Bcl-2 pathway0.46

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 EMD Millipore Pathway for CD40
        Apoptosis and survival Anti-apoptotic TNFs/NF-kB/Bcl-2 pathway

    2 R&D Systems Pathways for CD40
        TNF Superfamily - Human Ligand-Receptor Interactions & their Associated Functions
    A-beta Uptake & Degradation


    1 GeneGo (Thomson Reuters) Pathway for CD40
        Apoptosis and survival Anti-apoptotic TNFs/NF-kB/Bcl-2 pathway

    5 BioSystems Pathways for CD40
        NLR proteins
    Toll-like receptor signaling pathway
    IL-6 Signaling Pathway
    CD40/CD40L signaling
    Inflammatory Response Pathway

    3 Sino Biological Pathways for CD40 
        TNF Signaling
    Death Receptor Signaling
    NF-kB (NFkB) Pathway

    3        Reactome Pathways for CD40
        Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
    Adaptive Immune System
    Immune System


    5/16         Kegg Pathways  (Kegg details for CD40) (see all 16):
        Cytokine-cytokine receptor interaction
    NF-kappa B signaling pathway
    Cell adhesion molecules (CAMs)
    Toll-like receptor signaling pathway
    Intestinal immune network for IgA production


    CD40 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for CD40

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/77 Interacting proteins for CD40 (P259421, 3 ENSP000003613594) via UniProtKB, MINT, STRING, and/or I2D (see all 77)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    TRAF6Q9Y4K31, 3EBI-525714,EBI-359276 I2D: score=7 
    ENSG00000229802Q925043, ENSP000003917354I2D: score=2 STRING: ENSP00000391735
    SLC39A7Q925043, ENSP000003638074I2D: score=2 STRING: ENSP00000363807
    ENSG00000206288Q925043I2D: score=2 
    ENSG00000224399Q925043I2D: score=2 
    About this table

    Gene Ontology (GO): 5/24 biological process terms (GO ID links to tree view) (see all 24):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001934positive regulation of protein phosphorylation IMP--
    GO:0002768immune response-regulating cell surface receptor signaling pathway IEA--
    GO:0006461protein complex assembly TAS10748139
    GO:0006874cellular calcium ion homeostasis IMP--
    GO:0006954inflammatory response TAS2475341

    CD40 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    CD40 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for CD40 (TNR5)

    1 HMDB Compound for CD40    About this table
    CompoundSynonyms CAS #PubMed Ids
    Simvastatin(+)-Simvastatin (see all 28)79902-63-9--

    1 IUPHAR Ligand for CD40 (CD40)    About this table 
    LigandTypeActionAffinityPubmed IDs
    CD40 ligand
    NoneNone--

    10/116 Novoseek inferred chemical compound relationships for CD40 gene (see all 116)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    lfa703 69.8 4 15618295 (3), 17482516 (1)
    rantes 59.7 36 16864989 (8), 11274230 (5), 12122011 (3), 11754818 (1) (see all 18)
    blys 55.5 12 19421221 (3), 17567982 (2), 11015437 (1), 12154359 (1) (see all 6)
    ionomycin 48.9 9 1708162 (1), 16223731 (1), 9727564 (1), 7699321 (1) (see all 9)
    pdtc 47.1 3 20037166 (1), 12901869 (1), 16141529 (1)
    triazolopyrimidine 43.2 7 10600333 (5)
    sb 203580 43 5 16356505 (1), 11708812 (1), 12209089 (1), 17911635 (1)
    n-tosyl-l-phenylalanine chloromethyl ketone 37 1 10995749 (1)
    pd 98,059 36 5 16272352 (1), 16904975 (1), 19288477 (1), 10586056 (1)
    ly294002 35.9 2 15888255 (1), 18174238 (1)

    Search CenterWatch for drugs/clinical trials and news about CD40 / TNR5

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for CD40 gene (2 alternative transcripts): 
    NM_001250.4  NM_152854.2  

    Unigene Cluster for CD40:

