ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for KDM3B

Gene summary

Gene information	Gene symbol	KDM3B
	Gene ID	51780
	Gene name	lysine demethylase 3B
	Synonyms	5qNCA\|C5orf7\|JMJD1B\|NET22
	Cytomap	5q31.2
	Type of gene	protein-coding
	Description	lysine-specific demethylase 3BjmjC domain-containing histone demethylation protein 2Bjumonji domain containing 1Bjumonji domain-containing protein 1Blysine (K)-specific demethylase 3Bnuclear protein 5qNCA
	Modification date	20200313
	UniProtAcc	H0Y946, H0Y9V5, Q7LBC6,
	Context

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

Gene

GO ID

GO term

PubMed ID

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Gene structures and expression levels for KDM3B

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.

ENSG00000120733

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
HCC	UP	ENST00000542866.2	KDM3B-209:protein_coding:KDM3B	4.507955e+01	2.661160e+01	8.899337e-34	8.641256e-29

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 KDM3B

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_104719	chr5	138399860:138400012:138415132:138415239:138417483:138417610	138415132:138415239
exon_skip_109097	chr5	138420706:138420962:138424075:138424341:138425411:138425582	138424075:138424341
exon_skip_129192	chr5	138379584:138379708:138381516:138381590:138386022:138386190	138381516:138381590
exon_skip_179358	chr5	138399866:138400012:138415132:138415239:138417483:138417610	138415132:138415239
exon_skip_220210	chr5	138399862:138400012:138415132:138415239:138417483:138417610	138415132:138415239
exon_skip_272326	chr5	138418953:138419232:138420706:138420962:138424075:138424336	138420706:138420962
exon_skip_280985	chr5	138386577:138386621:138391013:138392261:138393171:138393372	138391013:138392261
exon_skip_28347	chr5	138381516:138381590:138386022:138386621:138391013:138392261	138386022:138386621
exon_skip_45785	chr5	138393171:138393372:138398178:138398392:138399860:138399899	138398178:138398392
exon_skip_47013	chr5	138430249:138430425:138431425:138431559:138435620:138436032	138431425:138431559
exon_skip_62399	chr5	138430249:138430425:138431425:138431559:138435620:138435812	138431425:138431559
exon_skip_7521	chr5	138418953:138419232:138420706:138420962:138424075:138424341	138420706:138420962
exon_skip_77839	chr5	138377811:138377825:138379584:138379708:138381516:138381590	138379584:138379708
exon_skip_84188	chr5	138417483:138417610:138418953:138419232:138420706:138420785	138418953:138419232

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

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Open reading frame (ORF) annotation in the exon skipping event for KDM3B

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
ENST00000314358	138379584	138379708	Frame-shift
ENST00000314358	138391013	138392261	Frame-shift
ENST00000314358	138398178	138398392	Frame-shift
ENST00000314358	138420706	138420962	Frame-shift
ENST00000314358	138381516	138381590	In-frame
ENST00000314358	138386022	138386621	In-frame
ENST00000314358	138415132	138415239	In-frame
ENST00000314358	138424075	138424341	In-frame
ENST00000314358	138431425	138431559	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
ENST00000314358	138420706	138420962	Frame-shift
ENST00000314358	138381516	138381590	In-frame
ENST00000314358	138386022	138386621	In-frame
ENST00000314358	138424075	138424341	In-frame
ENST00000314358	138431425	138431559	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
ENST00000314358	138391013	138392261	Frame-shift
ENST00000314358	138398178	138398392	Frame-shift
ENST00000314358	138418953	138419232	Frame-shift
ENST00000314358	138420706	138420962	Frame-shift
ENST00000314358	138381516	138381590	In-frame
ENST00000314358	138386022	138386621	In-frame
ENST00000314358	138415132	138415239	In-frame
ENST00000314358	138424075	138424341	In-frame
ENST00000314358	138431425	138431559	In-frame

