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Open reading frame (ORF) annotation in the exon skipping event | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon | |
Gene summary for PATL1 |
Gene summary |
Gene information | Gene symbol | PATL1 | Gene ID | 219988 |
Gene name | PAT1 homolog 1, processing body mRNA decay factor | |
Synonyms | Pat1b|hPat1b | |
Cytomap | 11q12.1 | |
Type of gene | protein-coding | |
Description | protein PAT1 homolog 1PAT1-like protein 1protein PAT1 homolog bprotein associated with topoisomerase II homolog 1 | |
Modification date | 20180523 | |
UniProtAcc | Q86TB9 | |
Context | PubMed: PATL1 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
PATL1 | GO:0000290 | deadenylation-dependent decapping of nuclear-transcribed mRNA | 20584987|20852261 |
PATL1 | GO:0033962 | cytoplasmic mRNA processing body assembly | 20584987 |
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Exon skipping events across known transcript of Ensembl for PATL1 from UCSC genome browser |
Skipped 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. |
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Gene isoform structures and expression levels for PATL1 |
Expression levels of gene isoforms across TCGA. |
Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for PATL1 |
Information of exkip skipping event in TCGA. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
exon_skip_71333 | 11 | 59418226:59418286:59419016:59419114:59419936:59420060 | 59419016:59419114 | ENSG00000166889.13 | ENST00000300146.9 |
exon_skip_71335 | 11 | 59422995:59423213:59423428:59423518:59423971:59424073 | 59423428:59423518 | ENSG00000166889.13 | ENST00000300146.9 |
exon_skip_71341 | 11 | 59423971:59424073:59425002:59425197:59426338:59426419 | 59425002:59425197 | ENSG00000166889.13 | ENST00000300146.9 |
exon_skip_71352 | 11 | 59426338:59426419:59426724:59426942:59434325:59434437 | 59426724:59426942 | ENSG00000166889.13 | ENST00000300146.9 |
PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PATL1 |
Information of exkip skipping event in GTEx |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
exon_skip_71333 | 11 | 59418226:59418286:59419016:59419114:59419936:59420060 | 59419016:59419114 | ENSG00000166889.13 | ENST00000300146.9 |
exon_skip_71335 | 11 | 59422995:59423213:59423428:59423518:59423971:59424073 | 59423428:59423518 | ENSG00000166889.13 | ENST00000300146.9 |
exon_skip_71341 | 11 | 59423971:59424073:59425002:59425197:59426338:59426419 | 59425002:59425197 | ENSG00000166889.13 | ENST00000300146.9 |
exon_skip_71352 | 11 | 59426338:59426419:59426724:59426942:59434325:59434437 | 59426724:59426942 | ENSG00000166889.13 | ENST00000300146.9 |
PSI values of skipped exons in GTEx. |
* Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for PATL1 |
Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000300146 | 59419016 | 59419114 | Frame-shift |
ENST00000300146 | 59426724 | 59426942 | Frame-shift |
ENST00000300146 | 59423428 | 59423518 | In-frame |
ENST00000300146 | 59425002 | 59425197 | In-frame |
Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000300146 | 59419016 | 59419114 | Frame-shift |
ENST00000300146 | 59426724 | 59426942 | Frame-shift |
ENST00000300146 | 59423428 | 59423518 | In-frame |
ENST00000300146 | 59425002 | 59425197 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PATL1 |
Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases. |
ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
ENST00000300146 | 4089 | 770 | 59425002 | 59425197 | 512 | 706 | 142 | 207 |
ENST00000300146 | 4089 | 770 | 59423428 | 59423518 | 809 | 898 | 241 | 271 |
Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases. |
ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
ENST00000300146 | 4089 | 770 | 59425002 | 59425197 | 512 | 706 | 142 | 207 |
ENST00000300146 | 4089 | 770 | 59423428 | 59423518 | 809 | 898 | 241 | 271 |
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 feature | Description of feature |
Q86TB9 | 142 | 207 | 1 | 659 | Alternative sequence | ID=VSP_031777;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.1 |
Q86TB9 | 142 | 207 | 1 | 143 | Alternative sequence | ID=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 |
Q86TB9 | 142 | 207 | 1 | 770 | Chain | ID=PRO_0000320963;Note=Protein PAT1 homolog 1 |
Q86TB9 | 142 | 207 | 155 | 338 | Compositional bias | Note=Pro-rich |
Q86TB9 | 142 | 207 | 177 | 177 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
Q86TB9 | 142 | 207 | 178 | 178 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q3TC46 |
Q86TB9 | 142 | 207 | 179 | 179 | Modified residue | Note=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 |
Q86TB9 | 142 | 207 | 184 | 184 | Modified residue | Note=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 |
Q86TB9 | 142 | 207 | 194 | 194 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
Q86TB9 | 142 | 207 | 1 | 397 | Region | Note=Involved in nuclear foci localization |
Q86TB9 | 142 | 207 | 85 | 388 | Region | Note=Region N%3B interaction with decapping machinery |
Q86TB9 | 142 | 207 | 160 | 160 | Sequence conflict | Note=Q->H;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q86TB9 | 241 | 271 | 1 | 659 | Alternative sequence | ID=VSP_031777;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.1 |
Q86TB9 | 241 | 271 | 242 | 271 | Alternative sequence | ID=VSP_040576;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q86TB9 | 241 | 271 | 1 | 770 | Chain | ID=PRO_0000320963;Note=Protein PAT1 homolog 1 |
Q86TB9 | 241 | 271 | 155 | 338 | Compositional bias | Note=Pro-rich |
Q86TB9 | 241 | 271 | 263 | 263 | Modified residue | Note=Asymmetric dimethylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315 |
Q86TB9 | 241 | 271 | 1 | 397 | Region | Note=Involved in nuclear foci localization |
Q86TB9 | 241 | 271 | 85 | 388 | Region | Note=Region N%3B interaction with decapping machinery |
Q86TB9 | 241 | 271 | 223 | 397 | Region | Note=Involved in RNA-binding |
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 feature | Description of feature |
Q86TB9 | 142 | 207 | 1 | 659 | Alternative sequence | ID=VSP_031777;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.1 |
Q86TB9 | 142 | 207 | 1 | 143 | Alternative sequence | ID=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 |
Q86TB9 | 142 | 207 | 1 | 770 | Chain | ID=PRO_0000320963;Note=Protein PAT1 homolog 1 |
Q86TB9 | 142 | 207 | 155 | 338 | Compositional bias | Note=Pro-rich |
Q86TB9 | 142 | 207 | 177 | 177 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
Q86TB9 | 142 | 207 | 178 | 178 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q3TC46 |
Q86TB9 | 142 | 207 | 179 | 179 | Modified residue | Note=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 |
Q86TB9 | 142 | 207 | 184 | 184 | Modified residue | Note=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 |
Q86TB9 | 142 | 207 | 194 | 194 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
Q86TB9 | 142 | 207 | 1 | 397 | Region | Note=Involved in nuclear foci localization |
Q86TB9 | 142 | 207 | 85 | 388 | Region | Note=Region N%3B interaction with decapping machinery |
Q86TB9 | 142 | 207 | 160 | 160 | Sequence conflict | Note=Q->H;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q86TB9 | 241 | 271 | 1 | 659 | Alternative sequence | ID=VSP_031777;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.1 |
Q86TB9 | 241 | 271 | 242 | 271 | Alternative sequence | ID=VSP_040576;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q86TB9 | 241 | 271 | 1 | 770 | Chain | ID=PRO_0000320963;Note=Protein PAT1 homolog 1 |
Q86TB9 | 241 | 271 | 155 | 338 | Compositional bias | Note=Pro-rich |
Q86TB9 | 241 | 271 | 263 | 263 | Modified residue | Note=Asymmetric dimethylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315 |
Q86TB9 | 241 | 271 | 1 | 397 | Region | Note=Involved in nuclear foci localization |
Q86TB9 | 241 | 271 | 85 | 388 | Region | Note=Region N%3B interaction with decapping machinery |
Q86TB9 | 241 | 271 | 223 | 397 | Region | Note=Involved in RNA-binding |
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SNVs in the skipped exons for PATL1 |
- Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
- Differential PSIs between mutated versus non-mutated samples. |
PATL1_ESCA_exon_skip_71341_psi_boxplot.png |
PATL1_KIRC_exon_skip_71341_psi_boxplot.png |
PATL1_LUAD_exon_skip_71341_psi_boxplot.png |
