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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

CD40 Gene

protein-coding GIFtS: 68
GCID: GC20P044746

CD40 molecule, TNF receptor superfamily member 5

(Previous names: tumor necrosis factor receptor superfamily, member 5 )
(Previous symbol: TNFRSF5)

Explore 177 diseases affiliated with
CD40 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
CD40 Molecule, TNF Receptor Superfamily Member 5¹ ²		B Cell Surface Antigen CD40²
TNFRSF5¹ ² ³ ⁵		B Cell-Associated Molecule²
Bp50¹ ² ³		CD40 Antigen (TNF Receptor Superfamily Member 5)²
P50¹		CD40 Type II Isoform²
Tumor Necrosis Factor Receptor Superfamily, Member 5¹ ²		Nerve Growth Factor Receptor-Related B-Lymphocyte Activation Molecule²
B-Cell Surface Antigen CD40² ³		Tumor Necrosis Factor Receptor Superfamily Member 5²
CD40L Receptor² ³		CDw40³
CDW40²		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:

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)

UniProtKB/Swiss-Prot: TNR5_HUMAN, P25942

Function: Receptor for TNFSF5/CD40LG

Gene Wiki entry for CD40

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000020.10 NC_018931.1 NT_011362.10

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 ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
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

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_P25942

CD40 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins (2 alternative transcripts):

NP_001241.1 NP_690593.1

ENSEMBL proteins:

ENSP00000361359 ENSP00000361350 ENSP00000434825

Reactome Protein details: P25942
Human Recombinant Protein Products:

	Browse Purified and Recombinant Proteins at EMD Millipore
	R&D Systems Recombinant & Natural Proteins for CD40 (CD40/TNFRSF5)
	Enzo Life Sciences proteins for CD40
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	GenScript Purified and Recombinant Proteins for CD40
	Novus Biologicals CD40 Proteins Novus Biologicals CD40 Lysates
	Sino Biological Recombinant Protein for CD40
	Browse ProSpec Recombinant Proteins
	Uscn Proteins for CD40

Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005576	extracellular region	IEA	--
GO:0005886	plasma membrane	TAS	--
GO:0005887	integral to plasma membrane	TAS	10748139
GO:0009897	external side of plasma membrane	IEA	--
GO:0035631	CD40 receptor complex	ISS	--

CD40 for ontologies About GeneDecksing

CD40 Antibody Products:

	Browse EMD Millipore's Extensive Line of Mono- and Polyclonal Antibodies
	R&D Systems Antibodies for CD40 (CD40/TNFRSF5)
	Browse OriGene Antibodies OriGene Custom Antibody Services for CD40
	GenScript Custom Superior Antibodies Services for CD40
	Novus Biologicals CD40 Antibodies
	Search for Antibodies for CD40 at Abcam
	Uscn Antibodies for CD40
	ThermoFisher Antibodies for CD40

Assay Products for CD40:

	Browse Kits and Assays available from EMD Millipore
	OriGene Custom Immunoassay Development Browse OriGene Fluorogenic Cell Assay Kits
	R&D Systems ELISAs for CD40 (CD40/TNFRSF5) (see all)
	GenScript Custom Assay Services for CD40
	Enzo Life Sciences assays for CD40
	Uscn ELISAs and CLIAs for CD40

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

CD40 for domains About GeneDecksing

2 InterPro domains/families:

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 families:

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

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

UniProtKB/Swiss-Prot: TNR5_HUMAN, P25942

Function: Receptor for TNFSF5/CD40LG

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

		OriGene 3'-UTR Clone (see all 2): CD40 Browse MicroRNA Expression Plasmids
		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 plasmid: CD40 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for CD40 (see all 7) OriGene shRNA RFP: CD40 OriGene siRNA: CD40
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat CD40

Gene Editing
Products:

DNA2.0 Custom Protein Engineering Service for CD40

Clone Products:		Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for CD40 (see all 7) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for CD40 (see all 2) 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
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		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CD40

Cell Line Products:		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

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0004871	signal transducer activity	TAS	9671306
GO:0004872	receptor activity	TAS	10092834
GO:0005515	protein binding	IPI	--
GO:0019899	enzyme binding	IPI	12223522
GO:0031625	ubiquitin protein ligase binding	IPI	11279055

CD40 for ontologies           About GeneDecksing

Animal Models:
     Mouse knock-outs for CD40: Cd40^tm1Geha Cd40^tm1Kik Cd40^tm1Arah
     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