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Infer the effects of exon skipping event on protein functional features for KDM3B

p-ENSG00000120733_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
ENST00000314358	6830	1761	138381516	138381590	907	980	235	260
ENST00000314358	6830	1761	138386022	138386621	982	1580	260	460
ENST00000314358	6830	1761	138415132	138415239	3401	3507	1067	1102
ENST00000314358	6830	1761	138424075	138424341	4174	4439	1324	1413
ENST00000314358	6830	1761	138431425	138431559	5272	5405	1690	1735

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
ENST00000314358	6830	1761	138381516	138381590	907	980	235	260
ENST00000314358	6830	1761	138386022	138386621	982	1580	260	460
ENST00000314358	6830	1761	138424075	138424341	4174	4439	1324	1413
ENST00000314358	6830	1761	138431425	138431559	5272	5405	1690	1735

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
ENST00000314358	6830	1761	138381516	138381590	907	980	235	260
ENST00000314358	6830	1761	138386022	138386621	982	1580	260	460
ENST00000314358	6830	1761	138415132	138415239	3401	3507	1067	1102
ENST00000314358	6830	1761	138424075	138424341	4174	4439	1324	1413
ENST00000314358	6830	1761	138431425	138431559	5272	5405	1690	1735

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
Q7LBC6	235	260	1	1002	Alternative sequence	ID=VSP_018298;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q7LBC6	235	260	1	344	Alternative sequence	ID=VSP_018299;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11087669;Dbxref=PMID:11087669
Q7LBC6	235	260	2	1761	Chain	ID=PRO_0000234373;Note=Lysine-specific demethylase 3B
Q7LBC6	235	260	256	256	Natural variant	ID=VAR_026221;Note=A->T;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:10470851,ECO:0000269\|PubMed:11687974,ECO:0000269\|PubMed:15489334,ECO:0000269\|Ref.6;Dbxref=dbSNP:rs6865472,PMID:10470851,PMID:11687974,PMID:15
Q7LBC6	260	460	1	1002	Alternative sequence	ID=VSP_018298;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q7LBC6	260	460	1	344	Alternative sequence	ID=VSP_018299;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11087669;Dbxref=PMID:11087669
Q7LBC6	260	460	345	349	Alternative sequence	ID=VSP_018300;Note=In isoform 2. TFVPQ->MGAME;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11087669;Dbxref=PMID:11087669
Q7LBC6	260	460	2	1761	Chain	ID=PRO_0000234373;Note=Lysine-specific demethylase 3B
Q7LBC6	260	460	361	361	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
Q7LBC6	1067	1102	2	1761	Chain	ID=PRO_0000234373;Note=Lysine-specific demethylase 3B
Q7LBC6	1324	1413	1382	1385	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1324	1413	1390	1394	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1324	1413	2	1761	Chain	ID=PRO_0000234373;Note=Lysine-specific demethylase 3B
Q7LBC6	1324	1413	1401	1410	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1324	1413	1386	1389	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1690	1735	1689	1704	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1690	1735	2	1761	Chain	ID=PRO_0000234373;Note=Lysine-specific demethylase 3B
Q7LBC6	1690	1735	1498	1721	Domain	Note=JmjC;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00538
Q7LBC6	1690	1735	1707	1709	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1690	1735	1710	1719	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D

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
Q7LBC6	235	260	1	1002	Alternative sequence	ID=VSP_018298;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q7LBC6	235	260	1	344	Alternative sequence	ID=VSP_018299;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11087669;Dbxref=PMID:11087669
Q7LBC6	235	260	2	1761	Chain	ID=PRO_0000234373;Note=Lysine-specific demethylase 3B
Q7LBC6	235	260	256	256	Natural variant	ID=VAR_026221;Note=A->T;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:10470851,ECO:0000269\|PubMed:11687974,ECO:0000269\|PubMed:15489334,ECO:0000269\|Ref.6;Dbxref=dbSNP:rs6865472,PMID:10470851,PMID:11687974,PMID:15
Q7LBC6	260	460	1	1002	Alternative sequence	ID=VSP_018298;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q7LBC6	260	460	1	344	Alternative sequence	ID=VSP_018299;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11087669;Dbxref=PMID:11087669
Q7LBC6	260	460	345	349	Alternative sequence	ID=VSP_018300;Note=In isoform 2. TFVPQ->MGAME;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11087669;Dbxref=PMID:11087669
Q7LBC6	260	460	2	1761	Chain	ID=PRO_0000234373;Note=Lysine-specific demethylase 3B
Q7LBC6	260	460	361	361	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
Q7LBC6	1324	1413	1382	1385	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1324	1413	1390	1394	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1324	1413	2	1761	Chain	ID=PRO_0000234373;Note=Lysine-specific demethylase 3B
Q7LBC6	1324	1413	1401	1410	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1324	1413	1386	1389	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1690	1735	1689	1704	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1690	1735	2	1761	Chain	ID=PRO_0000234373;Note=Lysine-specific demethylase 3B
Q7LBC6	1690	1735	1498	1721	Domain	Note=JmjC;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00538
Q7LBC6	1690	1735	1707	1709	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1690	1735	1710	1719	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D

