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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for INPP4A |
 Gene summary |
| Gene information | Gene symbol | INPP4A | Gene ID | 3631 |
| Gene name | inositol polyphosphate-4-phosphatase type I A | |
| Synonyms | INPP4|TVAS1 | |
| Cytomap | 2q11.2 | |
| Type of gene | protein-coding | |
| Description | inositol polyphosphate-4-phosphatase type I Ainositol polyphosphate-4-phosphatase, type I, 107kDinositol polyphosphate-4-phosphatase, type I, 107kDatype I inositol 3,4-bisphosphate 4-phosphatase | |
| Modification date | 20200322 | |
| UniProtAcc | ||
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
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Gene structures and expression levels for INPP4A |
| Skipped exons in the ROSMAP, MSBB, and Mayo 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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ENSG00000040933
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for INPP4A |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_122025 | chr2 | 98520049:98520154:98520687:98520731:98533377:98533456 | 98520687:98520731 |
| exon_skip_128457 | chr2 | 98564640:98564763:98565640:98565766:98566029:98566169 | 98565640:98565766 |
| exon_skip_175778 | chr2 | 98555553:98555691:98559463:98559495:98563465:98563637 | 98559463:98559495 |
| exon_skip_177555 | chr2 | 98555553:98555808:98559463:98559495:98563465:98563637 | 98559463:98559495 |
| exon_skip_203897 | chr2 | 98543877:98544007:98545969:98546073:98546586:98546694 | 98545969:98546073 |
| exon_skip_233972 | chr2 | 98546586:98546694:98548955:98548969:98552786:98552969 | 98548955:98548969 |
| exon_skip_238184 | chr2 | 98568571:98568668:98568883:98569008:98569158:98569412 | 98568883:98569008 |
| exon_skip_252264 | chr2 | 98546586:98546694:98548955:98548969:98552786:98552879 | 98548955:98548969 |
| exon_skip_36814 | chr2 | 98552786:98552969:98554271:98554489:98555553:98555691 | 98554271:98554489 |
| exon_skip_54743 | chr2 | 98538891:98538981:98539528:98539675:98543877:98544007 | 98539528:98539675 |
| exon_skip_56768 | chr2 | 98444950:98445085:98518964:98519025:98519946:98520154 | 98518964:98519025 |
| exon_skip_62348 | chr2 | 98533377:98533495:98535729:98535845:98536129:98536208 | 98535729:98535845 |
| exon_skip_73283 | chr2 | 98555556:98555691:98559463:98559495:98563465:98563637 | 98559463:98559495 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_73283 | Mayo_CB | 6.815854e-01 | 7.926087e-01 | -1.110233e-01 | 8.045535e-06 |
| exon_skip_248494 | Mayo_TC | 4.358537e-01 | 5.485714e-01 | -1.127178e-01 | 1.118855e-04 |
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Open reading frame (ORF) annotation in the exon skipping event for INPP4A |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000074304 | 98565640 | 98565766 | Frame-shift |
| ENST00000523221 | 98565640 | 98565766 | Frame-shift |
| ENST00000074304 | 98520687 | 98520731 | In-frame |
| ENST00000523221 | 98520687 | 98520731 | In-frame |
| ENST00000074304 | 98545969 | 98546073 | In-frame |
| ENST00000523221 | 98545969 | 98546073 | In-frame |
| ENST00000074304 | 98548955 | 98548969 | In-frame |
| ENST00000523221 | 98548955 | 98548969 | In-frame |
| ENST00000074304 | 98554271 | 98554489 | In-frame |
| ENST00000523221 | 98554271 | 98554489 | In-frame |
| ENST00000074304 | 98559463 | 98559495 | In-frame |
| ENST00000523221 | 98559463 | 98559495 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000074304 | 98539528 | 98539675 | Frame-shift |
| ENST00000523221 | 98539528 | 98539675 | Frame-shift |
| ENST00000074304 | 98545969 | 98546073 | In-frame |
| ENST00000523221 | 98545969 | 98546073 | In-frame |
| ENST00000074304 | 98548955 | 98548969 | In-frame |
| ENST00000523221 | 98548955 | 98548969 | In-frame |
| ENST00000074304 | 98559463 | 98559495 | In-frame |
| ENST00000523221 | 98559463 | 98559495 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000074304 | 98518964 | 98519025 | 5UTR-5UTR |
| ENST00000074304 | 98565640 | 98565766 | Frame-shift |
| ENST00000523221 | 98565640 | 98565766 | Frame-shift |
| ENST00000074304 | 98520687 | 98520731 | In-frame |
| ENST00000523221 | 98520687 | 98520731 | In-frame |
| ENST00000074304 | 98535729 | 98535845 | In-frame |