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
About This Section

Unified GeneCards pathways - 5/17 super-pathways (see all 17) About this table

See pathways by source

Super-pathway

contained gene-specific pathways

Allograft rejection

Allograft rejection	1.00	Intestinal immune network for IgA production	0.38
Autoimmune thyroid disease	0.60	Viral myocarditis	0.33
Asthma	0.44

Immune System

Immune System

1.00

Adaptive Immune System

0.59

Apoptosis and survival_Anti-apoptotic TNFs/NF-kB/Bcl-2 pathway

Apoptosis and survival Anti-apoptotic TNFs/NF-kB/Bcl-2 pathway

1.00

Apoptosis and survival_Anti-apoptotic TNFs/NF-kB/Bcl-2 pathway

1.00

Toll-like receptor signaling pathway

Toll-like receptor signaling pathway

1.00

Toll-like receptor signaling pathway

0.97

IL-6 Signaling Pathway

IL-6 Signaling Pathway

1.00

Pathway sources
See GeneCards unified pathways
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
	IL-6 Signaling Pathway
	Toll-like receptor signaling pathway
	CD40/CD40L signaling
	Inflammatory Response Pathway

3 Reactome Pathways for CD40

	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
	Adaptive Immune System
	Immune System

5/12 Kegg Pathways (Kegg details for CD40) (see all 12):

	Cytokine-cytokine receptor interaction
	Cell adhesion molecules (CAMs)
	Toll-like receptor signaling pathway
	Intestinal immune network for IgA production
	Malaria

CD40 for pathways About GeneDecksing

Interactions:

SABiosciences Gene Network Central^TM Interacting Genes and Proteins Network for CD40

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

5/73 Interacting proteins for CD40 (P25942^{1, 3} ENSP00000361359⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 73)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
TRAF6	Q9Y4K3¹^,³	EBI-1056393,EBI-359276 I2D: score=7
TRAF3	Q13114¹^,³, ENSP00000332468⁴	EBI-1056393,EBI-357631 I2D: score=8 STRING: ENSP00000332468
TRAF5	O00463³, ENSP00000261464⁴	I2D: score=4 STRING: ENSP00000261464
BIRC3	Q13489³, ENSP00000263464⁴	I2D: score=3 STRING: ENSP00000263464
CAV1	Q03135³, ENSP00000339191⁴	I2D: score=3 STRING: ENSP00000339191

About this table

Gene Ontology (GO): 5/25 biological process terms (GO ID links to tree view) (see all 25): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001934	positive regulation of protein phosphorylation	IMP	--
GO:0002768	immune response-regulating cell surface receptor signaling pathway	IEA	--
GO:0006461	protein complex assembly	TAS	10748139
GO:0006874	cellular calcium ion homeostasis	IMP	--
GO:0006954	inflammatory response	TAS	2475341

CD40 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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

1 HMDB Compound for CD40 About this table

Compound	Synonyms	CAS #	PubMed Ids
Simvastatin	(+)-Simvastatin (see all 28)	79902-63-9	--

10/116 Novoseek 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 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
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, 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

miRNA Products:		OriGene 3'-UTR Clone (see all 2): CD40 Browse OriGene MicroRNA Expression Plasmids
		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 plasmid: CD40 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for CD40 (see all 7) OriGene shRNA RFP: CD40 OriGene siRNA: CD40
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat CD40

Clone Products:		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for CD40 (see all 7) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for CD40 (see all 2) 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)
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for CD40
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CD40

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for CD40 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay in human, mouse, rat CD40
		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CD40
		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CD40

Additional cDNA 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):

AI620202 CK826276 CA305932 H50599 AI674469 BM477258 BQ548631 NM_152854

AA876065 BC012419 AI791563 CR619622 AA913214 BU623275 BM707407 BF797410

AA806068 CA417566 NM_001250 AA886208 AA749024 AA767182 CA944736 AI267899

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)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --

About this image

CD40 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

4 LifeMap In Vivo Development Anatomical Compartments/Cells

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Blood

Myeloid Dendritic Cells

Blood

Skeletal Muscle

Hyoid Arch Muscles

Myoblasts

Skeletal Muscle

Mandibular Arch Muscles

Myoblasts

Skeletal Muscle

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

Stem Cell Differentiation: 1 LifeMap Cell

Name

Category

Intervertebral disc (IVD) annulus fibrosus (AF) cells (Differentiation of s...)