    CD40 molecule, TNF receptor superfamily member 5
    Hs.472860  [show with all ESTs]
    Unigene Representative Sequence: AB209660
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000372285(uc002xrf.1 uc002xrg.1 uc002xrh.1 uc002xrj.1 uc002xrk.1)
    ENST00000372276 ENST00000466205 ENST00000489304 ENST00000477696 ENST00000461171

    Congresses - knowledge worth sharing:  
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

    miRNA
    Products:
         
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat CD40
    8 QIAGEN miScript miRNA Assays for microRNAs that regulate CD40:
    hsa-miR-30c-2* hsa-miR-30c-1* hsa-miR-575 hsa-miR-145 hsa-miR-3165 hsa-miR-3155 hsa-miR-3155b hsa-miR-484
    SwitchGear 3'UTR luciferase reporter plasmidCD40 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for CD40
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat CD40
    Clone
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    OriGene clones in human, mouse for CD40 (see all 16)
    OriGene ORF clones in mouse, rat for CD40
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    GenScript: all cDNA clones in your preferred vector (see all 2): CD40 (NM_152854)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CD40
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CD40
    Sirion Biotech Customized lentivirus for stable overexpression of CD40 
                         Customized lentivirus expression plasmids for stable overexpression of CD40 
    Primer
    Products:
        
    OriGene qPCR primer pairs and template standards for CD40
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CD40
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CD40

    Additional mRNA sequence: 

    AB209660.1 AJ300189.1 AK222896.1 AY225405.1 BC012419.1 BC064518.1 BT019901.1 

    9 DOTS entries:

    DT.451574  DT.100791759  DT.86853137  DT.100791764  DT.92423397  DT.102104  DT.95170181  DT.40204598 
    DT.95170183 

    24/119 AceView cDNA sequences (see all 119):

    BI759406 AI267899 CA307201 CA944736 CR619622 BM708033 BM456032 AI791563 
    BC012419 AA934395 NM_001250 NM_152854 BM707407 CK826276 AI620202 CA417566 
    AA749024 BF797410 AA767182 CA305932 AI674469 H50599 BQ548631 AA876065 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for CD40    About this scheme

    ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8
    SP1:              -                                   -           -         
    SP2:              -                       -     -                 -         
    SP3:                                      -           -           -         
    SP4:                                                  -                     


    ECgene alternative splicing isoforms for CD40

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    CD40 expression in normal human tissues (normalized intensities)      CD40 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    CD40 Expression
    About this image


    CD40 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/11 selected tissues (see all 11) fully expand
     
     Blood (Hematopoietic System)    fully expand to see all 11 entries
             Monocytes Peripheral Blood
             Immunosuppressive dendritic cells
             b cells   
     
     Dermis (Integumentary System)    fully expand to see all 3 entries
             Dermal Fibroblasts Dorsal Dermis
     
     Bone (Muscoskeletal System)    fully expand to see all 2 entries
             Zeugopod Periosteum
             Bone marrow-derived mesenchymal stem cells
     
     Lymph (Hematopoietic System)    fully expand to see all 2 entries
             LYMPH NODE   
     
     Spleen (Hematopoietic System)
             spleen ; cells in white pulp   

    See CD40 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CD40

    SOURCE GeneReport for Unigene cluster: Hs.472860

    UniProtKB/Swiss-Prot: TNR5_HUMAN, P25942
    Tissue specificity: B-cells and in primary carcinomas

        SABiosciences Expression via Pathway-Focused PCR Arrays including CD40 (see all 21): 
              Cell Surface Markers in human mouse rat
              Antiviral Response in human mouse rat
              Multiple Sclerosis in human mouse rat
              Lymphoma in human mouse rat
              T-cell & B-cell Activation in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for CD40 gene from 4/9 species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Cd401 , 5 CD40 antigen1, 5 71.29(n)1
    62.77(a)1
      2 (85.38 cM)5
    219391  NM_011611.21  NP_035741.21 
     1650556275 
    chicken
    (Gallus gallus)
    Aves CD401 CD40 molecule, TNF receptor superfamily member 5 52.58(n)
    42.64(a)
      395385  NM_204665.1  NP_989996.1 
    lizard
    (Anolis carolinensis)
    Reptilia CD406
    Uncharacterized protein
    37(a)
    1 ↔ 1
    GL343871.1(80493-94195)
    zebrafish
    (Danio rerio)
    Actinopterygii cd406
    CD40 antigen
    24(a)
    1 ↔ 1
    23(37916785-37929019)


