Cd40 MGI Mouse Gene Detail - MGI:88336

Symbol

Cd40
Name

CD40 antigen
Synonyms

Bp50, Cd40, p50, Tnfrsf5

Feature Type

protein coding gene
IDs

MGI:88336
NCBI Gene: 21939
Alliance

gene page
Transcription Start Sites

22 TSS

Sequence Map

Chr2:164897535-164913574 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 85.38 cM
Mapping Data

20 experiments

SNPs within 2kb

126 from dbSNP Build 142
Strain Annotations

18
RFLP

5

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_88336	protein coding gene	Chr2:164897535-164914868 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0026886	protein coding gene	Chr2:170580341-170601129 (+)
A/J	MGP_AJ_G0026853	protein coding gene	Chr2:163597709-163615011 (+)
AKR/J	MGP_AKRJ_G0026824	protein coding gene	Chr2:168480309-168497625 (+)
BALB/cJ	MGP_BALBcJ_G0026862	protein coding gene	Chr2:163963664-163980936 (+)
C3H/HeJ	MGP_C3HHeJ_G0026604	protein coding gene	Chr2:168829016-168850285 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0027309	protein coding gene	Chr2:175521507-175545135 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0024680	protein coding gene	Chr2:157004526-157021220 (+)
CAST/EiJ	MGP_CASTEiJ_G0026062	protein coding gene	Chr2:169244718-169265734 (+)
CBA/J	MGP_CBAJ_G0026581	protein coding gene	Chr2:181892231-181913443 (+)
DBA/2J	MGP_DBA2J_G0026719	protein coding gene	Chr2:162763078-162781514 (+)
FVB/NJ	MGP_FVBNJ_G0026685	protein coding gene	Chr2:161197415-161215414 (+)
LP/J	MGP_LPJ_G0026821	protein coding gene	Chr2:170633725-170654117 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0026704	protein coding gene	Chr2:185431860-185451614 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0027366	protein coding gene	Chr2:168370542-168389832 (+)
PWK/PhJ	MGP_PWKPhJ_G0025799	protein coding gene	Chr2:162365787-162384135 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0025600	protein coding gene	Chr2:167282344-167301630 (+)
WSB/EiJ	MGP_WSBEiJ_G0026135	protein coding gene	Chr2:169260239-169283775 (+)

Human Ortholog

CD40, CD40 molecule

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CD40, CD40 molecule
Synonyms

