ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for RAD51D

Gene summary

Gene information	Gene symbol	RAD51D
	Gene ID	5892
	Gene name	RAD51 paralog D
	Synonyms	BROVCA4\|R51H3\|RAD51L3\|TRAD
	Cytomap	17q12
	Type of gene	protein-coding
	Description	DNA repair protein RAD51 homolog 4RAD51 homolog DRAD51-like protein 3recombination repair protein
	Modification date	20200313
	UniProtAcc	H0UID0, K7EJ58, K7EKG7, K7EMF1, K7EN92, K7ERM7, K7ESI1, K7ESL4, O75771,
	Context

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
RAD51D	GO:0042148	strand invasion	11834724

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Gene structures and expression levels for RAD51D

Skipped exons in the ROSMAP, MSBB, and Mayo 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.

ENSG00000185379

Differentially expressed gene analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

Base mean exp.

log2FC(AD/control)

P-value

Adj. p-value

Differentially expressed isoform analysis across multiple brain tissues between AD and control.

Tissue type	DEG direction	ENST	Transcript info.	Base mean exp.	log2FC(AD/control)	P-value	Adjc. p-value
CB	DOWN	ENST00000585343.5	RAD51D-206:nonsense_mediated_decay:RAD51D	1.908808e+00	-1.230391e+00	1.827450e-04	1.232884e-03

Landscape of isoform expressions across multiple brain tissues between AD and control.

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for RAD51D

Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).

All exon skipping events in AD cohorts.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon
exon_skip_117757	chr17	35106386:35106481:35107366:35107447:35119111:35119172	35107366:35107447
exon_skip_132889	chr17	35106441:35106481:35106988:35107122:35107366:35107447	35106988:35107122
exon_skip_14317	chr17	35106988:35107122:35116859:35117037:35118501:35118619	35116859:35117037
exon_skip_202484	chr17	35103454:35103544:35106128:35106249:35106386:35106481	35106128:35106249
exon_skip_202499	chr17	35107366:35107447:35118501:35118619:35119111:35119172	35118501:35118619
exon_skip_205194	chr17	35106441:35106481:35106988:35107122:35118501:35118619	35106988:35107122
exon_skip_239472	chr17	35106441:35106481:35107366:35107447:35118501:35118619	35107366:35107447
exon_skip_249758	chr17	35107366:35107447:35116859:35117037:35118501:35118619	35116859:35117037
exon_skip_267949	chr17	35106441:35106481:35106988:35107122:35116859:35117037	35106988:35107122
exon_skip_282526	chr17	35106441:35106481:35107366:35107447:35116859:35117037	35107366:35107447
exon_skip_287866	chr17	35106988:35107122:35107366:35107447:35116859:35117037	35107366:35107447
exon_skip_35050	chr17	35116859:35117037:35118501:35118619:35119111:35119172	35118501:35118619
exon_skip_43902	chr17	35107366:35107447:35116859:35117037:35119111:35119172	35116859:35117037
exon_skip_4661	chr17	35106441:35106481:35116859:35117037:35118501:35118619	35116859:35117037
exon_skip_8256	chr17	35106988:35107122:35107366:35107447:35118501:35118619	35107366:35107447
exon_skip_86996	chr17	35106386:35106481:35106988:35107061:35107366:35107447	35106988:35107061

Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.

Exon skipping information	Tissue type	Avg(PSIs) in AD	Avg(PSIs) in control	Difference (PSI)	Adj. p-value
exon_skip_117757	Mayo_TC	2.973239e-01	4.021053e-01	-1.047813e-01	1.079426e-04

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Open reading frame (ORF) annotation in the exon skipping event for RAD51D

Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000345365	35107366	35107447	Frame-shift
ENST00000394589	35107366	35107447	Frame-shift
ENST00000345365	35118501	35118619	Frame-shift
ENST00000394589	35118501	35118619	Frame-shift
ENST00000345365	35106988	35107122	In-frame
ENST00000394589	35106988	35107122	In-frame

Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000345365	35118501	35118619	Frame-shift
ENST00000394589	35118501	35118619	Frame-shift
ENST00000345365	35106988	35107122	In-frame
ENST00000394589	35106988	35107122	In-frame

Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000345365	35107366	35107447	Frame-shift
ENST00000394589	35107366	35107447	Frame-shift
ENST00000345365	35118501	35118619	Frame-shift
ENST00000394589	35118501	35118619	Frame-shift
ENST00000345365	35106988	35107122	In-frame
ENST00000394589	35106988	35107122	In-frame

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Infer the effects of exon skipping event on protein functional features for RAD51D

p-ENSG00000185379_img4.png
boxplot

Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000345365	10005	328	35106988	35107122	602	735	115	159
ENST00000394589	2304	328	35106988	35107122	485	618	115	159

Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000345365	10005	328	35106988	35107122	602	735	115	159
ENST00000394589	2304	328	35106988	35107122	485	618	115	159

Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000345365	10005	328	35106988	35107122	602	735	115	159
ENST00000394589	2304	328	35106988	35107122	485	618	115	159

