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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 NPRL3

check button Gene summary
Gene informationGene symbol

NPRL3

Gene ID

8131

Gene nameNPR3 like, GATOR1 complex subunit
SynonymsC16orf35|CGTHBA|FFEVF3|HS-40|MARE|NPR3|RMD11
Cytomap

16p13.3

Type of geneprotein-coding
DescriptionGATOR complex protein NPRL3-14 gene proteinalpha-globin regulatory element-containing gene proteinconserved gene telomeric to alpha globin cluster
Modification date20180523
UniProtAcc

Q12980

ContextPubMed: NPRL3 [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 NPRL3 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 NPRL3

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 NPRL3

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_13998616138781:138888:139710:139900:142593:142723139710:139900ENSG00000103148.11ENST00000405960.3,ENST00000445810.1,ENST00000399953.3,ENST00000428323.2,ENST00000399957.3,ENST00000399951.3
exon_skip_13999516139710:139900:142593:142723:143216:143323142593:142723ENSG00000103148.11ENST00000405960.3,ENST00000445810.1,ENST00000399953.3,ENST00000428323.2,ENST00000399957.3,ENST00000399951.3
exon_skip_14000316142593:142723:143216:143323:148142:148158143216:143323ENSG00000103148.11ENST00000405960.3,ENST00000445810.1,ENST00000399953.3,ENST00000428323.2,ENST00000399957.3,ENST00000399951.3
exon_skip_14000716143256:143323:148142:148299:150369:150507148142:148299ENSG00000103148.11ENST00000405960.3,ENST00000445810.1,ENST00000399953.3,ENST00000428323.2,ENST00000399957.3,ENST00000473674.1,ENST00000399951.3
exon_skip_14001416148227:148299:150369:150507:160522:160604150369:150507ENSG00000103148.11ENST00000483663.1,ENST00000468260.1,ENST00000405960.3,ENST00000457916.1,ENST00000445810.1,ENST00000399953.3,ENST00000428323.2,ENST00000399957.3,ENST00000473674.1,ENST00000399951.3
exon_skip_14001916150369:150507:160522:160604:162620:162774160522:160604ENSG00000103148.11ENST00000483663.1,ENST00000468260.1,ENST00000405960.3,ENST00000457916.1,ENST00000445810.1,ENST00000399953.3,ENST00000428323.2,ENST00000399957.3,ENST00000473674.1,ENST00000399951.3
exon_skip_14002216162658:162774:167299:167374:169124:169254167299:167374ENSG00000103148.11ENST00000483663.1,ENST00000419636.1,ENST00000468260.1,ENST00000405960.3,ENST00000457916.1,ENST00000399953.3,ENST00000473674.1
exon_skip_14002316162658:162774:167299:167374:180520:180590167299:167374ENSG00000103148.11ENST00000445810.1
exon_skip_14002416162658:162774:169124:169254:174935:175047169124:169254ENSG00000103148.11ENST00000456528.1
exon_skip_14002516162658:162774:169124:169254:180520:180590169124:169254ENSG00000103148.11ENST00000428323.2
exon_skip_14003216162658:162774:180520:180590:188148:188333180520:180590ENSG00000103148.11ENST00000399957.3,ENST00000399951.3
exon_skip_14003416167299:167374:169124:169254:180520:180590169124:169254ENSG00000103148.11ENST00000405960.3,ENST00000457916.1,ENST00000399953.3
exon_skip_14003916169124:169254:173505:173544:174935:175047173505:173544ENSG00000103148.11ENST00000468260.1
exon_skip_14004016169124:169254:173505:173544:180520:180590173505:173544ENSG00000103148.11ENST00000419636.1
exon_skip_14004416169124:169254:174935:175072:180520:180590174935:175072ENSG00000103148.11ENST00000456528.1
exon_skip_14004616169124:169254:180520:180590:188148:188333180520:180590ENSG00000103148.11ENST00000405960.3,ENST00000399953.3,ENST00000428323.2
exon_skip_14004716169124:169254:180520:180590:188230:188360180520:180590ENSG00000103148.11ENST00000457916.1
exon_skip_14005916173505:173544:174935:175072:180520:180590174935:175072ENSG00000103148.11ENST00000468260.1
exon_skip_14006016174935:175072:180520:180590:188148:188333180520:180590ENSG00000103148.11ENST00000456528.1
exon_skip_14006116180520:180590:188148:188333:188640:188665188148:188333ENSG00000103148.11ENST00000405960.3,ENST00000456528.1

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

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Exon skipping events with PSIs in GTEx for NPRL3

