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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in TCGA

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Exon skipping events with PSIs in GTEx

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for CD40

check button Gene summary
Gene informationGene symbol

CD40

Gene ID

958

Gene nameCD40 molecule
SynonymsBp50|CDW40|TNFRSF5|p50
Cytomap

20q13.12

Type of geneprotein-coding
Descriptiontumor necrosis factor receptor superfamily member 5B cell surface antigen CD40B cell-associated moleculeCD40 molecule, TNF receptor superfamily member 5CD40L receptor
Modification date20180522
UniProtAcc

P25942

ContextPubMed: CD40 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
CD40

GO:2000353

positive regulation of endothelial cell apoptotic process

12885753


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Exon skipping events across known transcript of Ensembl for CD40 from UCSC genome browser

check buttonSkipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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Gene isoform structures and expression levels for CD40

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for CD40

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3527162044747011:44747033:44750362:44750537:44750871:4475088244750362:44750537ENSG00000101017.9ENST00000477696.1
exon_skip_3527182044747011:44747033:44750458:44750537:44750871:4475088244750458:44750537ENSG00000101017.9ENST00000372276.3,ENST00000489304.1,ENST00000466205.1
exon_skip_3527202044751254:44751395:44751764:44751858:44755278:4475534044751764:44751858ENSG00000101017.9ENST00000489304.1,ENST00000372285.3
exon_skip_3527222044751248:44751395:44751764:44751858:44756776:4475684744751764:44751858ENSG00000101017.9ENST00000372276.3
exon_skip_3527312044751248:44751395:44755278:44755340:44756776:4475684744755278:44755340ENSG00000101017.9ENST00000477696.1,ENST00000466205.1
exon_skip_3527362044751764:44751858:44755278:44755340:44756776:4475684744755278:44755340ENSG00000101017.9ENST00000372285.3
exon_skip_3527442044755278:44755340:44755845:44755928:44756776:4475684744755845:44755928ENSG00000101017.9ENST00000489304.1
exon_skip_3527462044756776:44756863:44756968:44756997:44757520:4475764344756968:44756997ENSG00000101017.9ENST00000372276.3,ENST00000489304.1,ENST00000477696.1,ENST00000372285.3,ENST00000466205.1

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for CD40

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3527162044747011:44747033:44750362:44750537:44750871:4475088244750362:44750537ENSG00000101017.9ENST00000477696.1
exon_skip_3527182044747011:44747033:44750458:44750537:44750871:4475088244750458:44750537ENSG00000101017.9ENST00000372276.3,ENST00000466205.1,ENST00000489304.1
exon_skip_3527202044751254:44751395:44751764:44751858:44755278:4475534044751764:44751858ENSG00000101017.9ENST00000372285.3,ENST00000489304.1
exon_skip_3527222044751248:44751395:44751764:44751858:44756776:4475684744751764:44751858ENSG00000101017.9ENST00000372276.3
exon_skip_3527312044751248:44751395:44755278:44755340:44756776:4475684744755278:44755340ENSG00000101017.9ENST00000466205.1,ENST00000477696.1
exon_skip_3527362044751764:44751858:44755278:44755340:44756776:4475684744755278:44755340ENSG00000101017.9ENST00000372285.3
exon_skip_3527442044755278:44755340:44755845:44755928:44756776:4475684744755845:44755928ENSG00000101017.9ENST00000489304.1
exon_skip_3527462044756776:44756863:44756968:44756997:44757520:4475764344756968:44756997ENSG00000101017.9ENST00000372285.3,ENST00000372276.3,ENST00000466205.1,ENST00000489304.1,ENST00000477696.1

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for CD40

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003722854475176444751858Frame-shift
ENST000003722854475527844755340Frame-shift
ENST000003722854475696844756997Frame-shift

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003722854475176444751858Frame-shift
ENST000003722854475527844755340Frame-shift
ENST000003722854475696844756997Frame-shift

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Infer the effects of exon skipping event on protein functional features for CD40

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end

check button Lost protein functional features of individual exon skipping events in TCGA.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature


check button Lost protein functional features of individual exon skipping events in GTEx.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature


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SNVs in the skipped exons for CD40

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
LIHCTCGA-DD-A39Y-01exon_skip_352716
44750363447505374475049044750490Frame_Shift_DelA-p.E28fs
LIHCTCGA-DD-A39Y-01exon_skip_352718
44750459447505374475049044750490Frame_Shift_DelA-p.E28fs
LIHCTCGA-G3-A3CJ-01exon_skip_352716
44750363447505374475049044750490Frame_Shift_DelA-p.E28fs
LIHCTCGA-G3-A3CJ-01exon_skip_352718
44750459447505374475049044750490Frame_Shift_DelA-p.E28fs
LIHCTCGA-DD-A39Y-01exon_skip_352722
exon_skip_352720
44751765447518584475179944751799Frame_Shift_DelC-p.C146fs
LIHCTCGA-G3-A3CJ-01exon_skip_352722
exon_skip_352720
44751765447518584475183744751837Frame_Shift_DelA-p.E159fs
STADTCGA-HU-A4GT-01exon_skip_352736
exon_skip_352731
44755279447553404475529444755294Frame_Shift_DelC-p.D171fs
LIHCTCGA-DD-AACA-01exon_skip_352746
44756969447569974475697544756975Frame_Shift_DelT-p.V218fs
BRCATCGA-E2-A108-01exon_skip_352716
44750363447505374475051344750513Nonsense_MutationCTp.Q36*
BRCATCGA-E2-A108-01exon_skip_352718
44750459447505374475051344750513Nonsense_MutationCTp.Q36*
LUSCTCGA-66-2767-01exon_skip_352736
exon_skip_352731
44755279447553404475530744755307Nonsense_MutationCTp.Q176*
SKCMTCGA-D3-A3MR-06exon_skip_352716
44750363447505374475053844750538Splice_SiteGA.
SKCMTCGA-D3-A3MR-06exon_skip_352718
44750459447505374475053844750538Splice_SiteGA.

