ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for CDK11A

Gene summary

Gene information	Gene symbol	CDK11A
	Gene ID	728642
	Gene name	cyclin dependent kinase 11A
	Synonyms	CDC2L2\|CDC2L3\|CDK11-p110\|CDK11-p46\|CDK11-p58\|PITSLRE\|p58GTA
	Cytomap	1p36.33
	Type of gene	protein-coding
	Description	cyclin-dependent kinase 11APITSLRE BPITSLRE protein kinase beta SV1 isoformPITSLRE protein kinase beta SV16 isoformPITSLRE protein kinase beta SV17 isoformPITSLRE protein kinase beta SV18 isoformPITSLRE protein kinase beta SV2 isoformPITSLRE protei
	Modification date	20180523
	UniProtAcc	Q9UQ88
	Context	PubMed: CDK11A [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

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

Gene	GO ID	GO term	PubMed ID
CDK11A	GO:0006468	protein phosphorylation	12501247
CDK11A	GO:0050684	regulation of mRNA processing	12501247

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Exon skipping events across known transcript of Ensembl for CDK11A from UCSC genome browser

Skipped 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.

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Gene isoform structures and expression levels for CDK11A

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for CDK11A

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_20531	1	1634319:1634438:1634518:1634708:1634914:1635063	1634518:1634708	ENSG00000008128.18	ENST00000460465.1,ENST00000378633.1,ENST00000356200.3,ENST00000357760.2,ENST00000404249.3,ENST00000356937.3,ENST00000509982.1,ENST00000378638.2,ENST00000463652.1,ENST00000358779.5
exon_skip_20535	1	1635262:1635379:1635477:1635783:1635988:1636024	1635477:1635783	ENSG00000008128.18	ENST00000356937.3
exon_skip_20536	1	1635306:1635434:1635661:1635783:1635988:1636024	1635661:1635783	ENSG00000008128.18	ENST00000495016.1
exon_skip_20542	1	1640232:1640391:1640476:1640572:1640956:1641079	1640476:1640572	ENSG00000008128.18	ENST00000460465.1,ENST00000356200.3,ENST00000357760.2,ENST00000378635.3,ENST00000404249.3,ENST00000356937.3,ENST00000378638.2,ENST00000358779.5
exon_skip_20543	1	1640956:1641079:1643702:1643839:1647784:1647917	1643702:1643839	ENSG00000008128.18	ENST00000460465.1,ENST00000378633.1,ENST00000356200.3,ENST00000404249.3,ENST00000509982.1,ENST00000378638.2,ENST00000358779.5
exon_skip_20546	1	1640956:1641079:1643702:1643866:1647784:1647917	1643702:1643866	ENSG00000008128.18	ENST00000357760.2,ENST00000356937.3
exon_skip_20548	1	1640956:1641079:1647784:1647917:1650796:1650894	1647784:1647917	ENSG00000008128.18	ENST00000378635.3
exon_skip_20549	1	1643702:1643839:1647784:1647917:1650766:1650894	1647784:1647917	ENSG00000008128.18	ENST00000460465.1,ENST00000356200.3,ENST00000404249.3,ENST00000509982.1,ENST00000378638.2
exon_skip_20550	1	1643702:1643839:1647784:1647917:1650796:1650894	1647784:1647917	ENSG00000008128.18	ENST00000378633.1,ENST00000358779.5
exon_skip_20551	1	1650796:1650894:1653034:1653150:1654146:1654270	1653034:1653150	ENSG00000008128.18	ENST00000460465.1,ENST00000378633.1,ENST00000357760.2,ENST00000378635.3,ENST00000404249.3,ENST00000479362.1,ENST00000509982.1,ENST00000358779.5
exon_skip_20553	1	1653034:1653150:1654026:1654073:1654146:1654270	1654026:1654073	ENSG00000008128.18	ENST00000378638.2

