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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in TCGA

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Exon skipping events with PSIs in GTEx

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

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Exon skipping events in the canonical protein sequence

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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for CDKL3

check button Gene summary
Gene informationGene symbol

CDKL3

Gene ID

51265

Gene namecyclin dependent kinase like 3
SynonymsNKIAMRE
Cytomap

5q31.1

Type of geneprotein-coding
Descriptioncyclin-dependent kinase-like 3serine-threonine protein kinase NKIAMRE
Modification date20180523
UniProtAcc

Q8IVW4

ContextPubMed: CDKL3 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID

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Exon skipping events across known transcript of Ensembl for CDKL3 from UCSC genome browser

check buttonSkipped 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.
all structure

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Gene isoform structures and expression levels for CDKL3

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for CDKL3

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_4442185133622040:133622250:133637830:133637901:133638280:133638378133637830:133637901ENSG00000006837.7ENST00000435240.2,ENST00000520693.1
exon_skip_4442195133634319:133634401:133635346:133635441:133638280:133638378133635346:133635441ENSG00000006837.7ENST00000523054.1
exon_skip_4442205133634319:133634401:133637830:133637901:133638280:133638378133637830:133637901ENSG00000006837.7ENST00000518990.1
exon_skip_4442235133640095:133640258:133642299:133642393:133643828:133644157133642299:133642393ENSG00000006837.7ENST00000536186.1,ENST00000519312.1,ENST00000265334.4,ENST00000435240.2,ENST00000609654.1,ENST00000520693.1,ENST00000521118.1,ENST00000523054.1
exon_skip_4442335133642299:133642393:133643828:133644157:133647982:133648071133643828:133644157ENSG00000006837.7ENST00000519312.1
exon_skip_4442435133643828:133644157:133644264:133644418:133647982:133648071133644264:133644418ENSG00000006837.7ENST00000435211.1,ENST00000536186.1,ENST00000265334.4,ENST00000523832.1,ENST00000609654.1,ENST00000521118.1,ENST00000523054.1
exon_skip_4442445133643828:133644157:133644264:133644418:133655048:133655080133644264:133644418ENSG00000006837.7ENST00000435240.2,ENST00000520592.1,ENST00000520693.1
exon_skip_4442455133643828:133644157:133644264:133644418:133657481:133657594133644264:133644418ENSG00000006837.7ENST00000609383.1
exon_skip_4442485133643828:133644157:133647982:133648071:133655048:133655080133647982:133648071ENSG00000006837.7ENST00000519312.1
exon_skip_4442555133643828:133644157:133657481:133657594:133706688:133706695133657481:133657594ENSG00000006837.7ENST00000521755.1
exon_skip_4442595133644264:133644418:133647982:133648071:133655048:133655080133647982:133648071ENSG00000006837.7ENST00000435211.1,ENST00000265334.4,ENST00000523832.1,ENST00000609654.1,ENST00000521118.1,ENST00000523054.1
exon_skip_4442605133644264:133644418:133647982:133648071:133657481:133657594133647982:133648071ENSG00000006837.7ENST00000536186.1
exon_skip_4442635133644264:133644418:133655048:133655188:133657481:133657594133655048:133655188ENSG00000006837.7ENST00000435240.2,ENST00000520693.1
exon_skip_4442695133644264:133644418:133657481:133657594:133706688:133706695133657481:133657594ENSG00000006837.7ENST00000609383.1
exon_skip_4442785133647982:133648071:133655048:133655188:133657481:133657594133655048:133655188ENSG00000006837.7ENST00000435211.1,ENST00000519312.1,ENST00000265334.4,ENST00000523832.1,ENST00000609654.1,ENST00000521118.1,ENST00000523054.1
exon_skip_4442835133655048:133655188:133657481:133657594:133706688:133706695133657481:133657594ENSG00000006837.7ENST00000519312.1,ENST00000522501.1,ENST00000435240.2,ENST00000520693.1
exon_skip_4442935133657481:133657594:133685939:133686118:133695587:133695782133685939:133686118ENSG00000006837.7ENST00000435211.1,ENST00000265334.4,ENST00000523832.1,ENST00000521118.1,ENST00000523054.1
exon_skip_4443095133685984:133686118:133695587:133695782:133706688:133706695133695587:133695782ENSG00000006837.7ENST00000523054.1