Bp50, CDW40, p50, TNFRSF5
Links

HGNC:11919

NCBI Gene ID: 958

neXtProt AC: NX_P25942

UniProt: P25942
Chr Location

20q13.12; chr20:46118271-46129863 (+) GRCh38

MGI Vertebrate Homology

Cd40 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: CD40
Gene Tree

Cd40

Diseases

22 with human CD40 associations

				Human Disease	Mouse Models
				arthritis IDs arthritis DOID:848 ICD10CM:M19.90 MESH:D001168 NCI:C2883 UMLS_CUI:C0003864
				asthma IDs asthma DOID:2841 DOID:12703 DOID:13829 DOID:13830 DOID:2840 DOID:5783 ICD10CM:J45 ICD9CM:493 ICD9CM:493.9 KEGG:05310 MESH:D001249 NCI:C28397 OMIM:600807 UMLS_CUI:C0004096
				B-cell lymphoma IDs B-cell lymphoma DOID:707 MESH:D016393 NCI:C3457 UMLS_CUI:C0079731
				Burkitt lymphoma IDs Burkitt lymphoma DOID:8584 ICD10CM:C83.7 ICD9CM:200.2 MESH:D002051 NCI:C2912 OMIM:113970 ORDO:543 UMLS_CUI:C0006413
				Crohn's disease IDs Crohn's disease DOID:8778 DOID:8784 DOID:8855 DOID:8942 EFO:0000384 ICD10CM:K50.1 ICD9CM:555.1 MESH:D003424 NCI:C37262 UMLS_CUI:C0156147
				diffuse large B-cell lymphoma IDs diffuse large B-cell lymphoma DOID:0050745 MESH:D016403 NCI:C80280
				end stage renal disease IDs end stage renal disease DOID:783
				follicular lymphoma IDs follicular lymphoma DOID:0050873 MESH:D008224 OMIM:151430
				Graves' disease IDs Graves' disease DOID:12361 EFO:0004237 ICD10CM:E05.0 MESH:D006111 NCI:C3071 OMIM:275000 UMLS_CUI:C0018213
				hyperimmunoglobulin syndrome IDs hyperimmunoglobulin syndrome DOID:2959 NCI:C27579 UMLS_CUI:C1334069
				immunodeficiency with hyper IgM type 3 IDs immunodeficiency with hyper IgM type 3 DOID:0060023 NCI:C176416 OMIM:606843 ORDO:101090 UMLS_CUI:C1720957
				Kawasaki disease IDs Kawasaki disease DOID:13378 EFO:0004246 ICD10CM:M30.3 ICD9CM_2006:446.1 ICD9CM:446.1 MESH:D009080 NCI:C34825 OMIM:611775 UMLS_CUI:C0026691
				melanoma IDs melanoma DOID:1909 EFO:0000756 KEGG:05218 MESH:D008545 NCI:C3224 UMLS_CUI:C0025202
				multiple myeloma IDs multiple myeloma DOID:9538 EFO:0001378 ICD10CM:C90.0 ICD9CM:203.0 MESH:D009101 NCI:C3242 OMIM:254500 ORDO:29073 UMLS_CUI:C0026764
				multiple sclerosis IDs multiple sclerosis DOID:2377 ICD10CM:G35 ICD9CM:340 MESH:D009103 NCI:C3243 OMIM:612594 OMIM:612595 OMIM:612596 UMLS_CUI:C0026769
				non-Hodgkin lymphoma IDs non-Hodgkin lymphoma DOID:0060060 ICD10CM:C85.9 MESH:D008228 NCI:C3211 OMIM:605027 ORDO:547 UMLS_CUI:C0024305
				pancreatic ductal carcinoma IDs pancreatic ductal carcinoma DOID:3587 DOID:10023 ICD10CM:C25.3 ICD9CM:157.3 MESH:D021441 UMLS_CUI:C0153461 UMLS_CUI:C0887833
				pemphigus IDs pemphigus DOID:9182 ICD10CM:L10 ICD9CM:694.4 MESH:D010392 NCI:C34909 UMLS_CUI:C0030807
				plasma cell leukemia IDs plasma cell leukemia DOID:9513 ICD10CM:C90.1 ICD9CM:203.1 MESH:D007952 NCI:C3180 UMLS_CUI:C0023484
				psoriasis IDs psoriasis DOID:8893 EFO:0000676 ICD10CM:L40 MESH:D011565 NCI:C3346 OMIM:PS177900 UMLS_CUI:C0033860
				rheumatoid arthritis IDs rheumatoid arthritis DOID:7148 EFO:0000685 ICD10CM:M06.9 ICD9CM:714.0 KEGG:05323 MESH:D001172 NCI:C2884 OMIM:180300 UMLS_CUI:C0003873
				systemic lupus erythematosus IDs systemic lupus erythematosus DOID:9074 ICD10CM:M32.9 ICD9CM:710.0 KEGG:05322 MESH:D008180 NCI:C3201 OMIM:152700 OMIM:300809 OMIM:605480 OMIM:608437 OMIM:609903 OMIM:609939 OMIM:610065 OMIM:610066 OMIM:612254 OMIM:612378 OMIM:613145 OMIM:614420 ORDO:536 UMLS_CUI:C0024141

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

32 phenotypes from 5 alleles in 7 genetic backgrounds
28 phenotypes from multigenic genotypes
280 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

24
Chemically induced (ENU)

2
Endonuclease-mediated

9
Gene trapped

1
Targeted

10
Transgenic

2
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

48 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous inactivation of this gene may cause impaired immunoglobulin class switching and germinal center formation, reduced susceptibility to type II hypersensitivity reaction, impaired priming of T cells and control of M. tuberculosis infection, and altered response to transplant.

