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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 EXTL3

check button Gene summary
Gene informationGene symbol

EXTL3

Gene ID

2137

Gene nameexostosin like glycosyltransferase 3
SynonymsBOTV|EXTL1L|EXTR1|ISDNA|REGR|RPR
Cytomap

8p21.1

Type of geneprotein-coding
Descriptionexostosin-like 3EXT-related 1exostoses (multiple)-like 3exostosin tumor-like 3glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferasehereditary multiple exostoses gene isologputative tumor suppressor protein EXTL3reg receptor
Modification date20180527
UniProtAcc

O43909

ContextPubMed: EXTL3 [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
EXTL3

GO:0015012

heparan sulfate proteoglycan biosynthetic process

28132690|28148688


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Exon skipping events across known transcript of Ensembl for EXTL3 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 EXTL3

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 EXTL3

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_482491828480277:28480327:28494818:28494946:28570973:2857103028494818:28494946ENSG00000012232.4ENST00000519288.1
exon_skip_482503828494853:28494946:28543402:28543525:28570973:2857103028543402:28543525ENSG00000012232.4ENST00000520940.1
exon_skip_482505828494853:28494946:28570973:28571067:28573101:2857312728570973:28571067ENSG00000012232.4ENST00000519288.1
exon_skip_482506828559121:28559176:28570973:28571067:28573101:2857312728570973:28571067ENSG00000012232.4ENST00000220562.4,ENST00000519886.1
exon_skip_482513828570973:28571067:28573101:28575724:28588739:2858886728573101:28575724ENSG00000012232.4ENST00000220562.4
exon_skip_482520828595035:28595180:28600602:28600731:28608173:2860824128600602:28600731ENSG00000012232.4ENST00000220562.4,ENST00000517738.1,ENST00000523149.1

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

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Exon skipping events with PSIs in GTEx for EXTL3

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_482491828480277:28480327:28494818:28494946:28570973:2857103028494818:28494946ENSG00000012232.4ENST00000519288.1
exon_skip_482505828494853:28494946:28570973:28571067:28573101:2857312728570973:28571067ENSG00000012232.4ENST00000519288.1
exon_skip_482506828559121:28559176:28570973:28571067:28573101:2857312728570973:28571067ENSG00000012232.4ENST00000220562.4,ENST00000519886.1
exon_skip_482513828570973:28571067:28573101:28575724:28588739:2858886728573101:28575724ENSG00000012232.4ENST00000220562.4
exon_skip_482520828595035:28595180:28600602:28600731:28608173:2860824128600602:28600731ENSG00000012232.4ENST00000523149.1,ENST00000220562.4,ENST00000517738.1

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 EXTL3

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
ENST0000022056228573101285757245CDS-5UTR
ENST0000022056228570973285710675UTR-5UTR
ENST000002205622860060228600731In-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
ENST0000022056228573101285757245CDS-5UTR
ENST0000022056228570973285710675UTR-5UTR
ENST000002205622860060228600731In-frame

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Infer the effects of exon skipping event on protein functional features for EXTL3

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
ENST000002205626500919286006022860073133243452807850

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
ENST000002205626500919286006022860073133243452807850

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
O43909807850833833Active siteOntology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9ES89
O439098078501919ChainID=PRO_0000149657;Note=Exostosin-like 3
O43909807850831879Disulfide bondOntology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9ES89
O43909807850829833RegionNote=Substrate binding;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9ES89
O4390980785052919Topological domainNote=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255


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
O43909807850833833Active siteOntology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9ES89
O439098078501919ChainID=PRO_0000149657;Note=Exostosin-like 3
O43909807850831879Disulfide bondOntology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9ES89
O43909807850829833RegionNote=Substrate binding;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9ES89
O4390980785052919Topological domainNote=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255


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SNVs in the skipped exons for EXTL3

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-A3A1-01exon_skip_482513
28573102285757242857361228573612Frame_Shift_DelG-p.A12fs
COADTCGA-G4-6588-01exon_skip_482513
28573102285757242857498528574985Frame_Shift_DelT-p.L470fs
BRCATCGA-B6-A0RE-01exon_skip_482513
28573102285757242857438528574386Frame_Shift_Ins-Cp.H271fs
THYMTCGA-ZB-A964-01exon_skip_482513
28573102285757242857461028574611Frame_Shift_Ins-Cp.Q346fs
CHOLTCGA-4G-AAZO-01exon_skip_482513
28573102285757242857366828573668Nonsense_MutationGAp.W31*
LUADTCGA-49-4506-01exon_skip_482513
28573102285757242857404828574048Nonsense_MutationCTp.R158*
LUADTCGA-97-8172-01exon_skip_482513
28573102285757242857437428574374Nonsense_MutationGAp.W266*
SKCMTCGA-EE-A2GP-06exon_skip_482513
28573102285757242857449528574495Nonsense_MutationCTp.Q307*
SKCMTCGA-EE-A2GP-06exon_skip_482513
28573102285757242857449528574495Nonsense_MutationCTp.Q307X
COADTCGA-AD-6964-01exon_skip_482513
28573102285757242857512428575124Nonsense_MutationGAp.W516X
SKCMTCGA-GN-A4U8-06exon_skip_482513
28573102285757242857552728575527Nonsense_MutationCTp.Q651*

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
HEC59_ENDOMETRIUM28573102285757242857515328575153Frame_Shift_DelT-p.I526fs
RERFLCAD1_LUNG28573102285757242857373828573739In_Frame_Ins-GATGAGGCTp.55_55D>DEAD
REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28573102285757242857359028573590Missense_MutationCTp.T5I
REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28573102285757242857359528573595Missense_MutationCAp.L7M
EFE184_ENDOMETRIUM28573102285757242857361328573613Missense_MutationGAp.G13R
JHOS3_OVARY28573102285757242857365228573652Missense_MutationCTp.R26C
MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28573102285757242857371528573715Missense_MutationGAp.A47T
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28573102285757242857381128573811Missense_MutationGAp.V79M
KM12_LARGE_INTESTINE28573102285757242857381128573811Missense_MutationGAp.V79M
HUG1N_STOMACH28573102285757242857383928573839Missense_MutationCTp.S88L
2313287_STOMACH28573102285757242857383928573839Missense_MutationCTp.S88L
HEC1A_ENDOMETRIUM28573102285757242857391928573919Missense_MutationGAp.E115K
HEC1_ENDOMETRIUM28573102285757242857391928573919Missense_MutationGAp.E115K
HEC1B_ENDOMETRIUM28573102285757242857391928573919Missense_MutationGAp.E115K
GA10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28573102285757242857393528573935Missense_MutationGAp.S120N
FARAGE_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28573102285757242857403428574034Missense_MutationTGp.L153R
M00921_SKIN28573102285757242857407328574073Missense_MutationCTp.A166V
NCIH2172_LUNG28573102285757242857408228574082Missense_MutationCTp.P169L
ISHIKAWAHERAKLIO02ER_ENDOMETRIUM28573102285757242857408828574088Missense_MutationCTp.P171L
EFO27_OVARY28573102285757242857410828574108Missense_MutationCTp.R178W
P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28573102285757242857423428574234Missense_MutationGTp.A220S
JIYOYEP2003_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28573102285757242857423428574234Missense_MutationGTp.A220S
SW48_LARGE_INTESTINE28573102285757242857431928574319Missense_MutationCTp.P248L
NCIH2052_PLEURA28573102285757242857436028574360Missense_MutationTCp.S262P
SNU1040_LARGE_INTESTINE28573102285757242857437628574376Missense_MutationGAp.R267Q
RKO_LARGE_INTESTINE28573102285757242857441428574414Missense_MutationCGp.R280G
SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28573102285757242857441528574415Missense_MutationGAp.R280H
NB13_AUTONOMIC_GANGLIA28573102285757242857449728574497Missense_MutationGCp.Q307H
RKO_LARGE_INTESTINE28573102285757242857473028574730Missense_MutationCTp.A385V
LOVO_LARGE_INTESTINE28573102285757242857480228574802Missense_MutationCTp.P409L
JHH7_LIVER28573102285757242857483228574832Missense_MutationAGp.E419G
SARC9371_BONE28573102285757242857486728574867Missense_MutationGAp.A431T
SNU685_ENDOMETRIUM28573102285757242857491328574913Missense_MutationGTp.G446V
AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28573102285757242857502328575023Missense_MutationCGp.L483V
SKMES1_LUNG28573102285757242857510528575105Missense_MutationGTp.R510L
SNUC4_LARGE_INTESTINE28573102285757242857518628575186Missense_MutationGTp.R537L
SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28573102285757242857518628575186Missense_MutationGAp.R537H
T84_LARGE_INTESTINE28573102285757242857518828575188Missense_MutationAGp.I538V
L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28573102285757242857521728575217Missense_MutationATp.E547D
SNU175_LARGE_INTESTINE28573102285757242857522228575222Missense_MutationCTp.A549V
SNU1079_BILIARY_TRACT28573102285757242857522728575227Missense_MutationGAp.A551T
SW156_KIDNEY28573102285757242857534728575347Missense_MutationCGp.R591G
SNGM_ENDOMETRIUM28573102285757242857534828575348Missense_MutationGAp.R591H
SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28573102285757242857550128575501Missense_MutationGTp.G642V
PCI6A_UPPER_AERODIGESTIVE_TRACT28573102285757242857551328575513Missense_MutationCAp.S646Y
NCIH747_LARGE_INTESTINE28573102285757242857553428575534Missense_MutationCTp.A653V
CORL303_LUNG28573102285757242857557528575575Missense_MutationAGp.M667V
OVCAR4_OVARY28600603286007312860070528600705Missense_MutationCAp.H842N
WM35_SKIN28573102285757242857437428574374Nonsense_MutationGAp.W266*
KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28573102285757242857481128574811Nonsense_MutationGAp.W412*
JSC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28573102285757242857499328574993Nonsense_MutationCTp.Q473*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for EXTL3

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 EXTL3


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for EXTL3


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RelatedDrugs for EXTL3

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 EXTL3

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