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for CDKL3

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_4442185133622040:133622250:133637830:133637901:133638280:133638378133637830:133637901ENSG00000006837.7ENST00000520693.1,ENST00000435240.2
exon_skip_4442195133634319:133634401:133635346:133635441:133638280:133638378133635346:133635441ENSG00000006837.7ENST00000523054.1
exon_skip_4442205133634319:133634401:133637830:133637901:133638280:133638378133637830:133637901ENSG00000006837.7ENST00000518990.1
exon_skip_4442235133640095:133640258:133642299:133642393:133643828:133644157133642299:133642393ENSG00000006837.7ENST00000609654.1,ENST00000536186.1,ENST00000520693.1,ENST00000435240.2,ENST00000519312.1,ENST00000265334.4,ENST00000523054.1,ENST00000521118.1
exon_skip_4442335133642299:133642393:133643828:133644157:133647982:133648071133643828:133644157ENSG00000006837.7ENST00000519312.1
exon_skip_4442435133643828:133644157:133644264:133644418:133647982:133648071133644264:133644418ENSG00000006837.7ENST00000609654.1,ENST00000536186.1,ENST00000265334.4,ENST00000523054.1,ENST00000521118.1,ENST00000523832.1,ENST00000435211.1
exon_skip_4442445133643828:133644157:133644264:133644418:133655048:133655080133644264:133644418ENSG00000006837.7ENST00000520693.1,ENST00000435240.2,ENST00000520592.1
exon_skip_4442455133643828:133644157:133644264:133644418:133657481:133657594133644264:133644418ENSG00000006837.7ENST00000609383.1
exon_skip_4442485133643828:133644157:133647982:133648071:133655048:133655080133647982:133648071ENSG00000006837.7ENST00000519312.1
exon_skip_4442555133643828:133644157:133657481:133657594:133706688:133706695133657481:133657594ENSG00000006837.7ENST00000521755.1
exon_skip_4442595133644264:133644418:133647982:133648071:133655048:133655080133647982:133648071ENSG00000006837.7ENST00000609654.1,ENST00000265334.4,ENST00000523054.1,ENST00000521118.1,ENST00000523832.1,ENST00000435211.1
exon_skip_4442605133644264:133644418:133647982:133648071:133657481:133657594133647982:133648071ENSG00000006837.7ENST00000536186.1
exon_skip_4442635133644264:133644418:133655048:133655188:133657481:133657594133655048:133655188ENSG00000006837.7ENST00000520693.1,ENST00000435240.2
exon_skip_4442695133644264:133644418:133657481:133657594:133706688:133706695133657481:133657594ENSG00000006837.7ENST00000609383.1
exon_skip_4442785133647982:133648071:133655048:133655188:133657481:133657594133655048:133655188ENSG00000006837.7ENST00000609654.1,ENST00000519312.1,ENST00000265334.4,ENST00000523054.1,ENST00000521118.1,ENST00000523832.1,ENST00000435211.1
exon_skip_4442815133647982:133648071:133657481:133657594:133706688:133706695133657481:133657594ENSG00000006837.7ENST00000536186.1
exon_skip_4442835133655048:133655188:133657481:133657594:133706688:133706695133657481:133657594ENSG00000006837.7ENST00000520693.1,ENST00000435240.2,ENST00000519312.1,ENST00000522501.1
exon_skip_4442935133657481:133657594:133685939:133686118:133695587:133695782133685939:133686118ENSG00000006837.7ENST00000265334.4,ENST00000523054.1,ENST00000521118.1,ENST00000523832.1,ENST00000435211.1
exon_skip_4443075133685939:133686118:133695587:133695782:133702049:133702214133695587:133695782ENSG00000006837.7ENST00000265334.4,ENST00000521118.1,ENST00000523832.1,ENST00000435211.1
exon_skip_4443095133685984:133686118:133695587:133695782:133706688:133706695133695587:133695782ENSG00000006837.7ENST00000523054.1
exon_skip_4443135133695587:133695782:133702049:133702235:133702667:133702761133702049:133702235ENSG00000006837.7ENST00000265334.4,ENST00000521118.1,ENST00000435211.1

