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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for ACTA1 |
 Gene summary |
| Gene information | Gene symbol | ACTA1 | Gene ID | 58 |
| Gene name | actin, alpha 1, skeletal muscle | |
| Synonyms | ACTA|ASMA|CFTD|CFTD1|CFTDM|MPFD|NEM1|NEM2|NEM3|SHPM | |
| Cytomap | 1q42.13 | |
| Type of gene | protein-coding | |
| Description | actin, alpha skeletal musclenemaline myopathy type 3 | |
| Modification date | 20180520 | |
| UniProtAcc | P68133 | |
| Context | PubMed: ACTA1 [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 |
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Exon skipping events across known transcript of Ensembl for ACTA1 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 ACTA1 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for ACTA1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_37927 | 1 | 229567740:229567932:229568016:229568178:229568302:229568627 | 229568016:229568178 | ENSG00000143632.10 | ENST00000366684.3 |
| exon_skip_37929 | 1 | 229568404:229568627:229568733:229568874:229569750:229569841 | 229568733:229568874 | ENSG00000143632.10 | ENST00000366683.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for ACTA1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_37927 | 1 | 229567740:229567932:229568016:229568178:229568302:229568627 | 229568016:229568178 | ENSG00000143632.10 | ENST00000366684.3 |
| exon_skip_37929 | 1 | 229568404:229568627:229568733:229568874:229569750:229569841 | 229568733:229568874 | ENSG00000143632.10 | ENST00000366683.2 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for ACTA1 |
| 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 |
| ENST00000366684 | 229568016 | 229568178 | 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 |
| ENST00000366684 | 229568016 | 229568178 | In-frame |
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Infer the effects of exon skipping event on protein functional features for ACTA1 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| 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 |
| ENST00000366684 | 1508 | 377 | 229568016 | 229568178 | 558 | 719 | 151 | 205 |
| 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 |
| ENST00000366684 | 1508 | 377 | 229568016 | 229568178 | 558 | 719 | 151 | 205 |
| 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 |
| P68133 | 151 | 205 | 2 | 377 | Chain | ID=PRO_0000442803;Note=Actin%2C alpha skeletal muscle%2C intermediate form;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P62737 |
| P68133 | 151 | 205 | 3 | 377 | Chain | ID=PRO_0000442804;Note=Actin%2C alpha skeletal muscle;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P68135 |
| P68133 | 151 | 205 | 156 | 156 | Natural variant | ID=VAR_062447;Note=In NEM3. D->N |
| P68133 | 151 | 205 | 165 | 165 | Natural variant | ID=VAR_011684;Note=In MPCETM. V->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10508519,ECO:0000269|PubMed:15198992;Dbxref=dbSNP:rs121909522,PMID:10508519,PMID:15198992 |
| P68133 | 151 | 205 | 165 | 165 | Natural variant | ID=VAR_062448;Note=In NEM3%3B results in sequestration of sarcomeric and Z line proteins into intranuclear aggregates%3B there is some evidence of muscle regeneration suggesting a compensatory effect. V->M;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269 |
| P68133 | 151 | 205 | 172 | 172 | Natural variant | ID=VAR_062449;Note=In NEM3. A->G |
| P68133 | 151 | 205 | 181 | 181 | Natural variant | ID=VAR_062450;Note=In NEM3. D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15236405;Dbxref=PMID:15236405 |
| P68133 | 151 | 205 | 181 | 181 | Natural variant | ID=VAR_062451;Note=In NEM3. D->H |
| P68133 | 151 | 205 | 181 | 181 | Natural variant | ID=VAR_062452;Note=In NEM3. D->N |
| P68133 | 151 | 205 | 184 | 184 | Natural variant | ID=VAR_015580;Note=In NEM3%3B mild. G->D;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10508519,ECO:0000269|PubMed:15236405;Dbxref=PMID:10508519,PMID:15236405 |
| P68133 | 151 | 205 | 185 | 185 | Natural variant | ID=VAR_015582;Note=In NEM3%3B severe. R->C;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10508519;Dbxref=PMID:10508519 |
| P68133 | 151 | 205 | 185 | 185 | Natural variant | ID=VAR_062453;Note=In NEM3%3B requires 2 nucleotide substitutions. R->D |
| P68133 | 151 | 205 | 185 | 185 | Natural variant | ID=VAR_015581;Note=In NEM3%3B autosomal dominant%3B severe. R->G;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:11333380,ECO:0000269|PubMed:15198992,ECO:0000269|PubMed:15236405;Dbxref=PMID:11333380,PMID:15198992,PMID:1523640 |
| P68133 | 151 | 205 | 185 | 185 | Natural variant | ID=VAR_062454;Note=In NEM3. R->S;Dbxref=dbSNP:rs1064794287 |
| P68133 | 151 | 205 | 197 | 197 | Natural variant | ID=VAR_076426;Note=In SHPM%3B no effect on cytoskeleton structure. E->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25938801;Dbxref=dbSNP:rs869312739,PMID:25938801 |
| P68133 | 151 | 205 | 198 | 198 | Natural variant | ID=VAR_062455;Note=In NEM3. R->L |