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_13998616138781:138888:139710:139900:142593:142723139710:139900ENSG00000103148.11ENST00000445810.1,ENST00000428323.2,ENST00000399957.3,ENST00000399953.3,ENST00000399951.3,ENST00000405960.3
exon_skip_13999516139710:139900:142593:142723:143216:143323142593:142723ENSG00000103148.11ENST00000445810.1,ENST00000428323.2,ENST00000399957.3,ENST00000399953.3,ENST00000399951.3,ENST00000405960.3
exon_skip_14000316142593:142723:143216:143323:148142:148158143216:143323ENSG00000103148.11ENST00000445810.1,ENST00000428323.2,ENST00000399957.3,ENST00000399953.3,ENST00000399951.3,ENST00000405960.3
exon_skip_14000716143256:143323:148142:148299:150369:150507148142:148299ENSG00000103148.11ENST00000445810.1,ENST00000428323.2,ENST00000399957.3,ENST00000399953.3,ENST00000399951.3,ENST00000405960.3,ENST00000473674.1
exon_skip_14001416148227:148299:150369:150507:160522:160604150369:150507ENSG00000103148.11ENST00000445810.1,ENST00000428323.2,ENST00000399957.3,ENST00000399953.3,ENST00000399951.3,ENST00000405960.3,ENST00000473674.1,ENST00000483663.1,ENST00000457916.1,ENST00000468260.1
exon_skip_14001916150369:150507:160522:160604:162620:162774160522:160604ENSG00000103148.11ENST00000445810.1,ENST00000428323.2,ENST00000399957.3,ENST00000399953.3,ENST00000399951.3,ENST00000405960.3,ENST00000473674.1,ENST00000483663.1,ENST00000457916.1,ENST00000468260.1
exon_skip_14002216162658:162774:167299:167374:169124:169254167299:167374ENSG00000103148.11ENST00000399953.3,ENST00000405960.3,ENST00000473674.1,ENST00000483663.1,ENST00000457916.1,ENST00000468260.1,ENST00000419636.1
exon_skip_14002316162658:162774:167299:167374:180520:180590167299:167374ENSG00000103148.11ENST00000445810.1
exon_skip_14002416162658:162774:169124:169254:174935:175047169124:169254ENSG00000103148.11ENST00000456528.1
exon_skip_14002516162658:162774:169124:169254:180520:180590169124:169254ENSG00000103148.11ENST00000428323.2
exon_skip_14003216162658:162774:180520:180590:188148:188333180520:180590ENSG00000103148.11ENST00000399957.3,ENST00000399951.3
exon_skip_14003416167299:167374:169124:169254:180520:180590169124:169254ENSG00000103148.11ENST00000399953.3,ENST00000405960.3,ENST00000457916.1
exon_skip_14003916169124:169254:173505:173544:174935:175047173505:173544ENSG00000103148.11ENST00000468260.1
exon_skip_14004016169124:169254:173505:173544:180520:180590173505:173544ENSG00000103148.11ENST00000419636.1
exon_skip_14004416169124:169254:174935:175072:180520:180590174935:175072ENSG00000103148.11ENST00000456528.1
exon_skip_14004616169124:169254:180520:180590:188148:188333180520:180590ENSG00000103148.11ENST00000428323.2,ENST00000399953.3,ENST00000405960.3
exon_skip_14004716169124:169254:180520:180590:188230:188360180520:180590ENSG00000103148.11ENST00000457916.1
exon_skip_14005916173505:173544:174935:175072:180520:180590174935:175072ENSG00000103148.11ENST00000468260.1
exon_skip_14006016174935:175072:180520:180590:188148:188333180520:180590ENSG00000103148.11ENST00000456528.1
exon_skip_14006116180520:180590:188148:188333:188640:188665188148:188333ENSG00000103148.11ENST00000405960.3,ENST00000456528.1

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 NPRL3

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

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

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Infer the effects of exon skipping event on protein functional features for NPRL3

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 NPRL3

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_140014
150370150507150403150403Frame_Shift_DelG-p.P245fs
LIHCTCGA-G3-A3CJ-01exon_skip_140019
160523160604160578160578Frame_Shift_DelG-p.H193fs
LIHCTCGA-DD-A1EG-01exon_skip_140019
160523160604160583160583Frame_Shift_DelG-p.P190fs
LIHCTCGA-G3-A3CJ-01exon_skip_140019
160523160604160583160583Frame_Shift_DelG-p.P190fs
LIHCTCGA-DD-A3A0-01167300167374167321167321Frame_Shift_DelA-p.F124fs
STADTCGA-BR-4361-01167300167374167321167321Frame_Shift_DelA-p.N125fs
SKCMTCGA-FR-A8YD-06exon_skip_140061
188149188333188184188184Frame_Shift_DelA-p.F28fs
HNSCTCGA-BA-A6D8-01exon_skip_140024
exon_skip_140025
exon_skip_140034
169125169254169169169169Nonsense_MutationGAp.R92*
PAADTCGA-IB-7651-01exon_skip_140024
exon_skip_140025
exon_skip_140034
169125169254169169169169Nonsense_MutationGAp.R92*
CESCTCGA-DG-A2KK-01167300167374167375167375Splice_SiteCTe4-1