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for CDKL3

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST00000265334133642299133642393Frame-shift
ENST00000265334133644264133644418Frame-shift
ENST00000265334133647982133648071Frame-shift
ENST00000265334133655048133655188Frame-shift
ENST00000265334133685939133686118Frame-shift

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000002653341337020491337022353UTR-3CDS
ENST00000265334133642299133642393Frame-shift
ENST00000265334133644264133644418Frame-shift
ENST00000265334133647982133648071Frame-shift
ENST00000265334133655048133655188Frame-shift
ENST00000265334133685939133686118Frame-shift
ENST00000265334133695587133695782In-frame

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Infer the effects of exon skipping event on protein functional features for CDKL3

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

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000265334214459213369558713369578228547955120

check button 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 featureDescription of feature


check button 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 featureDescription of feature
Q8IVW4551206569Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ZDU
Q8IVW4551207274Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ZDU
Q8IVW4551207680Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ZDU
Q8IVW4551208385Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ZDU
Q8IVW4551201592ChainID=PRO_0000085820;Note=Cyclin-dependent kinase-like 3
Q8IVW4551204286DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159
Q8IVW4551204556HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ZDU
Q8IVW4551208692HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ZDU
Q8IVW45512099118HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ZDU


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SNVs in the skipped exons for CDKL3

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

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
LIHCTCGA-DD-A1EG-01exon_skip_444243
exon_skip_444245
exon_skip_444244
133644265133644418133644309133644309Frame_Shift_DelT-p.T331fs
LIHCTCGA-G3-A3CJ-01exon_skip_444243
exon_skip_444245
exon_skip_444244
133644265133644418133644309133644309Frame_Shift_DelT-p.T331fs
LIHCTCGA-G3-A3CJ-01exon_skip_444259
exon_skip_444248
exon_skip_444260
133647983133648071133648022133648022Frame_Shift_DelA-p.L281fs
LIHCTCGA-DD-A3A0-01exon_skip_444293
133685940133686118133686084133686084Frame_Shift_DelA-p.L132fs
LIHCTCGA-G3-A3CJ-01exon_skip_444293
133685940133686118133686098133686098Frame_Shift_DelT-p.K127fs
UCECTCGA-B5-A0K9-01exon_skip_444293
133685940133686118133686098133686098Frame_Shift_DelT-p.K127fs
LGGTCGA-HT-7477-01exon_skip_444309
133695588133695782133695594133695594Frame_Shift_DelA-p.S118fs
BLCATCGA-FD-A6TE-01exon_skip_444309
133695588133695782133695761133695761Frame_Shift_DelC-p.V63fs
LIHCTCGA-DD-A39Y-01exon_skip_444309
133695588133695782133695766133695766Frame_Shift_DelT-p.N61fs
HNSCTCGA-T2-A6X2-01exon_skip_444233
133643829133644157133644119133644119Nonsense_MutationGAp.Q42*
BLCATCGA-XF-A9T6-01exon_skip_444293
133685940133686118133685984133685984Nonsense_MutationCTp.W165*
READTCGA-F5-6814-01exon_skip_444309
133695588133695782133695617133695617Nonsense_MutationGAp.R111X
UCECTCGA-BS-A0UV-01exon_skip_444309
133695588133695782133695617133695617Nonsense_MutationGAp.R111*
STADTCGA-BR-8589-01exon_skip_444255
exon_skip_444283
exon_skip_444269
133657482133657594133657596133657596Splice_SiteTC.
STADTCGA-BR-8589-01exon_skip_444255
exon_skip_444283
exon_skip_444269
133657482133657594133657596133657596Splice_SiteTCp.K180_splice

