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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 GLB1L3

check button Gene summary
Gene informationGene symbol

GLB1L3

Gene ID

112937

Gene namegalactosidase beta 1 like 3
Synonyms-
Cytomap

11q25

Type of geneprotein-coding
Descriptionbeta-galactosidase-1-like protein 3
Modification date20180523
UniProtAcc

Q8NCI6

ContextPubMed: GLB1L3 [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 GLB1L3 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 GLB1L3

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 GLB1L3

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_6694411134146634:134146657:134147219:134147345:134147593:134147806134147219:134147345ENSG00000166105.11ENST00000431683.2
exon_skip_6694611134147593:134147806:134151270:134151339:134151918:134152014134151270:134151339ENSG00000166105.11ENST00000431683.2,ENST00000389887.5
exon_skip_6694711134153630:134153739:134158691:134158784:134162025:134162107134158691:134158784ENSG00000166105.11ENST00000431683.2,ENST00000389887.5
exon_skip_6695511134163038:134163103:134182242:134182383:134182709:134182781134182242:134182383ENSG00000166105.11ENST00000498012.1
exon_skip_6695711134177085:134177102:134179519:134179657:134180464:134180545134179519:134179657ENSG00000166105.11ENST00000431683.2
exon_skip_6695811134177085:134177102:134179521:134179657:134180464:134180545134179521:134179657ENSG00000166105.11ENST00000455971.2
exon_skip_6695911134179521:134179657:134180464:134180545:134180957:134181064134180464:134180545ENSG00000166105.11ENST00000431683.2,ENST00000455971.2
exon_skip_6696011134180464:134180545:134180957:134181064:134182242:134182383134180957:134181064ENSG00000166105.11ENST00000431683.2,ENST00000455971.2
exon_skip_6696211134182709:134182781:134183289:134183368:134183834:134183922134183289:134183368ENSG00000166105.11ENST00000431683.2,ENST00000410100.2
exon_skip_6696311134183834:134183922:134184223:134184335:134188524:134188641134184223:134184335ENSG00000166105.11ENST00000431683.2,ENST00000455971.2,ENST00000486034.1,ENST00000467068.1,ENST00000498012.1

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

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Exon skipping events with PSIs in GTEx for GLB1L3

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_6694411134146634:134146657:134147219:134147345:134147593:134147806134147219:134147345ENSG00000166105.11ENST00000431683.2
exon_skip_6694611134147593:134147806:134151270:134151339:134151918:134152014134151270:134151339ENSG00000166105.11ENST00000389887.5,ENST00000431683.2
exon_skip_6694711134153630:134153739:134158691:134158784:134162025:134162107134158691:134158784ENSG00000166105.11ENST00000389887.5,ENST00000431683.2
exon_skip_6695511134163038:134163103:134182242:134182383:134182709:134182781134182242:134182383ENSG00000166105.11ENST00000498012.1
exon_skip_6695911134179521:134179657:134180464:134180545:134180957:134181064134180464:134180545ENSG00000166105.11ENST00000431683.2,ENST00000455971.2
exon_skip_6696011134180464:134180545:134180957:134181064:134182242:134182383134180957:134181064ENSG00000166105.11ENST00000431683.2,ENST00000455971.2
exon_skip_6696211134182709:134182781:134183289:134183368:134183834:134183922134183289:134183368ENSG00000166105.11ENST00000431683.2,ENST00000410100.2
exon_skip_6696311134183834:134183922:134184223:134184335:134188524:134188641134184223:134184335ENSG00000166105.11ENST00000431683.2,ENST00000486034.1,ENST00000498012.1,ENST00000455971.2,ENST00000467068.1

