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Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for TPM3 |
Gene summary |
Gene information | Gene symbol | TPM3 | Gene ID | 7170 |
Gene name | tropomyosin 3 | |
Synonyms | CAPM1|CFTD|HEL-189|HEL-S-82p|NEM1|OK/SW-cl.5|TM-5|TM3|TM30|TM30nm|TM5|TPM3nu|TPMsk3|TRK|hscp30 | |
Cytomap | 1q21.3 | |
Type of gene | protein-coding | |
Description | tropomyosin alpha-3 chainalpha-tropomyosin, slow skeletalcytoskeletal tropomyosin TM30epididymis luminal protein 189epididymis secretory sperm binding protein Li 82pheat-stable cytoskeletal protein 30 kDatropomyosin 3 nutropomyosin gammatropomyosi | |
Modification date | 20200328 | |
UniProtAcc | A0A087WWU8, A0A0S2Z4G4, | |
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 TPM3 |
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. |
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 |
DLPFC | DOWN | ENST00000302206.9 | TPM3-202:protein_coding:TPM3 | 3.694297e+00 | -1.071762e+00 | 6.627483e-05 | 5.351096e-03 |
PG | UP | ENST00000312970.13 | TPM3-203:lncRNA:TPM3 | 9.747140e+01 | 1.592222e+00 | 1.177576e-04 | 3.099953e-03 |
CB | UP | ENST00000509409.5 | TPM3-219:nonsense_mediated_decay:TPM3 | 4.637579e+01 | 1.225351e+00 | 4.842818e-04 | 2.803783e-03 |
TC | DOWN | ENST00000611659.4 | TPM3-223:protein_coding:TPM3 | 1.299612e+01 | -1.354099e+00 | 3.593313e-03 | 2.612345e-02 |
TC | UP | ENST00000509409.5 | TPM3-219:nonsense_mediated_decay:TPM3 | 8.771746e+01 | 8.998524e-01 | 4.363330e-03 | 3.023536e-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 TPM3 |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
exon_skip_115535 | chr1 | 154157658:154157721:154169305:154169383:154170400:154170469 | 154169305:154169383 |
exon_skip_117459 | chr1 | 154173084:154173201:154176115:154176248:154182988:154183042 | 154176115:154176248 |
exon_skip_126955 | chr1 | 154170707:154170711:154172029:154172104:154172908:154172978 | 154172029:154172104 |
exon_skip_131329 | chr1 | 154170707:154170711:154171413:154171488:154172908:154172978 | 154171413:154171488 |
exon_skip_167413 | chr1 | 154167742:154167940:154169305:154169383:154170400:154170469 | 154169305:154169383 |
exon_skip_171229 | chr1 | 154173084:154173201:154176115:154176248:154178114:154178183 | 154176115:154176248 |
exon_skip_182091 | chr1 | 154173160:154173201:154176115:154176248:154182988:154183042 | 154176115:154176248 |
exon_skip_192862 | chr1 | 154157686:154157721:154158898:154159048:154170400:154170469 | 154158898:154159048 |
exon_skip_22662 | chr1 | 154157488:154157721:154158898:154159048:154170400:154170469 | 154158898:154159048 |
exon_skip_239333 | chr1 | 154157488:154157721:154169305:154169383:154170400:154170469 | 154169305:154169383 |
exon_skip_241283 | chr1 | 154157583:154157721:154158898:154159048:154170400:154170469 | 154158898:154159048 |
exon_skip_275015 | chr1 | 154170707:154170711:154171413:154171488:154172029:154172091 | 154171413:154171488 |
exon_skip_27691 | chr1 | 154173084:154173201:154176115:154176248:154176854:154176952 | 154176115:154176248 |
exon_skip_290641 | chr1 | 154171413:154171488:154172029:154172104:154172908:154172978 | 154172029:154172104 |
exon_skip_290903 | chr1 | 154157033:154157721:154158898:154159048:154170400:154170469 | 154158898:154159048 |
exon_skip_30751 | chr1 | 154173084:154173201:154176115:154176248:154182988:154183147 | 154176115:154176248 |
exon_skip_68804 | chr1 | 154170400:154170469:154170649:154170711:154172029:154172104 | 154170649:154170711 |
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 TPM3 |
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 |
ENST00000368530 | 154170649 | 154170711 | In-frame |
ENST00000368530 | 154172029 | 154172104 | 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 |
ENST00000368530 | 154169305 | 154169383 | Frame-shift |
ENST00000368530 | 154172029 | 154172104 | 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 |
ENST00000368530 | 154169305 | 154169383 | Frame-shift |
ENST00000368530 | 154172029 | 154172104 | In-frame |
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Infer the effects of exon skipping event on protein functional features for TPM3 |
p-ENSG00000143549_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 |
ENST00000368530 | 1540 | 285 | 154170649 | 154170711 | 836 | 897 | 214 | 234 |
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 |
P06753 | 214 | 234 | 2 | 285 | Chain | ID=PRO_0000205632;Note=Tropomyosin alpha-3 chain |
P06753 | 214 | 234 | 1 | 285 | Coiled coil | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
P06753 | 214 | 234 | 216 | 216 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P58775 |
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 TPM3 |
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 TPM3 |
- 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 TPM3 |
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 TPM3 |
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 TPM3 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
IFG | MBNL1 | exon_skip_126955 | 4.680863e-01 | 1.200405e-02 |
STG | HNRNPD | exon_skip_275015 | 4.166467e-01 | 5.016795e-04 |
STG | CELF1 | exon_skip_275015 | 4.092430e-01 | 6.450787e-04 |
STG | NOVA1 | exon_skip_275015 | 4.394086e-01 | 2.231896e-04 |
TC | NOVA1 | exon_skip_275015 | 4.681474e-01 | 4.894473e-10 |
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RelatedDrugs for TPM3 |
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 TPM3 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |