ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for KDM5C

Gene summary

Gene information	Gene symbol	KDM5C
	Gene ID	8242
	Gene name	lysine demethylase 5C
	Synonyms	DXS1272E\|JARID1C\|MRX13\|MRXJ\|MRXSCJ\|MRXSJ\|SMCX\|XE169
	Cytomap	Xp11.22
	Type of gene	protein-coding
	Description	lysine-specific demethylase 5CJmjC domain-containing protein SMCXJumonji, AT rich interactive domain 1C (RBP2-like)Jumonji/ARID domain-containing protein 1CSmcx homolog, X chromosomeSmcy homolog, X-linkedhistone demethylase JARID1Clysine (K)-specif
	Modification date	20200313
	UniProtAcc	F8W7H7, F8WDK1, F8WF56, L8E945, P41229,
	Context

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

Gene	GO ID	GO term	PubMed ID
KDM5C	GO:0034720	histone H3-K4 demethylation	17320160

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Gene structures and expression levels for KDM5C

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.

ENSG00000126012

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

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 KDM5C

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_107889	chrX	53217853:53217966:53220839:53220916:53224740:53225176	53220839:53220916
exon_skip_118257	chrX	53218315:53218398:53218564:53218712:53220839:53220916	53218564:53218712
exon_skip_119937	chrX	53217796:53217966:53220839:53220916:53224740:53224907	53220839:53220916
exon_skip_150629	chrX	53220839:53220916:53221688:53221730:53224740:53224907	53221688:53221730
exon_skip_162786	chrX	53193782:53193851:53194139:53194738:53194931:53195068	53194139:53194738
exon_skip_166696	chrX	53217796:53217966:53220839:53220916:53224740:53225422	53220839:53220916
exon_skip_171980	chrX	53220839:53220916:53221688:53221730:53224740:53225176	53221688:53221730
exon_skip_199989	chrX	53217853:53217966:53218276:53218398:53220839:53220916	53218276:53218398
exon_skip_201137	chrX	53210414:53210576:53210676:53210857:53211497:53211655	53210676:53210857
exon_skip_224694	chrX	53218315:53218398:53220839:53220916:53224740:53225176	53220839:53220916
exon_skip_280213	chrX	53193782:53193851:53194139:53194738:53194931:53194954	53194139:53194738
exon_skip_35401	chrX	53198977:53199158:53201550:53201744:53201854:53201973	53201550:53201744
exon_skip_75636	chrX	53220839:53220916:53221688:53221730:53224740:53225208	53221688:53221730
exon_skip_98840	chrX	53220839:53220916:53221688:53221730:53224740:53225123	53221688:53221730

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 KDM5C

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
ENST00000375401	53210676	53210857	Frame-shift
ENST00000375401	53194139	53194738	In-frame
ENST00000375401	53201550	53201744	In-frame
ENST00000375401	53218276	53218398	In-frame
ENST00000375401	53220839	53220916	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
ENST00000375401	53210676	53210857	Frame-shift
ENST00000375401	53201550	53201744	In-frame
ENST00000375401	53218276	53218398	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
ENST00000375401	53210676	53210857	Frame-shift
ENST00000375401	53194139	53194738	In-frame
ENST00000375401	53201550	53201744	In-frame
ENST00000375401	53218276	53218398	In-frame
ENST00000375401	53220839	53220916	In-frame

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Infer the effects of exon skipping event on protein functional features for KDM5C

p-ENSG00000126012_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
ENST00000375401	6048	1560	53220839	53220916	684	760	50	75
ENST00000375401	6048	1560	53218276	53218398	762	883	76	116
ENST00000375401	6048	1560	53201550	53201744	2400	2593	622	686
ENST00000375401	6048	1560	53194139	53194738	3972	4570	1146	1345

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
ENST00000375401	6048	1560	53218276	53218398	762	883	76	116
ENST00000375401	6048	1560	53201550	53201744	2400	2593	622	686

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
ENST00000375401	6048	1560	53220839	53220916	684	760	50	75
ENST00000375401	6048	1560	53218276	53218398	762	883	76	116
ENST00000375401	6048	1560	53201550	53201744	2400	2593	622	686
ENST00000375401	6048	1560	53194139	53194738	3972	4570	1146	1345

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
P41229	50	75	51	76	Alternative sequence	ID=VSP_043752;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P41229	50	75	1	1560	Chain	ID=PRO_0000200586;Note=Lysine-specific demethylase 5C
P41229	50	75	14	55	Domain	Note=JmjN;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00537
P41229	50	75	73	76	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	76	116	51	76	Alternative sequence	ID=VSP_043752;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P41229	76	116	77	117	Alternative sequence	ID=VSP_026410;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P41229	76	116	1	1560	Chain	ID=PRO_0000200586;Note=Lysine-specific demethylase 5C
P41229	76	116	79	169	Domain	Note=ARID;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00355
P41229	76	116	73	76	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	76	116	82	94	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	76	116	112	122	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	76	116	87	87	Natural variant	ID=VAR_032986;Note=In MRXSCJ%3B no effect on subcellular location and enzymatic activity. D->G;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:16541399,ECO:0000269\|PubMed:17468742;Dbxref=PMID:16541399,PMID:17468742
P41229	76	116	79	81	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	76	116	95	97	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	622	686	1	1560	Chain	ID=PRO_0000200586;Note=Lysine-specific demethylase 5C
P41229	622	686	468	634	Domain	Note=JmjC;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00538
P41229	622	686	620	622	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5FWJ
P41229	622	686	623	636	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5FWJ
P41229	622	686	644	652	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5FWJ
P41229	622	686	655	657	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5FWJ
P41229	622	686	660	687	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5FWJ
P41229	622	686	640	640	Natural variant	ID=VAR_065091;Note=De novo mutation found in a patient with mental retardation. C->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21076407;Dbxref=PMID:21076407
P41229	622	686	642	642	Natural variant	ID=VAR_032988;Note=In MRXSCJ%3B impairs enzymatic activity. F->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:16541399,ECO:0000269\|PubMed:17320160;Dbxref=PMID:16541399,PMID:17320160
P41229	1146	1345	1	1560	Chain	ID=PRO_0000200586;Note=Lysine-specific demethylase 5C
P41229	1146	1345	1199	1199	Sequence conflict	Note=A->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
P41229	1146	1345	1187	1248	Zinc finger	Note=PHD-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00146

