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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 TPM4 |
 Gene summary |
| Gene information | Gene symbol | TPM4 | Gene ID | 7171 |
| Gene name | tropomyosin 4 | |
| Synonyms | HEL-S-108 | |
| Cytomap | 19p13.12-p13.11 | |
| Type of gene | protein-coding | |
| Description | tropomyosin alpha-4 chainTM30p1epididymis secretory protein Li 108 | |
| Modification date | 20200320 | |
| UniProtAcc | A0A2R8Y5V9, A0A2R8YE05, A0A2R8YEU4, A0A2R8YGX3, A0A2R8YH90, | |
| 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 TPM4 |
| 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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ENSG00000167460
| 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 |
| PCC | UP | ENST00000663894.1 | TPM4-232:retained_intron:TPM4 | 3.977882e+01 | 2.174432e+00 | 3.994230e-05 | 3.303490e-03 |
| HCC | UP | ENST00000663894.1 | TPM4-232:retained_intron:TPM4 | 1.184227e+01 | 2.058539e+00 | 5.533110e-06 | 9.184017e-04 |
| CB | DOWN | ENST00000663894.1 | TPM4-232:retained_intron:TPM4 | 9.491069e+02 | -1.589415e+00 | 2.130419e-10 | 1.196489e-08 |
| CB | DOWN | ENST00000591645.3 | TPM4-213:lncRNA:TPM4 | 5.310006e+02 | -1.051301e+00 | 1.790813e-08 | 4.952098e-07 |
| TC | DOWN | ENST00000657915.1 | TPM4-228:lncRNA:TPM4 | 1.071364e+02 | -8.549357e-01 | 7.172691e-11 | 1.455231e-08 |
| TC | DOWN | ENST00000647037.1 | TPM4-222:nonsense_mediated_decay:TPM4 | 2.816828e+02 | -1.365117e+00 | 4.213824e-07 | 2.006358e-05 |
| TC | UP | ENST00000646974.2 | TPM4-221:protein_coding:TPM4 | 4.496416e+01 | 1.511897e+00 | 1.625554e-05 | 3.813827e-04 |
| TC | DOWN | ENST00000663894.1 | TPM4-232:retained_intron:TPM4 | 1.503420e+02 | -1.457483e+00 | 1.149466e-04 | 1.806833e-03 |
| TC | DOWN | ENST00000588410.2 | TPM4-208:retained_intron:TPM4 | 8.751621e+00 | -1.231965e+00 | 7.273873e-04 | 7.721014e-03 |
| TC | UP | ENST00000659595.1 | TPM4-231:nonsense_mediated_decay:TPM4 | 1.038584e+02 | 1.070603e+00 | 2.428165e-03 | 1.943696e-02 |
| 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 TPM4 |
| 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_103837 | chr19 | 16080765:16081343:16081441:16081538:16081913:16082046 | 16081441:16081538 |
| exon_skip_122252 | chr19 | 16076091:16076172:16086423:16086540:16088027:16088097 | 16086423:16086540 |
| exon_skip_145584 | chr19 | 16076652:16076697:16086423:16086540:16088027:16088097 | 16086423:16086540 |
| exon_skip_148305 | chr19 | 16093735:16093753:16095264:16095357:16101264:16101409 | 16095264:16095357 |
| exon_skip_160772 | chr19 | 16093684:16093753:16095264:16095893:16101264:16101409 | 16095264:16095893 |
| exon_skip_161405 | chr19 | 16081913:16082046:16086423:16086540:16088027:16088097 | 16086423:16086540 |
| exon_skip_169406 | chr19 | 16076645:16076697:16081020:16081075:16081913:16081936 | 16081020:16081075 |
| exon_skip_174856 | chr19 | 16089047:16089120:16093536:16093598:16093684:16093746 | 16093536:16093598 |
| exon_skip_175391 | chr19 | 16077021:16077130:16080915:16081075:16081913:16081936 | 16080915:16081075 |
| exon_skip_194078 | chr19 | 16076645:16076697:16081020:16081075:16081913:16082046 | 16081020:16081075 |
| exon_skip_221306 | chr19 | 16089045:16089120:16093536:16093598:16093684:16093746 | 16093536:16093598 |
| exon_skip_222997 | chr19 | 16093735:16093753:16095264:16095893:16101264:16101409 | 16095264:16095893 |
| exon_skip_224537 | chr19 | 16093684:16093753:16095264:16095357:16101264:16101409 | 16095264:16095357 |
| exon_skip_244876 | chr19 | 16076091:16076172:16081913:16082046:16086423:16086540 | 16081913:16082046 |
| exon_skip_265602 | chr19 | 16076652:16076697:16081913:16082046:16086423:16086540 | 16081913:16082046 |
| exon_skip_271034 | chr19 | 16089045:16089120:16093040:16093132:16093536:16093598 | 16093040:16093132 |
| exon_skip_28007 | chr19 | 16076687:16076697:16081913:16082046:16086423:16086540 | 16081913:16082046 |
| exon_skip_282607 | chr19 | 16086423:16086540:16088027:16089120:16093536:16093598 | 16088027:16089120 |
| exon_skip_295977 | chr19 | 16067733:16067738:16076047:16076172:16081913:16082046 | 16076047:16076172 |
| exon_skip_32372 | chr19 | 16093684:16093753:16095264:16095893:16101264:16101547 | 16095264:16095893 |
| exon_skip_42671 | chr19 | 16093684:16093753:16095264:16095893:16101264:16102948 | 16095264:16095893 |
| exon_skip_43241 | chr19 | 16077957:16078149:16081020:16081075:16081913:16082046 | 16081020:16081075 |
| exon_skip_43608 | chr19 | 16089047:16089120:16093040:16093132:16093536:16093598 | 16093040:16093132 |
| exon_skip_49257 | chr19 | 16076449:16076697:16081913:16082046:16086423:16086540 | 16081913:16082046 |
| exon_skip_50208 | chr19 | 16076679:16076697:16081913:16082046:16086423:16086540 | 16081913:16082046 |