    ENSEMBL Gene Tree for CD40 (if available)
    TreeFam Gene Tree for CD40 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CD40 gene
    TNFRSF212  TNFRSF11A2  TNFRSF6B2  LTBR2  TNFRSF11B2  TNFRSF142  TNFRSF1B2  
    3 SIMAP similar genes for CD40 using alignment to 3 protein entries:     TNR5_HUMAN (see all proteins):
    TNFRSF11A    TNFRSF1B    TNFR1B

    CD40 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/351 SNPs in CD40 are shown (see all 351)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0393024
    Bladder carcinoma cell line Hu5494--see VAR_0393022 S G mis40--------
    VAR_0393014
    Bladder carcinoma cell line Hu5494--see VAR_0393012 C Q mis40--------
    VAR_0393034
    Bladder carcinoma cell line Hu5494--see VAR_0393032 S T mis40--------
    rs289315861,2,4
    CImmunodeficiency with hyper-IgM 3 (HIGM3)4 pathogenic144721508(+) AATACC/TGCGAC 4 R C mis1 ese30--------
    rs1171553251,2
    F--44715482(+) GTGAGG/ATCTGG 2 -- us2k11Minor allele frequency- A:0.01NA 120
    rs1464637011,2
    --44715658(+) GAGTGC/TTAACA 2 -- us2k10--------
    rs1841378741,2
    --44715916(+) GAGCCG/TAGATC 2 -- us2k10--------
    rs1148092601,2
    F--44715976(+) AACCCA/CAAAAC 2 -- us2k11Minor allele frequency- C:0.08WA 118
    rs1899009391,2
    --44716005(+) CCAAAA/GAACAA 2 -- us2k10--------
    rs731150051,2
    C,F--44716413(+) CTCAAG/CCAATC 2 -- us2k11Minor allele frequency- C:0.04WA 118

    HapMap Linkage Disequilibrium report for CD40 (44746906 - 44758502 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for CD40:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv833993CNV Gain17160897
    dgv1329e1CNV Complex17122850


    Human Gene Mutation Database (HGMD): CD40

    Locus Specific Mutation Databases (LSDB): CD40
    SABiosciences Cancer Mutation PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for CD40

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 109535   
    OMIM disorders: 606843  
    UniProtKB/Swiss-Prot: TNR5_HUMAN, P25942
  • Immunodeficiency with hyper-IgM 3 (HIGM3) [MIM:606843]: A rare immunodeficiency syndrome characterized by
    normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to
    bacterial infections. Note=The disease is caused by mutations affecting the gene represented in this entry

  • 20/166 diseases for CD40 (see all 166):    About MalaCards
    cd40 deficiency    chromosome 20q deletion    critical limb ischemia    plasma cell leukemia
    x-linked hyper igm syndrome    frozen shoulder    macroglobulinemia    waldenstrom macroglobulinemia
    monocytic leukemia    autoimmune thrombocytopenic purpura    hiv-1, resistance to    cervical squamous cell carcinoma
    graves' disease    langerhans-cell histiocytosis    aphthous stomatitis    acute monocytic leukemia
    histiocytosis    agammaglobulinemia    primary immunodeficiency disease    lupus nephritis

    12 diseases from the University of Copenhagen DISEASES database for CD40:
    Lymphoma     Hypersensitivity reaction type II disease     Primary immunodeficiency disease     Leukemia
    Atherosclerosis     Connective tissue disease     Multiple sclerosis     Multiple myeloma
    Blood protein disease     Rheumatoid arthritis     Tetanus     Hyperthyroidism

    CD40 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:  
    The International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD) 9 - 13 March 2014
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