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
P41229	76	116	51	76	Alternative sequence	ID=VSP_043752;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P41229	76	116	77	117	Alternative sequence	ID=VSP_026410;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P41229	76	116	1	1560	Chain	ID=PRO_0000200586;Note=Lysine-specific demethylase 5C
P41229	76	116	79	169	Domain	Note=ARID;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00355
P41229	76	116	73	76	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	76	116	82	94	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	76	116	112	122	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	76	116	87	87	Natural variant	ID=VAR_032986;Note=In MRXSCJ%3B no effect on subcellular location and enzymatic activity. D->G;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:16541399,ECO:0000269\|PubMed:17468742;Dbxref=PMID:16541399,PMID:17468742
P41229	76	116	79	81	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	76	116	95	97	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	622	686	1	1560	Chain	ID=PRO_0000200586;Note=Lysine-specific demethylase 5C
P41229	622	686	468	634	Domain	Note=JmjC;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00538
P41229	622	686	620	622	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5FWJ
P41229	622	686	623	636	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5FWJ
P41229	622	686	644	652	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5FWJ
P41229	622	686	655	657	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5FWJ
P41229	622	686	660	687	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5FWJ
P41229	622	686	640	640	Natural variant	ID=VAR_065091;Note=De novo mutation found in a patient with mental retardation. C->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21076407;Dbxref=PMID:21076407
P41229	622	686	642	642	Natural variant	ID=VAR_032988;Note=In MRXSCJ%3B impairs enzymatic activity. F->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:16541399,ECO:0000269\|PubMed:17320160;Dbxref=PMID:16541399,PMID:17320160

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
P41229	50	75	51	76	Alternative sequence	ID=VSP_043752;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P41229	50	75	1	1560	Chain	ID=PRO_0000200586;Note=Lysine-specific demethylase 5C
P41229	50	75	14	55	Domain	Note=JmjN;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00537
P41229	50	75	73	76	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	76	116	51	76	Alternative sequence	ID=VSP_043752;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P41229	76	116	77	117	Alternative sequence	ID=VSP_026410;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P41229	76	116	1	1560	Chain	ID=PRO_0000200586;Note=Lysine-specific demethylase 5C
P41229	76	116	79	169	Domain	Note=ARID;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00355
P41229	76	116	73	76	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	76	116	82	94	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	76	116	112	122	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	76	116	87	87	Natural variant	ID=VAR_032986;Note=In MRXSCJ%3B no effect on subcellular location and enzymatic activity. D->G;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:16541399,ECO:0000269\|PubMed:17468742;Dbxref=PMID:16541399,PMID:17468742
P41229	76	116	79	81	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	76	116	95	97	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2JRZ
P41229	622	686	1	1560	Chain	ID=PRO_0000200586;Note=Lysine-specific demethylase 5C
P41229	622	686	468	634	Domain	Note=JmjC;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00538
P41229	622	686	620	622	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5FWJ
P41229	622	686	623	636	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5FWJ
P41229	622	686	644	652	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5FWJ
P41229	622	686	655	657	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5FWJ
P41229	622	686	660	687	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5FWJ
P41229	622	686	640	640	Natural variant	ID=VAR_065091;Note=De novo mutation found in a patient with mental retardation. C->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21076407;Dbxref=PMID:21076407
P41229	622	686	642	642	Natural variant	ID=VAR_032988;Note=In MRXSCJ%3B impairs enzymatic activity. F->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:16541399,ECO:0000269\|PubMed:17320160;Dbxref=PMID:16541399,PMID:17320160
P41229	1146	1345	1	1560	Chain	ID=PRO_0000200586;Note=Lysine-specific demethylase 5C
P41229	1146	1345	1199	1199	Sequence conflict	Note=A->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
P41229	1146	1345	1187	1248	Zinc finger	Note=PHD-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00146

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3'-UTR located exon skipping events that lost miRNA binding sites in KDM5C

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 KDM5C

- 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 KDM5C

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 KDM5C

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 KDM5C

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for KDM5C

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 KDM5C

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 KDM5C

Gene structures and expression levels for KDM5C

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for KDM5C

Open reading frame (ORF) annotation in the exon skipping event for KDM5C

Infer the effects of exon skipping event on protein functional features for KDM5C

3'-UTR located exon skipping events that lost miRNA binding sites in KDM5C

SNVs in the skipped exons for KDM5C

AD stage-associated exon skippint events for KDM5C

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for KDM5C

Correlation with RNA binding proteins (RBPs) for KDM5C

RelatedDrugs for KDM5C

RelatedDiseases for KDM5C