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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 SIPA1L3

check button Gene summary
Gene informationGene symbol

SIPA1L3

Gene ID

23094

Gene namesignal induced proliferation associated 1 like 3
SynonymsCTRCT45|SPAL3|SPAR3
Cytomap

19q13.13-q13.2

Type of geneprotein-coding
Descriptionsignal-induced proliferation-associated 1-like protein 3SIPA1-like protein 3SPA-1-like protein 3
Modification date20180519
UniProtAcc

O60292

ContextPubMed: SIPA1L3 [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
SIPA1L3

GO:0003382

epithelial cell morphogenesis

26231217

SIPA1L3

GO:0090162

establishment of epithelial cell polarity

26231217


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Exon skipping events across known transcript of Ensembl for SIPA1L3 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 SIPA1L3

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 SIPA1L3

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3064131938422985:38423332:38519728:38519796:38571895:3857208838519728:38519796ENSG00000105738.6ENST00000476317.2
exon_skip_3064151938519728:38519796:38571895:38573739:38579360:3857949138571895:38573739ENSG00000105738.6ENST00000222345.6
exon_skip_3064181938591691:38591866:38597176:38597280:38600866:3860095538597176:38597280ENSG00000105738.6ENST00000222345.6
exon_skip_3064231938610472:38610522:38621137:38621412:38631823:3863207538621137:38621412ENSG00000105738.6ENST00000222345.6
exon_skip_3064251938631823:38632075:38633212:38633350:38643479:3864360738633212:38633350ENSG00000105738.6ENST00000222345.6
exon_skip_3064261938633212:38633350:38643479:38643607:38652892:3865301138643479:38643607ENSG00000105738.6ENST00000222345.6
exon_skip_3064271938643479:38643607:38652892:38653011:38655118:3865554638652892:38653011ENSG00000105738.6ENST00000222345.6
exon_skip_3064281938655410:38655546:38673158:38673380:38682784:3868295038673158:38673380ENSG00000105738.6ENST00000222345.6
exon_skip_3064301938664265:38664312:38673158:38673380:38682784:3868295038673158:38673380ENSG00000105738.6ENST00000601054.1
exon_skip_3064321938682784:38682950:38684176:38684420:38689028:3868917238684176:38684420ENSG00000105738.6ENST00000222345.6
exon_skip_3064331938684176:38684420:38689028:38689172:38692501:3869263738689028:38689172ENSG00000105738.6ENST00000222345.6
exon_skip_3064361938689028:38689172:38692501:38692637:38694766:3869484838692501:38692637ENSG00000105738.6ENST00000222345.6

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

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Exon skipping events with PSIs in GTEx for SIPA1L3

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3064171938591691:38591866:38596928:38597280:38600866:3860095538596928:38597280ENSG00000105738.6ENST00000595384.1
exon_skip_3064181938591691:38591866:38597176:38597280:38600866:3860095538597176:38597280ENSG00000105738.6ENST00000222345.6
exon_skip_3064231938610472:38610522:38621137:38621412:38631823:3863207538621137:38621412ENSG00000105738.6ENST00000222345.6
exon_skip_3064251938631823:38632075:38633212:38633350:38643479:3864360738633212:38633350ENSG00000105738.6ENST00000222345.6
exon_skip_3064271938643479:38643607:38652892:38653011:38655118:3865554638652892:38653011ENSG00000105738.6ENST00000222345.6
exon_skip_3064281938655410:38655546:38673158:38673380:38682784:3868295038673158:38673380ENSG00000105738.6ENST00000222345.6
exon_skip_3064301938664265:38664312:38673158:38673380:38682784:3868295038673158:38673380ENSG00000105738.6ENST00000601054.1
exon_skip_3064321938682784:38682950:38684176:38684420:38689028:3868917238684176:38684420ENSG00000105738.6ENST00000222345.6
exon_skip_3064331938684176:38684420:38689028:38689172:38692501:3869263738689028:38689172ENSG00000105738.6ENST00000222345.6
exon_skip_3064361938689028:38689172:38692501:38692637:38694766:3869484838692501:38692637ENSG00000105738.6ENST00000222345.6

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 SIPA1L3

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
ENST0000022234538571895385737395CDS-5UTR
ENST000002223453859717638597280Frame-shift
ENST000002223453862113738621412Frame-shift
ENST000002223453864347938643607Frame-shift
ENST000002223453865289238653011Frame-shift
ENST000002223453868417638684420Frame-shift
ENST000002223453869250138692637Frame-shift
ENST000002223453863321238633350In-frame
ENST000002223453867315838673380In-frame
ENST000002223453868902838689172In-frame