    10/93 Novoseek inferred disease relationships for CD40 gene (see all 93)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    hyper-igm syndrome 80.7 23 9058789 (3), 14752331 (2), 11358428 (2), 10559240 (1) (see all 14)
    higm3 77.3 3 15661021 (1), 14610488 (1), 12893749 (1)
    necrosis 74.5 256 9511754 (3), 14517219 (2), 10096561 (2), 10318845 (2) (see all 99)
    tumors 61.1 374 8623911 (6), 11304696 (6), 10980464 (5), 10473114 (4) (see all 99)
    m syndrome 59 2 15661021 (1), 8914765 (1)
    inflammation 56.9 68 11488834 (2), 19183933 (2), 12209092 (2), 19834879 (2) (see all 52)
    autoimmune diseases 49.4 15 9617563 (1), 17114447 (1), 12223069 (1), 19421221 (1) (see all 12)
    atherosclerosis 48 21 17967972 (2), 15921025 (1), 16904975 (1), 19896127 (1) (see all 19)
    lymphocytic leukemia chronic b-cell 44.7 7 1281692 (2), 11313271 (1), 11426465 (1), 9531577 (1) (see all 6)
    lymphoma 43.3 52 7530508 (3), 7541711 (3), 11825564 (3), 9137085 (2) (see all 30)

    Genetic Association Database (GAD): CD40
    Human Genome Epidemiology (HuGE) Navigator: CD40 (89 documents)

    Export disorders for CD40 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for CD40 gene, integrated from 9 sources (see all 1592):
    (articles sorted by number of sources associating them with CD40)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. CD40-tumor necrosis factor receptor-associated factor (TRAF) interactions: regulation of CD40 signaling through multiple TRAF binding sites and TRAF hetero-oligomerization. (PubMed id 9718306)1, 2, 9 Pullen S.S....Kehry M.R. (1998)
    2. Association analysis of CD40 polymorphisms with asthma and the level of serum total IgE. (PubMed id 17255560)1, 4, 9 Park J.H....Shin H.D. (2007)
    3. Allelic variants of CD40 and CD40L genes interact to promote antibiotic-induced cutaneous allergic reactions. (PubMed id 19735272)1, 4, 9 Kim S.H....Park H.W. (2009)
    4. Individual and epistatic effects of genetic polymorphisms of B-cell co-stimulatory molecules on susceptibility to pemphigus foliaceus. (PubMed id 19421221)1, 4, 9 Malheiros D. and Petzl-Erler M.L. (2009)
    5. Downstream regulator TANK binds to the CD40 recognition site on TRAF3. (PubMed id 12005438)1, 2, 9 Li C.... Ely K.R. (2002)
    6. Determination of carbohydrate structures N-linked to soluble CD154 and characterization of the interactions of CD40 with CD154 expressed in Pichia pastoris and Chinese hamster ovary cells. (PubMed id 11676606)1, 2, 9 Khandekar S.S....Fishman-Lobell J. (2001)
    7. Molecular basis for CD40 signaling mediated by TRAF3. (PubMed id 10984535)1, 2, 9 Ni C.Z.... Ely K.R. (2000)
    8. The role of polar interactions in the molecular recognition of CD40L with its receptor CD40. (PubMed id 9605317)1, 2, 9 Singh J.... Thomas D. (1998)
    9. Association of CD40 gene polymorphism (C-1T) with susceptibility and phenotype of Graves' disease. (PubMed id 16279844)1, 4, 9 Kurylowicz A....Bednarczuk T. (2005)
    10. Cloning and characterization of a cDNA encoding the human homolog of tumor necrosis factor receptor-associated factor 5 (TRAF5). (PubMed id 9511754)1, 2, 9 Mizushima S.... Inoue J. (1998)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 958 HGNC: 11919 AceView: TNFRSF5 Ensembl:ENSG00000101017 euGenes: HUgn958
    ECgene: CD40 Kegg: 958 H-InvDB: CD40

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for CD40 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for CD40 Genetics and Cytogenetics in Oncology and Haematology
    CD40basehttp://bioinf.uta.fi/CD40base/
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CD40
    NIEHS-SNPshttp://egp.gs.washington.edu/data/tnfrsf5/
    Wikipedia http://en.wikipedia.org/wiki/CD40

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for CD40 gene:
    Search GeneIP for patents involving CD40

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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