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All GO Annotations

68
GO References

31

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	non-membrane-bounded organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

768
Tissues

57
cDNA Data

25
Literature Summary

9

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA CD40

Xenbase cd40

ZFIN cd40

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All Sequences

72
RefSeq

13
UniProt

3
CCDS

CCDS17069.1, CCDS17070.1, CCDS17071.1

Ensembl

ENSMUSG00000017652 (Evidence)
NCBI Gene

21939

			Length	Strain/Species	Flank
genomic	21939	NCBI Gene Model \| MGI Sequence Detail	16040	C57BL/6J	± kb
transcript	NR_027852	RefSeq \| MGI Sequence Detail	1784	ZRU/MplStud
polypeptide	P27512	UniProt \| EBI \| MGI Sequence Detail	289	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000001961 tumor necrosis factor receptor superfamily member 5

(term hierarchy)
InterPro Domains

IPR001368 TNFR/NGFR cysteine-rich region

IPR020435 Tumour necrosis factor receptor 5

IPR034021 Tumour necrosis factor receptor 5, N-terminal

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All nucleic 38

Genomic 10

cDNA 25

Primer pair 3

Microarray probesets 6

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MGD-MRK-1859, MGI:2138913

Summaries

All 500

Developmental Gene Expression 9

Gene Ontology 31

Phenotypes 280
Earliest

J:3170 Morse HC 3rd, Genetic nomenclature for loci controlling surface antigens of mouse hemopoietic cells [published erratum appears in J Immunol 1993 Mar 15;150(6):2563]. J Immunol. 1992 Nov 15;149(10):3129-34
Latest

J:342049 Calzada-Fraile D, et al., Immune synapse formation promotes lipid peroxidation and MHC-I upregulation in licensed dendritic cells for efficient priming of CD8(+) T cells. Nat Commun. 2023 Oct 25;14(1):6772

TSS for Cd40:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr21701	Chr2:164897545-164897581 (+)	28 bp
Tssr21702	Chr2:164897588-164897610 (+)	64 bp
Tssr21703	Chr2:164900179-164900190 (+)	2,650 bp
Tssr21704	Chr2:164901211-164901224 (+)	3,683 bp
Tssr21705	Chr2:164901842-164901851 (+)	4,312 bp
Tssr21706	Chr2:164904231-164904240 (+)	6,701 bp
Tssr21707	Chr2:164905477-164905489 (+)	7,948 bp
Tssr21708	Chr2:164906056-164906083 (+)	8,535 bp
Tssr21709	Chr2:164906114-164906125 (+)	8,585 bp
Tssr21710	Chr2:164906848-164906859 (+)	9,319 bp
Tssr21711	Chr2:164906911-164906922 (+)	9,382 bp
Tssr21712	Chr2:164906928-164906945 (+)	9,402 bp
Tssr21713	Chr2:164907621-164907639 (+)	10,095 bp
Tssr21714	Chr2:164908579-164908604 (+)	11,057 bp
Tssr21715	Chr2:164908625-164908638 (+)	11,097 bp
Tssr21716	Chr2:164908679-164908688 (+)	11,149 bp
Tssr21717	Chr2:164908766-164908781 (+)	11,239 bp
Tssr21718	Chr2:164908812-164908828 (+)	11,285 bp
Tssr21719	Chr2:164908903-164908922 (+)	11,378 bp
Tssr21720	Chr2:164909106-164909115 (+)	11,576 bp
Tssr21721	Chr2:164909149-164909160 (+)	11,620 bp
Tssr21722	Chr2:164910019-164910025 (+)	12,487 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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