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for CDK11A

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_20531	1	1634319:1634438:1634518:1634708:1634914:1635063	1634518:1634708	ENSG00000008128.18	ENST00000356200.3,ENST00000463652.1,ENST00000356937.3,ENST00000378638.2,ENST00000509982.1,ENST00000404249.3,ENST00000460465.1,ENST00000357760.2,ENST00000358779.5,ENST00000378633.1
exon_skip_20535	1	1635262:1635379:1635477:1635783:1635988:1636024	1635477:1635783	ENSG00000008128.18	ENST00000356937.3
exon_skip_20536	1	1635306:1635434:1635661:1635783:1635988:1636024	1635661:1635783	ENSG00000008128.18	ENST00000495016.1
exon_skip_20542	1	1640232:1640391:1640476:1640572:1640956:1641079	1640476:1640572	ENSG00000008128.18	ENST00000356200.3,ENST00000356937.3,ENST00000378638.2,ENST00000404249.3,ENST00000460465.1,ENST00000357760.2,ENST00000358779.5,ENST00000378635.3
exon_skip_20543	1	1640956:1641079:1643702:1643839:1647784:1647917	1643702:1643839	ENSG00000008128.18	ENST00000356200.3,ENST00000378638.2,ENST00000509982.1,ENST00000404249.3,ENST00000460465.1,ENST00000358779.5,ENST00000378633.1
exon_skip_20546	1	1640956:1641079:1643702:1643866:1647784:1647917	1643702:1643866	ENSG00000008128.18	ENST00000356937.3,ENST00000357760.2
exon_skip_20548	1	1640956:1641079:1647784:1647917:1650796:1650894	1647784:1647917	ENSG00000008128.18	ENST00000378635.3
exon_skip_20549	1	1643702:1643839:1647784:1647917:1650766:1650894	1647784:1647917	ENSG00000008128.18	ENST00000356200.3,ENST00000378638.2,ENST00000509982.1,ENST00000404249.3,ENST00000460465.1
exon_skip_20550	1	1643702:1643839:1647784:1647917:1650796:1650894	1647784:1647917	ENSG00000008128.18	ENST00000358779.5,ENST00000378633.1
exon_skip_20551	1	1650796:1650894:1653034:1653150:1654146:1654270	1653034:1653150	ENSG00000008128.18	ENST00000509982.1,ENST00000404249.3,ENST00000460465.1,ENST00000357760.2,ENST00000358779.5,ENST00000378633.1,ENST00000378635.3,ENST00000479362.1
exon_skip_20553	1	1653034:1653150:1654026:1654073:1654146:1654270	1654026:1654073	ENSG00000008128.18	ENST00000378638.2

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for CDK11A

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000378633	1634518	1634708	Frame-shift
ENST00000378633	1643702	1643839	Frame-shift
ENST00000378633	1647784	1647917	Frame-shift
ENST00000378633	1653034	1653150	Frame-shift

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000378633	1634518	1634708	Frame-shift
ENST00000378633	1643702	1643839	Frame-shift
ENST00000378633	1647784	1647917	Frame-shift
ENST00000378633	1653034	1653150	Frame-shift

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Infer the effects of exon skipping event on protein functional features for CDK11A

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

Loci of skipped exons in TCGA 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

Loci of skipped exons in GTEx 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

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 feature

Description of feature

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 feature

Description of feature

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SNVs in the skipped exons for CDK11A

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

- Differential PSIs between mutated versus non-mutated samples.

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

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
STAD	TCGA-BR-8363-01	exon_skip_20535	1635478	1635783	1635530	1635530	Frame_Shift_Del	G	-	p.P581fs
LIHC	TCGA-DD-A1EG-01	exon_skip_20551	1653035	1653150	1653038	1653038	Frame_Shift_Del	T	-	p.D41fs
LIHC	TCGA-BC-A3KG-01	exon_skip_20551	1653035	1653150	1653065	1653065	Frame_Shift_Del	G	-	p.P32fs
UCEC	TCGA-D1-A103-01	exon_skip_20550 exon_skip_20549 exon_skip_20548	1647785	1647917	1647897	1647897	Nonsense_Mutation	C	A	p.E126*

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons

Mutation description

- 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
U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1634519	1634708	1634535	1634535	Missense_Mutation	A	C	p.L748R
BEN_LUNG	1634519	1634708	1634551	1634551	Missense_Mutation	G	A	p.P743S
HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1634519	1634708	1634551	1634551	Missense_Mutation	G	A	p.P743S
HS683_CENTRAL_NERVOUS_SYSTEM	1634519	1634708	1634551	1634551	Missense_Mutation	G	A	p.P743S
HS706T_BONE	1634519	1634708	1634551	1634551	Missense_Mutation	G	A	p.P743S
HS834T_FIBROBLAST	1634519	1634708	1634551	1634551	Missense_Mutation	G	A	p.P743S
HS934T_FIBROBLAST	1634519	1634708	1634551	1634551	Missense_Mutation	G	A	p.P743S
K562_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1634519	1634708	1634551	1634551	Missense_Mutation	G	A	p.P743S
MELHO_SKIN	1634519	1634708	1634551	1634551	Missense_Mutation	G	A	p.P743S
NCIH146_LUNG	1634519	1634708	1634551	1634551	Missense_Mutation	G	A	p.P743S
PLB985_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1634519	1634708	1634551	1634551	Missense_Mutation	G	A	p.P743S
SW780_URINARY_TRACT	1634519	1634708	1634551	1634551	Missense_Mutation	G	A	p.P743S
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1634519	1634708	1634575	1634575	Missense_Mutation	C	A	p.V735L
CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1635478	1635783	1635533	1635533	Missense_Mutation	G	C	p.T583S
KHYG_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1635478	1635783	1635549	1635549	Missense_Mutation	G	T	p.P578T
NMCG1_CENTRAL_NERVOUS_SYSTEM	1635478	1635783	1635549	1635549	Missense_Mutation	G	T	p.P578T
JHH4_LIVER	1635478	1635783	1635549	1635549	Missense_Mutation	G	T	p.P578T
EGI1_BILIARY_TRACT	1635662	1635783	1635673	1635673	Missense_Mutation	C	T	p.G562S
EGI1_BILIARY_TRACT	1635478	1635783	1635673	1635673	Missense_Mutation	C	T	p.G562S
PECAPJ41CLONED2_UPPER_AERODIGESTIVE_TRACT	1647785	1647917	1647797	1647797	Missense_Mutation	G	A	p.S149F
AN3CA_ENDOMETRIUM	1647785	1647917	1647806	1647806	Missense_Mutation	C	A	p.R146M
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1647785	1647917	1647809	1647809	Missense_Mutation	G	A	p.A145V
LB373EBV_MATCHED_NORMAL_TISSUE	1647785	1647917	1647902	1647902	Missense_Mutation	A	G	p.V114A
LB373MELD_SKIN	1647785	1647917	1647902	1647902	Missense_Mutation	A	G	p.V114A
JHOS2_OVARY	1653035	1653150	1653110	1653111	Missense_Mutation	CC	TG	p.G51Q
SNU478_BILIARY_TRACT	1653035	1653150	1653110	1653111	Missense_Mutation	CC	TG	p.G51Q
KYSE520_OESOPHAGUS	1653035	1653150	1653110	1653111	Missense_Mutation	CC	TG	p.G51Q
SNU16_STOMACH	1653035	1653150	1653110	1653111	Missense_Mutation	CC	TG	p.G51Q
HCC56_LARGE_INTESTINE	1653035	1653150	1653126	1653126	Missense_Mutation	C	T	p.D46N
HEC108_ENDOMETRIUM	1653035	1653150	1653129	1653129	Missense_Mutation	G	A	p.R45W
SNU886_LIVER	1653035	1653150	1653141	1653141	Missense_Mutation	G	A	p.R41W
NCIH661_LUNG	1653035	1653150	1653141	1653141	Missense_Mutation	G	A	p.R41W
KYSE410_OESOPHAGUS	1653035	1653150	1653061	1653061	Nonsense_Mutation	A	C	p.Y67*
NCIH2342_LUNG	1653035	1653150	1653108	1653108	Nonsense_Mutation	C	A	p.E52*
RCM1_LARGE_INTESTINE	1653035	1653150	1653150	1653150	Splice_Site	A	T	p.S38T

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CDK11A

sQTL information located at the skipped exons.

Exon skip ID

Chromosome

Three exons

Skippped exon

ENST

Cancer type

SNP id

Location

DNA change (ref/var)

P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CDK11A

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CDK11A

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RelatedDrugs for CDK11A

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

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for CDK11A

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 TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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Gene summary for CDK11A

Exon skipping events across known transcript of Ensembl for CDK11A from UCSC genome browser

Gene isoform structures and expression levels for CDK11A

Exon skipping events with PSIs in TCGA for CDK11A

Exon skipping events with PSIs in GTEx for CDK11A

Open reading frame (ORF) annotation in the exon skipping event for CDK11A

Infer the effects of exon skipping event on protein functional features for CDK11A

SNVs in the skipped exons for CDK11A

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CDK11A

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CDK11A

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CDK11A

RelatedDrugs for CDK11A

RelatedDiseases for CDK11A