| ENST00000523221 | 98535729 | 98535845 | In-frame |
| ENST00000074304 | 98545969 | 98546073 | In-frame |
| ENST00000523221 | 98545969 | 98546073 | In-frame |
| ENST00000074304 | 98548955 | 98548969 | In-frame |
| ENST00000523221 | 98548955 | 98548969 | In-frame |
| ENST00000074304 | 98559463 | 98559495 | In-frame |
| ENST00000523221 | 98559463 | 98559495 | In-frame |
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Infer the effects of exon skipping event on protein functional features for INPP4A |
p-ENSG00000040933_img4.png |
| Loci of skipped exons in ROSMAP 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 |
| ENST00000074304 | 6769 | 977 | 98520687 | 98520731 | 501 | 544 | 36 | 50 |
| ENST00000523221 | 2951 | 977 | 98520687 | 98520731 | 108 | 151 | 36 | 50 |
| ENST00000074304 | 6769 | 977 | 98545969 | 98546073 | 1344 | 1447 | 317 | 351 |
| ENST00000523221 | 2951 | 977 | 98545969 | 98546073 | 951 | 1054 | 317 | 351 |
| ENST00000074304 | 6769 | 977 | 98554271 | 98554489 | 1757 | 1974 | 454 | 527 |
| ENST00000523221 | 2951 | 977 | 98554271 | 98554489 | 1364 | 1581 | 454 | 527 |
| ENST00000074304 | 6769 | 977 | 98559463 | 98559495 | 2232 | 2263 | 613 | 623 |
| ENST00000523221 | 2951 | 977 | 98559463 | 98559495 | 1839 | 1870 | 613 | 623 |
| Loci of skipped exons in MSBB 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 |
| ENST00000074304 | 6769 | 977 | 98545969 | 98546073 | 1344 | 1447 | 317 | 351 |
| ENST00000523221 | 2951 | 977 | 98545969 | 98546073 | 951 | 1054 | 317 | 351 |
| ENST00000074304 | 6769 | 977 | 98559463 | 98559495 | 2232 | 2263 | 613 | 623 |
| ENST00000523221 | 2951 | 977 | 98559463 | 98559495 | 1839 | 1870 | 613 | 623 |
| Loci of skipped exons in Mayo 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 |
| ENST00000074304 | 6769 | 977 | 98520687 | 98520731 | 501 | 544 | 36 | 50 |
| ENST00000523221 | 2951 | 977 | 98520687 | 98520731 | 108 | 151 | 36 | 50 |
| ENST00000074304 | 6769 | 977 | 98535729 | 98535845 | 665 | 780 | 90 | 129 |
| ENST00000523221 | 2951 | 977 | 98535729 | 98535845 | 272 | 387 | 90 | 129 |
| ENST00000074304 | 6769 | 977 | 98545969 | 98546073 | 1344 | 1447 | 317 | 351 |
| ENST00000523221 | 2951 | 977 | 98545969 | 98546073 | 951 | 1054 | 317 | 351 |
| ENST00000074304 | 6769 | 977 | 98559463 | 98559495 | 2232 | 2263 | 613 | 623 |
| ENST00000523221 | 2951 | 977 | 98559463 | 98559495 | 1839 | 1870 | 613 | 623 |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| 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 |
| Q96PE3 | 36 | 50 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 36 | 50 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 36 | 50 | 31 | 137 | Domain | Note=C2 |
| Q96PE3 | 36 | 50 | 31 | 137 | Domain | Note=C2 |
| Q96PE3 | 317 | 351 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 317 | 351 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 454 | 527 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 454 | 527 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 454 | 527 | 487 | 487 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:23186163;Dbxref=PMID:19690332,PMID:23186163 |
| Q96PE3 | 454 | 527 | 487 | 487 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:23186163;Dbxref=PMID:19690332,PMID:23186163 |
| Q96PE3 | 613 | 623 | 574 | 613 | Alternative sequence | ID=VSP_015241;Note=In isoform 2 and isoform 4. GNPDSHAYWIRPEDPFCDVPSSPCPSTMPSTACHPHLTTH->D;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:7608176,ECO:0000303|PubMed:9295334;Dbxref=PMID:7608176,PMID:9295334 |
| Q96PE3 | 613 | 623 | 574 | 613 | Alternative sequence | ID=VSP_015241;Note=In isoform 2 and isoform 4. GNPDSHAYWIRPEDPFCDVPSSPCPSTMPSTACHPHLTTH->D;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:7608176,ECO:0000303|PubMed:9295334;Dbxref=PMID:7608176,PMID:9295334 |
| Q96PE3 | 613 | 623 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 613 | 623 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Lost protein functional features of individual exon skipping events in MSBB. |
| 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 |