PATL1_SKCM_exon_skip_71335_psi_boxplot.png |
- Non-synonymous mutations located in the skipped exons in TCGA. |
Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
SKCM | TCGA-EE-A2A2-06 | exon_skip_71335 | 59423429 | 59423518 | 59423460 | 59423460 | Frame_Shift_Del | A | - | p.L261fs |
LIHC | TCGA-G3-A3CJ-01 | exon_skip_71335 | 59423429 | 59423518 | 59423461 | 59423461 | Frame_Shift_Del | G | - | p.L261fs |
THCA | TCGA-ET-A2MX-01 | exon_skip_71335 | 59423429 | 59423518 | 59423492 | 59423492 | Frame_Shift_Del | A | - | p.F250fs |
LIHC | TCGA-DD-A3A0-01 | exon_skip_71341 | 59425003 | 59425197 | 59425006 | 59425006 | Frame_Shift_Del | T | - | p.Q207fs |
ESCA | TCGA-L5-A43J-01 | exon_skip_71341 | 59425003 | 59425197 | 59425146 | 59425146 | Frame_Shift_Del | G | - | p.Q160fs |
LIHC | TCGA-DD-A3A0-01 | exon_skip_71352 | 59426725 | 59426942 | 59426729 | 59426729 | Frame_Shift_Del | A | - | p.L114fs |
BLCA | TCGA-ZF-AA4W-01 | exon_skip_71341 | 59425003 | 59425197 | 59425145 | 59425146 | Frame_Shift_Ins | - | G | p.Q160fs |
KIRC | TCGA-A3-3372-01 | exon_skip_71341 | 59425003 | 59425197 | 59425145 | 59425146 | Frame_Shift_Ins | - | G | p.G160fs |
KIRC | TCGA-AK-3447-01 | exon_skip_71341 | 59425003 | 59425197 | 59425145 | 59425146 | Frame_Shift_Ins | - | G | p.G160fs |
KIRC | TCGA-AS-3777-01 | exon_skip_71341 | 59425003 | 59425197 | 59425145 | 59425146 | Frame_Shift_Ins | - | G | p.G160fs |
LUAD | TCGA-17-Z005-01 | exon_skip_71341 | 59425003 | 59425197 | 59425145 | 59425146 | Frame_Shift_Ins | - | G | p.G160fs |
LUAD | TCGA-44-2662-01 | exon_skip_71341 | 59425003 | 59425197 | 59425145 | 59425146 | Frame_Shift_Ins | - | G | p.G160fs |
UCEC | TCGA-BG-A0M0-01 | exon_skip_71341 | 59425003 | 59425197 | 59425145 | 59425146 | Frame_Shift_Ins | - | G | p.Q160fs |
STAD | TCGA-D7-A4YV-01 | exon_skip_71333 | 59419017 | 59419114 | 59419061 | 59419061 | Nonsense_Mutation | G | A | p.R494* |
STAD | TCGA-D7-A4YV-01 | exon_skip_71333 | 59419017 | 59419114 | 59419061 | 59419061 | Nonsense_Mutation | G | A | p.R494X |
UCEC | TCGA-AP-A051-01 | exon_skip_71333 | 59419017 | 59419114 | 59419112 | 59419112 | Nonsense_Mutation | G | A | p.Q477* |
UCEC | TCGA-AX-A05Z-01 | exon_skip_71335 | 59423429 | 59423518 | 59423519 | 59423519 | Splice_Site | C | A | e7-1 |
- Depth of coverage in the three exons composing exon skipping event |
- Non-synonymous mutations located in the skipped exons in CCLE. |
Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
RCCAB_KIDNEY | 59419017 | 59419114 | 59419085 | 59419085 | Frame_Shift_Del | T | - | p.T486fs |
CW2_LARGE_INTESTINE | 59423429 | 59423518 | 59423492 | 59423492 | Frame_Shift_Del | A | - | p.F250fs |
CAL51_BREAST | 59425003 | 59425197 | 59425146 | 59425146 | Frame_Shift_Del | G | - | p.Q160fs |
HCT116_LARGE_INTESTINE | 59426725 | 59426942 | 59426849 | 59426850 | Frame_Shift_Del | TC | - | p.D74fs |
REC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 59419017 | 59419114 | 59419043 | 59419043 | Missense_Mutation | C | A | p.V500F |
HT115_LARGE_INTESTINE | 59423429 | 59423518 | 59423452 | 59423452 | Missense_Mutation | C | T | p.A264T |
NCIH441_LUNG | 59423429 | 59423518 | 59423456 | 59423456 | Missense_Mutation | C | G | p.Q262H |
OC316_OVARY | 59425003 | 59425197 | 59425047 | 59425047 | Missense_Mutation | C | A | p.G193C |
OC314_OVARY | 59425003 | 59425197 | 59425047 | 59425047 | Missense_Mutation | C | A | p.G193C |
NCIH1651_LUNG | 59425003 | 59425197 | 59425061 | 59425061 | Missense_Mutation | C | G | p.R188T |
SCH_STOMACH | 59425003 | 59425197 | 59425122 | 59425122 | Missense_Mutation | G | A | p.L168F |
DANG_PANCREAS | 59426725 | 59426942 | 59426854 | 59426854 | Missense_Mutation | C | G | p.E72D |
CW2_LARGE_INTESTINE | 59426725 | 59426942 | 59426886 | 59426886 | Missense_Mutation | C | T | p.V62M |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PATL1 |
sQTL information located at the skipped exons. |
Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PATL1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PATL1 |
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RelatedDrugs for PATL1 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for PATL1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |