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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 PSTK

check button Gene summary
Gene informationGene symbol

PSTK

Gene ID

118672

Gene namephosphoseryl-tRNA kinase
SynonymsC10orf89
Cytomap

10q26.13

Type of geneprotein-coding
DescriptionL-seryl-tRNA(Sec) kinaseO-phosphoseryl-tRNA(Sec) kinase
Modification date20180524
UniProtAcc

Q8IV42

ContextPubMed: PSTK [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 PSTK 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 PSTK

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 PSTK

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_4581910124740046:124740211:124742248:124742540:124742787:124742986124742248:124742540ENSG00000179988.9ENST00000406217.2,ENST00000368887.3,ENST00000405485.1
exon_skip_4582110124742805:124742986:124745815:124745891:124746384:124746478124745815:124745891ENSG00000179988.9ENST00000406217.2,ENST00000368887.3,ENST00000483455.1,ENST00000496079.1,ENST00000497219.1
exon_skip_4582210124742805:124742986:124745815:124745891:124749689:124749851124745815:124745891ENSG00000179988.9ENST00000483755.1
exon_skip_4582410124742805:124742986:124745815:124747020:124749689:124749851124745815:124747020ENSG00000179988.9ENST00000405485.1
exon_skip_4583210124745815:124745891:124746384:124746478:124749689:124749851124746384:124746478ENSG00000179988.9ENST00000406217.2,ENST00000483455.1,ENST00000496079.1,ENST00000465232.1
exon_skip_4583710124746384:124746478:124746849:124747020:124749689:124749851124746849:124747020ENSG00000179988.9ENST00000368887.3,ENST00000497219.1

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

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Exon skipping events with PSIs in GTEx for PSTK

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_4581910124740046:124740211:124742248:124742540:124742787:124742986124742248:124742540ENSG00000179988.9ENST00000368887.3,ENST00000405485.1,ENST00000406217.2
exon_skip_4582110124742805:124742986:124745815:124745891:124746384:124746478124745815:124745891ENSG00000179988.9ENST00000368887.3,ENST00000406217.2,ENST00000483455.1,ENST00000497219.1,ENST00000496079.1
exon_skip_4582210124742805:124742986:124745815:124745891:124749689:124749851124745815:124745891ENSG00000179988.9ENST00000483755.1
exon_skip_4582410124742805:124742986:124745815:124747020:124749689:124749851124745815:124747020ENSG00000179988.9ENST00000405485.1
exon_skip_4583210124745815:124745891:124746384:124746478:124749689:124749851124746384:124746478ENSG00000179988.9ENST00000465232.1,ENST00000406217.2,ENST00000483455.1,ENST00000496079.1
exon_skip_4583710124746384:124746478:124746849:124747020:124749689:124749851124746849:124747020ENSG00000179988.9ENST00000368887.3,ENST00000497219.1

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 PSTK

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
ENST000004054851247458151247470203UTR-3CDS
ENST000003688871247468491247470203UTR-3CDS
ENST00000368887124742248124742540Frame-shift
ENST00000405485124742248124742540Frame-shift
ENST00000368887124745815124745891Frame-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
ENST000004054851247458151247470203UTR-3CDS
ENST000003688871247468491247470203UTR-3CDS
ENST00000368887124742248124742540Frame-shift
ENST00000405485124742248124742540Frame-shift
ENST00000368887124745815124745891Frame-shift

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

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

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


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SNVs in the skipped exons for PSTK