Cartilage

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

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for CD40 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay in human, mouse, rat CD40
		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CD40
		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CD40

In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CD40

(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 3/11 species (see all 11) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
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	--	36(a)	1 ↔ 1	GL343871.1(80493-94195)
zebrafish (Danio rerio)	Actinopterygii	cd40⁶	CD40 antigen	19(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 TNFRSF6B² TNFRSF1B² TNFRSF4² TNFRSF11A² NGFR² TNFRSF14² TNFRSF11B²

LTBR² TNFRSF9²

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, UniProtKB, 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

SNP ID	Valid	Clinical significance	Chr 20 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs73115005^1,2	C,F,	--	41487179(+)	`CTCAAG/CCAATC`	2	--	us2k¹		1		WA	118
rs112279312^1,2		--	41487252(+)	`TTTATT/CTTTAT`	2	--	us2k¹		2		CSA WA	119
rs13037724^1,2	C,H	--	41487848(+)	`CAGGAT/AACCTA`	2	--	us2k¹		4		NS EA	418
rs13041789^1,2	H	--	41488003(+)	`AAGAAG/AAAGAG`	2	--	us2k¹ trp³		4		NS EA	420
rs11569299^1,2	C,H,	--	41488141(+)	`CGATAA/C/GGTGGA`	2	--	us2k¹		5		NS EA	598
rs11569300^1,2	C,F,	--	41488197(+)	`AAGGCT/-GGGGC`	2	--	ut5¹		2		NS NA	214
rs11569302^1,2	C,F,H,	--	41488387(+)	`GACTTC/TGGGGA`	2	--	int¹		14		NS EA NA WA	1756
rs11569303^1,2	H	--	41488498(+)	`CTCCCG/AGGCTG`	2	--	int¹		2		NS	280
rs11569304^1,2	C,F,H,	--	41488593(+)	`AGCCTC/AAGAGG`	2	--	int¹		13		NS EA WA	1158
rs201828795^1,2	C	--	41488933(+)	`GACCCC/TTGGGG`	2	--	int¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for CD40 (44746906 - 44758502 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for CD40
1 CNV: 4102
Human Gene Mutation Database (HGMD): CD40

Locus Specific Mutation Databases (LSDB): CD40

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing CD40

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, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

CD40 for disorders           About GeneDecksing

OMIM gene information: 109535
OMIM disorders: 606843
UniProtKB/Swiss-Prot: TNR5_HUMAN, P25942

Defects in CD40 are the cause of immunodeficiency with hyper-IgM type 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

20/177 diseases for CD40 (see all 177): About MalaCards

langerhans-cell histiocytosis alzheimer's disease splenic marginal zone lymphoma b-cell non-hodgkin lymphoma

immunodeficiency with hyper igm common variable immunodeficiency diffuse large b-cell lymphoma waldenstrom macroglobulinemia

hypersensitivity reaction type ii disease frozen shoulder non-hodgkin lymphoma severe combined immunodeficiency

graft versus host disease arterial occlusive disease peripheral arterial occlusive disease critical limb ischemia

autoimmune thrombocytopenic purpura monocytic leukemia b-cell lymphomas plasma cell leukemia

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

Rheumatoid arthritis Tetanus Blood protein disease Hyperthyroidism

10/93 Novoseek 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)
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PubMed articles for CD40 gene, integrated from 9 sources (see all 1566):
(articles sorted by number of sources associating them with CD40)

Utopia: connect your pdf to the dynamic
world of online information

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)
Downstream regulator TANK binds to the CD40 recognition site on TRAF3. (PubMed id 12005438)^{1, 2, 9} Li C.... Ely K.R. (2002)
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)
Molecular basis for CD40 signaling mediated by TRAF3. (PubMed id 10984535)^{1, 2, 9} Ni C.Z.... Ely K.R. (2000)
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)
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)
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)
A C/T polymorphism in the 5' untranslated region of the CD40 gene is associated with later onset of Graves' disease in Japanese. (PubMed id 16127217)^{1, 4, 9} Mukai T....Yamada K. (2005)
Mutations of CD40 gene cause an autosomal recessive form of immunodeficiency with hyper IgM. (PubMed id 11675497)^{1, 2, 9} Ferrari S....Plebani A. (2001)
Tumor necrosis factor receptor-associated factor 6 (TRAF6) stimulates extracellular signal-regulated kinase (ERK) activity in CD40 signaling along a ras-independent pathway. (PubMed id 9432981)^{1, 2, 9} Kashiwada M.... Takemori T. (1998)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
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)
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Entrez Gene: 958	HGNC: 11919	AceView: TNFRSF5	Ensembl:ENSG00000101017	euGenes: HUgn958
ECgene: CD40	Kegg: 958	H-InvDB: CD40

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

Intellectual Property for CD40 gene
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Patent Information for CD40 gene:
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GeneCards and IP:
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CD40 molecule, TNF receptor superfamily member 5

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CD40 Gene

CD40 molecule, TNF receptor superfamily member 5

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