| P68133 | 151 | 205 | 199 | 199 | Natural variant | ID=VAR_062456;Note=In NEM3. G->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15236405;Dbxref=PMID:15236405 |
| 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 |
| P68133 | 151 | 205 | 2 | 377 | Chain | ID=PRO_0000442803;Note=Actin%2C alpha skeletal muscle%2C intermediate form;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P62737 |
| P68133 | 151 | 205 | 3 | 377 | Chain | ID=PRO_0000442804;Note=Actin%2C alpha skeletal muscle;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P68135 |
| P68133 | 151 | 205 | 156 | 156 | Natural variant | ID=VAR_062447;Note=In NEM3. D->N |
| P68133 | 151 | 205 | 165 | 165 | Natural variant | ID=VAR_011684;Note=In MPCETM. V->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10508519,ECO:0000269|PubMed:15198992;Dbxref=dbSNP:rs121909522,PMID:10508519,PMID:15198992 |
| P68133 | 151 | 205 | 165 | 165 | Natural variant | ID=VAR_062448;Note=In NEM3%3B results in sequestration of sarcomeric and Z line proteins into intranuclear aggregates%3B there is some evidence of muscle regeneration suggesting a compensatory effect. V->M;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269 |
| P68133 | 151 | 205 | 172 | 172 | Natural variant | ID=VAR_062449;Note=In NEM3. A->G |
| P68133 | 151 | 205 | 181 | 181 | Natural variant | ID=VAR_062450;Note=In NEM3. D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15236405;Dbxref=PMID:15236405 |
| P68133 | 151 | 205 | 181 | 181 | Natural variant | ID=VAR_062451;Note=In NEM3. D->H |
| P68133 | 151 | 205 | 181 | 181 | Natural variant | ID=VAR_062452;Note=In NEM3. D->N |
| P68133 | 151 | 205 | 184 | 184 | Natural variant | ID=VAR_015580;Note=In NEM3%3B mild. G->D;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10508519,ECO:0000269|PubMed:15236405;Dbxref=PMID:10508519,PMID:15236405 |
| P68133 | 151 | 205 | 185 | 185 | Natural variant | ID=VAR_015582;Note=In NEM3%3B severe. R->C;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10508519;Dbxref=PMID:10508519 |
| P68133 | 151 | 205 | 185 | 185 | Natural variant | ID=VAR_062453;Note=In NEM3%3B requires 2 nucleotide substitutions. R->D |
| P68133 | 151 | 205 | 185 | 185 | Natural variant | ID=VAR_015581;Note=In NEM3%3B autosomal dominant%3B severe. R->G;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:11333380,ECO:0000269|PubMed:15198992,ECO:0000269|PubMed:15236405;Dbxref=PMID:11333380,PMID:15198992,PMID:1523640 |
| P68133 | 151 | 205 | 185 | 185 | Natural variant | ID=VAR_062454;Note=In NEM3. R->S;Dbxref=dbSNP:rs1064794287 |
| P68133 | 151 | 205 | 197 | 197 | Natural variant | ID=VAR_076426;Note=In SHPM%3B no effect on cytoskeleton structure. E->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25938801;Dbxref=dbSNP:rs869312739,PMID:25938801 |
| P68133 | 151 | 205 | 198 | 198 | Natural variant | ID=VAR_062455;Note=In NEM3. R->L |
| P68133 | 151 | 205 | 199 | 199 | Natural variant | ID=VAR_062456;Note=In NEM3. G->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15236405;Dbxref=PMID:15236405 |
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SNVs in the skipped exons for ACTA1 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - 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 |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_37927 | 229568017 | 229568178 | 229568162 | 229568162 | Frame_Shift_Del | G | - | p.S157fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_37929 | 229568734 | 229568874 | 229568750 | 229568750 | Frame_Shift_Del | C | - | p.G38fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_37929 | 229568734 | 229568874 | 229568777 | 229568777 | Frame_Shift_Del | G | - | p.P29fs |
| UCS | TCGA-N7-A4Y8-01 | exon_skip_37929 | 229568734 | 229568874 | 229568733 | 229568733 | Splice_Site | C | A | . |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 229568734 | 229568874 | 229568742 | 229568742 | Frame_Shift_Del | G | - | p.R41fs |
| SKLU1_LUNG | 229568734 | 229568874 | 229568742 | 229568742 | Frame_Shift_Del | G | - | p.R41fs |
| KNS42_CENTRAL_NERVOUS_SYSTEM | 229568017 | 229568178 | 229568158 | 229568158 | Missense_Mutation | C | T | p.D159N |
| CCRFCEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 229568734 | 229568874 | 229568838 | 229568838 | Missense_Mutation | C | A | p.A9S |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ACTA1 |
| 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 ACTA1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ACTA1 |
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RelatedDrugs for ACTA1 |
| 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 ACTA1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| ACTA1 | C1834336 | Nemaline myopathy 3 | 13 | CTD_human;ORPHANET;UNIPROT |
| ACTA1 | C0546264 | Congenital Fiber Type Disproportion | 2 | CTD_human;ORPHANET;UNIPROT |
| ACTA1 | C0149721 | Left Ventricular Hypertrophy | 1 | CTD_human |
| ACTA1 | C4225181 | MYOPATHY, SCAPULOHUMEROPERONEAL | 1 | ORPHANET;UNIPROT |
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