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
CD40_44747011_44747033_44750362_44750537_44750871_44750882_TCGA-D3-A3MR-06Sample: TCGA-D3-A3MR-06
Cancer type: SKCM
ESID: exon_skip_352716
Skipped exon start: 44750363
Skipped exon end: 44750537
Mutation start: 44750538
Mutation end: 44750538
Mutation type: Splice_Site
Reference seq: G
Mutation seq: A
AAchange: .
CD40_44747011_44747033_44750362_44750537_44750871_44750882_TCGA-D3-A3MR-06Sample: TCGA-D3-A3MR-06
Cancer type: SKCM
ESID: exon_skip_352718
Skipped exon start: 44750459
Skipped exon end: 44750537
Mutation start: 44750538
Mutation end: 44750538
Mutation type: Splice_Site
Reference seq: G
Mutation seq: A
AAchange: .
exon_skip_13419_SKCM_TCGA-D3-A3MR-06.png
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exon_skip_346500_SKCM_TCGA-D3-A3MR-06.png
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exon_skip_352716_SKCM_TCGA-D3-A3MR-06.png
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exon_skip_38175_SKCM_TCGA-D3-A3MR-06.png
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exon_skip_477214_SKCM_TCGA-D3-A3MR-06.png
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CD40_44747011_44747033_44750362_44750537_44750871_44750882_TCGA-E2-A108-01Sample: TCGA-E2-A108-01
Cancer type: BRCA
ESID: exon_skip_352716
Skipped exon start: 44750363
Skipped exon end: 44750537
Mutation start: 44750513
Mutation end: 44750513
Mutation type: Nonsense_Mutation
Reference seq: C
Mutation seq: T
AAchange: p.Q36*
CD40_44747011_44747033_44750362_44750537_44750871_44750882_TCGA-E2-A108-01Sample: TCGA-E2-A108-01
Cancer type: BRCA
ESID: exon_skip_352718
Skipped exon start: 44750459
Skipped exon end: 44750537
Mutation start: 44750513
Mutation end: 44750513
Mutation type: Nonsense_Mutation
Reference seq: C
Mutation seq: T
AAchange: p.Q36*
exon_skip_352716_BRCA_TCGA-E2-A108-01.png
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CD40_44747011_44747033_44750362_44750537_44750871_44750882_TCGA-DD-A39Y-01Sample: TCGA-DD-A39Y-01
Cancer type: LIHC
ESID: exon_skip_352716
Skipped exon start: 44750363
Skipped exon end: 44750537
Mutation start: 44750490
Mutation end: 44750490
Mutation type: Frame_Shift_Del
Reference seq: A
Mutation seq: -
AAchange: p.E28fs
CD40_44747011_44747033_44750362_44750537_44750871_44750882_TCGA-DD-A39Y-01Sample: TCGA-DD-A39Y-01
Cancer type: LIHC
ESID: exon_skip_352718
Skipped exon start: 44750459
Skipped exon end: 44750537
Mutation start: 44750490
Mutation end: 44750490
Mutation type: Frame_Shift_Del
Reference seq: A
Mutation seq: -
AAchange: p.E28fs
CD40_44747011_44747033_44750362_44750537_44750871_44750882_TCGA-DD-A39Y-01Sample: TCGA-DD-A39Y-01
Cancer type: LIHC
ESID: exon_skip_352720
Skipped exon start: 44751765
Skipped exon end: 44751858
Mutation start: 44751799
Mutation end: 44751799
Mutation type: Frame_Shift_Del
Reference seq: C
Mutation seq: -
AAchange: p.C146fs
exon_skip_105023_LIHC_TCGA-DD-A39Y-01.png
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check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
SW684_SOFT_TISSUE44750363447505374475047544750475Missense_MutationCTp.P23L
SW684_SOFT_TISSUE44750459447505374475047544750475Missense_MutationCTp.P23L
RKO_LARGE_INTESTINE44750363447505374475050244750502Missense_MutationTCp.L32P
RKO_LARGE_INTESTINE44750459447505374475050244750502Missense_MutationTCp.L32P
HEC1A_ENDOMETRIUM44750363447505374475050244750502Missense_MutationTCp.L32P
HEC1A_ENDOMETRIUM44750459447505374475050244750502Missense_MutationTCp.L32P
KYSE150_OESOPHAGUS44750363447505374475053544750535Missense_MutationCTp.P43L
KYSE150_OESOPHAGUS44750459447505374475053544750535Missense_MutationCTp.P43L

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CD40

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CD40


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CD40


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RelatedDrugs for CD40

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for CD40

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
CD40C0003873Rheumatoid Arthritis3CTD_human
CD40C0026691Mucocutaneous Lymph Node Syndrome2CTD_human
CD40C1720957Hyper-IgM Immunodeficiency Syndrome, Type 32ORPHANET;UNIPROT
CD40C0026769Multiple Sclerosis1CTD_human
CD40C0038220Status Epilepticus1CTD_human
CD40C1458155Mammary Neoplasms1CTD_human