Lost protein functional features of individual exon skipping events in ROSMAP.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
O75771	115	159	50	328	Alternative sequence	ID=VSP_005559;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	50	328	Alternative sequence	ID=VSP_005559;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	50	161	Alternative sequence	ID=VSP_005560;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	50	161	Alternative sequence	ID=VSP_005560;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	88	118	Alternative sequence	ID=VSP_005563;Note=In isoform 6. SLDKLLDAGLYTGEVTEIVGGPGSGKTQVCL->RHGGRTQVGTWEDCSCLRSPQGDRGVGSGML;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	88	118	Alternative sequence	ID=VSP_005563;Note=In isoform 6. SLDKLLDAGLYTGEVTEIVGGPGSGKTQVCL->RHGGRTQVGTWEDCSCLRSPQGDRGVGSGML;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	116	160	Alternative sequence	ID=VSP_005561;Note=In isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	116	160	Alternative sequence	ID=VSP_005561;Note=In isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	119	328	Alternative sequence	ID=VSP_005564;Note=In isoform 6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	119	328	Alternative sequence	ID=VSP_005564;Note=In isoform 6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	1	328	Chain	ID=PRO_0000122942;Note=DNA repair protein RAD51 homolog 4
O75771	115	159	1	328	Chain	ID=PRO_0000122942;Note=DNA repair protein RAD51 homolog 4

Lost protein functional features of individual exon skipping events in MSBB.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
O75771	115	159	50	328	Alternative sequence	ID=VSP_005559;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	50	328	Alternative sequence	ID=VSP_005559;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	50	161	Alternative sequence	ID=VSP_005560;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	50	161	Alternative sequence	ID=VSP_005560;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	88	118	Alternative sequence	ID=VSP_005563;Note=In isoform 6. SLDKLLDAGLYTGEVTEIVGGPGSGKTQVCL->RHGGRTQVGTWEDCSCLRSPQGDRGVGSGML;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	88	118	Alternative sequence	ID=VSP_005563;Note=In isoform 6. SLDKLLDAGLYTGEVTEIVGGPGSGKTQVCL->RHGGRTQVGTWEDCSCLRSPQGDRGVGSGML;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	116	160	Alternative sequence	ID=VSP_005561;Note=In isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	116	160	Alternative sequence	ID=VSP_005561;Note=In isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	119	328	Alternative sequence	ID=VSP_005564;Note=In isoform 6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	119	328	Alternative sequence	ID=VSP_005564;Note=In isoform 6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	1	328	Chain	ID=PRO_0000122942;Note=DNA repair protein RAD51 homolog 4
O75771	115	159	1	328	Chain	ID=PRO_0000122942;Note=DNA repair protein RAD51 homolog 4

Lost protein functional features of individual exon skipping events in Mayo.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
O75771	115	159	50	328	Alternative sequence	ID=VSP_005559;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	50	328	Alternative sequence	ID=VSP_005559;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	50	161	Alternative sequence	ID=VSP_005560;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	50	161	Alternative sequence	ID=VSP_005560;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	88	118	Alternative sequence	ID=VSP_005563;Note=In isoform 6. SLDKLLDAGLYTGEVTEIVGGPGSGKTQVCL->RHGGRTQVGTWEDCSCLRSPQGDRGVGSGML;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	88	118	Alternative sequence	ID=VSP_005563;Note=In isoform 6. SLDKLLDAGLYTGEVTEIVGGPGSGKTQVCL->RHGGRTQVGTWEDCSCLRSPQGDRGVGSGML;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	116	160	Alternative sequence	ID=VSP_005561;Note=In isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	116	160	Alternative sequence	ID=VSP_005561;Note=In isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	119	328	Alternative sequence	ID=VSP_005564;Note=In isoform 6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	119	328	Alternative sequence	ID=VSP_005564;Note=In isoform 6. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O75771	115	159	1	328	Chain	ID=PRO_0000122942;Note=DNA repair protein RAD51 homolog 4
O75771	115	159	1	328	Chain	ID=PRO_0000122942;Note=DNA repair protein RAD51 homolog 4

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3'-UTR located exon skipping events that lost miRNA binding sites in RAD51D

3'-UTR exon skipping evnets lost miRNA binding.

Tissue type

ENST

Exon skip start

Exon skip end

microRNA

Binding site by TargetScan

Binding type by TargetScan

Bdinding site by miRanda

Score of miRanda

Energy by miRanda

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SNVs in the skipped exons for RAD51D

- Differential PSIs between mutated versus non-mutated samples.

- Depth of Coverage in the skipped exon of the mutated samples.

- Sashimi plot in the skipped exon of the mutated samples.

- Non-synonymous mutations located in the skipped exons.

Cancer type

Sample

ESID

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

- Non-synonymous mutations located in the skipped exons in CCLE.

Sample

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

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AD stage-associated exon skippint events for RAD51D

Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).

AD stage info

Cohort

Tissue

SE id

Coefficient

P-value

Chromosome

Strand

E1 start

E1 end

Skipped start

Skipped end

E2 start

E2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAD51D

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
TC	exon_skip_202499	rs2306508	chr17:35127396	2.307118e-04	3.183520e-02

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Correlation with RNA binding proteins (RBPs) for RAD51D

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	UNK	exon_skip_132889	-4.005261e-01	3.072279e-06
CB	PCBP4	exon_skip_22478	4.394240e-01	3.680303e-07
CB	UNK	exon_skip_22478	4.780925e-01	2.240228e-08
TC	RBM6	exon_skip_132889	5.214857e-01	1.076789e-11
TC	G3BP2	exon_skip_132889	-4.611979e-01	3.655671e-09
TC	MSI1	exon_skip_117757	-4.161452e-01	1.032088e-06
TC	SAMD4A	exon_skip_117757	-4.187987e-01	8.664731e-07
TC	KHDRBS2	exon_skip_117757	4.993574e-01	1.972767e-09

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RelatedDrugs for RAD51D

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for RAD51D

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

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