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.
PSTK_LIHC_exon_skip_45824_psi_boxplot.png
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PSTK_LUAD_exon_skip_45837_psi_boxplot.png
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check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
LIHCTCGA-G3-A3CJ-01exon_skip_45819
124742249124742540124742321124742321Frame_Shift_DelG-p.G97fs
LIHCTCGA-DD-A1EG-01exon_skip_45819
124742249124742540124742364124742364Frame_Shift_DelG-p.W111fs
LIHCTCGA-DD-A1EG-01exon_skip_45819
124742249124742540124742446124742446Frame_Shift_DelA-p.T138fs
LIHCTCGA-DD-A1EG-01exon_skip_45819
124742249124742540124742491124742491Frame_Shift_DelT-p.N153fs
LIHCTCGA-DD-A39Y-01exon_skip_45819
124742249124742540124742491124742491Frame_Shift_DelT-p.N153fs
LIHCTCGA-DD-A3A0-01exon_skip_45819
124742249124742540124742491124742491Frame_Shift_DelT-p.N153fs
LIHCTCGA-G3-A3CJ-01exon_skip_45819
124742249124742540124742491124742491Frame_Shift_DelT-p.N153fs
LIHCTCGA-DD-A39Y-01exon_skip_45821
exon_skip_45822
124745816124745891124745831124745831Frame_Shift_DelT-p.D241fs
LIHCTCGA-DD-A39Y-01exon_skip_45824
124745816124747020124745831124745831Frame_Shift_DelT-p.D241fs
LIHCTCGA-G3-A3CJ-01exon_skip_45821
exon_skip_45822
124745816124745891124745851124745851Frame_Shift_DelA-p.E248fs
LIHCTCGA-G3-A3CJ-01exon_skip_45824
124745816124747020124745851124745851Frame_Shift_DelA-p.E248fs
LUADTCGA-55-7570-01exon_skip_45824
124745816124747020124747013124747013Frame_Shift_DelG-p.T347fs
LUADTCGA-55-7570-01exon_skip_45837
124746850124747020124747013124747013Frame_Shift_DelG-p.T347fs
LIHCTCGA-BC-A112-01exon_skip_45819
124742249124742540124742320124742321Frame_Shift_Ins-Gp.V97fs
BLCATCGA-DK-A6B2-01exon_skip_45819
124742249124742540124742270124742270Nonsense_MutationCTp.R80*
KIRCTCGA-B0-5085-01exon_skip_45819
124742249124742540124742525124742525Nonsense_MutationCTp.Q165*
KIRCTCGA-B0-5085-01exon_skip_45819
124742249124742540124742525124742525Nonsense_MutationCTp.Q165X

