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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 ATP2B4 |
 Gene summary |
| Gene information | Gene symbol | ATP2B4 | Gene ID | 493 |
| Gene name | ATPase plasma membrane Ca2+ transporting 4 | |
| Synonyms | ATP2B2|MXRA1|PMCA4|PMCA4b|PMCA4x | |
| Cytomap | 1q32.1 | |
| Type of gene | protein-coding | |
| Description | plasma membrane calcium-transporting ATPase 4ATPase, Ca++ transporting, plasma membrane 4matrix-remodeling-associated protein 1sarcolemmal calcium pump | |
| Modification date | 20200327 | |
| 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 |
| ATP2B4 | GO:0006874 | cellular calcium ion homeostasis | 19278978|25798335 |
| ATP2B4 | GO:0010629 | negative regulation of gene expression | 25147342 |
| ATP2B4 | GO:0010751 | negative regulation of nitric oxide mediated signal transduction | 19278978 |
| ATP2B4 | GO:0016525 | negative regulation of angiogenesis | 25147342 |
| ATP2B4 | GO:0033138 | positive regulation of peptidyl-serine phosphorylation | 19278978 |
| ATP2B4 | GO:0043537 | negative regulation of blood vessel endothelial cell migration | 25147342 |
| ATP2B4 | GO:0045019 | negative regulation of nitric oxide biosynthetic process | 11591728|19278978 |
| ATP2B4 | GO:0051001 | negative regulation of nitric-oxide synthase activity | 11591728|17242280|19278978|19287093 |
| ATP2B4 | GO:0070885 | negative regulation of calcineurin-NFAT signaling cascade | 19287093|25147342 |
| ATP2B4 | GO:0071872 | cellular response to epinephrine stimulus | 19278978 |
| ATP2B4 | GO:0098736 | negative regulation of the force of heart contraction | 17242280 |
| ATP2B4 | GO:0140199 | negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process | 17242280 |
| ATP2B4 | GO:1900082 | negative regulation of arginine catabolic process | 19278978 |
| ATP2B4 | GO:1901660 | calcium ion export | 25798335 |
| ATP2B4 | GO:1902548 | negative regulation of cellular response to vascular endothelial growth factor stimulus | 25147342 |
| ATP2B4 | GO:1903078 | positive regulation of protein localization to plasma membrane | 15955804 |
| ATP2B4 | GO:1903249 | negative regulation of citrulline biosynthetic process | 19278978 |
| ATP2B4 | GO:2000481 | positive regulation of cAMP-dependent protein kinase activity | 19278978 |
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Gene structures and expression levels for ATP2B4 |
| 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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ENSG00000058668
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | UP | ENST00000367218.7 | ATP2B4-204:protein_coding:ATP2B4 | 1.900110e+03 | 8.131579e-01 | 1.825925e-06 | 2.502685e-05 |
| TC | UP | ENST00000357681.9 | ATP2B4-203:protein_coding:ATP2B4 | 1.336173e+03 | 9.166636e-01 | 1.119520e-07 | 6.678089e-06 |
| 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 ATP2B4 |
| 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_179483 | chr1 | 203722478:203722689:203723881:203723988:203727395:203727571 | 203723881:203723988 |
| exon_skip_211144 | chr1 | 203682809:203683398:203698157:203698354:203699460:203699717 | 203698157:203698354 |
| exon_skip_211896 | chr1 | 203703652:203703813:203707009:203707223:203707862:203708104 | 203707009:203707223 |
| exon_skip_244746 | chr1 | 203727395:203727571:203733223:203733400:203739546:203744081 | 203733223:203733400 |
| exon_skip_274057 | chr1 | 203700798:203700923:203702044:203702079:203703652:203703813 | 203702044:203702079 |