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
ENST000002223453859717638597280Frame-shift
ENST000002223453862113738621412Frame-shift
ENST000002223453865289238653011Frame-shift
ENST000002223453868417638684420Frame-shift
ENST000002223453869250138692637Frame-shift
ENST000002223453863321238633350In-frame
ENST000002223453867315838673380In-frame
ENST000002223453868902838689172In-frame

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Infer the effects of exon skipping event on protein functional features for SIPA1L3

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
ENST000002223458004178138633212386333503905404211321177
ENST000002223458004178138673158386733804718493914031476
ENST000002223458004178138689028386891725350549316131661

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
ENST000002223458004178138633212386333503905404211321177
ENST000002223458004178138673158386733804718493914031476
ENST000002223458004178138689028386891725350549316131661

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
O602921132117711781ChainID=PRO_0000056752;Note=Signal-induced proliferation-associated 1-like protein 3
O602921403147611781ChainID=PRO_0000056752;Note=Signal-induced proliferation-associated 1-like protein 3
O602921403147614481448Modified residueNote=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861
O602921403147614501450Natural variantID=VAR_025477;Note=P->A;Dbxref=dbSNP:rs3745945
O602921613166111781ChainID=PRO_0000056752;Note=Signal-induced proliferation-associated 1-like protein 3
O602921613166116191619Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:G3X9J0
O602921613166116221622Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:G3X9J0


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
O602921132117711781ChainID=PRO_0000056752;Note=Signal-induced proliferation-associated 1-like protein 3
O602921403147611781ChainID=PRO_0000056752;Note=Signal-induced proliferation-associated 1-like protein 3
O602921403147614481448Modified residueNote=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861
O602921403147614501450Natural variantID=VAR_025477;Note=P->A;Dbxref=dbSNP:rs3745945
O602921613166111781ChainID=PRO_0000056752;Note=Signal-induced proliferation-associated 1-like protein 3
O602921613166116191619Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:G3X9J0
O602921613166116221622Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:G3X9J0


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SNVs in the skipped exons for SIPA1L3

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.
SIPA1L3_STAD_exon_skip_306415_psi_boxplot.png
boxplot

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_306415
38571896385737393857257838572578Frame_Shift_DelC-p.P126fs
LIHCTCGA-DD-A39Y-01exon_skip_306415
38571896385737393857257838572578Frame_Shift_DelC-p.P126fs
LIHCTCGA-G3-A3CJ-01exon_skip_306415
38571896385737393857257838572578Frame_Shift_DelC-p.P126fs
COADTCGA-D5-6531-01exon_skip_306415
38571896385737393857275838572767Frame_Shift_DelGGGGAGCCGC-p.184_187del
STADTCGA-B7-A5TJ-01exon_skip_306415
38571896385737393857318338573183Frame_Shift_DelC-p.S326fs
LIHCTCGA-DD-A39Y-01exon_skip_306426
38643480386436073864351738643517Frame_Shift_DelC-p.P1191fs
TGCTTCGA-XY-A8S2-01exon_skip_306432
38684177386844203868428238684282Frame_Shift_DelC-p.P1568fs
GBMTCGA-26-5135-01exon_skip_306415
38571896385737393857232938572329Nonsense_MutationCTp.Q42*
UCSTCGA-NA-A4QV-01exon_skip_306425
38633213386333503863333338633333Nonsense_MutationCGp.Y1172*
UCSTCGA-NA-A4QV-01exon_skip_306425
38633213386333503863333338633333Nonsense_MutationCGp.Y1172X
SKCMTCGA-ER-A199-06exon_skip_306428
exon_skip_306430
38673159386733803867329238673292Nonsense_MutationATp.K1448*
SKCMTCGA-ER-A199-06exon_skip_306428
exon_skip_306430
38673159386733803867329238673292Nonsense_MutationATp.K1448X
BLCATCGA-E7-A7XN-01exon_skip_306428
exon_skip_306430
38673159386733803867332738673327Nonsense_MutationGAp.W1459*

