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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 SPHK2

check button Gene summary
Gene informationGene symbol

SPHK2

Gene ID

56848

Gene namesphingosine kinase 2
SynonymsSK 2|SK-2|SPK 2|SPK-2
Cytomap

19q13.33

Type of geneprotein-coding
Descriptionsphingosine kinase 2sphingosine kinase type 2
Modification date20180519
UniProtAcc

Q9NRA0

ContextPubMed: SPHK2 [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 SPHK2 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 SPHK2

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 SPHK2

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3089101949122708:49122800:49123658:49123810:49129147:4912943249123658:49123810ENSG00000063176.11ENST00000340932.3
exon_skip_3089111949123771:49123810:49129147:49129619:49130948:4913109849129147:49129619ENSG00000063176.11ENST00000598088.1,ENST00000245222.4,ENST00000340932.3
exon_skip_3089121949123658:49123810:49129206:49129619:49130948:4913109849129206:49129619ENSG00000063176.11ENST00000601712.1
exon_skip_3089131949123771:49123810:49129324:49129619:49130948:4913109849129324:49129619ENSG00000063176.11ENST00000600537.1
exon_skip_3089151949130948:49131098:49131231:49131326:49131418:4913153449131231:49131326ENSG00000063176.11ENST00000598088.1,ENST00000599748.1,ENST00000600537.1,ENST00000443164.1,ENST00000245222.4,ENST00000601712.1,ENST00000340932.3,ENST00000597434.1,ENST00000599029.1,ENST00000426514.2
exon_skip_3089191949131418:49131534:49131937:49132983:49133690:4913397349131937:49132983ENSG00000063176.11ENST00000443164.1,ENST00000599029.1

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

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Exon skipping events with PSIs in GTEx for SPHK2

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3089101949122708:49122800:49123658:49123810:49129147:4912943249123658:49123810ENSG00000063176.11ENST00000340932.3
exon_skip_3089111949123771:49123810:49129147:49129619:49130948:4913109849129147:49129619ENSG00000063176.11ENST00000245222.4,ENST00000340932.3,ENST00000598088.1
exon_skip_3089121949123658:49123810:49129206:49129619:49130948:4913109849129206:49129619ENSG00000063176.11ENST00000601712.1
exon_skip_3089131949123771:49123810:49129324:49129619:49130948:4913109849129324:49129619ENSG00000063176.11ENST00000600537.1
exon_skip_3089151949130948:49131098:49131231:49131326:49131418:4913153449131231:49131326ENSG00000063176.11ENST00000245222.4,ENST00000340932.3,ENST00000601712.1,ENST00000600537.1,ENST00000598088.1,ENST00000426514.2,ENST00000597434.1,ENST00000599748.1,ENST00000443164.1,ENST00000599029.1
exon_skip_3089191949131418:49131534:49131937:49132983:49133690:4913397349131937:49132983ENSG00000063176.11ENST00000443164.1,ENST00000599029.1

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 SPHK2

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
ENST000002452224912914749129619Frame-shift
ENST000005980884912914749129619Frame-shift
ENST000002452224913123149131326Frame-shift
ENST000005980884913123149131326Frame-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
ENST000002452224912914749129619Frame-shift
ENST000005980884912914749129619Frame-shift
ENST000002452224913123149131326Frame-shift
ENST000005980884913123149131326Frame-shift

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Infer the effects of exon skipping event on protein functional features for SPHK2

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 SPHK2

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.
SPHK2_CESC_exon_skip_308919_psi_boxplot.png
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SPHK2_LIHC_exon_skip_308911_psi_boxplot.png
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SPHK2_STAD_exon_skip_308911_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_308911
49129148491296194912928749129287Frame_Shift_DelC-p.A122fs
LIHCTCGA-G3-A3CJ-01exon_skip_308912
49129207491296194912928749129287Frame_Shift_DelC-p.A122fs
STADTCGA-B7-A5TI-01exon_skip_308911
49129148491296194912931149129311Frame_Shift_DelC-p.T130fs
STADTCGA-B7-A5TI-01exon_skip_308912
49129207491296194912931149129311Frame_Shift_DelC-p.T130fs
LIHCTCGA-DD-A1EG-01exon_skip_308911
49129148491296194912936749129367Frame_Shift_DelC-p.P149fs
LIHCTCGA-DD-A1EG-01exon_skip_308912
49129207491296194912936749129367Frame_Shift_DelC-p.P149fs
LIHCTCGA-DD-A1EG-01exon_skip_308913
49129325491296194912936749129367Frame_Shift_DelC-p.P149fs
LIHCTCGA-DD-A3A0-01exon_skip_308919
49131938491329834913223149132231Frame_Shift_DelC-p.T451fs
LIHCTCGA-DD-A39Y-01exon_skip_308919
49131938491329834913228849132288Frame_Shift_DelC-p.A470fs
LIHCTCGA-G3-A3CJ-01exon_skip_308919
49131938491329834913234749132347Frame_Shift_DelC-p.L427fs
LIHCTCGA-G3-A3CJ-01exon_skip_308919
49131938491329834913234749132347Frame_Shift_DelC-p.P490fs
CESCTCGA-DS-A1OB-01exon_skip_308919
49131938491329834913237949132380Frame_Shift_DelAG-p.PE500fs
CESCTCGA-DS-A1OC-01exon_skip_308919
49131938491329834913237949132380Frame_Shift_DelAG-p.PE500fs
CESCTCGA-DS-A1OD-01exon_skip_308919
49131938491329834913237949132380Frame_Shift_DelAG-p.PE500fs
COADTCGA-AD-6964-01exon_skip_308919
49131938491329834913253449132534Frame_Shift_DelC-p.A490fs
SARCTCGA-DX-A3M2-01exon_skip_308911
49129148491296194912928949129289Nonsense_MutationCTp.R123*
SARCTCGA-DX-A3M2-01exon_skip_308912
49129207491296194912928949129289Nonsense_MutationCTp.R123*
BLCATCGA-DK-A3X1-01exon_skip_308919
49131938491329834913230649132306Nonsense_MutationCAp.S414*
BLCATCGA-DK-A3X1-01exon_skip_308919
49131938491329834913230649132306Nonsense_MutationCAp.S476*
KIRPTCGA-GL-A9DC-01exon_skip_308919
49131938491329834913277449132774Nonsense_MutationGAp.W570X
CHOLTCGA-W5-AA39-01exon_skip_308919
49131938491329834913294949132949Nonsense_MutationTAp.Y690*