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
Q7LBC6	235	260	1	1002	Alternative sequence	ID=VSP_018298;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q7LBC6	235	260	1	344	Alternative sequence	ID=VSP_018299;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11087669;Dbxref=PMID:11087669
Q7LBC6	235	260	2	1761	Chain	ID=PRO_0000234373;Note=Lysine-specific demethylase 3B
Q7LBC6	235	260	256	256	Natural variant	ID=VAR_026221;Note=A->T;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:10470851,ECO:0000269\|PubMed:11687974,ECO:0000269\|PubMed:15489334,ECO:0000269\|Ref.6;Dbxref=dbSNP:rs6865472,PMID:10470851,PMID:11687974,PMID:15
Q7LBC6	260	460	1	1002	Alternative sequence	ID=VSP_018298;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q7LBC6	260	460	1	344	Alternative sequence	ID=VSP_018299;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11087669;Dbxref=PMID:11087669
Q7LBC6	260	460	345	349	Alternative sequence	ID=VSP_018300;Note=In isoform 2. TFVPQ->MGAME;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11087669;Dbxref=PMID:11087669
Q7LBC6	260	460	2	1761	Chain	ID=PRO_0000234373;Note=Lysine-specific demethylase 3B
Q7LBC6	260	460	361	361	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
Q7LBC6	1067	1102	2	1761	Chain	ID=PRO_0000234373;Note=Lysine-specific demethylase 3B
Q7LBC6	1324	1413	1382	1385	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1324	1413	1390	1394	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1324	1413	2	1761	Chain	ID=PRO_0000234373;Note=Lysine-specific demethylase 3B
Q7LBC6	1324	1413	1401	1410	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1324	1413	1386	1389	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1690	1735	1689	1704	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1690	1735	2	1761	Chain	ID=PRO_0000234373;Note=Lysine-specific demethylase 3B
Q7LBC6	1690	1735	1498	1721	Domain	Note=JmjC;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00538
Q7LBC6	1690	1735	1707	1709	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D
Q7LBC6	1690	1735	1710	1719	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4C8D

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3'-UTR located exon skipping events that lost miRNA binding sites in KDM3B

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 KDM3B

- 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 KDM3B

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

ADstage

MSBB

IFG

exon_skip_47013

-3.819242e-01

4.490183e-02

chr5

138430249

138430425

138431425

138431559

138435620

138436032

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for KDM3B

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for KDM3B

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	HNRNPDL	exon_skip_28347	-4.393731e-01	1.488202e-08
CB	RBM45	exon_skip_28347	-4.764976e-01	5.460413e-10

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RelatedDrugs for KDM3B

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 KDM3B

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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Gene summary for KDM3B

Gene structures and expression levels for KDM3B

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for KDM3B

Open reading frame (ORF) annotation in the exon skipping event for KDM3B

Infer the effects of exon skipping event on protein functional features for KDM3B

3'-UTR located exon skipping events that lost miRNA binding sites in KDM3B

SNVs in the skipped exons for KDM3B

AD stage-associated exon skippint events for KDM3B

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for KDM3B

Correlation with RNA binding proteins (RBPs) for KDM3B

RelatedDrugs for KDM3B

RelatedDiseases for KDM3B