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
PSTK_124746384_124746478_124746849_124747020_124749689_124749851_TCGA-55-7570-01Sample: TCGA-55-7570-01
Cancer type: LUAD
ESID: exon_skip_45837
Skipped exon start: 124746850
Skipped exon end: 124747020
Mutation start: 124747013
Mutation end: 124747013
Mutation type: Frame_Shift_Del
Reference seq: G
Mutation seq: -
AAchange: p.T347fs
PSTK_124746384_124746478_124746849_124747020_124749689_124749851_TCGA-55-7570-01Sample: TCGA-55-7570-01
Cancer type: LUAD
ESID: exon_skip_45824
Skipped exon start: 124745816
Skipped exon end: 124747020
Mutation start: 124747013
Mutation end: 124747013
Mutation type: Frame_Shift_Del
Reference seq: G
Mutation seq: -
AAchange: p.T347fs
exon_skip_45824_LUAD_TCGA-55-7570-01.png
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exon_skip_45837_LUAD_TCGA-55-7570-01.png
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exon_skip_514168_LUAD_TCGA-55-7570-01.png
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PSTK_124742805_124742986_124745815_124747020_124749689_124749851_TCGA-DD-A39Y-01Sample: TCGA-DD-A39Y-01
Cancer type: LIHC
ESID: exon_skip_45819
Skipped exon start: 124742249
Skipped exon end: 124742540
Mutation start: 124742491
Mutation end: 124742491
Mutation type: Frame_Shift_Del
Reference seq: T
Mutation seq: -
AAchange: p.N153fs
PSTK_124742805_124742986_124745815_124747020_124749689_124749851_TCGA-DD-A39Y-01Sample: TCGA-DD-A39Y-01
Cancer type: LIHC
ESID: exon_skip_45824
Skipped exon start: 124745816
Skipped exon end: 124747020
Mutation start: 124745831
Mutation end: 124745831
Mutation type: Frame_Shift_Del
Reference seq: T
Mutation seq: -
AAchange: p.D241fs
PSTK_124742805_124742986_124745815_124747020_124749689_124749851_TCGA-DD-A39Y-01Sample: TCGA-DD-A39Y-01
Cancer type: LIHC
ESID: exon_skip_45822
Skipped exon start: 124745816
Skipped exon end: 124745891
Mutation start: 124745831
Mutation end: 124745831
Mutation type: Frame_Shift_Del
Reference seq: T
Mutation seq: -
AAchange: p.D241fs
exon_skip_105023_LIHC_TCGA-DD-A39Y-01.png
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PSTK_124742805_124742986_124745815_124747020_124749689_124749851_TCGA-G3-A3CJ-01Sample: TCGA-G3-A3CJ-01
Cancer type: LIHC
ESID: exon_skip_45819
Skipped exon start: 124742249
Skipped exon end: 124742540
Mutation start: 124742321
Mutation end: 124742321
Mutation type: Frame_Shift_Del
Reference seq: G
Mutation seq: -
AAchange: p.G97fs
PSTK_124742805_124742986_124745815_124747020_124749689_124749851_TCGA-G3-A3CJ-01Sample: TCGA-G3-A3CJ-01
Cancer type: LIHC
ESID: exon_skip_45819
Skipped exon start: 124742249
Skipped exon end: 124742540
Mutation start: 124742491
Mutation end: 124742491
Mutation type: Frame_Shift_Del
Reference seq: T
Mutation seq: -
AAchange: p.N153fs
PSTK_124742805_124742986_124745815_124747020_124749689_124749851_TCGA-G3-A3CJ-01Sample: TCGA-G3-A3CJ-01
Cancer type: LIHC
ESID: exon_skip_45824
Skipped exon start: 124745816
Skipped exon end: 124747020
Mutation start: 124745851
Mutation end: 124745851
Mutation type: Frame_Shift_Del
Reference seq: A
Mutation seq: -
AAchange: p.E248fs
PSTK_124742805_124742986_124745815_124747020_124749689_124749851_TCGA-G3-A3CJ-01Sample: TCGA-G3-A3CJ-01
Cancer type: LIHC
ESID: exon_skip_45822
Skipped exon start: 124745816
Skipped exon end: 124745891
Mutation start: 124745851
Mutation end: 124745851
Mutation type: Frame_Shift_Del
Reference seq: A
Mutation seq: -
AAchange: p.E248fs
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PSTK_124742805_124742986_124745815_124747020_124749689_124749851_TCGA-55-7570-01Sample: TCGA-55-7570-01
Cancer type: LUAD
ESID: exon_skip_45837
Skipped exon start: 124746850
Skipped exon end: 124747020
Mutation start: 124747013
Mutation end: 124747013
Mutation type: Frame_Shift_Del
Reference seq: G
Mutation seq: -
AAchange: p.T347fs
PSTK_124742805_124742986_124745815_124747020_124749689_124749851_TCGA-55-7570-01Sample: TCGA-55-7570-01
Cancer type: LUAD
ESID: exon_skip_45824
Skipped exon start: 124745816
Skipped exon end: 124747020
Mutation start: 124747013
Mutation end: 124747013
Mutation type: Frame_Shift_Del
Reference seq: G
Mutation seq: -
AAchange: p.T347fs
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check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
HCT116_LARGE_INTESTINE124746385124746478124746474124746474Frame_Shift_DelA-p.A291fs
HCT116_LARGE_INTESTINE124745816124747020124746474124746474Frame_Shift_DelA-p.A291fs
MDAMB435S_SKIN124742249124742540124742264124742264Missense_MutationTGp.L78V
SNUC2A_LARGE_INTESTINE124742249124742540124742361124742361Missense_MutationTCp.M110T
SNUC2B_LARGE_INTESTINE124742249124742540124742361124742361Missense_MutationTCp.M110T
SLR23_KIDNEY124742249124742540124742407124742407Missense_MutationTGp.F125L
LS411N_LARGE_INTESTINE124746385124746478124746449124746449Missense_MutationTCp.I283T
LS411N_LARGE_INTESTINE124745816124747020124746449124746449Missense_MutationTCp.I283T
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE124746850124747020124746904124746904Missense_MutationAGp.N311S
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE124745816124747020124746904124746904Missense_MutationAGp.N311S
GP2D_LARGE_INTESTINE124746850124747020124746904124746904Missense_MutationAGp.N311S
GP2D_LARGE_INTESTINE124745816124747020124746904124746904Missense_MutationAGp.N311S
GP5D_LARGE_INTESTINE124746850124747020124746904124746904Missense_MutationAGp.N311S
GP5D_LARGE_INTESTINE124745816124747020124746904124746904Missense_MutationAGp.N311S
TGBC11TKB_STOMACH124746850124747020124746960124746960Missense_MutationGAp.A330T
TGBC11TKB_STOMACH124745816124747020124746960124746960Missense_MutationGAp.A330T
SKMEL1_SKIN124742249124742540124742260124742260Nonsense_MutationGAp.W76*
HCC56_LARGE_INTESTINE124742249124742540124742270124742270Nonsense_MutationCTp.R80*

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

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value
exon_skip_4582410124742805:124742986:124745815:124747020:124749689:124749851124745815:124747020ENST00000405485.1LGGrs7096614chr10:124746801T/G4.75e-04
exon_skip_4582410124742805:124742986:124745815:124747020:124749689:124749851124745815:124747020ENST00000405485.1LGGrs7096614chr10:124746801T/G3.81e-03

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


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


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RelatedDrugs for PSTK

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 PSTK

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