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
DOTC24510_CERVIX133655049133655188133655149133655149Frame_Shift_DelC-p.S231fs
MDAMB436_BREAST133655049133655188133655167133655185Frame_Shift_DelTGCAAGTGAGGTGACAAAT-p.NLSPHLQ219fs
HS675T_FIBROBLAST133695588133695782133695604133695605Frame_Shift_Ins-Ap.Y115fs
RERFLCFM_LUNG133642300133642393133642336133642336Missense_MutationCTp.M474I
SNU1_STOMACH133642300133642393133642367133642367Missense_MutationCTp.R464H
SNU81_LARGE_INTESTINE133643829133644157133643848133643848Missense_MutationGTp.L449I
OVTOKO_OVARY133643829133644157133644028133644028Missense_MutationCGp.E389Q
KYSE510_OESOPHAGUS133643829133644157133644033133644033Missense_MutationGAp.A387V
SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE133643829133644157133644043133644043Missense_MutationGCp.Q384E
HEC151_ENDOMETRIUM133643829133644157133644100133644100Missense_MutationCGp.G365R
OVTOKO_OVARY133643829133644157133644145133644145Missense_MutationCGp.E350Q
SKGIIIA_CERVIX133644265133644418133644314133644314Missense_MutationCAp.R329I
HCC2998_LARGE_INTESTINE133647983133648071133647992133647992Missense_MutationACp.F291C
HEC251_ENDOMETRIUM133647983133648071133647992133647993Missense_MutationAACGp.F291R
HEC251_ENDOMETRIUM133647983133648071133647993133647993Missense_MutationAGp.F291L
SNU1040_LARGE_INTESTINE133647983133648071133647995133647995Missense_MutationCTp.G290E
MDAMB436_BREAST133655049133655188133655062133655062Missense_MutationGAp.A260V
BIN67_OVARY133655049133655188133655095133655095Missense_MutationCTp.R249K
CME1_SOFT_TISSUE133655049133655188133655095133655095Missense_MutationCTp.R249K
COGN278_AUTONOMIC_GANGLIA133655049133655188133655095133655095Missense_MutationCTp.R249K
RH41_SOFT_TISSUE133655049133655188133655095133655095Missense_MutationCTp.R249K
SCMCRM2_SOFT_TISSUE133655049133655188133655095133655095Missense_MutationCTp.R249K
SCS214_SOFT_TISSUE133655049133655188133655095133655095Missense_MutationCTp.R249K
CME1_SOFT_TISSUE133655049133655188133655098133655098Missense_MutationGTp.A248E
SH10TC_STOMACH133655049133655188133655134133655134Missense_MutationCAp.G236V
WM793_SKIN133655049133655188133655155133655155Missense_MutationGAp.S229F
JHU028_LUNG133655049133655188133655166133655166Missense_MutationCAp.Q225H
HEC251_ENDOMETRIUM133685940133686118133685949133685949Missense_MutationGTp.S177Y
NCIH661_LUNG133685940133686118133685988133685988Missense_MutationCTp.R164H
SNU81_LARGE_INTESTINE133685940133686118133686022133686022Missense_MutationGAp.P153S
RH28_SOFT_TISSUE133685940133686118133686055133686055Missense_MutationACp.C142G
NH6_AUTONOMIC_GANGLIA133695588133695782133695607133695607Missense_MutationTAp.D114V
253J_URINARY_TRACT133695588133695782133695646133695646Missense_MutationCTp.R101Q
253JBV_URINARY_TRACT133695588133695782133695646133695646Missense_MutationCTp.R101Q
MFE319_ENDOMETRIUM133695588133695782133695650133695650Missense_MutationTCp.K100E
SNU81_LARGE_INTESTINE133695588133695782133695706133695706Missense_MutationACp.F81C
EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE133695588133695782133695771133695771Missense_MutationGTp.H59Q
HCC2998_LARGE_INTESTINE133644265133644418133644365133644365Nonsense_MutationACp.L312*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CDKL3

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CDKL3


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CDKL3


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RelatedDrugs for CDKL3

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for CDKL3

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource