ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for CDK12

Gene summary

Gene information	Gene symbol	CDK12
	Gene ID	51755
	Gene name	cyclin dependent kinase 12
	Synonyms	CRK7\|CRKR\|CRKRS
	Cytomap	17q12
	Type of gene	protein-coding
	Description	cyclin-dependent kinase 12CDC2-related protein kinase 7Cdc2-related kinase, arginine/serine-richcell division cycle 2-related protein kinase 7cell division protein kinase 12
	Modification date	20200313
	UniProtAcc	A0A2I6PNI6, A0A590UJE9, H0YLT2, J3QSD7, Q9NYV4,
	Context

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

Gene	GO ID	GO term	PubMed ID
CDK12	GO:0046777	protein autophosphorylation	11683387

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Gene structures and expression levels for CDK12

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.

ENSG00000167258

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	UP	ENST00000430627.6	CDK12-201:protein_coding:CDK12	2.526735e+02	1.007688e+00	3.614257e-07	6.306335e-06
CB	UP	ENST00000584632.5	CDK12-209:protein_coding:CDK12	1.867068e+02	8.984894e-01	4.407330e-05	3.694088e-04

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 CDK12

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_115087	chr17	39511529:39511630:39515731:39515808:39517440:39517556	39515731:39515808
exon_skip_132760	chr17	39551038:39551142:39556286:39556413:39564760:39564830	39556286:39556413
exon_skip_148420	chr17	39471514:39471763:39490557:39490733:39492751:39492890	39490557:39490733
exon_skip_181864	chr17	39492751:39492890:39494524:39494694:39501250:39501439	39494524:39494694
exon_skip_217027	chr17	39556286:39556413:39556864:39557058:39564760:39564907	39556864:39557058
exon_skip_224829	chr17	39556286:39556413:39556864:39557058:39564760:39564830	39556864:39557058
exon_skip_254765	chr17	39547821:39547830:39551038:39551142:39556286:39556413	39551038:39551142
exon_skip_54329	chr17	39517440:39517556:39519956:39520087:39524674:39524885	39519956:39520087
exon_skip_71850	chr17	39546617:39546758:39547768:39547830:39551038:39551141	39547768:39547830

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 CDK12

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
ENST00000447079	39490557	39490733	In-frame
ENST00000447079	39494524	39494694	In-frame
ENST00000447079	39515731	39515808	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
ENST00000447079	39515731	39515808	In-frame
ENST00000447079	39519956	39520087	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
ENST00000447079	39490557	39490733	In-frame
ENST00000447079	39494524	39494694	In-frame
ENST00000447079	39515731	39515808	In-frame
ENST00000447079	39519956	39520087	In-frame

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Infer the effects of exon skipping event on protein functional features for CDK12

p-ENSG00000167258_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
ENST00000447079	8353	1490	39490557	39490733	1966	2141	644	702
ENST00000447079	8353	1490	39494524	39494694	2283	2452	750	806
ENST00000447079	8353	1490	39515731	39515808	2803	2879	923	948

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
ENST00000447079	8353	1490	39515731	39515808	2803	2879	923	948
ENST00000447079	8353	1490	39519956	39520087	2998	3128	988	1031

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
ENST00000447079	8353	1490	39490557	39490733	1966	2141	644	702
ENST00000447079	8353	1490	39494524	39494694	2283	2452	750	806
ENST00000447079	8353	1490	39515731	39515808	2803	2879	923	948
ENST00000447079	8353	1490	39519956	39520087	2998	3128	988	1031

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
Q9NYV4	644	702	1	1490	Chain	ID=PRO_0000085715;Note=Cyclin-dependent kinase 12
Q9NYV4	644	702	655	655	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
Q9NYV4	644	702	644	644	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3MJK5
Q9NYV4	644	702	681	681	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:17081983,ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:18691976,ECO:0000244\|PubMed:19
Q9NYV4	644	702	685	685	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:17081983,ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:18691976,ECO:0000244\|PubMed:19369195,ECO:0
Q9NYV4	644	702	692	692	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:18691976,ECO:0000244\|PubMed:19369195,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:18691976,PMID:19369195,P
Q9NYV4	750	806	752	758	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	750	806	761	763	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5ACB
Q9NYV4	750	806	764	767	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4UN0
Q9NYV4	750	806	789	794	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	750	806	756	756	Binding site	Note=ATP
Q9NYV4	750	806	1	1490	Chain	ID=PRO_0000085715;Note=Cyclin-dependent kinase 12
Q9NYV4	750	806	727	1020	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q9NYV4	750	806	769	778	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	750	806	802	804	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5ACB
Q9NYV4	923	948	1	1490	Chain	ID=PRO_0000085715;Note=Cyclin-dependent kinase 12
Q9NYV4	923	948	727	1020	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q9NYV4	923	948	916	931	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	923	948	941	952	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST

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
Q9NYV4	923	948	1	1490	Chain	ID=PRO_0000085715;Note=Cyclin-dependent kinase 12
Q9NYV4	923	948	727	1020	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q9NYV4	923	948	916	931	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	923	948	941	952	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	988	1031	1	1490	Chain	ID=PRO_0000085715;Note=Cyclin-dependent kinase 12
Q9NYV4	988	1031	727	1020	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q9NYV4	988	1031	991	1000	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	988	1031	1011	1014	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	988	1031	1018	1021	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	988	1031	1025	1027	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	988	1031	986	988	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	988	1031	1005	1007	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST

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
Q9NYV4	644	702	1	1490	Chain	ID=PRO_0000085715;Note=Cyclin-dependent kinase 12
Q9NYV4	644	702	655	655	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
Q9NYV4	644	702	644	644	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3MJK5
Q9NYV4	644	702	681	681	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:17081983,ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:18691976,ECO:0000244\|PubMed:19
Q9NYV4	644	702	685	685	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:17081983,ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:18691976,ECO:0000244\|PubMed:19369195,ECO:0
Q9NYV4	644	702	692	692	Modified residue	Note=Phosphothreonine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:18691976,ECO:0000244\|PubMed:19369195,ECO:0000244\|PubMed:23186163;Dbxref=PMID:18669648,PMID:18691976,PMID:19369195,P
Q9NYV4	750	806	752	758	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	750	806	761	763	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5ACB
Q9NYV4	750	806	764	767	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4UN0
Q9NYV4	750	806	789	794	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	750	806	756	756	Binding site	Note=ATP
Q9NYV4	750	806	1	1490	Chain	ID=PRO_0000085715;Note=Cyclin-dependent kinase 12
Q9NYV4	750	806	727	1020	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q9NYV4	750	806	769	778	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	750	806	802	804	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5ACB
Q9NYV4	923	948	1	1490	Chain	ID=PRO_0000085715;Note=Cyclin-dependent kinase 12
Q9NYV4	923	948	727	1020	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q9NYV4	923	948	916	931	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	923	948	941	952	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	988	1031	1	1490	Chain	ID=PRO_0000085715;Note=Cyclin-dependent kinase 12
Q9NYV4	988	1031	727	1020	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
Q9NYV4	988	1031	991	1000	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	988	1031	1011	1014	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	988	1031	1018	1021	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	988	1031	1025	1027	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	988	1031	986	988	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST
Q9NYV4	988	1031	1005	1007	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4NST

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3'-UTR located exon skipping events that lost miRNA binding sites in CDK12

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 CDK12

- 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 CDK12

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 CDK12

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 CDK12

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	PCBP4	exon_skip_71850	4.563155e-01	9.030935e-09

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RelatedDrugs for CDK12

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 CDK12

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 CDK12

Gene structures and expression levels for CDK12

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CDK12

Open reading frame (ORF) annotation in the exon skipping event for CDK12

Infer the effects of exon skipping event on protein functional features for CDK12

3'-UTR located exon skipping events that lost miRNA binding sites in CDK12

SNVs in the skipped exons for CDK12

AD stage-associated exon skippint events for CDK12

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CDK12

Correlation with RNA binding proteins (RBPs) for CDK12

RelatedDrugs for CDK12

RelatedDiseases for CDK12