| exon_skip_50502 | chr19 | 16080765:16081343:16081441:16081538:16081913:16081936 | 16081441:16081538 |
| exon_skip_84767 | chr19 | 16081024:16081343:16081441:16081538:16081913:16082046 | 16081441:16081538 |
| exon_skip_91874 | chr19 | 16086423:16086540:16088027:16088097:16089045:16089120 | 16088027:16088097 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for TPM4 |
| 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 |
| ENST00000643579 | 16081913 | 16082046 | Frame-shift |
| ENST00000300933 | 16086423 | 16086540 | Frame-shift |
| ENST00000643579 | 16086423 | 16086540 | Frame-shift |
| ENST00000300933 | 16081020 | 16081075 | In-frame |
| ENST00000300933 | 16093536 | 16093598 | In-frame |
| ENST00000643579 | 16093536 | 16093598 | 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 |
| ENST00000643579 | 16081913 | 16082046 | Frame-shift |
| ENST00000300933 | 16093536 | 16093598 | In-frame |
| ENST00000643579 | 16093536 | 16093598 | 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 |
| ENST00000643579 | 16081913 | 16082046 | Frame-shift |
| ENST00000300933 | 16086423 | 16086540 | Frame-shift |
| ENST00000643579 | 16086423 | 16086540 | Frame-shift |
| ENST00000300933 | 16088027 | 16088097 | Frame-shift |
| ENST00000643579 | 16088027 | 16088097 | Frame-shift |
| ENST00000300933 | 16081020 | 16081075 | In-frame |
| ENST00000300933 | 16093536 | 16093598 | In-frame |
| ENST00000643579 | 16093536 | 16093598 | In-frame |
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Infer the effects of exon skipping event on protein functional features for TPM4 |
p-ENSG00000167460_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 |
| ENST00000300933 | 2683 | 248 | 16093536 | 16093598 | 793 | 854 | 177 | 198 |
| ENST00000643579 | 2424 | 248 | 16093536 | 16093598 | 596 | 657 | 177 | 198 |
| 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 |
| ENST00000300933 | 2683 | 248 | 16093536 | 16093598 | 793 | 854 | 177 | 198 |
| ENST00000643579 | 2424 | 248 | 16093536 | 16093598 | 596 | 657 | 177 | 198 |
| 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 |
| ENST00000300933 | 2683 | 248 | 16093536 | 16093598 | 793 | 854 | 177 | 198 |
| ENST00000643579 | 2424 | 248 | 16093536 | 16093598 | 596 | 657 | 177 | 198 |
| 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 |
| P67936 | 177 | 198 | 2 | 248 | Chain | ID=PRO_0000205635;Note=Tropomyosin alpha-4 chain |
| P67936 | 177 | 198 | 2 | 248 | Chain | ID=PRO_0000205635;Note=Tropomyosin alpha-4 chain |
| P67936 | 177 | 198 | 2 | 248 | Coiled coil | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P67936 | 177 | 198 | 2 | 248 | Coiled coil | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P67936 | 177 | 198 | 177 | 177 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P67936 | 177 | 198 | 177 | 177 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| 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 |
| P67936 | 177 | 198 | 2 | 248 | Chain | ID=PRO_0000205635;Note=Tropomyosin alpha-4 chain |
| P67936 | 177 | 198 | 2 | 248 | Chain | ID=PRO_0000205635;Note=Tropomyosin alpha-4 chain |
| P67936 | 177 | 198 | 2 | 248 | Coiled coil | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P67936 | 177 | 198 | 2 | 248 | Coiled coil | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P67936 | 177 | 198 | 177 | 177 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P67936 | 177 | 198 | 177 | 177 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| 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 |
| P67936 | 177 | 198 | 2 | 248 | Chain | ID=PRO_0000205635;Note=Tropomyosin alpha-4 chain |
| P67936 | 177 | 198 | 2 | 248 | Chain | ID=PRO_0000205635;Note=Tropomyosin alpha-4 chain |
| P67936 | 177 | 198 | 2 | 248 | Coiled coil | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P67936 | 177 | 198 | 2 | 248 | Coiled coil | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P67936 | 177 | 198 | 177 | 177 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P67936 | 177 | 198 | 177 | 177 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
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3'-UTR located exon skipping events that lost miRNA binding sites in TPM4 |
| 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 TPM4 |
| - 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 TPM4 |
| 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 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TPM4 |
| 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 TPM4 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for TPM4 |
| 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 TPM4 |
| 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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