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
SIPA1L3_38519728_38519796_38571895_38573739_38579360_38579491_TCGA-B7-A5TJ-01Sample: TCGA-B7-A5TJ-01
Cancer type: STAD
ESID: exon_skip_306415
Skipped exon start: 38571896
Skipped exon end: 38573739
Mutation start: 38573183
Mutation end: 38573183
Mutation type: Frame_Shift_Del
Reference seq: C
Mutation seq: -
AAchange: p.S326fs
exon_skip_306415_STAD_TCGA-B7-A5TJ-01.png
boxplot
exon_skip_505419_STAD_TCGA-B7-A5TJ-01.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
SNU175_LARGE_INTESTINE38571896385737393857296438572964Frame_Shift_DelC-p.G256fs
HEC6_ENDOMETRIUM38684177386844203868435638684356Frame_Shift_DelC-p.H1592fs
SNUC4_LARGE_INTESTINE38571896385737393857295738572958Frame_Shift_Ins-Gp.MG251fs
SNU1040_LARGE_INTESTINE38571896385737393857238038572381In_Frame_Ins-CCACCAp.59_60insTT
M14_SKIN38571896385737393857221938572219Missense_MutationGAp.R5Q
MDAMB435S_SKIN38571896385737393857221938572219Missense_MutationGAp.R5Q
JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE38571896385737393857226038572260Missense_MutationGTp.G19C
C33A_CERVIX38571896385737393857226338572263Missense_MutationGAp.A20T
KYSE150_OESOPHAGUS38571896385737393857227538572275Missense_MutationGAp.D24N
CAL51_BREAST38571896385737393857233938572339Missense_MutationGAp.S45N
GCT_SOFT_TISSUE38571896385737393857235338572353Missense_MutationCTp.L50F
SNU520_STOMACH38571896385737393857238038572380Missense_MutationGAp.A59T
HCT15_LARGE_INTESTINE38571896385737393857238338572383Missense_MutationAGp.T60A
HCT15_LARGE_INTESTINE38571896385737393857238638572386Missense_MutationGAp.A61T
NCIH1793_LUNG38571896385737393857243838572438Missense_MutationGTp.G78V
NCIH650_LUNG38571896385737393857244438572444Missense_MutationGCp.R80P
HEC6_ENDOMETRIUM38571896385737393857248938572489Missense_MutationAGp.E95G
YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE38571896385737393857249738572497Missense_MutationACp.N98H
CAL12T_LUNG38571896385737393857252738572527Missense_MutationATp.T108S
HCT15_LARGE_INTESTINE38571896385737393857253938572539Missense_MutationAGp.K112E
EN_ENDOMETRIUM38571896385737393857260838572608Missense_MutationTCp.S135P
HEC108_ENDOMETRIUM38571896385737393857267538572675Missense_MutationGAp.R157Q
AGS_STOMACH38571896385737393857269638572696Missense_MutationTAp.L164H
SNU1040_LARGE_INTESTINE38571896385737393857271138572711Missense_MutationGAp.R169H
SISO_CERVIX38571896385737393857280338572803Missense_MutationCTp.R200C
GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE38571896385737393857280338572803Missense_MutationCTp.R200C
HEC6_ENDOMETRIUM38571896385737393857283038572830Missense_MutationGAp.D209N
LU134A_LUNG38571896385737393857283938572839Missense_MutationGTp.G212C
MCF7_BREAST38571896385737393857288238572882Missense_MutationGTp.R226L
ES5_BONE38571896385737393857289938572899Missense_MutationGCp.A232P
UMUC14_URINARY_TRACT38571896385737393857290338572903Missense_MutationGAp.R233Q
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE38571896385737393857292338572923Missense_MutationGAp.E240K
HCT15_LARGE_INTESTINE38571896385737393857292338572923Missense_MutationGAp.E240K
HCC1359_LUNG38571896385737393857295838572958Missense_MutationGTp.M251I
CAL72_BONE38571896385737393857297138572971Missense_MutationGAp.G256R
KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE38571896385737393857299138572991Missense_MutationCAp.H262Q
HEC59_ENDOMETRIUM38571896385737393857300938573009Missense_MutationGTp.K268N
SW962_VULVA38571896385737393857302338573023Missense_MutationCAp.P273Q
RKO_LARGE_INTESTINE38571896385737393857305138573051Missense_MutationGTp.K282N
HS675T_FIBROBLAST38571896385737393857305238573052Missense_MutationGTp.A283S
HEC6_ENDOMETRIUM38571896385737393857314438573144Missense_MutationGTp.E313D
JHUEM2_ENDOMETRIUM38571896385737393857316738573167Missense_MutationCTp.A321V
42MGBA_CENTRAL_NERVOUS_SYSTEM38571896385737393857317238573172Missense_MutationGAp.E323K
NCIH630_LARGE_INTESTINE38571896385737393857320738573207Missense_MutationGTp.W334C
HEC108_ENDOMETRIUM38571896385737393857322738573227Missense_MutationCTp.A341V
SNUC4_LARGE_INTESTINE38571896385737393857323838573238Missense_MutationGAp.V345M
KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE38571896385737393857325838573258Missense_MutationCAp.D351E
NCIH684_LIVER38571896385737393857325938573259Missense_MutationCGp.L352V
NCIH1105_LUNG38571896385737393857330738573307Missense_MutationAGp.T368A
LS411N_LARGE_INTESTINE38571896385737393857332038573320Missense_MutationCTp.A372V
DERL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE38571896385737393857339438573394Missense_MutationCAp.P397T
HEC59_ENDOMETRIUM38571896385737393857349038573490Missense_MutationCTp.H429Y
SNU175_LARGE_INTESTINE38571896385737393857349638573496Missense_MutationCTp.R431C
C2BBE1_LARGE_INTESTINE38571896385737393857350838573508Missense_MutationGAp.G435R
CACO2_LARGE_INTESTINE38571896385737393857350838573508Missense_MutationGAp.G435R
JHC7_BONE38571896385737393857354438573544Missense_MutationGCp.A447P
MEL202_EYE38571896385737393857354438573544Missense_MutationGCp.A447P
ROS50_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE38571896385737393857355038573550Missense_MutationGAp.V449M
AN3CA_ENDOMETRIUM38571896385737393857359338573593Missense_MutationCTp.A463V
LB2518MEL_SKIN38571896385737393857364138573641Missense_MutationCTp.P479L
SNU1040_LARGE_INTESTINE38571896385737393857365538573655Missense_MutationCTp.R484W
MDAMB415_BREAST38571896385737393857368838573688Missense_MutationGAp.E495K
COLO792_SKIN38571896385737393857370438573704Missense_MutationGAp.G500D
CCRFCEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE38571896385737393857370938573709Missense_MutationCTp.R502C
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE38571896385737393857371038573710Missense_MutationGAp.R502H
NEC8_TESTIS38621138386214123862116338621163Missense_MutationTGp.V965G
NCIH660_PROSTATE38621138386214123862127838621278Missense_MutationGTp.Q1003H
PANC1_PANCREAS38621138386214123862129138621291Missense_MutationGAp.V1008M
KP1N_PANCREAS38621138386214123862129138621291Missense_MutationGAp.V1008M
FUOV1_OVARY38621138386214123862132938621329Missense_MutationCAp.H1020Q
KGN_OVARY38621138386214123862132938621329Missense_MutationCAp.H1020Q
KYSE180_OESOPHAGUS38643480386436073864353238643532Missense_MutationGAp.D1196N
MKN1_STOMACH38643480386436073864357138643571Missense_MutationACp.T1209P
L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE38643480386436073864359938643599Missense_MutationATp.Q1218L
U251MG_CENTRAL_NERVOUS_SYSTEM38652893386530113865299538652995Missense_MutationCTp.P1255L
NCIH2196_LUNG38673159386733803867331438673314Missense_MutationATp.H1455L
NCIH1155_LUNG38673159386733803867332038673320Missense_MutationCTp.T1457I
TOV21G_OVARY38673159386733803867335538673355Missense_MutationCTp.P1469S
HEC59_ENDOMETRIUM38684177386844203868429138684291Missense_MutationGAp.V1571M
MRKNU1_BREAST38684177386844203868434338684343Missense_MutationGAp.R1588H
KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE38684177386844203868436138684361Missense_MutationACp.H1594P
RL952_ENDOMETRIUM38684177386844203868441138684411Missense_MutationGAp.E1611K
CHP126_AUTONOMIC_GANGLIA38692502386926373869254338692543Missense_MutationCAp.L1676M
SLR26_KIDNEY38692502386926373869259938692599Missense_MutationGTp.E1694D
ISHIKAWAHERAKLIO02ER_ENDOMETRIUM38692502386926373869260638692606Missense_MutationCGp.P1697A
JSC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE38692502386926373869263538692635Missense_MutationGAp.M1706I
PACADD137_PANCREAS38571896385737393857257538572575Nonsense_MutationCTp.Q124*
SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE38571896385737393857262338572623Nonsense_MutationCTp.R140*
SISO_CERVIX38571896385737393857299838572998Nonsense_MutationCTp.Q265*
GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE38571896385737393857299838572998Nonsense_MutationCTp.Q265*
HCC1428_BREAST38571896385737393857368838573688Nonsense_MutationGTp.E495*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SIPA1L3

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 SIPA1L3


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SIPA1L3


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RelatedDrugs for SIPA1L3

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 SIPA1L3

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