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
NPRL3_162658_162774_167299_167374_180520_180590_TCGA-DG-A2KK-01Sample: TCGA-DG-A2KK-01
Cancer type: CESC
ESID:
Skipped exon start: 167300
Skipped exon end: 167374
Mutation start: 167375
Mutation end: 167375
Mutation type: Splice_Site
Reference seq: C
Mutation seq: T
AAchange: e4-1
exon_skip_140022_CESC_TCGA-DG-A2KK-01.png
boxplot
exon_skip_140023_CESC_TCGA-DG-A2KK-01.png
boxplot
NPRL3_162658_162774_167299_167374_169124_169254_TCGA-DG-A2KK-01Sample: TCGA-DG-A2KK-01
Cancer type: CESC
ESID:
Skipped exon start: 167300
Skipped exon end: 167374
Mutation start: 167375
Mutation end: 167375
Mutation type: Splice_Site
Reference seq: C
Mutation seq: T
AAchange: e4-1
exon_skip_140022_CESC_TCGA-DG-A2KK-01.png
boxplot
exon_skip_140023_CESC_TCGA-DG-A2KK-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
RAMOS2G64C10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE142594142723142657142665In_Frame_DelGGCAAGAAC-p.VLA364del
CHLA258_BONE139711139900139732139732Missense_MutationCTp.A444T
LS411N_LARGE_INTESTINE139711139900139732139732Missense_MutationCTp.A444T
HEC59_ENDOMETRIUM139711139900139753139753Missense_MutationGAp.R437C
H2369_PLEURA139711139900139819139819Missense_MutationAGp.S415P
MHHNB11_AUTONOMIC_GANGLIA139711139900139819139819Missense_MutationAGp.S415P
MFE319_ENDOMETRIUM142594142723142613142613Missense_MutationATp.L381Q
MCC13_SKIN142594142723142615142616Missense_MutationGGAAp.P380L
MCC13_SKIN142594142723142616142616Missense_MutationGAp.P380L
SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE142594142723142704142704Missense_MutationGTp.Q351K
SNU668_STOMACH142594142723142715142715Missense_MutationGAp.P347L
SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE142594142723142716142716Missense_MutationGAp.P347S
U87MG_CENTRAL_NERVOUS_SYSTEM143217143323143225143225Missense_MutationGCp.S341R
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE148143148299148213148213Missense_MutationAGp.V285A
CROAP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE148143148299148217148217Missense_MutationGAp.R284W
KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE150370150507150425150425Missense_MutationCTp.A238T
C33A_CERVIX150370150507150428150428Missense_MutationAGp.Y237H
HCT15_LARGE_INTESTINE150370150507150469150469Missense_MutationCTp.S223N
CW2_LARGE_INTESTINE160523160604160551160551Missense_MutationCTp.A201T
SNU1040_LARGE_INTESTINE160523160604160571160571Missense_MutationAGp.I194T
NCIH2887_LUNG167300167374167330167330Missense_MutationCGp.M121I
U2OS_BONE167300167374167330167330Missense_MutationCAp.M121I
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE169125169254169157169157Missense_MutationGTp.H96N
NHAHTDD_CENTRAL_NERVOUS_SYSTEM169125169254169168169168Missense_MutationCTp.R92Q
SNU1040_LARGE_INTESTINE180521180590180524180524Missense_MutationGTp.S62Y
HEC59_ENDOMETRIUM180521180590180569180569Missense_MutationGAp.A47V
SNU81_LARGE_INTESTINE188149188333188178188178Missense_MutationCAp.R30I
CHAGOK1_LUNG188149188333188254188254Missense_MutationTAp.T5S
GP2D_LARGE_INTESTINE188149188333188262188262Missense_MutationCGp.R2P
GP5D_LARGE_INTESTINE188149188333188262188262Missense_MutationCGp.R2P
MET2B160523160604160590160590Nonsense_MutationGAp.Q188*
SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE169125169254169169169169Nonsense_MutationGAp.R92*
SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE160523160604160523160523Splice_SiteCAp.S210I

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NPRL3

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 NPRL3


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NPRL3


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RelatedDrugs for NPRL3

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 NPRL3

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