ExonSkipDB Logo

Home

Download

Statistics

Landscape

Help

Contact

Center for Computational Systems Medicine
leaf

Gene summary

leaf

Gene structures and expression levels

leaf

Exon skipping events with PSIs in TCGA

leaf

Exon skipping events with PSIs in GTEx

leaf

Open reading frame (ORF) annotation in the exon skipping event

leaf

Exon skipping events in the canonical protein sequence

leaf

SNVs in the skipped exons with depth of coverage

leaf

Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

leaf

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

leaf

Related drugs with this gene

leaf

Related diseases with this gene

Gene summary for PATL1

check button Gene summary
Gene informationGene symbol

PATL1

Gene ID

219988

Gene namePAT1 homolog 1, processing body mRNA decay factor
SynonymsPat1b|hPat1b
Cytomap

11q12.1

Type of geneprotein-coding
Descriptionprotein PAT1 homolog 1PAT1-like protein 1protein PAT1 homolog bprotein associated with topoisomerase II homolog 1
Modification date20180523
UniProtAcc

Q86TB9

ContextPubMed: PATL1 [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
PATL1

GO:0000290

deadenylation-dependent decapping of nuclear-transcribed mRNA

20584987|20852261

PATL1

GO:0033962

cytoplasmic mRNA processing body assembly

20584987


Top

Exon skipping events across known transcript of Ensembl for PATL1 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

Top

Gene isoform structures and expression levels for PATL1

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


Top

Exon skipping events with PSIs in TCGA for PATL1

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_713331159418226:59418286:59419016:59419114:59419936:5942006059419016:59419114ENSG00000166889.13ENST00000300146.9
exon_skip_713351159422995:59423213:59423428:59423518:59423971:5942407359423428:59423518ENSG00000166889.13ENST00000300146.9
exon_skip_713411159423971:59424073:59425002:59425197:59426338:5942641959425002:59425197ENSG00000166889.13ENST00000300146.9
exon_skip_713521159426338:59426419:59426724:59426942:59434325:5943443759426724:59426942ENSG00000166889.13ENST00000300146.9

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

Top

Exon skipping events with PSIs in GTEx for PATL1

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_713331159418226:59418286:59419016:59419114:59419936:5942006059419016:59419114ENSG00000166889.13ENST00000300146.9
exon_skip_713351159422995:59423213:59423428:59423518:59423971:5942407359423428:59423518ENSG00000166889.13ENST00000300146.9
exon_skip_713411159423971:59424073:59425002:59425197:59426338:5942641959425002:59425197ENSG00000166889.13ENST00000300146.9
exon_skip_713521159426338:59426419:59426724:59426942:59434325:5943443759426724:59426942ENSG00000166889.13ENST00000300146.9

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

Top

Open reading frame (ORF) annotation in the exon skipping event for PATL1

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
ENST000003001465941901659419114Frame-shift
ENST000003001465942672459426942Frame-shift
ENST000003001465942342859423518In-frame
ENST000003001465942500259425197In-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
ENST000003001465941901659419114Frame-shift
ENST000003001465942672459426942Frame-shift
ENST000003001465942342859423518In-frame
ENST000003001465942500259425197In-frame

Top

Infer the effects of exon skipping event on protein functional features for PATL1

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
ENST0000030014640897705942500259425197512706142207
ENST0000030014640897705942342859423518809898241271

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
ENST0000030014640897705942500259425197512706142207
ENST0000030014640897705942342859423518809898241271

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
Q86TB91422071659Alternative sequenceID=VSP_031777;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.1
Q86TB91422071143Alternative sequenceID=VSP_031778;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334
Q86TB91422071770ChainID=PRO_0000320963;Note=Protein PAT1 homolog 1
Q86TB9142207155338Compositional biasNote=Pro-rich
Q86TB9142207177177Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648
Q86TB9142207178178Modified residueNote=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q3TC46
Q86TB9142207179179Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:21406692,PMID:23186163
Q86TB9142207184184Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:21406692,PMID:23186163
Q86TB9142207194194Modified residueNote=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163
Q86TB91422071397RegionNote=Involved in nuclear foci localization
Q86TB914220785388RegionNote=Region N%3B interaction with decapping machinery
Q86TB9142207160160Sequence conflictNote=Q->H;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q86TB92412711659Alternative sequenceID=VSP_031777;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.1
Q86TB9241271242271Alternative sequenceID=VSP_040576;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q86TB92412711770ChainID=PRO_0000320963;Note=Protein PAT1 homolog 1
Q86TB9241271155338Compositional biasNote=Pro-rich
Q86TB9241271263263Modified residueNote=Asymmetric dimethylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315
Q86TB92412711397RegionNote=Involved in nuclear foci localization
Q86TB924127185388RegionNote=Region N%3B interaction with decapping machinery
Q86TB9241271223397RegionNote=Involved in RNA-binding