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
SPHK2_49131418_49131534_49131937_49132983_49133690_49133973_TCGA-DS-A1OD-01Sample: TCGA-DS-A1OD-01
Cancer type: CESC
ESID: exon_skip_308919
Skipped exon start: 49131938
Skipped exon end: 49132983
Mutation start: 49132379
Mutation end: 49132380
Mutation type: Frame_Shift_Del
Reference seq: AG
Mutation seq: -
AAchange: p.PE500fs
exon_skip_308919_CESC_TCGA-DS-A1OD-01.png
boxplot
SPHK2_49123771_49123810_49129147_49129619_49130948_49131098_TCGA-DD-A1EG-01Sample: TCGA-DD-A1EG-01
Cancer type: LIHC
ESID: exon_skip_308912
Skipped exon start: 49129207
Skipped exon end: 49129619
Mutation start: 49129367
Mutation end: 49129367
Mutation type: Frame_Shift_Del
Reference seq: C
Mutation seq: -
AAchange: p.P149fs
SPHK2_49123771_49123810_49129147_49129619_49130948_49131098_TCGA-DD-A1EG-01Sample: TCGA-DD-A1EG-01
Cancer type: LIHC
ESID: exon_skip_308913
Skipped exon start: 49129325
Skipped exon end: 49129619
Mutation start: 49129367
Mutation end: 49129367
Mutation type: Frame_Shift_Del
Reference seq: C
Mutation seq: -
AAchange: p.P149fs
SPHK2_49123771_49123810_49129147_49129619_49130948_49131098_TCGA-DD-A1EG-01Sample: TCGA-DD-A1EG-01
Cancer type: LIHC
ESID: exon_skip_308911
Skipped exon start: 49129148
Skipped exon end: 49129619
Mutation start: 49129367
Mutation end: 49129367
Mutation type: Frame_Shift_Del
Reference seq: C
Mutation seq: -
AAchange: p.P149fs
exon_skip_103075_LIHC_TCGA-DD-A1EG-01.png
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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
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49131938491329834913253449132534Frame_Shift_DelC-p.A490fs
SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49131938491329834913267049132670Frame_Shift_DelG-p.E535fs
451LU_SKIN49129207491296194912947749129488In_Frame_DelCCGGCGCGGGGC-p.RRGA124del
451LU_SKIN49129325491296194912947749129488In_Frame_DelCCGGCGCGGGGC-p.RRGA124del
451LU_SKIN49129148491296194912947749129488In_Frame_DelCCGGCGCGGGGC-p.RRGA124del
SF172_CENTRAL_NERVOUS_SYSTEM49123659491238104912380049123800Missense_MutationATp.Q10L
SMZ1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49129207491296194912923349129233Missense_MutationCTp.P42L
SMZ1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49129148491296194912923349129233Missense_MutationCTp.P42L
ME1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49129207491296194912923349129233Missense_MutationCTp.P42L
ME1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49129148491296194912923349129233Missense_MutationCTp.P42L
SNU175_LARGE_INTESTINE49129207491296194912923349129233Missense_MutationCTp.P42L
SNU175_LARGE_INTESTINE49129148491296194912923349129233Missense_MutationCTp.P42L
NY_BONE49129207491296194912923349129233Missense_MutationCTp.P42L
NY_BONE49129148491296194912923349129233Missense_MutationCTp.P42L
KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49129207491296194912923349129233Missense_MutationCTp.P42L
KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49129148491296194912923349129233Missense_MutationCTp.P42L
SNU1040_LARGE_INTESTINE49129207491296194912932649129326Missense_MutationCTp.A73V
SNU1040_LARGE_INTESTINE49129325491296194912932649129326Missense_MutationCTp.A73V
SNU1040_LARGE_INTESTINE49129148491296194912932649129326Missense_MutationCTp.A73V
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49129207491296194912932949129329Missense_MutationTCp.L74P
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49129325491296194912932949129329Missense_MutationTCp.L74P
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49129148491296194912932949129329Missense_MutationTCp.L74P
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49129207491296194912937049129370Missense_MutationCGp.R88G
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49129325491296194912937049129370Missense_MutationCGp.R88G
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49129148491296194912937049129370Missense_MutationCGp.R88G
LAMA84_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49129207491296194912941249129412Missense_MutationACp.T102P
LAMA84_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49129325491296194912941249129412Missense_MutationACp.T102P
LAMA84_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49129148491296194912941249129412Missense_MutationACp.T102P
EW24_BONE49129207491296194912944349129443Missense_MutationCTp.A112V
EW24_BONE49129325491296194912944349129443Missense_MutationCTp.A112V
EW24_BONE49129148491296194912944349129443Missense_MutationCTp.A112V
IGROV1_OVARY49129207491296194912950049129500Missense_MutationCAp.A131D
IGROV1_OVARY49129325491296194912950049129500Missense_MutationCAp.A131D
IGROV1_OVARY49129148491296194912950049129500Missense_MutationCAp.A131D
CHLA06ATRT_SOFT_TISSUE49129207491296194912954849129548Missense_MutationGAp.R147H
CHLA06ATRT_SOFT_TISSUE49129325491296194912954849129548Missense_MutationGAp.R147H
CHLA06ATRT_SOFT_TISSUE49129148491296194912954849129548Missense_MutationGAp.R147H
EFO27_OVARY49131232491313264913124949131249Missense_MutationCTp.R227W
HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49131232491313264913125049131250Missense_MutationGAp.R227Q
KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49131938491329834913209549132095Missense_MutationGCp.D344H
HCT15_LARGE_INTESTINE49131938491329834913210449132104Missense_MutationATp.S347C
RL952_ENDOMETRIUM49131938491329834913231849132318Missense_MutationGAp.R418H
LS411N_LARGE_INTESTINE49131938491329834913235149132351Missense_MutationAGp.Q429R
SNU175_LARGE_INTESTINE49131938491329834913239549132395Missense_MutationCGp.L444V
SNU1040_LARGE_INTESTINE49131938491329834913241149132411Missense_MutationGTp.G449V
EW8_BONE49131938491329834913245649132456Missense_MutationCAp.P464Q
RH1_SOFT_TISSUE49131938491329834913245649132456Missense_MutationCAp.P464Q
SNU213_PANCREAS49131938491329834913249549132495Missense_MutationCTp.S477F
ECGI10_OESOPHAGUS49131938491329834913255249132552Missense_MutationCTp.S496F
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49131938491329834913261449132614Missense_MutationGCp.D517H
FLO1_OESOPHAGUS49131938491329834913265049132650Missense_MutationCTp.P529S
HCC2279_LUNG49131938491329834913267249132672Missense_MutationGCp.G536A
TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49131938491329834913267549132675Missense_MutationAGp.D537G
P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49131938491329834913272549132725Missense_MutationGCp.V554L
SAS_UPPER_AERODIGESTIVE_TRACT49131938491329834913272549132725Missense_MutationGCp.V554L
NCIH2342_LUNG49131938491329834913275349132753Missense_MutationAGp.D563G
MMACSF_SKIN49131938491329834913278049132780Missense_MutationGAp.R572H
HCT15_LARGE_INTESTINE49131938491329834913283049132830Missense_MutationCTp.R589C
HEC59_ENDOMETRIUM49131938491329834913286249132862Missense_MutationGTp.Q599H
HEC251_ENDOMETRIUM49131938491329834913287549132875Missense_MutationGAp.A604T
REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE49131938491329834913297449132974Missense_MutationCAp.P637T
JHUEM1_ENDOMETRIUM49131938491329834913193949131939Splice_SiteTGp.F292V

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SPHK2

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 SPHK2


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SPHK2


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RelatedDrugs for SPHK2

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 SPHK2

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
SPHK2C0025261Memory Disorders1CTD_human
SPHK2C0740392Infarction, Middle Cerebral Artery1CTD_human