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 GLB1L3

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
ENST00000431683134180957134181064Frame-shift
ENST00000431683134183289134183368Frame-shift
ENST00000431683134184223134184335Frame-shift
ENST00000431683134147219134147345In-frame
ENST00000431683134151270134151339In-frame
ENST00000431683134158691134158784In-frame
ENST00000431683134179519134179657In-frame
ENST00000431683134180464134180545In-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
ENST00000431683134180957134181064Frame-shift
ENST00000431683134183289134183368Frame-shift
ENST00000431683134184223134184335Frame-shift
ENST00000431683134147219134147345In-frame
ENST00000431683134151270134151339In-frame
ENST00000431683134158691134158784In-frame
ENST00000431683134180464134180545In-frame

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Infer the effects of exon skipping event on protein functional features for GLB1L3

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
ENST00000431683260065313414721913414734524149849
ENST000004316832600653134151270134151339363431121143
ENST000004316832600653134158691134158784637729212243
ENST0000043168326006531341795191341796579621099320366
ENST00000431683260065313418046413418054511001180366393

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
ENST00000431683260065313414721913414734524149849
ENST000004316832600653134151270134151339363431121143
ENST000004316832600653134158691134158784637729212243
ENST00000431683260065313418046413418054511001180366393

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
Q8NCI68491339Alternative sequenceID=VSP_024280;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q8NCI68491653ChainID=PRO_0000283028;Note=Beta-galactosidase-1-like protein 3
Q8NCI61211431339Alternative sequenceID=VSP_024280;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q8NCI61211431653ChainID=PRO_0000283028;Note=Beta-galactosidase-1-like protein 3
Q8NCI6212243227227Active siteNote=Proton donor;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q8NCI62122431339Alternative sequenceID=VSP_024280;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q8NCI62122431653ChainID=PRO_0000283028;Note=Beta-galactosidase-1-like protein 3
Q8NCI63203661339Alternative sequenceID=VSP_024280;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q8NCI6320366314653Alternative sequenceID=VSP_024284;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q8NCI63203661653ChainID=PRO_0000283028;Note=Beta-galactosidase-1-like protein 3
Q8NCI6366393314653Alternative sequenceID=VSP_024284;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q8NCI63663931653ChainID=PRO_0000283028;Note=Beta-galactosidase-1-like protein 3


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
Q8NCI68491339Alternative sequenceID=VSP_024280;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q8NCI68491653ChainID=PRO_0000283028;Note=Beta-galactosidase-1-like protein 3
Q8NCI61211431339Alternative sequenceID=VSP_024280;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q8NCI61211431653ChainID=PRO_0000283028;Note=Beta-galactosidase-1-like protein 3
Q8NCI6212243227227Active siteNote=Proton donor;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q8NCI62122431339Alternative sequenceID=VSP_024280;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q8NCI62122431653ChainID=PRO_0000283028;Note=Beta-galactosidase-1-like protein 3
Q8NCI6366393314653Alternative sequenceID=VSP_024284;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q8NCI63663931653ChainID=PRO_0000283028;Note=Beta-galactosidase-1-like protein 3


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SNVs in the skipped exons for GLB1L3