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
Q86TB91422071659Alternative sequenceID=VSP_031777;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.1
Q86TB91422071143Alternative sequenceID=VSP_031778;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334
Q86TB91422071770ChainID=PRO_0000320963;Note=Protein PAT1 homolog 1
Q86TB9142207155338Compositional biasNote=Pro-rich
Q86TB9142207177177Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648
Q86TB9142207178178Modified residueNote=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q3TC46
Q86TB9142207179179Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:21406692,PMID:23186163
Q86TB9142207184184Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:21406692,PMID:23186163
Q86TB9142207194194Modified residueNote=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163
Q86TB91422071397RegionNote=Involved in nuclear foci localization
Q86TB914220785388RegionNote=Region N%3B interaction with decapping machinery
Q86TB9142207160160Sequence conflictNote=Q->H;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q86TB92412711659Alternative sequenceID=VSP_031777;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.1
Q86TB9241271242271Alternative sequenceID=VSP_040576;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q86TB92412711770ChainID=PRO_0000320963;Note=Protein PAT1 homolog 1
Q86TB9241271155338Compositional biasNote=Pro-rich
Q86TB9241271263263Modified residueNote=Asymmetric dimethylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315
Q86TB92412711397RegionNote=Involved in nuclear foci localization
Q86TB924127185388RegionNote=Region N%3B interaction with decapping machinery
Q86TB9241271223397RegionNote=Involved in RNA-binding


Top

SNVs in the skipped exons for PATL1

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.
PATL1_ESCA_exon_skip_71341_psi_boxplot.png
boxplot
PATL1_KIRC_exon_skip_71341_psi_boxplot.png
boxplot
PATL1_LUAD_exon_skip_71341_psi_boxplot.png
boxplot
PATL1_SKCM_exon_skip_71335_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
SKCMTCGA-EE-A2A2-06exon_skip_71335
59423429594235185942346059423460Frame_Shift_DelA-p.L261fs
LIHCTCGA-G3-A3CJ-01exon_skip_71335
59423429594235185942346159423461Frame_Shift_DelG-p.L261fs
THCATCGA-ET-A2MX-01exon_skip_71335
59423429594235185942349259423492Frame_Shift_DelA-p.F250fs
LIHCTCGA-DD-A3A0-01exon_skip_71341
59425003594251975942500659425006Frame_Shift_DelT-p.Q207fs
ESCATCGA-L5-A43J-01exon_skip_71341
59425003594251975942514659425146Frame_Shift_DelG-p.Q160fs
LIHCTCGA-DD-A3A0-01exon_skip_71352
59426725594269425942672959426729Frame_Shift_DelA-p.L114fs
BLCATCGA-ZF-AA4W-01exon_skip_71341
59425003594251975942514559425146Frame_Shift_Ins-Gp.Q160fs
KIRCTCGA-A3-3372-01exon_skip_71341
59425003594251975942514559425146Frame_Shift_Ins-Gp.G160fs
KIRCTCGA-AK-3447-01exon_skip_71341
59425003594251975942514559425146Frame_Shift_Ins-Gp.G160fs
KIRCTCGA-AS-3777-01exon_skip_71341
59425003594251975942514559425146Frame_Shift_Ins-Gp.G160fs
LUADTCGA-17-Z005-01exon_skip_71341
59425003594251975942514559425146Frame_Shift_Ins-Gp.G160fs
LUADTCGA-44-2662-01exon_skip_71341
59425003594251975942514559425146Frame_Shift_Ins-Gp.G160fs
UCECTCGA-BG-A0M0-01exon_skip_71341
59425003594251975942514559425146Frame_Shift_Ins-Gp.Q160fs
STADTCGA-D7-A4YV-01exon_skip_71333
59419017594191145941906159419061Nonsense_MutationGAp.R494*
STADTCGA-D7-A4YV-01exon_skip_71333
59419017594191145941906159419061Nonsense_MutationGAp.R494X
UCECTCGA-AP-A051-01exon_skip_71333
59419017594191145941911259419112Nonsense_MutationGAp.Q477*
UCECTCGA-AX-A05Z-01exon_skip_71335
59423429594235185942351959423519Splice_SiteCAe7-1