| Q96PE3 | 317 | 351 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 317 | 351 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 613 | 623 | 574 | 613 | Alternative sequence | ID=VSP_015241;Note=In isoform 2 and isoform 4. GNPDSHAYWIRPEDPFCDVPSSPCPSTMPSTACHPHLTTH->D;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:7608176,ECO:0000303|PubMed:9295334;Dbxref=PMID:7608176,PMID:9295334 |
| Q96PE3 | 613 | 623 | 574 | 613 | Alternative sequence | ID=VSP_015241;Note=In isoform 2 and isoform 4. GNPDSHAYWIRPEDPFCDVPSSPCPSTMPSTACHPHLTTH->D;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:7608176,ECO:0000303|PubMed:9295334;Dbxref=PMID:7608176,PMID:9295334 |
| Q96PE3 | 613 | 623 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 613 | 623 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Lost protein functional features of individual exon skipping events in Mayo. |
| 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 |
| Q96PE3 | 36 | 50 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 36 | 50 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 36 | 50 | 31 | 137 | Domain | Note=C2 |
| Q96PE3 | 36 | 50 | 31 | 137 | Domain | Note=C2 |
| Q96PE3 | 90 | 129 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 90 | 129 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 90 | 129 | 31 | 137 | Domain | Note=C2 |
| Q96PE3 | 90 | 129 | 31 | 137 | Domain | Note=C2 |
| Q96PE3 | 317 | 351 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 317 | 351 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 613 | 623 | 574 | 613 | Alternative sequence | ID=VSP_015241;Note=In isoform 2 and isoform 4. GNPDSHAYWIRPEDPFCDVPSSPCPSTMPSTACHPHLTTH->D;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:7608176,ECO:0000303|PubMed:9295334;Dbxref=PMID:7608176,PMID:9295334 |
| Q96PE3 | 613 | 623 | 574 | 613 | Alternative sequence | ID=VSP_015241;Note=In isoform 2 and isoform 4. GNPDSHAYWIRPEDPFCDVPSSPCPSTMPSTACHPHLTTH->D;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:7608176,ECO:0000303|PubMed:9295334;Dbxref=PMID:7608176,PMID:9295334 |
| Q96PE3 | 613 | 623 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
| Q96PE3 | 613 | 623 | 1 | 977 | Chain | ID=PRO_0000190232;Note=Type I inositol 3%2C4-bisphosphate 4-phosphatase |
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3'-UTR located exon skipping events that lost miRNA binding sites in INPP4A |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for INPP4A |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - 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 |
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AD stage-associated exon skippint events for INPP4A |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
| ADstage | MSBB | IFG | exon_skip_73283 | -4.700197e-01 | 1.160900e-02 | chr2 | + | 98555556 | 98555691 | 98559463 | 98559495 | 98563465 | 98563637 |
| CDR | MSBB | IFG | exon_skip_73283 | -4.112108e-01 | 2.971114e-02 | chr2 | + | 98555556 | 98555691 | 98559463 | 98559495 | 98563465 | 98563637 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for INPP4A |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for INPP4A |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | TARDBP | exon_skip_290810 | 4.403986e-01 | 9.788900e-09 |
| CB | PUM1 | exon_skip_290810 | 4.329346e-01 | 1.842095e-08 |
| CB | CELF1 | exon_skip_290810 | 4.116025e-01 | 1.033765e-07 |
| CB | SRSF1 | exon_skip_290810 | 4.463685e-01 | 5.838556e-09 |
| CB | RBM6 | exon_skip_73283 | -4.122992e-01 | 1.438860e-07 |
| CB | CNOT4 | exon_skip_73283 | -6.133780e-01 | 5.641989e-17 |
| CB | PCBP1 | exon_skip_73283 | -4.442783e-01 | 1.101090e-08 |
| CB | TRA2A | exon_skip_73283 | -6.632831e-01 | 1.708220e-20 |
| CB | RC3H1 | exon_skip_73283 | -4.129171e-01 | 1.372561e-07 |
| HCC | TRNAU1AP | exon_skip_248494 | -4.713007e-01 | 4.649219e-16 |
| HCC | TRNAU1AP | exon_skip_233972 | -4.089247e-01 | 8.047347e-12 |
| TC | PUM1 | exon_skip_248494 | 5.975092e-01 | 4.433776e-16 |
| TC | CELF1 | exon_skip_248494 | 5.481429e-01 | 2.683910e-13 |
| TC | PUM1 | exon_skip_233972 | 6.070182e-01 | 2.351372e-15 |
| TC | CELF1 | exon_skip_233972 | 4.940507e-01 | 6.385209e-10 |
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RelatedDrugs for INPP4A |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for INPP4A |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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