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_66944
134147220134147345134147254134147254Frame_Shift_DelT-p.F21fs
LIHCTCGA-DD-A1EG-01exon_skip_66960
134180958134181064134181005134181005Frame_Shift_DelC-p.P411fs
LIHCTCGA-G3-A3CJ-01exon_skip_66962
134183290134183368134183337134183337Frame_Shift_DelT-p.N516fs
LUSCTCGA-22-5489-01exon_skip_66960
134180958134181064134181039134181039Nonsense_MutationGAp.W421*
ESCATCGA-L5-A891-01exon_skip_66962
134183290134183368134183296134183296Nonsense_MutationCTp.R503*
BLCATCGA-FD-A3NA-01exon_skip_66959
134180465134180545134180464134180464Splice_SiteGCp.D367_splice
UCECTCGA-B5-A0K1-01exon_skip_66960
134180958134181064134181065134181065Splice_SiteGTp.E429_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
HCC33_LUNG134182243134182383134182352134182352Frame_Shift_DelG-p.R466fs
NCIH1666_LUNG134147220134147345134147234134147234Missense_MutationGTp.W13L
KYSE30_OESOPHAGUS134147220134147345134147333134147333Missense_MutationCTp.P46L
NCIH250_LUNG134151271134151339134151291134151291Missense_MutationATp.H128L
HEC59_ENDOMETRIUM134158692134158784134158695134158695Missense_MutationCTp.R214C
NCIH358_LUNG134158692134158784134158696134158696Missense_MutationGAp.R214H
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE134158692134158784134158696134158696Missense_MutationGAp.R214H
TASK1_CENTRAL_NERVOUS_SYSTEM134158692134158784134158729134158729Missense_MutationAGp.E225G
NCIH358_LUNG134158692134158784134158755134158755Missense_MutationGTp.D234Y
NCIH650_LUNG134158692134158784134158774134158774Missense_MutationATp.Y240F
NBSUSSR_AUTONOMIC_GANGLIA134179520134179657134179594134179594Missense_MutationAGp.N346D
NBSUSSR_AUTONOMIC_GANGLIA134179522134179657134179594134179594Missense_MutationAGp.N346D
MZ7MEL_SKIN134179520134179657134179608134179608Missense_MutationGAp.M350I
MZ7MEL_SKIN134179522134179657134179608134179608Missense_MutationGAp.M350I
D247MG_CENTRAL_NERVOUS_SYSTEM134179520134179657134179612134179612Missense_MutationGAp.G352R
D247MG_CENTRAL_NERVOUS_SYSTEM134179522134179657134179612134179612Missense_MutationGAp.G352R
JAR_PLACENTA134180465134180545134180526134180526Missense_MutationACp.K387N
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE134180958134181064134180969134180969Missense_MutationCTp.P398S
JHUEM7_ENDOMETRIUM134180958134181064134180987134180987Missense_MutationCAp.P404T
KYSE270_OESOPHAGUS134180958134181064134181000134181000Missense_MutationTGp.V408G
GP2D_LARGE_INTESTINE134180958134181064134181021134181021Missense_MutationCTp.S415L
GP5D_LARGE_INTESTINE134180958134181064134181021134181021Missense_MutationCTp.S415L
HEC59_ENDOMETRIUM134180958134181064134181026134181026Missense_MutationTCp.Y417H
A549_LUNG134180958134181064134181029134181029Missense_MutationCAp.L418I
JHU028_LUNG134180958134181064134181029134181029Missense_MutationCAp.L418I
EMCBAC1_LUNG134180958134181064134181040134181040Missense_MutationGTp.W421C
MCC13_SKIN134180958134181064134181051134181051Missense_MutationCTp.S425F
SH10TC_STOMACH134182243134182383134182278134182278Missense_MutationCGp.N441K
NUGC3_STOMACH134182243134182383134182312134182312Missense_MutationGAp.G453R
EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE134182243134182383134182329134182329Missense_MutationGCp.E458D
MDAMB361_BREAST134182243134182383134182334134182334Missense_MutationCTp.S460F
SKNAS_AUTONOMIC_GANGLIA134183290134183368134183306134183306Missense_MutationGAp.R506K
MCIXC_AUTONOMIC_GANGLIA134183290134183368134183306134183306Missense_MutationGAp.R506K
NCIH810_LUNG134183290134183368134183307134183307Missense_MutationGCp.R506S
MN60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE134183290134183368134183314134183314Missense_MutationGAp.V509M
BB49EBV_MATCHED_NORMAL_TISSUE134184224134184335134184238134184238Missense_MutationCTp.T561I
HCC2157_BREAST134184224134184335134184271134184271Missense_MutationCTp.P572L

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for GLB1L3

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 GLB1L3


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for GLB1L3


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RelatedDrugs for GLB1L3

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 GLB1L3

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