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
PATL1_59423971_59424073_59425002_59425197_59426338_59426419_TCGA-L5-A43J-01Sample: TCGA-L5-A43J-01
Cancer type: ESCA
ESID: exon_skip_71341
Skipped exon start: 59425003
Skipped exon end: 59425197
Mutation start: 59425146
Mutation end: 59425146
Mutation type: Frame_Shift_Del
Reference seq: G
Mutation seq: -
AAchange: p.Q160fs
exon_skip_131502_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_142268_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_30909_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_30910_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_30912_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_319572_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_325050_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_342500_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_343170_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_344507_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_390317_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_390320_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_390321_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_445696_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_467372_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_489594_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_500520_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_504965_ESCA_TCGA-L5-A43J-01.png
boxplot
exon_skip_71341_ESCA_TCGA-L5-A43J-01.png
boxplot
PATL1_59423971_59424073_59425002_59425197_59426338_59426419_TCGA-A3-3372-01Sample: TCGA-A3-3372-01
Cancer type: KIRC
ESID: exon_skip_71341
Skipped exon start: 59425003
Skipped exon end: 59425197
Mutation start: 59425145
Mutation end: 59425146
Mutation type: Frame_Shift_Ins
Reference seq: -
Mutation seq: G
AAchange: p.G160fs
exon_skip_10881_KIRC_TCGA-A3-3372-01.png
boxplot
exon_skip_335781_KIRC_TCGA-A3-3372-01.png
boxplot
exon_skip_347690_KIRC_TCGA-A3-3372-01.png
boxplot
exon_skip_490731_KIRC_TCGA-A3-3372-01.png
boxplot
exon_skip_71341_KIRC_TCGA-A3-3372-01.png
boxplot
exon_skip_93534_KIRC_TCGA-A3-3372-01.png
boxplot
PATL1_59422995_59423213_59423428_59423518_59423971_59424073_TCGA-AX-A05Z-01Sample: TCGA-AX-A05Z-01
Cancer type: UCEC
ESID: exon_skip_71335
Skipped exon start: 59423429
Skipped exon end: 59423518
Mutation start: 59423519
Mutation end: 59423519
Mutation type: Splice_Site
Reference seq: C
Mutation seq: A
AAchange: e7-1
exon_skip_19387_UCEC_TCGA-AX-A05Z-01.png
boxplot
exon_skip_19397_UCEC_TCGA-AX-A05Z-01.png
boxplot
exon_skip_301197_UCEC_TCGA-AX-A05Z-01.png
boxplot
exon_skip_340619_UCEC_TCGA-AX-A05Z-01.png
boxplot
exon_skip_382353_UCEC_TCGA-AX-A05Z-01.png
boxplot
exon_skip_429532_UCEC_TCGA-AX-A05Z-01.png
boxplot
exon_skip_429535_UCEC_TCGA-AX-A05Z-01.png
boxplot
exon_skip_71335_UCEC_TCGA-AX-A05Z-01.png
boxplot
exon_skip_74728_UCEC_TCGA-AX-A05Z-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
RCCAB_KIDNEY59419017594191145941908559419085Frame_Shift_DelT-p.T486fs
CW2_LARGE_INTESTINE59423429594235185942349259423492Frame_Shift_DelA-p.F250fs
CAL51_BREAST59425003594251975942514659425146Frame_Shift_DelG-p.Q160fs
HCT116_LARGE_INTESTINE59426725594269425942684959426850Frame_Shift_DelTC-p.D74fs
REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE59419017594191145941904359419043Missense_MutationCAp.V500F
HT115_LARGE_INTESTINE59423429594235185942345259423452Missense_MutationCTp.A264T
NCIH441_LUNG59423429594235185942345659423456Missense_MutationCGp.Q262H
OC316_OVARY59425003594251975942504759425047Missense_MutationCAp.G193C
OC314_OVARY59425003594251975942504759425047Missense_MutationCAp.G193C
NCIH1651_LUNG59425003594251975942506159425061Missense_MutationCGp.R188T
SCH_STOMACH59425003594251975942512259425122Missense_MutationGAp.L168F
DANG_PANCREAS59426725594269425942685459426854Missense_MutationCGp.E72D
CW2_LARGE_INTESTINE59426725594269425942688659426886Missense_MutationCTp.V62M

Top

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PATL1

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value

Top

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PATL1


Top

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PATL1


Top

RelatedDrugs for PATL1

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

RelatedDiseases for PATL1

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