| exon_skip_30449 | chr1 | 203711960:203712139:203713165:203713252:203714171:203714277 | 203713165:203713252 |
| exon_skip_8113 | chr1 | 203727395:203727571:203733223:203733400:203739546:203739572 | 203733223:203733400 |
| 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_244746 | MSBB_PG | 5.517037e-01 | 6.980000e-01 | -1.462963e-01 | 5.899727e-03 |
| exon_skip_8113 | Mayo_TC | 4.101220e-01 | 5.414493e-01 | -1.313273e-01 | 1.366665e-04 |
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Open reading frame (ORF) annotation in the exon skipping event for ATP2B4 |
| 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 |
| 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 |
| 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 |
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Infer the effects of exon skipping event on protein functional features for ATP2B4 |
p-ENSG00000058668_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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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3'-UTR located exon skipping events that lost miRNA binding sites in ATP2B4 |
| 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 ATP2B4 |
| - 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 ATP2B4 |
| 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_30449 | -4.260682e-01 | 2.377595e-02 | chr1 | + | 203711960 | 203712139 | 203713165 | 203713252 | 203714171 | 203714277 |
| CDR | MSBB | IFG | exon_skip_30449 | -5.441951e-01 | 2.756331e-03 | chr1 | + | 203711960 | 203712139 | 203713165 | 203713252 | 203714171 | 203714277 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ATP2B4 |
| 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 ATP2B4 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | MSI1 | exon_skip_244746 | -5.833859e-01 | 1.100405e-14 |
| CB | RALYL | exon_skip_244746 | 5.310120e-01 | 5.391741e-12 |
| DLPFC | RBMS2 | exon_skip_244746 | -6.147740e-01 | 4.836944e-29 |
| DLPFC | MSI1 | exon_skip_244746 | -4.959316e-01 | 6.417926e-18 |
| DLPFC | KHDRBS2 | exon_skip_244746 | 5.809485e-01 | 2.088687e-25 |
| DLPFC | HNRNPF | exon_skip_244746 | -4.121108e-01 | 2.498915e-12 |
| FL | RBMS2 | exon_skip_244746 | -4.092205e-01 | 2.852434e-09 |
| FL | SRSF2 | exon_skip_244746 | 5.121938e-01 | 1.954777e-14 |
| FL | MSI1 | exon_skip_244746 | -5.988618e-01 | 2.306765e-20 |
| FL | FXR2 | exon_skip_244746 | 4.944958e-01 | 2.022951e-13 |
| FL | RBM24 | exon_skip_244746 | 4.911055e-01 | 3.117546e-13 |
| FL | HNRNPA0 | exon_skip_244746 | 5.168859e-01 | 1.028128e-14 |
| FL | PUM1 | exon_skip_244746 | 4.596003e-01 | 1.392666e-11 |
| FL | RALYL | exon_skip_244746 | 6.369824e-01 | 1.378922e-23 |
| FL | EIF4G2 | exon_skip_244746 | 4.373273e-01 | 1.631719e-10 |
| FL | RBM23 | exon_skip_244746 | 4.092672e-01 | 2.839520e-09 |
| HCC | RBMS2 | exon_skip_244746 | -5.847477e-01 | 2.413318e-26 |
| HCC | MSI1 | exon_skip_244746 | -5.782659e-01 | 1.135428e-25 |
| HCC | RBM6 | exon_skip_244746 | -5.084899e-01 | 2.724021e-19 |
| HCC | TRNAU1AP | exon_skip_244746 | -4.034030e-01 | 4.558517e-12 |
| HCC | PCBP4 | exon_skip_244746 | -4.982177e-01 | 1.802672e-18 |
| HCC | UNK | exon_skip_244746 | -4.849218e-01 | 1.896712e-17 |
| HCC | KHDRBS2 | exon_skip_244746 | 4.256895e-01 | 2.128154e-13 |
| HCC | EIF4G2 | exon_skip_244746 | -4.272048e-01 | 1.713568e-13 |
| HCC | SRSF4 | exon_skip_244746 | -4.024529e-01 | 5.168868e-12 |
| HCC | SRSF5 | exon_skip_244746 | -4.224131e-01 | 3.387402e-13 |
| HCC | HNRNPF | exon_skip_244746 | -5.333317e-01 | 2.147461e-21 |
| IFG | IGF2BP2 | exon_skip_244746 | -4.364514e-01 | 2.023269e-02 |
| IFG | RBM47 | exon_skip_244746 | -4.345322e-01 | 2.085274e-02 |
| IFG | RBM46 | exon_skip_244746 | -4.176222e-01 | 2.701790e-02 |
| IFG | KHDRBS2 | exon_skip_244746 | 5.322924e-01 | 3.548551e-03 |
| IFG | RBM24 | exon_skip_244746 | 5.767186e-01 | 1.315773e-03 |
| IFG | RALYL | exon_skip_244746 | 5.635553e-01 | 1.790997e-03 |
| PCC | RBMS2 | exon_skip_244746 | -7.188008e-01 | 3.323075e-34 |
| PCC | MSI1 | exon_skip_244746 | -5.700021e-01 | 3.129489e-19 |
| PCC | RBM6 | exon_skip_244746 | -4.618010e-01 | 2.490828e-12 |
| PCC | RBM47 | exon_skip_244746 | -4.169144e-01 | 4.133420e-10 |
| PCC | PCBP4 | exon_skip_244746 | -4.757034e-01 | 4.368642e-13 |
| PCC | PUM1 | exon_skip_244746 | 5.116239e-01 | 3.320214e-15 |
| PCC | RALYL | exon_skip_244746 | 5.074153e-01 | 6.060105e-15 |
| PCC | HNRNPF | exon_skip_244746 | -5.902157e-01 | 8.069502e-21 |
| PG | SRSF2 | exon_skip_244746 | 5.471851e-01 | 3.122281e-16 |
| PG | MSI1 | exon_skip_244746 | -4.618668e-01 | 1.980071e-11 |
| PG | CNOT4 | exon_skip_244746 | 5.287265e-01 | 4.466945e-15 |
| PG | TRNAU1AP | exon_skip_244746 | 4.174526e-01 | 2.071981e-09 |
| PG | FXR2 | exon_skip_244746 | 7.196521e-01 | 1.318334e-31 |
| PG | PCBP1 | exon_skip_244746 | 5.608791e-01 | 3.892124e-17 |
| PG | RC3H1 | exon_skip_244746 | 4.550132e-01 | 4.243046e-11 |
| PG | KHDRBS2 | exon_skip_244746 | 5.925486e-01 | 2.144234e-19 |
| PG | RBM24 | exon_skip_244746 | 7.164447e-01 | 3.236776e-31 |
| PG | ENOX1 | exon_skip_244746 | 4.937256e-01 | 4.546879e-13 |
| PG | HNRNPA0 | exon_skip_244746 | 6.069721e-01 | 1.651443e-20 |
| PG | PUM1 | exon_skip_244746 | 7.370951e-01 | 7.931425e-34 |
| PG | HNRNPDL | exon_skip_244746 | 5.825092e-01 | 1.185757e-18 |
| PG | HNRNPD | exon_skip_244746 | 5.882344e-01 | 4.503911e-19 |
| PG | RALYL | exon_skip_244746 | 8.014744e-01 | 7.637024e-44 |
| PG | EIF4G2 | exon_skip_244746 | 5.168837e-01 | 2.265699e-14 |
| PG | RBM23 | exon_skip_244746 | 5.185515e-01 | 1.809432e-14 |
| PG | SRSF4 | exon_skip_244746 | 4.162741e-01 | 2.323256e-09 |
| PG | SRSF5 | exon_skip_244746 | 5.502526e-01 | 1.974662e-16 |
| PG | ZCRB1 | exon_skip_244746 | 4.869422e-01 | 1.049572e-12 |
| STG | MSI1 | exon_skip_244746 | -4.352214e-01 | 2.522693e-05 |
| STG | HNRNPA0 | exon_skip_244746 | 4.248178e-01 | 4.110844e-05 |
| STG | RALYL | exon_skip_244746 | 5.458907e-01 | 4.541451e-08 |
| TC | RBMS2 | exon_skip_8113 | -5.878565e-01 | 2.097044e-15 |
| TC | SRSF2 | exon_skip_8113 | 5.356154e-01 | 1.378234e-12 |
| TC | MSI1 | exon_skip_8113 | -5.949593e-01 | 7.916392e-16 |
| TC | FXR2 | exon_skip_8113 | 6.132318e-01 | 5.765508e-17 |
| TC | KHDRBS2 | exon_skip_8113 | 8.236669e-01 | 1.548186e-38 |
| TC | RBM24 | exon_skip_8113 | 7.454400e-01 | 4.934257e-28 |
| TC | ENOX1 | exon_skip_8113 | 5.205104e-01 | 7.362449e-12 |
| TC | HNRNPA0 | exon_skip_8113 | 7.175338e-01 | 3.577312e-25 |
| TC | PUM1 | exon_skip_8113 | 6.685913e-01 | 6.578919e-21 |
| TC | HNRNPDL | exon_skip_8113 | 4.596379e-01 | 2.906283e-09 |
| TC | HNRNPD | exon_skip_8113 | 5.985698e-01 | 4.780180e-16 |
| TC | RALYL | exon_skip_8113 | 8.669585e-01 | 6.489992e-47 |
| TC | SRSF5 | exon_skip_8113 | 4.434974e-01 | 1.176184e-08 |
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RelatedDrugs for ATP2B4 |
| 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 ATP2B4 |
| 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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